Miracle-dz/UniFAR-FTUs huggingface dataset:
Development of a fermentation system to model sessile bacterial populations in the human colon

A fermentation system was designed to model the human colonic microflora in vitro . The system provided a framework of mucin beads to encourage the adhesion of bacteria, which was encased within a dialysis membrane. The void between the beads was inoculated with faeces from human donors. Water and metabolites were removed from the fermentation by osmosis using a solution of polyethylene glycol (PEG). The system was concomitantly inoculated alongside a conventional single-stage chemostat. Three fermentations were carried out using inocula from three healthy human donors. Bacterial populations from the chemostat and biofilm system were enumerated using fluorescence in situ hybridization. The culture fluid was also analysed for its short-chain fatty acid (SCFA) content. A higher cell density was achieved in the biofilm fermentation system (taking into account the contribution made by the bead-associated bacteria) as compared with the chemostat, owing to the removal of water and metabolites. Evaluation of the bacterial populations revealed that the biofilm system was able to support two distinct groups of bacteria: bacteria growing in association with the mucin beads and planktonic bacteria in the culture fluid. Furthermore, distinct differences were observed between populations in the biofilm fermenter system and the chemostat, with the former supporting higher populations of clostridia and Escherichia coli . SCFA levels were lower in the biofilm system than in the chemostat, as in the former they were removed via the osmotic effect of the PEG. These experiments demonstrated the potential usefulness of the biofilm system for investigating the complexity of the human colonic microflora and the contribution made by sessile bacterial populations.
Active Cardboard Box with Smart Internal Lining Based on Encapsulated Essential Oils for Enhancing the Shelf Life of Fresh Mandarins

Mandarins are usually sold in bulk and refrigerated in open cardboard boxes with a relatively short shelf-life (12–15 days) due to physiological and pathological disorders (rot, dehydration, internal breakdown, etc.). The influence of a controlled release of essential oils (EOs) from an active packaging (including β-cyclodextrin-EOs inclusion complex) was studied on the mandarin quality stability, comparing different sized cardboard trays and boxes, either non-active or active, at the pilot plant scale (experiment 1; commercialization simulation at room temperature after a previous simulation of short transportation/storage of 5 days at 8 °C). Then, the selected package was further validated at the industrial scale (experiment 2; cold storage at 8 °C up to 21 days). Among package types, the active large box (≈10 kg fruit per box) better maintained the mandarin quality, extending the shelf life from two weeks (non-active large box) to three weeks at room temperature. Particularly, the active large box highly controlled microbial growth (up to two log units), reduced weight losses (by 1.6-fold), reduced acidity, and increased soluble solids (highly appreciated in sensory analyses), while it minimized colour and controlled firmness changes after three weeks. Such trends were also observed during the validation experiment, extending the shelf life (based on sensory quality) from 14 to at least 21 days. In conclusion, the mandarin’s shelf life with this active cardboard box format was extended more than one week at 8 °C.
tRNA elbow modifications affect the tRNA pseudouridine synthase TruB and the methyltransferase TrmA

tRNAs constitute the most highly modified class of RNA. Every tRNA contains a unique set of modifications, and Ψ55, m5U54, and m7G46 are frequently found within the elbow of the tRNA structure. Despite the abundance of tRNA modifications, we are only beginning to understand the orchestration of modification enzymes during tRNA maturation. Here, we investigated whether pre-existing modifications impact the binding affinity or catalysis by tRNA elbow modification enzymes. Specifically, we focused on the Escherichia coli enzymes TruB, TrmA, and TrmB which generate Ψ55, m5U54, and m7G46, respectively. tRNAs containing a single modification were prepared, and the binding and activity preferences of purified E. coli TrmA, TruB, and TrmB were examined in vitro. TruB preferentially binds and modifies unmodified tRNA. TrmA prefers to modify unmodified tRNA, but binds most tightly to tRNA that already contains Ψ55. In contrast, binding and modification by TrmB is insensitive to the tRNA modification status. Our results suggest that TrmA and TruB are likely to act on mostly unmodified tRNA precursors during the early stages of tRNA maturation whereas TrmB presumably acts on later tRNA intermediates that are already partially modified. In conclusion, we uncover the mechanistic basis for the preferred modification order in the E. coli tRNA elbow region.
Projected impacts of climate change on the range and phenology of three culturally-important shrub species

Climate change is shifting both the habitat suitability and the timing of critical biological events, such as flowering and fruiting, for plant species across the globe. Here, we ask how both the distribution and phenology of three food-producing shrubs native to northwestern North America might shift as the climate changes. To address this question, we compared gridded climate data with species location data to identify climate variables that best predicted the current bioclimatic niches of beaked hazelnut (Corylus cornuta), Oregon grape (Mahonia aquifolium), and salal (Gaultheria shallon). We also developed thermal-sum models for the timing of flowering and fruit ripening for these species. We then used multi-model ensemble future climate projections to estimate how species range and phenology may change under future conditions. Modelling efforts showed extreme minimum temperature, climate moisture deficit, and mean summer precipitation were predictive of climatic suitability across all three species. Future bioclimatic niche models project substantial reductions in habitat suitability across the lower elevation and southern portions of the species’ current ranges by the end of the 21st century. Thermal-sum phenology models for these species indicate that flowering and the ripening of fruits and nuts will advance an average of 25 days by the mid-21st century, and 36 days by the late-21st century under a high emissions scenario (RCP 8.5). Future changes in the climatic niche and phenology of these important food-producing species may alter trophic relationships, with cascading impacts on regional ecosystems.
Corn Flour Intake, Aflatoxin B1 Exposure, and Risk of Esophageal Precancerous Lesions in a High-Risk Area of Huai’an, China: A Case-Control Study

Aflatoxin B1 (AFB1), which has potent toxicity and carcinogenicity, is a common contaminant of important agricultural commodities. This study aimed to investigate the frequency of corn flour intake and assess the exposure to AFB1 via direct detection of AFB1 in the diet and serum AFB1 exposure biomarker, so as to evaluate their associations with the risk of esophageal precancerous lesions (EPL). A case-control study based on three-day duplicate diet samples was performed in Huai’an District. One hundred EPL cases and 100 healthy controls were enrolled and required to be age- (±2 years) and gender-matched. The concentration of AFB1 in food samples and the level of serum AFB1-albumin (AFB1-Alb) adduct were quantitatively analyzed. Results showed that corn flour intake was positively associated with serum AFB1-Alb adduct level (p for trend = 0.003), dietary AFB1 exposure (p for trend < 0.001), and the risk of EPL (p for trend = 0.017). Increased serum AFB1-Alb adduct level was associated with an increased risk of EPL as well (p for trend < 0.001). In conclusion, corn flour may be an essential source of AFB1 in Huai’an District, whereas high exposure to AFB1 is likely to be an important risk factor contributing to the progression of EPL.
Factors Affecting the Abscission of Reproductive Organs in Yellow Lupins ( Lupinus luteus L.) III. ENDOGENOUS GROWTH SUBSTANCES IN VIRUS-INFECTED AND HEALTHY PLANTS AND THEIR EFFECT ON ABSCISSION

Extracts of small and mature-size lupin pods yielded four substances affecting the growth of wheat-coleoptile sections : one acid promotor (A), two acid inhibitors {B and X), and one neutral inhibitor ( Y). Inhibitor B was extremely active, however, coleoptile sections showed no signs of toxic effects ; they resumed growth at a rapid rate after rinsing them and adding /3-indolylacetic acid (IAA) to the medium. I /xg of IAA was required to counter act the effect of 'B' extracted from 230 mg. of tissue. On an equal fresh weight basis the inhibiting action of 'B' in lupin pods was 500-1,500 times more potent than that of 'inhibitor /? ' in etiolated pea seedlings. Small pods of plants infected with pea-mosaic virus yielded 3 times the amount of 'A' of healthy plants (equivalent to 1 /xg. IAA and 0 3 /xg. IAA per 25 g. of tissue respectively), and approximately § the amount of 'B'. Mature pods of virus-infected plants again yielded more 'A', but also z \ times more 'B' than pods of healthy plants. Healthy pods yielded more ' Y' than virus-infected pods, and there was no difference in 'X'.
Lipid Composition and Associated Gene Expression Patterns during Pollen Germination and Pollen Tube Growth in Olive (Olea europaea L.)

Abstract Pollen lipids are essential for sexual reproduction, but our current knowledge regarding lipid dynamics in growing pollen tubes is still very scarce. Here, we report unique lipid composition and associated gene expression patterns during olive pollen germination. Up to 376 genes involved in the biosynthesis of all lipid classes, except suberin, cutin and lipopolysaccharides, are expressed in olive pollen. The fatty acid profile of olive pollen is markedly different compared with other plant organs. Triacylglycerol (TAG), containing mostly C12–C16 saturated fatty acids, constitutes the bulk of olive pollen lipids. These compounds are partially mobilized, and the released fatty acids enter the β-oxidation pathway to yield acetyl-CoA, which is converted into sugars through the glyoxylate cycle during the course of pollen germination. Our data suggest that fatty acids are synthesized de novo and incorporated into glycerolipids by the ‘eukaryotic pathway’ in elongating pollen tubes. Phosphatidic acid is synthesized de novo in the endomembrane system during pollen germination and seems to have a central role in pollen tube lipid metabolism. The coordinated action of fatty acid desaturases FAD2–3 and FAD3B might explain the increase in linoleic and alpha-linolenic acids observed in germinating pollen. Continuous synthesis of TAG by the action of diacylglycerol acyltransferase 1 (DGAT1) enzyme, but not phosphoplipid:diacylglycerol acyltransferase (PDAT), also seems plausible. All these data allow for a better understanding of lipid metabolism during the olive reproductive process, which can impact, in the future, on the increase in olive fruit yield and, therefore, olive oil production.
Special Series : Palliative Care

Background: First defined in 2002 by Catlin and Carter, neonatal palliative care (NPC) is a relatively new model of care in neonatal pediatrics, first appearing in the medical literature in the early 1980s. Purpose: The purpose of this article is to suggest a conceptual definition of NPC that encompasses all the essential concepts as a way of moving NPC forward by having a consistent approach. Methods: Following a review of the NPC literature, a thematic analysis as a method for identifying, analyzing, and interpreting patterns of meaning in the definitions (“themes”) within the literature was undertaken. Findings: The major themes identified included philosophies of care, support, culture and spirituality, the team, and clinical management. Implications for Research: At the heart of NPC is the primacy of maintaining quality of life, while providing ethical and humane care that supports a “good death. ” The extensive elements presented in this article are considered essential to a comprehensive and conceptual definition of NPC proposed here.
Elliptical-fire perimeter- and area-intensity distributions

Equations are presented for determining the proportion of the total perimeter and area burned for a simple elliptically shaped fire for any specified range of Byram's fireline intensities. The same principles apply to any characteristic that is dependent on fireline intensity. Only three inputs are required: head-fire intensity; the elliptical shape factor; and the backfire spread rate. This last quantity is not required if it is assumed that the ignition point is at one focus of the ellipse. The spatial distributions produced have potential application to fire management.
Modified Pearson Model for High-Energy Multi-Charge Implantation and Impurity Activation for Sensor Microsystems

The mathematical Gauss and Pearson models, that qualitatively determine the physical processes of ion doping of acceptor (p) and donor (n) impurities, are used for the simulation of silicon submicron large scale integrated (LSI) structures. Such models are the basis of CAD-technology for calculating the concentration profiles of diode and transistor structures. This paper presents a modified Pearson model, which with high accuracy simulates the process of dual multicharge implantation of boron (B+, B++) and phosphorus (P+, P++) ions at the process of the formation of the isotype p+ -p and n+ -n contacts, which at present form the basis of combined drain-source areas of the CMOS submicron high speed structures.
Development of a Green-Based Quantitative Assay Using Time Series to Detect Risks

Designing efficient algorithms for forecasting of the state of the environment is one of the most important challenges in the field of time series analysis and accurate prediction. With the exponential rate of development of remote sensing and with the availability of fast computing platforms, it has now become possible to effectively and efficiently make use of vulnerability indicators forest stands.
DC/DC Full-Bridge Converter for Cathodic Protection Application with Phase-Shift Control Method and No Auxiliary Circuit

Cathodic protection (CP) DC/DC converters are the external power sources used in CP applications in which the fix DC voltage converts to variable output DC voltage and bring about variable output current as well. In low to medium output voltages, where the duty cycle is less than 30%, zero voltage switching (ZVS) is unattainable. Therefore, a switching control method which is the combination of ZVS and variable frequency pulse width modulation (VFPWM) is suggested in the article. By using this hybrid control method, the DC/DC full bridge structure operates under an extended range of voltage up to 75V in the output and the output current from 0 to 25A with high efficiency. Simulation results demonstrate the accuracy of this method.
A New Method for Specific Emitter Identification With Results on Real Radar Measurements

Specific Emitter Identification (SEI) is the process of specifically identifying mobile transmitters by extracting unique features from the precise measurements of their emitted signals. A novel signal processing scheme with two stages is proposed for the identification of specific radar emitters. In the first stage, the received radar pulses are accurately time aligned and coherently integrated in order to increase the Signal-to-Noise (SNR) ratio. Using this technique, measurements with SNR improvements of more than 25 dB are obtained, enabling detection of subtle differences between different emitters. In the second step, Variational Mode Decomposition (VMD) is used to decompose both the envelope and the instantaneous frequency of the received signal into a set of modes. Then, these mod signals are characterized by using a group of features for identification. We demonstrate highly successful identification performance with the proposed method on real radar datasets.
Fault Diagnosis of Broken Rotor Bars in Induction Motors Using Finite Element Analysis

This paper intends to portray a method for analyzing the performance of induction motors and the detection of broken rotor bar fault using finite element (FE) analysis. Two types of broken rotor bar faults and the effects of the faults on induction motors characteristics in terms of flux density distributions, current, and torque is studied. Moreover, several different methods such as measuring the induced voltage in search coils, comparison of current harmonics in healthy motors and broken rotor bar motors, motor current signature analysis (MCSA) are used for early detection. Using finite element software, the motor broken bar mechanical fault is fully simulated in conditions matching that of real circumstances. An advantage of this method is its simplicity since due to using a finite element software, fault detection with high accuracy is possible without extensive and complex calculations. As a result, fault components are easily detectable in the study of the stator current frequency spectrum. Ultimately, by comparing the behavior and function of the motor in healthy and faulty conditions a pattern can be constructed for early detection of faults.
ML-based Reinforcement Learning Approach for Power Management in SoCs

This paper presents a machine learning-based reinforcement learning approach, mapping Finite State Machines, traditionally used for power management control in SoCs, to Markov Decision Process (MDP)-based agents for controlling power management features of Integrated Circuits with application to complex multiprocessor-based SoCs such as CPUs, APUs and GPUs. We present the problem of decision-based control of a number of power management features in ICs consisting of numerous heterogeneous IPs. An infinite-horizon fully observable MDPs are utilized to obtain a policy of actions maximizing the expectation of the formulated Power Management utility function. The approach balances the demand for desired performance while providing an optimal power saving as opposed to commonly used FSM-based power management techniques. MDP framework was employed for power management decision-making under conditions of uncertainly for reinforcement learning. We describe in detail converting power management FSMs into infinite-horizon fully observable MDPs. The approach optimizes itself using reinforcement learning based on specified reward structure and previous performance, yielding an optimal and dynamically adjusted power management mechanism in respect to the formulated model.
Multiphase Multipurpose High power Variable Speed Drive: Design and implementation

This is a summary report of the design and implementation procedure of a special kind of variable speed drive. This drive can control any type of electric motors (synchronous, Asynchronous, DC, BLDC, PMSM, and SR) with a maximum of 7 phases and up to 500kW. Different control algorithms (with real feedback sensor or sensorless) are embedded in it for different applications and situations. This project has lots of details, and so many tasks have been done in it. Only some technical aspects of the implementation phase have been presented here.
Fast and Scalable Simulation Framework for Large In-Order Chip Multiprocessors

As chip technology advances, the number of cores in mainstream chip multiprocessors (CMP) increases, so chips with hundreds of cores may become common within a decade. One of the challenges this trend sets to computer architects is to make the current CMP designs scalable to larger numbers of cores. A tool set that would allow us to predict how various design decisions may affect the performance of larger CMPs is therefore necessary. In this paper, we present a trace-based simulation framework we devised for Elbrus microprocessor family. Its core component, the CMP simulator is scalable to at least one thousand of cores and allows to evaluate the kilo-core CMP performance in just a few days using a mainstream 16-core host computer. It is also highly flexible and architecture-agnostic and, therefore, could be used to simulate other in-order architectures. We validated the framework against a real machine and achieved an average accuracy of 18 percent in single-core tests and 15 percent in four-core, an average error in relative slowdown evaluation of 2.6 percent, and average absolute errors in L2 and L3 cache miss rates within 0.3 bytes per cycle.
Formation of Epitaxial Layers of CuO on Al (100) Surface

In order to understand the local mechanisms that occur on the surface during the growth of the Al/CuO film, a theoretical calculation was performed based on the method of functional theory and first principles calculations. Dissociative CuO adsorption on Al is observed during the first deposition stage. We have focused our attention on such processes as: diffusion of Cu atoms on the Al (100) surface; Interactions between Cu and O on the film surface; penetration of Cu atoms into the surface layers and deeper into the substrate.As a result of our calculations, it is shown that CuO undergoes dissociative chemisorption on the Al (100) surface, which causes the Cu and O atoms to tend to separate from each other. Copper deposition promotes the introduction of Cu into the Al surface layers, especially during clustering, which lowers the penetration activation barrier.
Design of a Novel Axial Flux Rotor Consequent-Pole Permanent Magnet Machine

This paper proposes a novel axial flux rotor consequent-pole permanent magnet (AFRCPPM) machine with improved torque density. The key is to place the PMs between the adjacent rotor teeth with switched-flux feature compared to the stator permanent magnet (PM) dual-stator axial switched-flux PM (DS-ASFPM) machine. This will be able to obtain simple stator structure, high power density and large torque output capability. In the following paper, the topology, operating principle and winding configuration are analyzed in detail. According to the theoretical derivation, the major parameters of the AFRCPPM machine are acquired. Based on 3-D finite-element (FE) method, the electromagnetic performance of the AFRCPPM machine and DS-ASFPM machine is comparatively investigated to evaluate their characteristics. The FE-predicted results indicate that the AFRCPPM machine exhibits simple stator structure, sinusoidal back-EMF and high power/torque density. Moreover, under the same armature current, the AFRCPPM machine has larger output torque compared to the DS-ASFPM machine. Hence, it has a good prospect in electric vehicle (EV) or hybrid EV.
Performance Analysis of TMG FinFETs for Low Power Application with Improved Analog/RF Characteristics

In this manuscript, a 3D simulation model of FinFET is proposed. The device is designed in such a manner that the gate is made with three metals of different work functions, so it’s named as Tri-Metal Gate (TMG) FinFET. The work function at source/channel junction is kept high in comparison to the drain/channel junction to reduce DIBL and improve transconductance. This structure improves ONstate current, with suppressed OFF-state current. Further DC and analog/RF characteristics such as transfer characteristics, parasitic capacitance (Cgd, Cgs), transconductance (gm), cut off frequency (fT), output transconductance (gds), transconductance generation factor(TGF) are investigated. A comparative analysis of the proposed device with an existing device is also performed and results are studies. Above parameters support its utility at ultra-low power VLSI. The device has been simulated using TCAD simulator.