Miracle-dz/UniFAR-FTUs huggingface dataset:
A Trio of Ubiquitin Ligases Sequentially Drive Ubiquitylation and Autophagic Degradation of Dysfunctional Yeast Proteasomes

As central effectors of ubiquitin (Ub)-mediated proteolysis, proteasomes are regulated at multiple levels, including degradation of unwanted or dysfunctional particles via autophagy (termed proteaphagy). In yeast, inactive proteasomes are exported from the nucleus, sequestered into cytoplasmic aggresomes via the Hsp42 chaperone, extensively ubiquitylated, and then tethered to the expanding phagophore by the autophagy receptor Cue5. Here, we demonstrate the need for ubiquitylation driven by the trio of Ub ligases (E3s) San1, Rsp5 and Hul5, which, together with their corresponding E2s, work sequentially to promote nuclear export and Cue5 recognition. Whereas San1 functions prior to nuclear export, Rsp5 and Hul5 likely decorate aggresome-localized proteasomes in concert. Ultimately, topologically complex Ub chain(s) containing both K48 and K63 Ub-Ub linkages are assembled, mainly on the regulatory particle, to generate autophagy-competent substrates. As San1, Rsp5, Hul5, Hsp42, and Cue5 also participate in general proteostasis, proteaphagy likely engages an essential mechanism for eliminating inactive/misfolded proteins. HIGHLIGHTS Ubiquitylation is essential for the autophagic turnover of dysfunctional proteasomes. The San1, Rsp5 and Hul5 E3s act sequentially to drive proteaphagy. The E2s Ubc1, Ubc4 and Ubc5 are collectively required. Both K48- and K63-mediated Ub-Ub linkages are assembled for efficient proteaphagy.
Optimization Parameter of the 1P Keys Interpolation Kernel Implemented in the Correlation Algorithm for Estimating the Fundamental Frequency of the Speech Signal

The first part of this paper describes an algorithm for estimating the fundamental frequency F0 of a speech signal, using an autocorrelation algorithm. After that, it was shown that, due to the discrete structure of the autocorrelation function, the accuracy of the fundamental frequency estimate largely depends on the sampling period TS. Then, in order to increase the accuracy of the estimation, an interpolation of the correlation function is performed. Interpolation is performed using a one parameter (1P) Keys interpolation kernel. The second part of the paper presents an experiment in which the optimization of the 1P Keys kernel parameter was performed. The experiment was performed on test Sine and Speech signals, in the conditions of ambient disturbances (N8 Babble noise, SNR = 5 to -10 dB). MSE was used as a measure of the accuracy of the fundamental frequency estimate. Kernel parameter optimization was performed on the basis of the MSE minimum. The results are presented graphically and tabularly. Finally, a comparative analysis of the results was performed. Based on the comparative analysis, the window function, in which the smallest estimation error was achieved for all ambient noise conditions, was chosen.
Design of the Fermilab Pre-Series Cold Mass for the HL-LHC Accelerator Upgrade Project

As part of the U.S. contribution to the HL-LHC Accelerator Upgrade Project (AUP), Fermilab is designing and building cold masses suitable for use in the LHC interaction regions. The cold mass provides a vacuum-tight helium enclosure for the magnets. Two magnets are aligned both axially and in cross section at Fermilab based on survey and warm magnetic measurements. Bus work and instrumentation is added. A welded stainless steel vacuum-tight shell surrounds the two magnets, and the structure is prepared for insertion into the cryostat. This paper summarizes the design of the cold mass including alignment, bus work, weld details, and instrumentation.
The genome sequence of the orange-striped anemone, Diadumene lineata (Verrill, 1869)

We present a genome assembly from an individual Diadumene lineata (the orange-striped anemone; Cnidaria; Anthozoa; Actiniaria; Diadumenidae). The genome sequence is 313 megabases in span. The majority of the assembly (96.03%) is scaffolded into 16 chromosomal pseudomolecules. The complete mitochondrial genome was also assembled and is 17.6 kilobases in length.
Challenges in electric vehicle adoption and vehicle-grid integration

With rapid innovation in vehicle and battery technology and strong support from governmental bodies and regulators, electric vehicles (EV) sales are poised to rise. While a better and cleaner world is likely in the near future, wide adoption of EVs also raises many challenges. First, to promote wide adoption of EVs requires sufficient amount of charging infrastructures, which we do not currently have. Meanwhile, utilities, energy system operators and system planners are concerned that large EV charging load would greatly affect the energy system operation and increase generation cost. Thus, new operation schemes are badly needed for the system to better adapt to large EV load. From the perspective of system reliability, EV charging might cause many reliability issues, especially at the distribution level. This dissertation addresses these challenges by developing new analytical models using a range of operation research, simulation, and statistical methodologies. The outcome will facilitate governmental bodies in developing technology and policy roadmaps for accelerating electric vehicle deployment, and also help utilities, energy system operators, and system planners to properly recognize challenges in vehicle-grid integration and develop compatible operation and planning strategies.
Autogenic knickpoints in laboratory landscape experiments

Abstract. The upstream propagation of knickpoints in river longitudinal profiles is commonly assumed to be related to discrete changes in tectonics, climate or base level. However, the recognition that some knickpoints may form autogenically, independent of any external perturbation, may challenge these assumptions. We investigate here the genesis and dynamics of such autogenic knickpoints in laboratory experiments at the drainage basin scale, where landscapes evolved in response to constant rates of base level fall and precipitation. Despite these constant forcings, we observe that knickpoints regularly initiate in rivers at the catchments' outlet throughout the duration of experiments. The upstream knickpoint propagation rate does not decrease monotonically in relationship with the decrease in drainage area, as predicted by stream-power-based models, instead the propagation rate first increases until the mid-part of catchments before decreasing. To investigate the dynamics of the knickpoints, we calculated hydraulic information (water depth, river width, discharge and shear stress) using a hydrodynamic model. We show that knickpoint initiation at the outlet coincides with a fairly abrupt river narrowing entailing an increase in their shear stress. Then, once knickpoints have propagated upward, rivers widen causing a decrease in shear stress and incision rate, and making the river incision less than the base level fall rate. This creates an unstable situation which drives the formation of a new knickpoint. The experiments suggest a new autocyclic model of knickpoint generation controlled by river width dynamics independent of variations in climate or tectonics. This questions an interpretation of landscape records focusing only on climate and tectonic changes without considering autogenic processes.
Novel Hardware Trojan Attack on Activation Parameters of FPGA-Based DNN Accelerators

Deep neural network (DNN) hardware accelerators are being deployed widely to accelerate the inference process. Security of such accelerators is a major challenge, especially when being deployed in safety-critical systems such as autonomous vehicles. In this letter, we present novel Hardware Trojan (HT) attacks on two DNN hardware accelerators, which modifies the activation parameters of the DNN in a field-programmable gate array-based accelerator implementation. The proposed HT is agnostic to the detailed architecture of the DNN. Experimental results demonstrate that the proposed HT is extremely stealthy, and when activated can result in significant degradation in inference accuracy.
Efficacy of using zinc oxide nanoparticle as a substitute to antibiotic growth promoter and zinc sulphate for growth performance, antioxidant capacity, immunity and intestinal barrier function in broilers

Abstract Dietary zinc oxide nanoparticle (ZnO NP) possessing multiple biological activities might be a potential substitute for the combination of ZnSO4 and antibiotic growth promoter in broiler diets. Therefore, this study was conducted to investigate the efficacy of dietary ZnO NP as a substitute to the combination of ZnSO4 and xanthomycin for growth, antioxidant capacity, immunity, intestinal barrier and liver function in broilers. Arbor Acres chicks (n = 320) were assigned to 5 treatments with 8 replicates. Birds received a basal diet supplemented with 80 mg/kg ZnSO4 plus 5 mg/kg xanthomycin (ZnSO4 + Xanthomycin) or 0 (negative control, NC), 40, 80, and 160 mg/kg ZnO NP for 42 days. The average daily gain, average daily feed intake and feed-to-gain ratio showed dose-dependent increases with the increasing level of dietary ZnO NP during the 21–42 day and 1–42 day stages. The final body weight (42 d) and serum concentrations of insulin-like growth factor 1 and growth hormone increased linearly with the increasing level of dietary ZnO NP. In addition, 80 mg/kg ZnO NP increased the serum concentrations of IgA, IgG, IgM, andinterleukin-10 and peroxidase activity, the jejunal mucosal villus height, villus width and goblet cell numbers. Dietary 80 or 160 mg/kg ZnO NP significantly altered mRNA abundances of genes related to antioxidant status, intestinal barrier and immunity in the jejunal mucosa. These results indicated that dietary supplementation with 40–160 mg/kg ZnO NP caused no obvious negative effects on liver function, but effectively improved growth performance, intestinal barrier function, immunity and antioxidant capacity. Highlights Dietary 40–160 mg/kg zinc oxide nanoparticle (ZnO NP) improved growth performance and enhanced immunity of broilers without obvious negative effects on liver function. Dietary 40–160 mg/kg ZnO NP improved intestinal barrier and intestinal morphology, and enhanced antioxidant capacity via Nrf2/HO-1 pathway. Doses of 40–80 mg/kg ZnO NP were suggested to alternate the combination of 80 mg/kg ZnSO4 and 5 mg/kg xanthomycin in diets of broilers.
Billet Temperature Model of Reheating Furnace Based on Independent Component Regression

Reheating furnace is a multivariable nonlinear system with large inertia, net lag and crossed coupling. So the estimate of main guide line of its product quality--billet temperature--is all along a puzzle in the process. Independent component regression (ICR) model between billet temperature variable and process variable was established with multi-statistic projection principle and ICA method. Based on a steel works actual data and reckoning model parameter, analyzing check and error indicate that this model can forecast billet steel outlet temperature, and the forecasting error can satisfy industry application accuracy demands.
No Evidence for a Causal Link between Serum Uric Acid and Nonalcoholic Fatty Liver Disease from the Dongfeng-Tongji Cohort Study

Background and Aims Elevated serum uric acid (SUA) is associated with an increased risk of nonalcoholic fatty liver disease (NAFLD); however, whether this association is causal is undetermined. Methods Each participant from the Dongfeng-Tongji cohort study based on 27,009 retirees was interviewed face-to-face following a clinical examination. Covariance, logistic regression analysis, and instrumental variables were used to assess associations between SUA and (severity of) NAFLD and the causal link. Results Among 8,429 subjects free of NAFLD at baseline, 2,007 participants developed NAFLD after 5 years of follow-up. The multivariable-adjusted odds ratio (OR) for NAFLD for individuals in the fourth quartile of SUA level versus those in the first was 1.71 (95% CI: 1.45-2.01, P for trend <0.001) and was more dramatic in women or normal-weight persons. Furthermore, SUA was materially associated with greater mean markers of hepatic necroinflammation and greater probabilities of fibrosis. In genetic analyses, both single nucleotide polymorphisms (rs11722228 to SLC2A9 and rs2231142 to ABCG2) were pronouncedly associated with increased SUA concentrations, ranging from 0.19 to 0.22 mg/dl. No significant associations were observed between SNPs and potential confounders. No association was observed between the SUA-increasing allele and NAFLD, with an OR of 0.98 (95% CI: 0.90-1.08) per genetic score. This was not significantly different (P = 0.25) from what was expected (1.03, 95% CI: 1.03-1.03). Conclusions SUA was positively associated with NAFLD incidence especially in female and normal-weight individuals and the suspected progression risk of newly developed NAFLD. However, the Mendelian randomization analyses lend no causal evidence, suggesting high SUA as a marker and not a cause of NAFLD.
Stakeholders’ Perceptions Concerning Greek Protected Areas Governance

In this paper, we are interested in assessing the Greek protected areas’ (PAs) operation, and in particular, to what extent the stakeholders engaged in their management consider that the “good environmental governance” criteria are met. Through the use of Q-methodology, we find that, despite the very different circumstances of each PA, the stakeholders’ views cluster around four distinctive main perspectives (or factors). Furthermore, we find that stakeholders do not consider, overall, that the Greek PAs management strongly meets any of the “good environmental governance” criteria, with particularly poor assessments on crucial governance aspects such as a shared vision guiding the PA management, the rule of law, and the effectiveness/efficiency of the procedures, which suggests that the environmental governance of Greek PAs is suboptimal at least.
Lexical Associations in the L1 Turkish Mental Lexicon: Can L1 Lexical Intuition and a Representative Corpus Guide Teaching of Turkish as a Foreign Language Materials?

Studies to date using corpus linguistic and psycholinguistic approaches have investigated the collocational links in both the L1 and L2 brain from different angles. They have attempted to test the role collocations play in the mental lexicon and question how corpus data can guide us in our investigations. However, there have been almost no attempts to explore the relationship between the L1 Turkish users’ subjective judgements of collocational use (frequency) and the association strength of collocational items in Turkish evidenced in representative corpora. This research, mainly with a corpus-linguistic approach, aims to (a) detect the possible relationship between the collocational links in the L1 Turkish mental lexicon and the collocational frequency profiles on the TNC (Turkish National Corpus) (b) and thus question if L1 speaker intuitions (familiarity) regarding collocational frequency and the frequency profiles of the items, as evidenced through representative corpora, can/should be exploited in an attempt to create target vocabulary lists or vocabulary teaching materials for teaching Turkish as a foreign language. The results indicate that the collocational links in L1 Turkish users’ mental lexicon seem to resemble the lexical associations represented in the TNC. To be more precise, higher Delta-P (1 > word 2) scores are associated with stronger collocational intuitions. Additionally, the Delta-P (1 > word 2) as well as the CEFR 1 level are significant predictors of subjective judgements for frequent collocational use. The results have been discussed in light of the psycholinguistic research highlighting collocational processing, and some pedagogical conclusions have been drawn.
Tryptophan capped gold-aryl nanoparticles for energy transfer study with SARS-CoV-2 spike proteins

ABSTRACT Current research on coronavirus 2 disease (SARS-CoV-2) has been focused on developing reliable gold nanomaterials and methods for the detection of viral spike protein (S-proteins). Here, we describe the fluorescence quenching of spike proteins in the presence of robust gold-aryl nanoparticles. The obtained results demonstrated a strong binding affinity between S-proteins and tryptophan immobilized on gold-carbon nanoparticles (Trp-AuNPs) based on the binding constant value of 11.098 M−1. Förster non-radiative energy transfer (FRET) calculations showed an average binding distance of r = 3.06 nm and a critical energy transfer distance of R0 = 2.5 nm. Time-resolved fluorescence studies of conjugated S-proteins onto Trp-AuNPs revealed a short fluorescence lifetime and dynamic quenching.
Development of the Turbulent Diffusion Model of Fine Suspended Substances in the Lower Atmosphere Layer

A promising direction for solving the problem of air pollution by fine substances is the use of numerical modeling in the development of mathematical models of the transport of pollutants in the atmosphere. An urgent problem in applying mathematical models with numerical algorithms and software is constructing a qualitative model that would meet both the physical parameters and fulfill all the optimal conditions of numerical analysis. The main objective of this study was to develop an algorithm of a mathematical model based on the equation of distribution of impurities in a turbulent medium. That allows considering the simultaneous influence of wind speed, turbulence of atmospheric air, pollution parameters, direction, and wind force on the size of scattering zones. The unique feature of the study is the use of the coordinate splitting equation of impurities distribution in a turbulent environment with subsequent normalization and parameterization of conditions. Finding integrands functions in the calculation algorithm allows obtaining a stable computational algorithm of the proposed propagation model of fine suspended particles. The solution of the function implemented in the Mathcad Prime 7 software. Distributions of concentrations and their levels for various values of turbulence of atmospheric air and dangerous wind speed are received. The most significant number of fine particles is at a distance of up to 4 km from the emission source. Still, there is also the transfer of contaminants at more than 5 km (up to 57 % of the initial emission concentration). The model has convenient software and algorithmic software, the time of calculation of graphic visualizations up to 20 minutes on medium-power computers. The obtained mathematical model can use in systems of forecasting man-caused load on the environment for the prompt solution of environmental problems.
Comparison of CCM- and CRM-Based Boost Parallel Active Power Decoupler for PV Microinverter

Single-phase inverter or rectifier systems often make use of an active power decoupler (APD) to balance the mismatch between constant dc power and fluctuating ac power. This article deals with the comparison of continuous conduction mode (CCM) and critical conduction mode (CRM) operation-based design of a parallel boost-type APD for photovoltaic microinverter applications. From a design perspective, multiobjective analysis of efficiency, volume, and cost is explored within a decision space including planar inductors, gallium nitride based devices, film capacitors, switching frequency, and modulation (CCM vs. CRM). The theoretical study analyzes all possible design configurations within CCM and CRM and identifies Pareto-optimal designs, from which the selected CRM design can achieve reduced system volume and lower cost with the use of smaller inductor core, while operating with similar California Energy Commission efficiency drop as the selected CCM design. From a control perspective, a pulsewidth modulation based control strategy is proposed to implement closed-loop CRM modulation that does not rely on zero-crossing detection. Closed-loop systems are designed for the optimal CCM and CRM realizations, and the final system characteristics are compared. Experimental results, obtained using two separate 40-V, 400-W hardware prototypes for CCM and CRM, are presented to verify the analyses.
Radiometal-Labeled Chitosan Microspheres as Transarterial Radioembolization Agents against Hepatocellular Carcinoma

Transarterial radioembolization (TARE) is an emerging treatment for patients with unresectable hepatocellular carcinoma (HCC). This study successfully developed radiometal-labeled chitosan microspheres (111In/177Lu-DTPA-CMS) with a diameter of 36.5 ± 5.3 μm for TARE. The radiochemical yields of 111In/177Lu-DTPA-CMS were greater than 90% with high radiochemical purities (>98%). Most of the 111In/177Lu-DTPA-CMS were retained in the hepatoma and liver at 1 h after intraarterial (i.a.) administration. Except for liver accumulation, radioactivity in each normal organ was less than 1% of the injected radioactivity (%IA) at 72 h after injection. At 10 days after injection of 177Lu-DTPA-CMS (18.6 ± 1.3 MBq), the size of the hepatoma was significantly reduced by around 81%, while that of the rats in the control group continued to grow. This study demonstrated the effectiveness of 177Lu-DTPA-CMS in the treatment of N1-S1 hepatoma. 111In/177Lu-DTPA-CMS have the potential to be a superior theranostic pair for the treatment of clinical hepatoma.
Altitudinal distribution of the functional feeding groups of aquatic macroinvertebrates using an ecological network in Andean streams

Introduction: Analysis of functional feeding groups (FFG) in aquatic macroinvertebrates is important in understanding the structure, function, and dynamics of ecological processes ecosystems. Modularity refers to the degree of compartmentalization of food webs and varies between -1 and 1. A network with a modularity value close to 1 is resilient to disturbances and can be interpreted as an indicating factor for the stability of communities. Objective: In this study, we analyzed the trophic structure of benthic macroinvertebrates in La Nitrera stream, the San Juan River, and the Cauca River. Methods: The study was supported by ecological networking techniques using Gephi software. We studied nine sites in dry, rainy, and transition seasons in 2017 and 2018, monitoring changes in the altitude gradient. At each of the sites, the organisms were captured and determined, and physicochemical and hydraulic information was obtained. Results: The variance component analysis allowed to explain the variability of the data by relating the following environmental variables: FFG, diversity, richness, modularity, season, and time. Simple multifactorial ANOVA indicated that significant changes in FFG were associated with altitude, and modularity to time. The allocation of the FFG was done by stomach analysis and secondary information. Conclusion: The transition season had the highest modularity, possibly due to the recolonization of some biotopes caused by the decrease in riverbed velocity. La Nitrera and San Juan presented higher values than the Cauca, which may indicate that the altitudinal change and velocity of water currents affects the compartmentalization of the network.