Miracle-dz/UniFAR-FTUs huggingface dataset:
Joint Subcarrier-Pair and Power Allocation Based on SWIPT in Multi-Relay OFDM System

In this paper, we address the transmission rate optimization problem for a multi-relay orthogonal frequency division multiplexing (OFDM) system with simultaneous wireless information and power transfer (SWIPT), where each amplify-and-forward (AF) relay does not consume its own energy. By introducing a subcarrier-pair factor, we provide the joint subcarrier-pair and power allocation scheme based on the Hungarian algorithm and Lagrange dual method to maximize the transmission rate. Simulations show that the proposed algorithm can perform better on information transmission rate than other algorithms.
ISAR Imaging of the Maneuvering Target with Sparse Aperture Based on the Modified Orthogonal Matching Pursuit

Inverse synthetic aperture radar (ISAR) imaging of maneuveirng target with sparse aperture is very important in the filed of radar signal processing. In this paper, a novel ISAR imaging algorithm of maneuvering target with sparse aperture via the modified orthogonal matching pursuit (OMP) is proposed. First, the minimum entropy class algorithms are used to complete the high-precision motion compensation for the sparse echoes. Then, the echo of each range cell is approximated as a multi-component chirp signal, and the initial frequency and chirp rate of the signal are estimated by the parameter estimation method. Besides, the chirp-Fourier basis is established using the estimated parameters, and the sparse ISAR images can be constructed as a sparse optimization problem. Finally, the high-resolution ISAR image of maneuvering target is achieved after the modified OMP algorithm is used. The effectiveness of the new approach is demonstrated by the experiment results.
3-D Imaging Methods for Highly Squinted Tomo-SAR on Accelerated Motion Platform

This paper studies the three-dimensional imaging method for tomography synthetic aperture radar (Tomo-SAR) on accelerated motion platforms operating in highly squinted imaging mode. A new method using the nonuniform fast factorized back-projection (NUFFBP) algorithm is proposed to tackle the accelerated issue. The elevation resolution is achieved by utilizing array antenna in this paper. The compressive sensing (CS) theory is adopted to achieve the super-resolution in elevation direction. The SAR imageries in the range and azimuthal directions, combined with the elevation resolution, construct the three-dimensional (3-D) SAR image. Simulated data results show the good performance of the method.
The Association Between Helicobacter pylori Infection and Rosacea

Introduction: Helicobacterpylori ( H.pylori )isonethemostinfectiousmicroorganismof humandiseasefoundinhalf of theworld’s population. Despiteintenseinvestigationsintothespreadofrosacea,thepreciseetiologyremainsunclear. Therearetheories,which suggest H. pylori as a predisposing factor for the occurrence. This study aimed at determining the prevalence of H. pylori in patients with rosacea. Methods: This analytical-descriptive study was conducted on patients with rosacea disease attending Tabriz University of Medical Sciences Dermatology Clinics from October 2011 to January 2011. Patients, who were 18- to 65-year-olds with conﬁrmed rosacea diagnosis, were included in the study. All patients were referred to a dermatologist and the severity of rosacea was categorized in 3 gradesof mild,moderateandsevere. Then H.pylori infectionwasinvestigatedusing H.pylori stoolantigen. Pvaluesof lessthan0.05 were considered statistically signiﬁcant. Results: Out of 63 patients with rosacea, 35 patients (55.55%) were male and 28 patients (44.44%) were female. Based on the rosacea categorization, 11 (17.46%), 32 (50.79%), and 20 (31.74%) patients had respectively severe, moderate, and mild rosacea. There was no statistical signiﬁcant diﬀerence regarding age and gender between diﬀerent severities (P = 0.39). Forty patients (63.4%) out of all 63 werepositivefor H.pylori onstoolantigenexamination. Therewasnostatisticallysigniﬁcantassociationbetween H.pylori infection and gender (P = 0.87) or age (P = 0.62). There was a statistically signiﬁcant diﬀerence between patients with H. pylori negative and positive test results considering severity (P = 0.013). Conclusions: Inconclusion, althoughnoassociationbetweenrosaceaand H.pylori infectionwasseen, therewasasigniﬁcantasso-ciation between H. pylori infection and cases of severe rosacea.
Nitrogen Addition Decreases Soil Respiration without Changing the Temperature Sensitivity in a Semiarid Grassland

Abstract: The mechanisms underlying the response of soil respiration (Rs) to nitrogen (N) addition remain to be explored in semiarid ecosystems. This study was conducted to determine the effect of N addition on soil microbial composition, Rs and the temperature sensitivity of Rs (Q10). The N addition experiment was carried out in a semiarid grassland in China, with N fertilizer application rates of 0, 2, 4, 8, 16, or 32 g N m–2 yr–1. Microbial phospholipid fatty acids (PLFAs), Rs and Q10 were measured, and their relationships with soil properties were determined for three growing seasons. The results showed that N addition significantly increased the content of soil dissolved organic carbon (DOC) and inorganic nitrogen (IN), and decreased soil pH. With respect to soil microbes, N addition reduced soil PLFAs, reduced the fungi to bacteria ratio (F:B) and increased the gram-positive bacteria to gram-negative bacteria ratio (G+:G–). Rs under the N2, N4, N8, N16 and N32 treatments decreased by 2.58%, 14.86%, 22.62%, 23.97% and 19.87%, respectively, compared to the N0 (control) treatment. The results of structural equation models showed that N addition reduced Rs by lowering soil PLFAs and altering the microbial composition. However, N addition had no significant effect on either Q10, soil total organic carbon (TOC) or total nitrogen (TN), indicating that N addition alleviated soil carbon loss and was unlikely to change the potential for a bigger loss under global warming.
Bipartite network analysis of ant-task associations reveals task groups and absence of colonial daily activity

Social insects are one of the best examples of complex self-organised systems exhibiting task allocation. How task allocation is achieved is the most fascinating question in behavioural ecology and complex systems science. However, it is difficult to comprehensively characterise task allocation patterns due to behavioural complexity, such as the individual variation, context dependency, and chronological variation. Thus, it is imperative to quantify individual behaviours and integrate them into colony levels. Here, we applied bipartite network analyses to characterise individual-behaviour relationships. We recorded the behaviours of all individuals with verified age in ant colonies and analysed the individual-behaviour relationship at the individual, module, and network levels. Bipartite network analysis successfully detected the module structures, illustrating that certain individuals performed a subset of behaviours (i.e., task groups). We confirmed age polyethism by comparing age between modules. Additionally, to test the daily rhythm of the executed tasks, the data were partitioned between daytime and nighttime, and a bipartite network was re-constructed. This analysis supported that there was no daily rhythm in the tasks performed. These findings suggested that bipartite network analyses could untangle complex task allocation patterns and provide insights into understanding the division of labour.
The potential SARS-CoV-2 entry inhibitor

Outbreak of coronavirus disease 2019 (COVID-19) occurred in Wuhan and has rapidly spread to almost all parts of world. In coronaviruses, the receptor binding domain (RBD) in the distal part of S1 subunit of SARS-CoV-2 spike protein can directly bind to angiotensin converting enzyme 2 (ACE2). RBD promote viral entry into the host cells and is an important therapeutic target. In this study, we discovered that theaflavin showed the lower idock score (idock score: −7.95 kcal/mol). To confirm the result, we discovered that theaflavin showed FullFitness score of −991.21 kcal/mol and estimated ΔG of −8.53 kcal/mol for the most favorable interaction with contact area of SARS-CoV-2 RBD by SwissDock service. Regarding contact modes, hydrophobic interactions contribute significantly in binding and additional hydrogen bonds were formed between theaflavin and Arg454, Phe456, Asn460, Cys480, Gln493, Asn501 and Val503 of SARS-CoV-2 RBD, near the direct contact area with ACE2. Our results suggest that theaflavin could be the candidate of SARS-CoV-2 entry inhibitor for further study.
Dynamic Normalization

The normalization model has been applied to explain neural activity in diverse neural systems including primary visual cortex (V1). The model’s defining characteristic is that the response of each neuron is divided by a factor that includes a weighted sum of activity of a pool of neurons. In spite of the success of the normalization model, there are 3 unresolved issues. 1) Experimental evidence suggests that normalization in V1 operates via recurrent amplification, i.e., amplifying weak inputs more than strong inputs. It is unknown how normalization arises from recurrent amplification. 2) Experiments have demonstrated that normalization is weighted such each weight specifies how one neuron contributes to another’s normalization pool. It is unknown how weighted normalization arises from a recurrent circuit. 3) Neural activity in V1 exhibits complex dynamics, including gamma oscillations, linked to normalization. It is unknown how these dynamics emerge from normalization. Here, a new family of recurrent circuit models is reported, each of which comprises coupled neural integrators to implement normalization via recurrent amplification with arbitrary normalization weights, some of which can recapitulate key experimental observations of the dynamics of neural activity in V1. Significance Statement A family of recurrent circuit models is proposed to explain the dynamics of neural activity in primary visual cortex (V1). Each of the models in this family exhibits steady state output responses that are already known to fit a wide range of experimental data from diverse neural systems. These models can recapitulate the complex dynamics of V1 activity, including oscillations (so-called gamma oscillations, ~30-80 Hz). This theoretical framework also explains key aspects of working memory and motor control. Consequently, the same circuit architecture is applicable to a variety of neural systems, and V1 can be used as a model system for understanding the neural computations in many brain areas.
Melatonin Protects T-2 toxin-induced neuronal stress through Acetylcholinesterase & Cytochrome P450 receptor-mediated signaling

T-2 toxin is one of the potent mycotoxins responsible for several pathological conditions in humans and animals. This nonvolatile low molecular weight toxin compound shows strong resistance to degradation at room temperature as well as at autoclaving temperature. The inhibition of acetylcholinesterase and cytochrome P450 receptor by T-2 toxin leads to many pathological conditions as these two receptors involved in many pathways. Here, we have used melatonin as a protection agent against T-2 toxin in both receptor systems. Using molecular docking, molecular dynamics simulation and free energy calculations we have shown that melatonin can act as a potent inhibitor of T-2 toxin in acetylcholinesterase and cytochrome P450.
Decreased confidence in loss-avoidance contexts is a primary meta-cognitive bias of human reinforcement learning

In simple probabilistic instrumental-learning tasks, humans learn to seek reward and to avoid punishment equally well. Despite this remarkable symmetry in choice accuracy between gain and loss contexts, two recent effects of valence have been independently documented in reinforcement learning. First, decisions in a loss-context are slower, which is consistent with the Pavlovian-instrumental transfer hypothesis. Second, the loss context decreases individuals’ confidence in their choices. Whether these two effects are two facets of a single process or two independent effects of valence is still unknown. Here, across five experiments, we assessed the relative merit of the two hypotheses. Our results show that, in loss-contexts, the decrease in confidence in one’s choices can be robustly observed in the absence of the response time bias. This suggests that the effects of valence on motor and metacognitive responses, although concomitant in most cases, are dissociable. Jointly, these results highlight new important constraints that should be incorporated in mechanistic models of decision-making that integrate choice, reaction times and confidence.
Identification and Expression Analysis of Heat Shock Proteins in Wheat Infected with Powdery Mildew and Stripe Rust

Heat shock proteins (HSPs), which are encoded by conserved gene families in plants, are crucial for development and responses to diverse stresses. However, the wheat (Triticum aestivum) HSPs have not been systematically classified, especially those involved in protecting plants from disease. Here, we classified 119 DnaJ (Hsp40) proteins (TaDnaJs; encoded by 313 genes) and 41 Hsp70 proteins (TaHsp70s; encoded by 95 genes) into six and four groups, respectively, via a phylogenetic analysis. An examination of protein structures and a multiple sequence alignment revealed diversity in the TaDnaJ structural organization, but a highly conserved J-domain, which was usually characterized by an HPD motif followed by DRD or DED motifs. The expression profiles of these HSP-encoding homologous genes varied in response to Blumeria graminis f. sp. tritici and Puccinia striiformis f. sp. tritici. A quantitative real-time PCR analysis indicated a lack of similarity in the expression of DnaJ70b, Hsp70-30b, and Hsp90-4b in wheat infected by B. graminis f. sp. tritici, although the expression levels of these genes were abnormal in the infected resistant and susceptible lines. Furthermore, a direct interaction between DnaJ70 and TaHsp70-30 was not detected in a yeast two-hybrid assay. This study revealed the structure and expression profiles of the HSP-encoding genes in wheat. The resulting data may be useful for future functional analyses and for further elucidating the roles of wheat HSPs during responses to fungal infections.
In-cell destabilization of a homodimeric protein complex detected by DEER spectroscopy

Significance The question how does the intracellular environment affect the structure, dynamics, and stability of a protein and protein–protein interactions has been a center of interest in the context of understanding proteins function in their native environment. We addressed this question by exploring the conformational space and the stability of a homodimeric protein complex in human cells as compared to in dilute buffer solution and cell lysates. We showed that the dimer is destabilized in the cells, which is opposite to the theoretical predictions. Based on complementary in vitro measurements, we suggest that the destabilization originates from a combination of the crowding and shape of the dimer, the higher ionic strength in the cell, and potential attractive chemical interactions. The complexity of the cellular medium can affect proteins’ properties, and, therefore, in-cell characterization of proteins is essential. We explored the stability and conformation of the first baculoviral IAP repeat (BIR) domain of X chromosome-linked inhibitor of apoptosis (XIAP), BIR1, as a model for a homodimer protein in human HeLa cells. We employed double electron–electron resonance (DEER) spectroscopy and labeling with redox stable and rigid Gd3+ spin labels at three representative protein residues, C12 (flexible region), E22C, and N28C (part of helical residues 26 to 31) in the N-terminal region. In contrast to predictions by excluded-volume crowding theory, the dimer–monomer dissociation constant KD was markedly higher in cells than in solution and dilute cell lysate. As expected, this increase was partially recapitulated under conditions of high salt concentrations, given that conserved salt bridges at the dimer interface are critically required for association. Unexpectedly, however, also the addition of the crowding agent Ficoll destabilized the dimer while the addition of bovine serum albumin (BSA) and lysozyme, often used to represent interaction with charged macromolecules, had no effect. Our results highlight the potential of DEER for in-cell study of proteins as well as the complexities of the effects of the cellular milieu on protein structures and stability.
Drivers of change and ecosystem status in a temperate lake over the last Post-Glacial period from 14.5 kyr

Understanding the long-term dynamics of ecological communities on the centuries-to-millennia scale is important for explaining present-day biodiversity patterns. Placing these patterns in a historical context could yield reliable tools for predicting possible future scenarios. Paleoarchives of macro+ and micro-fossil remains, and most importantly biomarkers such as fossil pigments and ancient DNA present in various sedimentary deposits, allow long term changes in ecological communities to be analysed. We use recent compilations of data including fossil pigments, metabarcoding of sedimentary ancient DNA and microfossils together with data analysis to understand the impact of gradual versus abrupt climate changes on a lake`s ecosystem status over the last 14.5 kyr. We give examples of hypotheses that need long-term data, which can be addressed using well-established paleoproxy variables. These variables describe the climate, together with vegetation change and the appearance of anthropogenic forcing, either as a gradual change or an abrupt event. We were able to detect abrupt changes in the lake ecosystem during the stable period of the Holocene Thermal Maximum and we highlight the increased frequency and degree of perturbation in lakes due to non-immediate human activity over a larger region. Both observations demonstrate an impaired relationship between a gradual external driver and ecosystem response and apply to future scenarios of climate warming and increased human impact in north-eastern Europe.
Roads as conduits of taxonomic, functional and phylogenetic degradation in caatinga vegetation

Road networks cause disturbances that can alter the biodiversity and the functioning of the Caatinga ecosystems. We tested the hypotheses that (i) Caatinga vegetation near roads is less taxonomically, functionally and phylogenetically diverse, (ii) phylogenetically and functionally more clustered than vegetation further from roads, (iii) plant traits associated with herbivory deterrence are conserved within the phylogenetic lineages, and (iv) Caatinga vegetation near roads selects for disturbance-related traits. We sampled herbaceous and woody component of vegetation in four plots near roads and four plots further from roads to test these hypothesis. Sampled species were classified according to their resprouting capacity, nitrogen fixation, succulence/spines, urticancy/toxicity, lifeform, endozoochory, maximum height and maximum diameter, before we calculated the taxonomic, functional and phylogenetic diversity of plant communities. Species richness, taxonomic, functional and phylogenetic diversities were lower in plots close to the roads, confirming roads as sources of disturbances. The phylogenetic structure of the Caatinga vegetation near roads was clustered, indicating environmental filtering by herbivory as the main pervasive disturbance in Caatinga ecosystems, since traits related to herbivory deterrence were conserved within phylogenetic lineages and were filtered in near roads. Thus, roads should be considered degradation conduits causing taxonomic, phylogenetic and functional impoverishment of Caatinga vegetation.
Decision model for evaluating strategies to prevent mother-to-child transmission of HIV. Version 2.0 - draft.

The mother-to-child transmission (MTCT) model contains seven possible treatment choices: long course ZDV; short course ZDV following the Thailand PETRA Arm A and PETRA Arm B regmines; intrapartum and neonatal ZDV only; the HIVNET 012 regimen of single dose Nevirapine to the mother and child; and universal Nevirpine (Nevirpine provided to all women and children at the time of delivery without checking for HIV status). In addition to these seven treatment options the model also allows the user to choose the proportion of women undergoing a Cesarean section as well as the proportion of women that breastfeed their infants exclusively and with mixed breastfeeding and food supplements. Each of the treatment choices requires the user to supply various data including the costs of these interventions and possible user fees to offset these costs. The vertical transmission rate of the HIV virus varies by treatment option and can be manipulated by the user. Finally the user may specify a separate scenario and compare the scenario results with the results from the original base case. (excerpt)
Pinpointing of cysteine oxidation sites in vivo by high-resolution proteomics reveals mechanism of redox-dependent inhibition of STING

Protein function is regulated by post-translational modifications, among which reversible oxidation of Cys (Cys ox-PTM) emerged as a key regulatory mechanism of cellular responses. The redox regulation of virus-host interactions is well documented, but in most cases, proteins subjected to Cys ox-PTM remain unknown. The identification of Cys ox-PTM sites in vivo is essential to underpin our understanding of the mechanisms of the redox regulation. In this study, we present a proteome-wide identification of reversible Cys ox-PTM sites in vivo during stimulation by oxidants using a maleimide-based bioswitch method coupled to mass spectrometry. We identified 2720 unique Cys ox-PTM sites encompassing 1473 proteins with distinct abundance, location and functions. Label-free quantification (LFQ)-based analysis revealed the enrichment of ox-PTM in numerous pathways, many relevant to virus-host interaction. Here, we focused on the oxidation of STING, the central adaptor of the innate immune type I interferon pathway induced upon detection of cytosolic DNA. We provide the first in vivo demonstration of reversible oxidation of Cys148 and Cys206 of STING. Molecular analyses led us to establish a new model in which Cys148 oxidation is constitutive, while Cys206 oxidation is inducible by oxidative stress or by the natural ligand 2’3’-cGAMP. We show that oxidation of Cys206 has an inhibitory function to prevent STING hyperactivation through the constraint of a conformational change associated with the formation of inactive polymers containing intermolecular disulfide bonds. This provides new ground for the design of therapies targeting STING relevant to autoinflammatory disorders, immunotherapies and vaccines. Brief summary of the main results The function of proteins is regulated by post-translational modifications, among which reversible oxidation of Cys recently emerged as a key component. Comprehension of redox regulation of cellular responses requires identification of specific oxidation sites in vivo. Using a bioswitch method to specifically label Cys subjected to reversible oxidation coupled to mass spectrometry, we identified thousands of novel oxidation sites. Many are relevant to virus-host interaction pathways. Here, we focused on the oxidation of STING, an adaptor critical for activating the innate immune type I interferon pathway engaged upon cytosolic DNA sensing. Molecular studies led us to establish a new model in which STING Cys148 is oxidized at basal levels, while Cys206 oxidation is induced by oxidative stress and ligand binding. We show that oxidation of Cys206 has an inhibitory function to prevent STING hyperactivation. This study provides ground for novel research avenues aimed at designing therapeutics that target this pathway.