Miracle-dz/UniFAR-FTUs huggingface dataset:
Stabilization and l 2 gain control for networked control systems with actuator saturation

This paper is concerned with the stabilization and l 2 gain control problems for a class of networked control systems with actuator saturation. By using the switched system model, the regional stabilization condition is firstly obtained. Then, the corresponding optimization problem is given to maximize the estimate of the domain of attraction. Under zero initial condition, the state feedback controller is also designed under which the l 2 gain from disturbances to the controlled output is less than a given positive scalar. As the further discussion, the improved stabilization condition is proposed by exploring a more relaxed inequality. Finally, a simulation example is given to illustrate the effectiveness and values of the obtained results in this paper.
Mathematics Learning Assisted by GeoGebra Software to Improve SMK Student’s Spatial Ability and Mathematical Communication

Tujuan penelitian ini untuk mengetahui keefektifan pembelajaran Computer Assisted Instruction (CAI) Berbantuan Software GeoGebra terhadap kemampuan spasial dan kemampuan komunikasi matematis siswa pada materi transformasi Geometri. Populasi dalam penelitian ini adalah siswa kelas XI SMKN 3 Kuningan tahun pelajaran 2013/2014. Pemilihan sampel dengan cara purposed random sampling, pada pemilihan sampel diperoleh siswa XI-TSM 2 sebagai kelas eksperimen dan kelas XI-TSM 4 sebagai kelas kontrol. Kelas eksperimen diajar dengan pembelajaran Computer Assisted Instruction (CAI) Berbantuan Software GeoGebra, sedangkan kelas kontrol diajar dengan pembelajaran ekspositori. Pengambilan data diperoleh dengan hasil pretest dan postest untuk mendapatkan data nilai kemampuan spasial dan kemampuan komunikasi matematis siswa yang kemudian dianalisis dengan uji perbedaan rata-rata. Hasil penelitian adalah (1) Peningkatan kemampuan spasial siswa kelas eksperimen lebih baik daripada kelas kontrol. (2) Peningkatan kemampuan komunikasi matematis siswa kelas eksperimen lebih baik daripada kelas kontrol. (3) Terdapat korelasi yang positif antara kemampuan spasial dan kemampuan komunikasi matematis. The purpose of this study to determine the effectiveness of study Computer Assisted Instruction (CAI) aided software GeoGebra on spatial ability and mathematical communication skills of students in the material transformation of Geometry. The population in this study is class XI student of SMKN 3 Kuningan in the academic year 2014/2015. Election purposed sample by random sampling, sample obtained by the students XI-2 as the experimental class TSM and TSM class XI-4 as the control class. Experimental class taught by CAI aided Software GeoGebra, while the control class was taught by expository. Data obtained with the results of the pretest and posttest then analyzed with the average difference. The results are:(1) Improvement of spatial ability students experimental class is better than the control class. (2)The increase in students' mathematical communication skills experimental class is better than the control class. (3)There is a positive correlation between spatial ability and mathematical communication skills.
Automated escape system: identifying prey’s kinematic and behavioral features critical for predator evasion

Identifying the kinematic and behavioral variables of prey that influence the evasion from predator attacks is essential not only for comprehending the determinants of successful predator evasion but also for shedding light on the evolution of specific traits and the dynamics of predator-prey relationships on a larger scale. However, quantifying the relationship between these variables and the success or failure of predator evasion is challenging, particularly for variables with small variations within prey species. One promising approach to address this challenge is the use of a simulated prey system, which allows us to manipulate the kinematic and behavioral features of prey and expose them to real predators. Nevertheless, creating a system that moves comparably to real prey animals remains difficult, especially for invertebrate and lower vertebrate species that respond quickly to predators and escape rapidly. In this study, we have developed an automated escape system that is comparable to real prey species, responding to a predator within tens of milliseconds and escaping at over 1.0 m/s. The system automatically detects an approaching predator and pulls the prey away from the predator once the predator reaches a predetermined threshold distance. Reaction distance, response latency, as well as escaping speed, duration, and direction can be adjusted in the system. By repeatedly measuring the response latency and escaping speed of the system, we demonstrated the system’s ability to exhibit fast and rapid responses while maintaining consistency across successive trials. As a case study, we manipulated the escape speed and reaction distance of the prey to expose them to a predatory fish, Coreoperca kawamebari. The results show that both variables significantly affect the outcome of predator-prey interactions. These findings indicate that the developed escape system is useful for identifying kinematic and behavioral features of prey that are critical for predator evasion. Moreover, due to its relatively low cost and customizability, we propose that this system can be applied to investigate various aspects of animal behaviors (e.g., eliciting escape responses by artificial stimuli) in different animal species.
Well-posedness for the coupling between a viscous incompressible fluid and an elastic structure

In this paper, we consider a system modeling the interaction between a viscous incompressible fluid and an elastic structure. The fluid motion is represented by the classical Navier–Stokes equations while the elastic displacement is described by the linearized elasticity equation. The elastic structure is immersed in the fluid and the whole system is confined into a general bounded smooth domain of . Our main result is the local in time existence and uniqueness of a strong solution of the corresponding system.
Interrogation of RNA-protein interaction dynamics in bacterial growth

Characterising RNA-protein interaction dynamics is fundamental to understand how bacteria respond to their environment. In this study, we have analysed the dynamics of 91% of the Escherichia coli expressed proteome and the RNA-interaction properties of 271 RNA-binding proteins (RBPs) at different growth phases. We find that 68% of RBPs differentially bind RNA across growth phases and characterise 17 previously unannotated proteins as bacterial RBPs including YfiF, a ncRNA-binding protein. While these new RBPs are mostly present in Proteobacteria, two of them have human orthologs in the form of mitochondrial proteins associated with rare metabolic disorders. Moreover, we reveal novel RBP functions for proteins such as the chaperone HtpG, a new stationary phase tRNA-binding protein. Altogether, we provide the first dynamic RBPome of a bacterium, showcasing how this approach can reveal the function of uncharacterised proteins, and identify critical RNA-protein interactions for cell growth which could inform new antimicrobial therapies.
SGLT2 transcriptomic expression atlas supports a kidney-centric role for empagliflozin’s benefits in heart failure

Sodium-glucose cotransporter 2 inhibitors (SGLT2i), such as empagliflozin, have shown remarkable benefits in reducing cardiovascular events and mortality in patients with heart failure (HF) irrespective of diabetic status. Because of the magnitude of the benefits and broad application in both HF with reduced and preserved ejection fraction (EF), there have been concerted efforts to identify a mechanism for the observed benefits. One hypothesis is that SGLT2i act directly on the heart. Given empagliflozin’s high specificity to SGLT2, we reasoned that SGLT2 expression would be a requirement for cells to respond to treatment. Here, we present a comprehensive transcriptomic analysis of SLC5A2, which encodes SGLT2, at the single cell level in multiple datasets, confirming SLC5A2 expression in a subset of kidney epithelial cells but no meaningful expression in other cell types. This was true irrespective of developmental stage, disease state, sequencing method or depth, and species. Our findings support a kidney-centric role for the cardiovascular improvements reported in patients treated with SGLT2i.
Sex difference in the facilitation of fear learning by prior fear conditioning

There is now ample evidence that the strength and underlying mechanisms of memory formation can be drastically altered by prior experience. However, the prior work using rodent models on this topic has used only males as subjects, and as a result, we do know whether or not the effects of prior experience on subsequent learning are similar in both sexes. As a first step towards addressing this shortcoming rats of both sexes were given auditory fear conditioning, or fear conditioning with unsignaled shocks, followed an hour or a day later by a single pairing of light and shock. Fear memory for each experience was assessed by measuring freezing behavior to the auditory cue and fear-potentiated startle to the light. Results showed that males trained with auditory fear conditioning showed facilitated learning to the subsequent visual fear conditioning session when the two training sessions were separated by one hour or one day. Females showed evidence of facilitation in rats given auditory conditioning when they were spaced by an hour, but not when they were spaced by one day. Contextual fear conditioning did not support the facilitation of subsequent learning under any conditions. These results indicate that the mechanism by which prior fear conditioning facilitates subsequent learning differs between sexes, and they set the stage for mechanistic studies to understand the neurobiological basis of this sex difference.
A Molecular Communication model for cellular metabolism

Understanding cellular engagement with its environment is essential to control and monitor metabolism. Molecular Communication theory (MC) offers a computational means to identify environmental perturbations that direct or signify cellular behaviors by quantifying the information about a molecular environment that is transmitted through a metabolic system. We developed an model that integrates conventional flux balance analysis metabolic modeling (FBA) and MC to mechanistically expand the scope of MC, and thereby uniquely blends mechanistic biology and information theory to understand how substrate consumption is captured reaction activity, metabolite excretion, and biomass growth. This is enabled by defining several channels through which environmental information transmits in a metabolic network. The information flow in bits that is calculated through this workflow further determines the maximal metabolic effect of environmental perturbations on cellular metabolism and behaviors, since FBA simulates maximal efficiency of the metabolic system. We exemplify this method on two intestinal symbionts – Bacteroides thetaiotaomicron and Methanobrevibacter smithii – and visually consolidated the results into constellation diagrams that facilitate interpretation of information flow from given environments and thereby cultivate the design of controllable biological systems. The unique confluence of metabolic modeling and information theory in this model advances basic understanding of cellular metabolism and has applied value for the Internet of Bio-Nano Things, synthetic biology, microbial ecology, and autonomous laboratories.
Environmental enrichment promotes adaptive responding during tests of behavioral regulation in male heterogeneous stock rats

Organisms must regulate their behavior flexibly in the face of environmental challenges. Failure can lead to a host of maladaptive behavioral traits associated with a range of neuropsychiatric disorders, including attention deficit hyperactivity disorder, autism, and substance use disorders. This maladaptive dysregulation of behavior is influenced by genetic and environmental factors. For example, environmental enrichment produces beneficial neurobehavioral effects in animal models of such disorders. The present study determined the effects of environmental enrichment on a range of measures related to behavioral regulation using a large cohort of male, outbred heterogeneous stock (HS) rats as subjects to mimic the genetic variability found in the human population. Subjects were reared from late adolescence onwards either in pairs in standard housing with minimal enrichment (n=200) or in groups of 16 in a highly enriched environment consisting of a large multi-level cage filled with toys, running wheels, and shelters (n=64). Rats were subjected to a battery of tests, including: (i) locomotor response to novelty, (iI) light reinforcement, (iii) social reinforcement, (iv) reaction time, (v) a patch-depletion foraging test, (vi) Pavlovian conditioned approach, (vii) conditioned reinforcement, and (viii) cocaine conditioned cue preference. Results indicated that rats housed in the enriched environment were able to filter out irrelevant stimuli more effectively and thereby regulate their behavior more efficiently than standard-housing rats. The dramatic impact of environmental enrichment suggests that behavioral studies using standard housing conditions may not generalize to more complex environments that may be more ethologically relevant.
The substrate quality of CK2 target sites has a determinant role on their function and evolution

Most biological processes are regulated by peptide-recognition modules (PRMs) that bind to short linear motifs (SLiMs). Such interactions are rapidly reversible and often occur at low affinity. The protein kinase domain represents one such binding module, and known substrates may have full or only partial matches to the kinase recognition motif, a property known as ‘substrate quality’. However, it is not yet clear whether differences in substrate quality represent neutral variation along the phosphosite sequence or if these differences have functional consequences that are subject to selection. We explore this question in detail for the acidophilic kinase CK2. CK2 is well-characterised, clinically important, and a fundamental enzyme for many aspects of cell biology. We show that optimal CK2 sites are phosphorylated at maximal stoichiometries and found in many conditions whereas minimal substrates are phosphorylated at lower stoichiometries, are more dynamic during the cell cycle, and have regulatory functions. Optimal CK2 sites also tend to be older and more conserved than minimal sites, and evolutionary simulations indicate that the substrate quality of CK2 phosphosites is often tuned by selection. For intermediate target sites, increases or decreases to substrate quality may be deleterious, which we demonstrate experimentally for a CK2 substrate at the kinetochore. The results together suggest that minimal and optimal phosphosites are strongly differentiated in terms of their functional and evolutionary properties.
Benchmark of RF Photoinjector and Dipole Using ASTRA, GPT, and OPAL

With the rapid improvement in computing resources and codes in recent years, accelerator facilities can now achieve and rely on accurate beam dynamics simulations. These simulations include single particle effects (e.g. particle tracking in a magnetic field) as well as collective effects such as space charge (SC), and coherent synchrotron radiation (CSR). Using portions of the Argonne Wakefield Accelerator (AWA) as the benchmark model, we simulated beam dynamics with three particle tracking codes. The AWA rf photoinjector was benchmarked, primarily to study SC, in ASTRA, GPT, and OPAL-T using a 1 nC beam. A 20° dipole magnet was used to benchmark CSR effects in GPT and OPAL-T by bending a 1nC beam at energies between 2 MeV and 100 MeV. In this paper we present the results, and discuss the similarities and differences between the codes.
Hippocampal contributions to novel spatial learning are both age-related and age-invariant

Older adults show declines in spatial memory, although the extent of these alterations is not uniform across the healthy older population. Here, we investigate the stability of neural representations for the same and different spatial environments in a sample of younger and older adults using high-resolution functional magnetic resonance imaging (fMRI) of the medial temporal lobe. Older adults showed, on average, lower neural pattern similarity for retrieving the same environment and more variable neural patterns compared to young adults. We also found a positive association between spatial distance discrimination and the distinctiveness of neural patterns between environments. Our analyses suggested that one source for this association was the extent of informational connectivity to CA1 from other subfields, which was dependent on age, while another source was the fidelity of signals within CA1 itself, which was independent of age. Together, our findings suggest both age-dependent and independent neural contributions to spatial memory performance. Significance Statement Spatial memory declines with age, although some older adults show little cognitive decline, even into their 80s. One important lead for age-related changes comes from electrophysiological studies of older rats, who have less stable neural representations for a spatial environment, termed “place cells. ” Using high-resolution fMRI targeting the human hippocampus, we demonstrate that older adults also have less stable neural representations within the same environment. Our results reveal, however, that there are both age and performance dependent differences driving these effects. While older adults, on average, showed alterations in information flow within the hippocampal circuit, better performing individuals showed more differentiated neural representations regardless of age. Together, these findings provide novel insight into the impact of age on spatial memory.
Revisiting the role of mean annual precipitation in shaping functional trait distributions at a continental scale

Mean annual precipitation (MAP) plays an undisputed role in determining the spatial distribution of the vegetative ecosystems on Earth. Nevertheless, the relationship between MAP and plant functional traits remains unclear. Here, we test the relationship between eight key functional traits and MAP. Our analysis reveals a strong, coordinated response of several plant traits including leaf mass per area, leaf nitrogen, the leaf carbon isotope ratio and plant height from resource-conservative to resource-acquisitive values as MAP increased. These results establish an important role for MAP in driving trait selection across space and, therefore, a need for these effects to be included in future theoretical frameworks.
Restriction of the growth and biofilm formation of ESKAPE pathogens by caprine gut-derived probiotic bacteria

The accelerated rise of antimicrobial resistance (AMR) poses a significant global health risk, necessitating the exploration of alternative strategies for combating pathogenic infections. Biofilm-related infections, which are unresponsive to standard antibiotics, often require the use of higher-order antimicrobials with toxic side effects and a potential for disrupting the microbiome. Probiotic therapy, with its diverse benefits and inherent safety, is emerging as a promising approach for preventing and treating various infections and as an alternative to antibiotic therapy. In this study, we isolated novel probiotic bacteria from the gut of domestic goats (Capra hircus) and evaluated their antimicrobial and antibiofilm activities against the ‘ESKAPE’ group of pathogens. We performed comprehensive microbiological, biochemical, and molecular characterizations, including analysis of the 16S-rRNA gene V1-V3 region and the 16S-23S ISR region, on 20 caprine gut-derived lactic acid bacteria (LAB). Among these, six selected LABs demonstrated substantial biofilm formation in anaerobic conditions, and exhibited robust cell surface hydrophobicity and autoaggregation properties highlighting their superior enteric colonization capability. Notably, these LAB isolates exhibited broad-spectrum growth inhibitory and anti-biofilm properties against ‘ESKAPE’ pathogens. Additionally, the LAB isolates were susceptible to antibiotics listed by the European Food Safety Authority (EFSA), within the prescribed Minimum Inhibitory Concentration limits, suggesting their safety as feed additives. The remarkable probiotic characteristics exhibited by the caprine gut-derived LAB isolates in this study strongly endorse their potential as compelling alternatives to antibiotics and as direct-fed microbial (DFM) feed supplements in the livestock industry, addressing the escalating need for antibiotic-free animal products.
A unified framework to identify demographic buffering in natural populations

The Demographic Buffering Hypothesis (DBH) predicts that natural selection reduces the temporal fluctuations in demographic processes (such as survival, development, and reproduction), due to their negative impacts on population dynamics. However, a comprehensive approach that allows for the examination of demographic buffering patterns across multiple species is still lacking. Here, we propose a three-step framework aimed at identifying and quantifying demographic buffering. Firstly, we categorize species along a continuum of variance based on their stochastic elasticities. Secondly, we examine the linear selection gradients, followed by the examination of nonlinear selection gradients as the third step. With these three steps, our framework overcomes existing limitations of conventional approaches to identify and quantify demographic buffering, allows for multi-species comparisons, and offers an insight into the evolutionary forces that shape demographic buffering. We apply this framework to mammal species and discuss both the advantages and potential of our framework.
Multi-omics characterization of partial chemical reprogramming reveals evidence of cell rejuvenation

Partial reprogramming by cyclic short-term expression of Yamanaka factors holds promise for shifting cells to younger states and consequently delaying the onset of many diseases of aging. However, the delivery of transgenes and potential risk of teratoma formation present challenges for in vivo applications. Recent advances include the use of cocktails of compounds to reprogram somatic cells, but the characteristics and mechanisms of partial cellular reprogramming by chemicals remain unclear. Here, we report a multi-omics characterization of partial chemical reprogramming in fibroblasts from young and aged mice. We measured the effects of partial chemical reprogramming on the epigenome, transcriptome, proteome, phosphoproteome, and metabolome. At the transcriptome, proteome, and phosphoproteome levels, we saw widescale changes induced by this treatment, with the most notable signature being an upregulation of mitochondrial oxidative phosphorylation. Furthermore, at the metabolome level, we observed a reduction in the accumulation of aging-related metabolites. Using both transcriptomic and epigenetic clock-based analyses, we show that partial chemical reprogramming reduces the biological age of mouse fibroblasts. We demonstrate that these changes have functional impacts, as evidenced by changes in cellular respiration and mitochondrial membrane potential. Taken together, these results illuminate the potential for chemical reprogramming reagents to rejuvenate aged biological systems and warrant further investigation into adapting these approaches for in vivo age reversal.