Miracle-dz/UniFAR-FTUs huggingface dataset:
The Ubiquitin Conjugating Enzyme: An Important Ubiquitin Transfer Platform in Ubiquitin-Proteasome System

Owing to a sessile lifestyle in nature, plants are routinely faced with diverse hostile environments such as various abiotic and biotic stresses, which lead to accumulation of free radicals in cells, cell damage, protein denaturation, etc., causing adverse effects to cells. During the evolution process, plants formed defense systems composed of numerous complex gene regulatory networks and signal transduction pathways to regulate and maintain the cell homeostasis. Among them, ubiquitin-proteasome pathway (UPP) is the most versatile cellular signal system as well as a powerful mechanism for regulating many aspects of the cell physiology because it removes most of the abnormal and short-lived peptides and proteins. In this system, the ubiquitin-conjugating enzyme (E2) plays a critical role in transporting ubiquitin from the ubiquitin-activating enzyme (E1) to the ubiquitin-ligase enzyme (E3) and substrate. Nevertheless, the comprehensive study regarding the role of E2 enzymes in plants remains unexplored. In this review, the ubiquitination process and the regulatory role that E2 enzymes play in plants are primarily discussed, with the focus particularly put on E2′s regulation of biological functions of the cell.
Changes in the Cellular Distribution of Tyrosine Phosphorylation and Its Relationship with the Acrosomal Exocytosis and Plasma Membrane Integrity during In Vitro Capacitation of Frozen/Thawed Bull Spermatozoa

During sperm capacitation, intracellular signaling leads to protein tyrosine phosphorylation (PTP) of multiple cellular structures. However, the connection of this molecular signaling to the physiology of capacitated spermatozoa is not completely understood. This is the case of the short lifespan of capacitated spermatozoa and their increased susceptibility to initiate acrosomal exocytosis (AE) during incubation. Herein, by employing frozen/thawed bull spermatozoa, we aimed to study the relationship between PTP with AE and with plasma membrane integrity (PMI) at the cellular level. For this, we employed double staining following immunofluorescence for PTP combined with fluorescence probes for the acrosome (PNA-FITC) and PMI (LIVE/DEAD Fixable Dead Cell Stain Kit). Our results revealed that the presence of PTP at sperm head was less abundant in the sperm fraction that triggered the AE after 3 h of incubation under capacitating conditions, or by its induction with calcium ionophore, compared to the unreacted fraction. Furthermore, PTP at the equatorial region of the head (PTP-EQ) was enriched in the fraction showing damaged membrane while induction of AE with calcium ionophore did not alter the PMI and its relation to PTP-EQ. These results suggest that spontaneous AE and induced AE trigger similar cellular events regarding PTP and the spermatozoa showing PTP-EQ are more prone to suffer plasma membrane damage.
Evaluation of CAN Bus Security Challenges †

The automobile industry no longer relies on pure mechanical systems; instead, it benefits from many smart features based on advanced embedded electronics. Although the rise in electronics and connectivity has improved comfort, functionality, and safe driving, it has also created new attack surfaces to penetrate the in-vehicle communication network, which was initially designed as a close loop system. For such applications, the Controller Area Network (CAN) is the most-widely used communication protocol, which still suffers from various security issues because of the lack of encryption and authentication. As a result, any malicious/hijacked node can cause catastrophic accidents and financial loss. This paper analyses the CAN bus comprehensively to provide an outlook on security concerns. It also presents the security vulnerabilities of the CAN and a state-of-the-art attack surface with cases of implemented attack scenarios and goes through different solutions that assist in attack prevention, mainly based on an intrusion detection system (IDS).
A Population-Based Analysis of Interpersonal Trauma, Psychosis, and Suicide: Evidence, Pathways, and Implications

Subthreshold psychotic experiences (PEs) are known to confer a risk for suicidality. Yet, despite evidence of a strong etiological trauma–psychosis pathway, the coalesced effect of such concurrences on suicide risk is largely discounted. Our aims were to examine the impact of different manifestations of life span trauma and PEs on the risk of suicidal thoughts and attempts, using an exploratory person-centered approach. Data from the Adult Psychiatric Morbidity Survey (N = 7,403) were analyzed. PEs were assessed using the Psychosis Screening Questionnaire (PSQ) alongside items probing childhood and adult trauma, in addition to 12-month suicide thoughts and attempt. A manual three-step latent class analysis elicited four distinct profiles, namely, a socially disconnected/high PE, a sexual victimization/moderate PE, a life span trauma/low PE, and a baseline class. The socially disconnected class, characterized by a moderate likelihood of social disconnection, a high probability of various PE endorsements, yet a low likelihood of other significant trauma, showed the greatest risk of 12-month suicide ideation (odds ratio [OR] = 13.0, 95% confidence interval [CI] = [8.539, 19.021) and attempt (OR = 24.2, 95% CI = [10.349, 56.860). Neither multiple nor recurrent traumatic experiences invariably result in the emergence of PEs. Instead, a sense of social disconnection may be either resultant of PEs or alone sufficient to cultivate such symptom presentations, even in the absence of prior traumas. Moreover, just as traumatic encounters increase the risk of suicidality, so too might seemingly more innocuous adversities, such as poor-quality social relationships, further elevate the risk, particularly when proximal and coupled with the simultaneity of PEs.
Increased Risk of Chronic Periodontitis in Chronic Rhinosinusitis Patients: A Longitudinal Follow-Up Study Using a National Health-Screening Cohort

This study compared the risk of chronic periodontitis (CP) between chronic rhinosinusitis (CRS) and non-chronic rhinosinusitis (control) patients using a national cohort dataset from the Korean Health Insurance Review and Assessment Service. CRS (n = 5951) and control participants (n = 23,804) were selected after 1:4 ratio matching for age, sex, income, region of residence, and preoperative CP visits. Postoperative CP visits were measured between 2002 and 2015. The margin of equivalence of the difference between the CRS and control groups was set between −0.5 and 0.5. Statistical significance was noted in the post-index date (ID) of the third, fourth, and fifth year periods. In subgroup analyses according to age and sex, statistical significance was observed in 40–59-year-old males in post-ID third, fourth, and fifth year periods, ≥60-year-old males in post-ID third and fourth year periods, and ≥60-year-old females in post-ID fifth year period (p < 0.05, each). In another subgroup analysis based on the number of pre-ID CP visits, statistical significance was observed for pre-ID CP (0 time) in the third, fourth, and fifth year periods (p < 0.05, each). This study revealed that CRS participants were likely to receive CP diagnosis and treatment.
Near-infrared light-steered graphene aerogel micromotor with high speed and precise navigation for active transport and micro-assembly.

Fuel-free light-driven micromotors have attracted increasing attention since the advantages of reversible, noninvasive and remote manoeuvre on demand with excellent spatial and temporal resolution. However they are suffering from challenging bottleneck of the rather modest motion speed, which hinders their applications needing to overcome the water flow movement in environmental water. Herein, we demonstrate a near-infrared light (NIR)-steered, precise navigation-controlled micromotor based on reduced graphene oxide aerogel microsphere (RGOAM), which possess isotropic structure and is easily prepared by one-step electrospray approach other than conventional light-propelled micromotors with Janus structure. Benefiting from ultralight weight of aerogel and lesser fluid resistance on the water surface, the RGOAM motors show the higher motion speed (up to 17.60 mm/s) than that in the published literatures, letting it overcomes counter flow. Taking advantage of photothermal conversion capacity of RGOAM under asymmetric light field, it is capable of moving both on the water driven by the Marangoni effect and under the water via light-manipulated density change. The motion direction and speed on water, as well as "start/stop" state can be precisely steered by NIR light even in a complicated maze. Due to its strong adsorption and loading capacity, the RGOAM can be applied for active loading-transport-release of dyes on-demand, as well as micro-parts assembling and shaping. Our work provides a strategy to achieve high speed, precise navigation control as well as functional extensibility simultaneously for micromotors, which may offers considerable promise for the broad biomedical and environmental applications.
Factors Influencing Emerging Adults’ Use of Outpatient Mental Health Services

ABSTRACT Rates of treatment utilization decline as adolescents make the transition to adulthood even though young adults are particularly vulnerable to the negative outcomes of untreated mental illness. Although a variety of factors have been explored to explain decreased treatment utilization in this age group, previous research has almost exclusively employed cross-sectional methods rather than following a group of youth as they enter adulthood. The current study aims to address this methodological limitation by assessing treatment utilization in emerging adults who began participating in a longitudinal study during childhood. One hundred and thirty seven youth who turned 18 during the 96-month follow-up period were included in the current analyses. Demographic and socioeconomic variables such as sex, race, and insurance status and clinical variables such as psychiatric diagnoses and perceptions of treatment effectiveness were investigated as factors potentially associated with outpatient treatment use before and after age 18. Prior to age 18, youth reported using outpatient services at 75% of their visits, but after age 18, outpatient treatment utilization dropped to around 50%. White race, increased parental stress, and increased parental perception of treatment usefulness were associated with greater treatment use prior to age 18, whereas only increased youth perception of symptom-related dysfunction were associated with increased treatment use after age 18. Findings point to the importance of including youth preferences and perceptions of dysfunction in treatment decisions across adolescence in order to optimize treatment use following the transition to adulthood.
Hospitalization for Lactic Acidosis Among Patients With Reduced Kidney Function Treated With Metformin or Sulfonylureas

OBJECTIVE To compare the risk of lactic acidosis hospitalization between patients treated with metformin versus sulfonylureas following development of reduced kidney function. RESEARCH DESIGN AND METHODS This retrospective cohort combined data from the National Veterans Health Administration, Medicare, Medicaid, and the National Death Index. New users of metformin or sulfonylureas were followed from development of reduced kidney function (estimated glomerular filtration rate [eGFR] <60 mL/min/1.73 m2 or serum creatinine ≥1.4 mg/dL [female] or 1.5 mg/dL [male]) through hospitalization for lactic acidosis, death, loss to follow-up, or study end. Lactic acidosis hospitalization was defined as a composite of primary discharge diagnosis or laboratory-confirmed lactic acidosis (lactic acid ≥2.5 mmol/L and either arterial blood pH <7.35 or serum bicarbonate ≤19 mmol/L within 24 h of admission). We report the cause-specific hazard of lactic acidosis hospitalization between metformin and sulfonylureas from a propensity score–matched weighted cohort and conduct an additional competing risks analysis to account for treatment change and death. RESULTS The weighted cohort included 24,542 metformin users and 24,662 sulfonylurea users who developed reduced kidney function (median age 70 years, median eGFR 55.8 mL/min/1.73 m2). There were 4.18 (95% CI 3.63, 4.81) vs. 3.69 (3.19, 4.27) lactic acidosis hospitalizations per 1,000 person-years among metformin and sulfonylurea users, respectively (adjusted hazard ratio [aHR] 1.21 [95% CI 0.99, 1.50]). Results were consistent for both primary discharge diagnosis (aHR 1.11 [0.87, 1.44]) and laboratory-confirmed lactic acidosis (1.25 [0.92, 1.70]). CONCLUSIONS Among veterans with diabetes who developed reduced kidney function, occurrence of lactic acidosis hospitalization was uncommon and not statistically different between patients who continued metformin and those patients who continued sulfonylureas.
Thrips as the Transmission Bottleneck for Mixed Infection of Two Orthotospoviruses

Mixed infections provide opportunities for viruses to increase genetic diversity by facilitating genomic reassortment or recombination, and they may lead to the emergence of new virus species. Mixed infections of two economically important orthotospoviruses, Tomato spotted wilt orthotospovirus (TSWV) and Impatiens necrotic spot orthotospovirus (INSV), were found in recent years, but no natural reassortants between INSV and TSWV were ever reported. The goal of this study was to establish how vector preferences and the ability to transmit INSV and TSWV influence transmission and establishment of mixed infections. Our results demonstrate that thrips prefer to oviposit on TSWV and INSV mixed-infected plants over singly infected or healthy plants, providing young nymphs with the opportunity to acquire both viruses. Conversely, we observed that thrips served as a bottleneck during transmission and favored transmission of one of the two viruses over the second one, or over transmission of both viruses simultaneously. This constraint was relaxed in plants, when transmission of TSWV and INSV occurred sequentially, demonstrating that plants serve as orthotospovirus permissive hosts, while thrips serve as a bottleneck. Viral fitness, as measured by virus replication, transmission, and competition with other viral strains, is not well studied in mixed infection. Our study looks at the success of transmission during mixed infection of orthotopoviruses, enhancing the understanding of orthotospovirus epidemiology and evolution.
Metabolic Gene Expression in the Muscle and Blood Parameters of Broiler Chickens Stimulated In Ovo with Synbiotics

Simple Summary Poultry production plays a major role in providing meat products to global markets. Hence, there is a continued interest of researchers in the possibilities of improving the production parameters of broiler chickens. A direct response from muscles and their metabolism to in ovo synbiotic stimulation on day 12 of egg incubation has already been widely documented. However, it is necessary to analyze the molecular mechanisms determining the phenotypic effects. The present research aimed to explain the molecular background of the quality of broiler chicken meat after injection of synbiotics based on Lactobacillus strains into the air chamber of the egg. Characterization of the meat quality is based on the signature of the metabolic gene expression closely related to muscles and basic physiological parameters. Abstract To better understand the effects of synbiotics administered at early stages of embryonic development in poultry, it is necessary to analyze direct effects (meat quality) and the molecular background. The molecular interpretation of poultry meat properties after in ovo administration of synbiotics remains to be reported. The purpose of the present study was to analyze the molecular background of meat quality based on gene expression and basic physiological parameters. Eggs were injected with (S1) Lactobacillus salivarius with galacto-oligosaccharides or (S2) Lactobacillus plantarum with raffinose family oligosaccharides. The pectoral muscle was collected at two time points (day 7 and day 42) and subjected to RNA isolation. Gene expression analysis was performed by RT-qPCR for a panel of eight genes associated with metabolism. The concentration of glucose and hormones (insulin, glucagon, and leptin (S1 p = 0.04)) was also increased. The obtained results showed that metabolic gene expression in the muscle was more differential due to synbiotic stimulation on day 7 (FST in S1 p = 0.03; PDK4 in S1 p = 0.02 and S2 p = 0.01; CEBPB in S1 p = 0.01 and S2 p = 0.008; PHKB in S1 p = 0.01; PRKAG3 in S1 p = 0.02) than on day 42 (PDK4 in S1 p = 0.04). On the basis of the results obtained, it can be concluded that in ovo stimulation with S1 triggered the most potent and favorable changes in the pectoral muscle gene expression in broiler chickens.
Influence of Carbyne Content on the Mechanical Performance of Nanothick Amorphous Carbon Coatings

This study concerns the evaluation of the coefficient of friction, at different temperatures, of amorphous carbon thin films, deposited onto nanocrystalline sputtered copper coatings by clean-technology rf magnetron sputtering. The aim is to access the capacity of carbon thin films, with different contents of sp2 and sp1 bonds, to act as a solid lubricant for copper surfaces. Raman spectroscopy revealed that all the as-deposited coatings consist of amorphous carbon with low defect content and decreasing carbyne concentration with increasing thickness. The tribological tests at 25 °C and 200 °C revealed that, for the higher temperature, the 15 nm carbon coating present 0.001 friction coefficients at 2 N load. Overall, the study presents a one-step technology for the greener production of solid lubrication systems for micro- and nano-components, avoiding the environmental impact of lubricants.
Transcriptomics in Toxicogenomics, Part I: Experimental Design, Technologies, Publicly Available Data, and Regulatory Aspects

The starting point of successful hazard assessment is the generation of unbiased and trustworthy data. Conventional toxicity testing deals with extensive observations of phenotypic endpoints in vivo and complementing in vitro models. The increasing development of novel materials and chemical compounds dictates the need for a better understanding of the molecular changes occurring in exposed biological systems. Transcriptomics enables the exploration of organisms’ responses to environmental, chemical, and physical agents by observing the molecular alterations in more detail. Toxicogenomics integrates classical toxicology with omics assays, thus allowing the characterization of the mechanism of action (MOA) of chemical compounds, novel small molecules, and engineered nanomaterials (ENMs). Lack of standardization in data generation and analysis currently hampers the full exploitation of toxicogenomics-based evidence in risk assessment. To fill this gap, TGx methods need to take into account appropriate experimental design and possible pitfalls in the transcriptomic analyses as well as data generation and sharing that adhere to the FAIR (Findable, Accessible, Interoperable, and Reusable) principles. In this review, we summarize the recent advancements in the design and analysis of DNA microarray, RNA sequencing (RNA-Seq), and single-cell RNA-Seq (scRNA-Seq) data. We provide guidelines on exposure time, dose and complex endpoint selection, sample quality considerations and sample randomization. Furthermore, we summarize publicly available data resources and highlight applications of TGx data to understand and predict chemical toxicity potential. Additionally, we discuss the efforts to implement TGx into regulatory decision making to promote alternative methods for risk assessment and to support the 3R (reduction, refinement, and replacement) concept. This review is the first part of a three-article series on Transcriptomics in Toxicogenomics. These initial considerations on Experimental Design, Technologies, Publicly Available Data, Regulatory Aspects, are the starting point for further rigorous and reliable data preprocessing and modeling, described in the second and third part of the review series.
The Rostrolateral Prefrontal Cortex Mediates a Preference for High-Agency Environments

The ability to exert flexible instrumental control over one's environment is a defining feature of adaptive decision-making. Here, we investigated neural substrates mediating a preference for environments with greater instrumental divergence, the distance between outcome probability distributions associated with alternative actions. A formal index of agency, instrumental divergence allows an organism to flexibly obtain the currently most desired outcome as preferences change. As such, it may have intrinsic utility, guiding decisions toward environments that maximize instrumental power. Consistent with this notion, we found that a measure of expected value that treats instrumental divergence as a reward surrogate provided a better account of male and female human participants' choice preferences than did a conventional model, sensitive only to monetary reward. Using model-based fMRI, we found that activity in the rostrolateral and ventromedial PFC, regions associated with abstract cognitive inferences and subjective value computations, respectively, scaled with the divergence-based account of expected value. Implications for a neural common currency of information theoretic and motivational variables are discussed. SIGNIFICANCE STATEMENT Agency is a central concept in philosophy and psychology. While research thus far has focused on cognitive and perceptual measures of agency, recent work demonstrating a strong preference for high-agency environments indicates a salient motivational dimension. Here, using instrumental divergence, the distance between outcome distributions associated with alternative actions, as a formal index of agency, we found that brain regions associated with directed exploration and subjective value computations, respectively, were selectively modulated by a model that treated agency as a reward surrogate, over models that assigned utility only to monetary payoffs. In a subset of regions, such effects were predicted by the influence of instrumental divergence on economic choice preferences. Our results elucidate neural mechanisms mediating the utility of agency.