Miracle-dz/UniFAR-FTUs huggingface dataset:
Virus and Viroid-Derived Small RNAs as Modulators of Host Gene Expression: Molecular Insights Into Pathogenesis

Virus-derived siRNAs (vsiRNAs) generated by the host RNA silencing mechanism are effectors of plant’s defense response and act by targeting the viral RNA and DNA in post-transcriptional gene silencing (PTGS) and transcriptional gene silencing (TGS) pathways, respectively. Contrarily, viral suppressors of RNA silencing (VSRs) compromise the host RNA silencing pathways and also cause disease-associated symptoms. In this backdrop, reports describing the modulation of plant gene(s) expression by vsiRNAs via sequence complementarity between viral small RNAs (sRNAs) and host mRNAs have emerged. In some cases, silencing of host mRNAs by vsiRNAs has been implicated to cause characteristic symptoms of the viral diseases. Similarly, viroid infection results in generation of sRNAs, originating from viroid genomic RNAs, that potentially target host mRNAs causing typical disease-associated symptoms. Pathogen-derived sRNAs have been demonstrated to have the propensity to target wide range of genes including host defense-related genes, genes involved in flowering and reproductive pathways. Recent evidence indicates that vsiRNAs inhibit host RNA silencing to promote viral infection by acting as decoy sRNAs. Nevertheless, it remains unclear if the silencing of host transcripts by viral genome-derived sRNAs are inadvertent effects due to fortuitous pairing between vsiRNA and host mRNA or the result of genuine counter-defense strategy employed by viruses to enhance its survival inside the plant cell. In this review, we analyze the instances of such cross reaction between pathogen-derived vsiRNAs and host mRNAs and discuss the molecular insights regarding the process of pathogenesis.
Velocity-Porosity-Mineralogy Model for Unconventional Shale and Its Applications to Digital Rock Physics

By examining wireline data from Woodford and Wolfcamp gas shale, we find that the primary controls on the elastic-wave velocity are the total porosity, kerogen content, and mineralogy. At a fixed porosity, both V p and V s strongly depend on the clay content, as well as on the kerogen content. Both velocities are also strong functions of the sum of the above two components. Even better discrimination of the elastic properties at a fixed porosity is attained if we use the elastic-wave velocity of the solid matrix (including kerogen) of rock as the third variable. This finding, fairly obvious in retrospect, helps combine all mineralogical factors into only two variables, V p and V s of the solid phase. The constant-cement rock physics model, whose mathematical form is the modified lower Hashin-Shtrikman elastic bound, accurately describes the data. The inputs to this model include the elastic moduli and density of the solid component (minerals plus kerogen), those of the formation fluid, the differential pressure, and the critical porosity and coordination number (the average number of grain-to-grain contacts at the critical porosity). We show how this rock physics model can be used to predict the elastic properties from digital images of core, as well as 2D scanning electron microscope images of very small rock fragments.
An Activated Potassium Phosphate Fertilizer Solution for Stimulating the Growth of Agricultural Plants

This study aimed to develop a sustainable industrial chemical engineering technology to improve the interaction between technology, plants, and soil in agriculture. The signaling crosstalk between H2O2 and NO and that between H2O2 and Ca2+ influence plant developmental and physiological processes. Many promising technologies for crop stimulation and protection are based on a thorough study of the environmental impact of various physical factors. A low-temperature, high-frequency plasma was generated via cathode high-frequency glow discharge and used for the electrolysis of an aqueous solution of a low concentration of the strong electrolyte KH2PO4, with an electrolysis-activated solution named Plasmolite. The Plasmolite solution yielded a Raman (red) scattering spectrum with a maximum at 1,640 cm−1, which was associated with hydrogen atom vibrations, and other bands at 875, 930, 1,050, and 1,123 cm−1, which were associated with the aqueous electrolyte solution plasma treatment. Based on the goal of producing an optimal H2O2 concentration of 100 μM, two types of seeds were exposed to a Plasmolite-based 2 × 10–5 M KH2PO4 solution moisturizing medium for three days. Approximately 92% of the spring spelled seeds (grade “Gremme”) that were exposed to this test solution sprouted, compared with 76% of the seeds exposed to a control solution. The spring rye seeds (grade “Onokhoyskaya”) that were exposed to the test solution sprouted at a rate of 90% compared with 75% in the control. The percentage of seeds that sprouted with a root length of more than 6 mm was approximately 80% for the test solution, compared to 50% for the control. Based on these results, the use of Plasmolite is considered to be promising for the production of activated H2O2 for protecting plants and stimulating growth, particularly for enhancing the functions of K and P2O5 of fertilizers.
Sub-Regional Differences of the Human Amniotic Membrane and Their Potential Impact on Tissue Regeneration Application

For more than 100 years, the human amniotic membrane (hAM) has been used in multiple tissue regeneration applications. The hAM consists of cells with stem cell characteristics and a rich layer of extracellular matrix. Undoubtedly, the hAM with viable cells has remarkable properties such as the differentiation potential into all three germ layers, immuno-modulatory, and anti-fibrotic properties. At first sight, the hAM seems to be one structural entity. However, by integrating its anatomical location, the hAM can be divided into placental, reflected, and umbilical amniotic membrane. Recent studies show that cells of these amniotic sub-regions differ considerably in their properties such as morphology, structure, and content/release of certain bioactive factors. The aim of this review is to summarize these findings and discuss the relevance of these different properties for tissue regeneration. In summary, reflected amnion seems to be more immuno-modulatory and could have a higher reprogramming efficiency, whereas placental amnion seems to be pro-inflammatory, pro-angiogenic, with higher proliferation and differentiation capacity (e.g., chondrogenic and osteogenic), and could be more suitable for certain graft constructions. Therefore, we suggest that the respective hAM sub-region should be selected in consideration of its desired outcome. This will help to optimize and fine-tune the clinical application of the hAM.
Predictive Value of Prognostic Nutritional Index on COVID-19 Severity

Background: The prognostic nutritional index (PNI) has been described as a simple risk-stratified tool for several diseases. We explored the predictive role of the PNI on coronavirus disease 2019 (COVID-19) severity. Methods: A total of 101 patients with COVID-19 were included in this retrospective study from January 2020 to March 2020. They were divided into two groups according to COVID-19 severity: non-critical (n = 56) and critical (n = 45). The PNI was calculated upon hospital admission: 10 × serum albumin (g/dL) + 0.005 × total lymphocyte count (/mm3). Critical COVID-19 was defined as having one of the following features: respiratory failure necessitating mechanical ventilation; shock; organ dysfunction necessitating admission to the intensive care unit (ICU). The correlation between the PNI with COVID-19 severity was analyzed. Results: The PNI was significantly lower in critically ill than that in non-critically ill patients (P < 0.001). The receiver operating characteristic curve indicated that the PNI was a good discrimination factor for identifying COVID-19 severity (P < 0.001). Multivariate logistic regression analysis showed the PNI to be an independent risk factor for critical illness due to COVID-19 (P = 0.002). Conclusions: The PNI is a valuable biomarker that could be used to discriminate COVID-19 severity.
Bullying Victimization and Trauma

Bullying victimization and trauma research traditions operate quite separately. Hence, it is unclear from the literature whether bullying victimization should be considered as a form of interpersonal trauma. We review studies that connect bullying victimization with symptoms of PTSD, and in doing so, demonstrate that a conceptual understanding of the consequences of childhood bullying needs to be framed within a developmental perspective. We discuss two potential diagnoses that ought to be considered in the context of bullying victimization: (1) developmental trauma disorder, which was suggested but not accepted as a new diagnosis in the DSM-5 and (2) complex post-traumatic stress disorder, which has been included in the ICD-11. Our conclusion is that these frameworks capture the complexity of the symptoms associated with bullying victimization better than PTSD. We encourage practitioners to understand how exposure to bullying interacts with development at different ages when addressing the consequences for targets and when designing interventions that account for the duration, intensity, and sequelae of this type of interpersonal trauma.
hiPSC-Derived Neurons Provide a Robust and Physiologically Relevant In Vitro Platform to Test Botulinum Neurotoxins

Botulinum neurotoxins (BoNTs) are zinc metalloproteases that block neurotransmitter release at the neuromuscular junction (NMJ). Their high affinity for motor neurons combined with a high potency have made them extremely effective drugs for the treatment of a variety of neurological diseases as well as for aesthetic applications. Current in vitro assays used for testing and developing BoNT therapeutics include primary rodent cells and immortalized cell lines. Both models have limitations concerning accuracy and physiological relevance. In order to improve the translational value of preclinical data there is a clear need to use more accurate models such as human induced Pluripotent Stem Cells (hiPSC)-derived neuronal models. In this study we have assessed the potential of four different human iPSC-derived neuronal models including Motor Neurons for BoNT testing. We have characterized these models in detail and found that all models express all proteins needed for BoNT intoxication and showed that all four hiPSC-derived neuronal models are sensitive to both serotype A and E BoNT with Motor Neurons being the most sensitive. We showed that hiPSC-derived Motor Neurons expressed authentic markers after only 7 days of culture, are functional and able to form active synapses. When cultivated with myotubes, we demonstrated that they can innervate myotubes and induce contraction, generating an in vitro model of NMJ showing dose-responsive sensitivity BoNT intoxication. Together, these data demonstrate the promise of hiPSC-derived neurons, especially Motor Neurons, for pharmaceutical BoNT testing and development.
Proprioception in Action: A Matter of Ecological and Social Interaction

The aim of this paper is to provide a theoretical and formal framework to understand how the proprioceptive and kinesthetic system learns about body position and possibilities for movement in ongoing action and interaction. Whereas most weak embodiment accounts of proprioception focus on positionalist descriptions or on its role as a source of parameters for internal motor control, we argue that these aspects are insufficient to understand how proprioception is integrated into an active organized system in continuous and dynamic interaction with the environment. Our strong embodiment thesis is that one of the main theoretical principles to understand proprioception, as a perceptual experience within concrete situations, is the coupling with kinesthesia and its relational constitution—self, ecological, and social. In our view, these aspects are underdeveloped in current accounts, and an enactive sensorimotor theory enriched with phenomenological descriptions may provide an alternative path toward explaining this skilled experience. Following O'Regan and Noë (2001) sensorimotor contingencies conceptualization, we introduce three distinct notions of proprioceptive kinesthetic-sensorimotor contingencies (PK-SMCs), which we describe conceptually and formally considering three varieties of perceptual experience in action: PK-SMCs-self, PK-SMCs-self-environment, and PK-SMC-self-other. As a proof of concept of our proposal, we developed a minimal PK model to discuss these elements in detail and show their explanatory value as important guides to understand the proprioceptive/kinesthetic system. Finally, we also highlight that there is an opportunity to develop enactive sensorimotor theory in new directions, creating a bridge between the varieties of experiences of oneself and learning skills.
Minor Clinical Impact of COVID-19 Pandemic on Patients With Primary Immunodeficiency in Israel

In the last few months the world has witnessed a global pandemic due to severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2) infection causing coronavirus disease 2019 (COVID-19). Obviously, this pandemic affected individuals differently, with a significant impact on populations considered to be at high-risk. One such population, was assumed to be patients with primary genetic defect involving components or pathways of the immune system. While human immunity against COVID-19 is not fully understood, it is, so far, well documented, that both adaptive and innate cells have a critical role in protection against SARS-CoV-2. Here, we aimed to summarize the clinical and laboratory data on primary immunodeficiency (PID) patients in Israel, who were tested positive for SARS-CoV-2, in order to estimate the impact of COVID-19 on such patients. Data was collected from mid-February to end-September. During this time Israel experienced two “waves” of COVID-19 diseases; the first, from mid-February to mid-May and the second from mid-June and still ongoing at the end of data collection. A total of 20 PID patients, aged 4 months to 60 years, were tested positive for SARS-CoV-2, all but one, were detected during the second wave. Fourteen of the patients were on routine monthly IVIG replacement therapy at the time of virus detection. None of the patients displayed severe illness and none required hospitalization; moreover, 7/20 patients were completely asymptomatic. Possible explanations for the minimal clinical impact of COVID-19 pandemic observed in our PID patients include high level of awareness, extra-precautions, and even self-isolation. It is also possible that only specific immune pathways (e.g. type I interferon signaling), may increase the risk for a more severe course of disease and these are not affected in many of the PID patients. In some cases, lack of an immune response actually may be a protective measure against the development of COVID-19 sequelae.
Identification of Key Genes in Purine Metabolism as Prognostic Biomarker for Hepatocellular Carcinoma

Background Deregulated purine metabolism is critical for fast-growing tumor cells by providing nucleotide building blocks and cofactors. Importantly, purine antimetabolites belong to the earliest developed anticancer drugs and are still prescribed in clinics today. However, these antimetabolites can inhibit non-tumor cells and cause undesired side effects. As liver has the highest concentration of purines, it makes liver cancer a good model to study important nodes of dysregulated purine metabolism for better patient selection and precisive cancer treatment. Methods By using a training dataset from TCGA, we investigated the differentially expressed genes (DEG) of purine metabolism pathway (hsa00230) in hepatocellular carcinoma (HCC) and determined their clinical correlations to patient survival. A prognosis model was established by Lasso‐penalized Cox regression analysis, and then validated through multiple examinations including Cox regression analysis, stratified analysis, and nomogram using another ICGC test dataset. We next treated HCC cells using chemical drugs of the key enzymes in vitro to determine targetable candidates in HCC. Results The DEG analysis found 43 up-regulated and 2 down-regulated genes in the purine metabolism pathway. Among them, 10 were markedly associated with HCC patient survival. A prognostic correlation model including five genes (PPAT, DCK, ATIC, IMPDH1, RRM2) was established and then validated using the ICGC test dataset. Multivariate Cox regression analysis found that both prognostic risk model (HR = 4.703 or 3.977) and TNM stage (HR = 2.303 or 2.957) independently predicted HCC patient survival in the two datasets respectively. The up-regulations of the five genes were further validated by comparing between 10 pairs of HCC tissues and neighboring non-tumor tissues. In vitro cellular experiments further confirmed that inhibition of IMPDH1 significantly repressed HCC cell proliferation. Conclusion In summary, this study suggests that purine metabolism is deregulated in HCC. The prognostic gene correlation model based on the five purine metabolic genes may be useful in predicting HCC prognosis and patient selection. Moreover, the deregulated genes are targetable by specific inhibitors.
e-Banking Adoption: An Opportunity for Customer Value Co-creation

The development of information and communication technologies offers innovative opportunities to establish business strategies focused on customer value co-creation. This situation is especially notable in the banking industry. e-Banking activities can support competitive advantages. However, the adoption of e-banking is not yet well-established among consumers. In this sense, the technology acceptance model (TAM) is considered essential in studying consumer behavior applied to adopt a particular technology. According to the TAM model, this study analyses the factors which influence bank customers to adopt e-banking to facilitate their banking services and support the process of value co-creation. Consequently, the authors examine five main aspects of the technology adoption model to provide a broad understanding of bank customers’ consumption of e-banking. A partial least squares structural equation modeling (PLS-SEM) analysis is conducted to evaluate proposed relationships between factors and customers’ e-banking adoption.
Long-Term Dietary Restriction Leads to Development of Alternative Fighting Strategies

In competition for food, mates and territory, most animal species display aggressive behavior through visual threats and/or physical attacks. Such naturally-complex social behaviors have been shaped by evolution. Environmental pressure, such as the one imposed by dietary regimes, forces animals to adapt to specific conditions and ultimately to develop alternative behavioral strategies. The quality of the food resource during contests influence animals' aggression levels. However, little is known regarding the effects of a long-term dietary restriction-based environmental pressure on the development of alternative fighting strategies. To address this, we employed two lines of the wild-type Drosophila melanogaster Canton-S (CS) which originated from the same population but raised under two distinct diets for years. One diet contained both proteins and sugar, while the second one was sugar-free. We set up male-male aggression assays using both CS lines and found differences in aggression levels and the fighting strategies employed to establish dominance relationships. CS males raised on a sugar-containing diet started fights with a physical attack and employed a high number of lunges for establishing dominance but displayed few wing threats throughout the fight. In contrast, the sugar-free-raised males favored wing threats as an initial aggressive demonstration and used fewer lunges to establish dominance, but displayed a higher number of wing threats. This study demonstrates that fruit flies that have been raised under different dietary conditions have adapted their patterns of aggressive behavior and developed distinct fighting strategies: one favoring physical attacks, while the other one favoring visual threats.
Characterization of QTL and Environmental Interactions Controlling Flowering Time in Andean Common Bean (Phaseolus vulgaris L.)

Genetic variation for response of flowering time to photoperiod plays an important role in adaptation to environments with different photoperiods, and as consequence is an important contributor to plant productivity and yield. To elucidate the genetic control of flowering time [days to flowering (DTF); growing degree days (GDD)] in common bean, a facultative short-day plant, a quantitative trait loci (QTL) analysis was performed in a recombinant inbred mapping population derived from a cultivated accession and a photoperiod sensitive landrace, grown in different long-day (LD) and short-day (SD) environments by using a multiple-environment QTL model approach. A total of 37 QTL across 17 chromosome regions and 36 QTL-by-QTL interactions were identified for six traits associated with time to flowering and response to photoperiod. The DTF QTL accounted for 28 and 11% on average of the phenotypic variation in the population across LD and SD environments, respectively. Of these, a genomic region on chromosome 4 harboring the major DTF QTL was associated with both flowering time in LD and photoperiod response traits, controlling more than 60% of phenotypic variance, whereas a major QTL on chromosome 9 explained up to 32% of flowering time phenotypic variation in SD. Different epistatic interactions were found in LD and SD environments, and the presence of significant QTL × environment (QE) and epistasis × environment interactions implies that flowering time control may rely on different genes and genetic pathways under inductive and non-inductive conditions. Here, we report the identification of a novel major locus controlling photoperiod sensitivity on chromosome 4, which might interact with other loci for controlling common bean flowering time and photoperiod response. Our results have also demonstrated the importance of these interactions for flowering time control in common bean, and point to the likely complexity of flowering time pathways. This knowledge will help to identify and develop opportunities for adaptation and breeding of this legume crop.