Miracle-dz/UniFAR-FTUs huggingface dataset:
Indoleacetic Acid Levels in Wheat and Rice Seedlings under Oxygen Deficiency and Subsequent Reoxygenation

The lack of oxygen and post-anoxic reactions cause significant alterations of plant growth and metabolism. Plant hormones are active participants in these alterations. This study focuses on auxin–a phytohormone with a wide spectrum of effects on plant growth and stress tolerance. The indoleacetic acid (IAA) content in plants was measured by ELISA. The obtained data revealed anoxia-induced accumulation of IAA in wheat and rice seedlings related to their tolerance of oxygen deprivation. The highest IAA accumulation was detected in rice roots. Subsequent reoxygenation was accompanied with a fast auxin reduction to the control level. A major difference was reported for shoots: wheat seedlings contained less than one-third of normoxic level of auxin during post-anoxia, while IAA level in rice seedlings rapidly recovered to normoxic level. It is likely that the mechanisms of auxin dynamics resulted from oxygen-induced shift in auxin degradation and transport. Exogenous IAA treatment enhanced plant survival under anoxia by decreased electrolyte leakage, production of hydrogen peroxide and lipid peroxidation. The positive effect of external IAA application coincided with improvement of tolerance to oxygen deprivation in the 35S:iaaM × 35S:iaaH lines of transgene tobacco due to its IAA overproduction.
A neural circuit model for a contextual association task inspired by recommender systems

Behavioral data shows that humans and animals have the capacity to learn rules of associations applied to specific examples, and generalize these rules to a broad variety of contexts. This article focuses on neural circuit mechanisms to perform a context‐dependent association task that requires linking sensory stimuli to behavioral responses and generalizing to multiple other symmetrical contexts. The model uses neural gating units that regulate the pattern of physiological connectivity within the circuit. These neural gating units can be used in a learning framework that performs low‐rank matrix factorization analogous to recommender systems, allowing generalization with high accuracy to a wide range of additional symmetrical contexts. The neural gating units are trained with a biologically inspired framework involving traces of Hebbian modification that are updated based on the correct behavioral output of the network. This modeling demonstrates potential neural mechanisms for learning context‐dependent association rules and for the change in selectivity of neurophysiological responses in the hippocampus. The proposed computational model is evaluated using simulations of the learning process and the application of the model to new stimuli. Further, human subject behavioral experiments were performed and the results validate the key observation of a low‐rank synaptic matrix structure linking stimuli to responses.
Diabetes Management According to Health Status in Older Adults with Type 2 Diabetes Staying in Geriatric Care Facilities

Background: About 25% of adults >70 years suffer from type 2 diabetes. Due to the heterogeneity of the geriatric population, guidelines emphasize the need to individualize glycemic goals and simplify treatment strategies with the main focus of avoiding hypoglycemia. The aim of this study was to assess glycemic control in patients with type 2 diabetes in geriatric care facilities based on their individual health status. Methods: 170 medical records of older adults with type 2 diabetes in geriatric care facilities were retrospectively assessed (64.7% female, age 80 ± 9 years; glycated hemoglobin 6.8% ± 3.6% [51 ± 16 mmol/mol]; body mass index 27.9 ± 5.8 kg/m2). Based on the individual health status, patients were allocated to three groups (healthy n = 27, complex n = 86, and poor n = 57). Results: The overall blood glucose (BG) value was highest in the poor health group with 188 ± 47 mg/dL (poor) vs 167 ± 42 mg/dL (complex) vs 150 ± 34 mg/dL (healthy). BG values of 1.6% (poor) vs 2.8% (complex) vs 1.5% (healthy) of patients were below 90 mg/dL. 36.8% (poor) vs 23.4% (complex) vs 18.5% (healthy) of patients received insulin as the main diabetes therapy, but of these only 14.3% (poor) vs 20% (complex) vs 40% (healthy) were treated with basal insulin. Conclusions: Overall, BG values were higher in the poor and complex health group. There were a few low BG values in all groups. Although recommended by international guidelines, basal insulin therapy with its low complexity and low hypoglycemic risk is still underused, especially in the poor health group. Therefore, simplification of diabetes therapy should be considered further.
Deep Learning in Physiological Signal Data: A Survey

Deep Learning (DL), a successful promising approach for discriminative and generative tasks, has recently proved its high potential in 2D medical imaging analysis; however, physiological data in the form of 1D signals have yet to be beneficially exploited from this novel approach to fulfil the desired medical tasks. Therefore, in this paper we survey the latest scientific research on deep learning in physiological signal data such as electromyogram (EMG), electrocardiogram (ECG), electroencephalogram (EEG), and electrooculogram (EOG). We found 147 papers published between January 2018 and October 2019 inclusive from various journals and publishers. The objective of this paper is to conduct a detailed study to comprehend, categorize, and compare the key parameters of the deep-learning approaches that have been used in physiological signal analysis for various medical applications. The key parameters of deep-learning approach that we review are the input data type, deep-learning task, deep-learning model, training architecture, and dataset sources. Those are the main key parameters that affect system performance. We taxonomize the research works using deep-learning method in physiological signal analysis based on: (1) physiological signal data perspective, such as data modality and medical application; and (2) deep-learning concept perspective such as training architecture and dataset sources.
Talin: A potential drug target for Cancer therapy.

Talin is an intracellular cytoskeletal protein and one of the major components of the focal adhesion complex. It mainly acts as an interlink between transmembrane integrin receptors and cytosolic F-actin. Apart from integrins and actin, it also interacts with various other proteins in the adhesion complex to regulate their functional dynamics. Talin undergoes a variety of post-translational modifications and they are implicated in the control of cell motility. There are two talin isoforms (talin1 and talin2) in mammals and they are encoded by TLN1 and TLN2 genes. Recent studies showed that both the isoforms have some mechanistic dissimilarities in terms of their interaction with membrane-bound Integrins. Among the two isoforms, talin1 was well studied and most of the information available till now comes from talin1. The present review was aimed to provide an updated overview on the cellular significance of talin in normal and cancerous cells.
Molecular Mechanisms Involved in the Impairment of Boar Sperm Motility by Peroxynitrite-Induced Nitrosative Stress

Excessive levels of reactive nitrogen species (RNS) produce nitrosative stress. Among RNS is peroxynitrite, a highly reactive free radical generated when nitric oxide reacts with superoxide anion. Peroxynitrite effects have been mainly studied in somatic cells, and in spermatozoa the majority of studies are focused in humans. The aim of this study is to investigate the in vitro peroxynitrite effect on boar spermatozoa functions and the molecular mechanisms involved. Spermatozoa were exposed to the donor 3-morpholinosydnonimine (SIN-1) in non-capacitating or capacitating medium, motility was evaluated by CASA, functional parameters by flow cytometry and sperm protein phosphorylation by Western blotting. SIN-1 treatment, that significantly increases peroxynitrite levels in boar spermatozoa, potentiates the capacitating-stimulated phosphorylation of cAMP-dependent protein kinase 1 (PKA) substrates and GSK-3α. SIN-1 induced peroxynitrite does not decrease sperm viability, but significantly reduces sperm motility, progressive motility, velocities and motility coefficients. Concomitantly, peroxynitrite does not affect mitochondrial membrane potential, plasma membrane fluidity, or A23187-induced acrosome reaction. However, peroxynitrite significantly increases sperm lipid peroxidation in both media. In conclusion, peroxynitrite compromises boar sperm motility without affecting mitochondrial activity. Although peroxynitrite potentiates the phosphorylation of pathways leading to sperm motility, it also causes oxidative stress that might explain, at least partially, the motility impairment.
Chronic Stress Induces Maladaptive Behaviors by Activating Corticotropin-Releasing Hormone Signaling in the Mouse Oval Bed Nucleus of the Stria Terminalis

The bed nucleus of the stria terminalis (BNST) is a forebrain region highly responsive to stress that expresses corticotropin-releasing hormone (CRH) and is implicated in mood disorders, such as anxiety. However, the exact mechanism by which chronic stress induces CRH-mediated dysfunction in BNST and maladaptive behaviors remains unclear. Here, we first confirmed that selective acute optogenetic activation of the oval nucleus BNST (ovBNST) increases maladaptive avoidance behaviors in male mice. Next, we found that a 6 week chronic variable mild stress (CVMS) paradigm resulted in maladaptive behaviors and increased cellular excitability of ovBNST CRH neurons by potentiating mEPSC amplitude, altering the resting membrane potential, and diminishing M-currents (a voltage-gated K+ current that stabilizes membrane potential) in ex vivo slices. CVMS also increased c-fos+ cells in ovBNST following handling. We next investigated potential molecular mechanism underlying the electrophysiological effects and observed that CVMS increased CRH+ and pituitary adenylate cyclase-activating polypeptide+ (PACAP; a CRH upstream regulator) cells but decreased striatal-enriched protein tyrosine phosphatase+ (a STEP CRH inhibitor) cells in ovBNST. Interestingly, the electrophysiological effects of CVMS were reversed by CRHR1-selective antagonist R121919 application. CVMS also activated protein kinase A (PKA) in BNST, and chronic infusion of the PKA-selective antagonist H89 into ovBNST reversed the effects of CVMS. Coadministration of the PKA agonist forskolin prevented the beneficial effects of R121919. Finally, CVMS induced an increase in surface expression of phosphorylated GluR1 (S845) in BNST. Collectively, these findings highlight a novel and indispensable stress-induced role for PKA-dependent CRHR1 signaling in activating BNST CRH neurons and mediating maladaptive behaviors. SIGNIFICANCE STATEMENT Chronic stress and acute activation of oval bed nucleus of the stria terminalis (ovBNST) induces maladaptive behaviors in rodents. However, the precise molecular and electrophysiological mechanisms underlying these effects remain unclear. Here, we demonstrate that chronic variable mild stress activates corticotropin-releasing hormone (CRH)-associated stress signaling and CRH neurons in ovBNST by potentiating mEPSC amplitude and decreasing M-current in male mice. These electrophysiological alterations and maladaptive behaviors were mediated by BNST protein kinase A-dependent CRHR1 signaling. Our results thus highlight the importance of BNST CRH dysfunction in chronic stress-induced disorders.
Investigating Effects of Bordered Pit Membrane Morphology and Properties on Plant Xylem Hydraulic Functions—A Case Study from 3D Reconstruction and Microflow Modelling of Pit Membranes in Angiosperm Xylem

Pit membranes in between neighboring conduits of xylem play a crucial role in plant water transport. In this review, the morphological characteristics, chemical composition and mechanical properties of bordered pit membranes were summarized and linked with their functional roles in xylem hydraulics. The trade-off between xylem hydraulic efficiency and safety was closely related with morphology and properties of pit membranes, and xylem embolism resistance was also determined by the pit membrane morphology and properties. Besides, to further investigate the effects of bordered pit membranes morphology and properties on plant xylem hydraulic functions, here we modelled three-dimensional structure of bordered pit membranes by applying a deposition technique. Based on reconstructed 3D pit membrane structures, a virtual fibril network was generated to model the microflow pattern across inter-vessel pit membranes. Moreover, the mechanical behavior of intervessel pit membranes was estimated from a single microfibril’s mechanical property. Pit membranes morphology varied among different angiosperm and gymnosperm species. Our modelling work suggested that larger pores of pit membranes do not necessarily contribute to major flow rate across pit membranes; instead, the obstructed degree of flow pathway across the pit membranes plays a more important role. Our work provides useful information for studying the mechanism of microfluid flow transport across pit membranes and also sheds light on investigating the response of pit membranes both at normal and stressed conditions, thus improving our understanding on functional roles of pit membranes in xylem hydraulic function. Further work could be done to study the morphological and mechanical response of bordered pit membranes under different dehydrated conditions, as well as the related microflow behavior, based on our constructed model.
Current status and perspectives of xanthones production using cultured plant biocatalyst models aided by in-silico tools for its optimization

Abstract With an increasing interest in exploring the biocatalyst potential for the production of natural products (NP), research in NP biotechnology now follows. Xanthones constitute an important class of phytochemicals exhibiting a myriad of bioactivities and potential for interacting with multimolecular targets, and xanthones are considered to be privileged phytochemical scaffolds in medicinal chemistry. Recent advances in xanthones biosynthetic pathways are outlined and their metabolic engineering. This review summarizes the state-of-the-art processes for the biotechnological production of xanthones, its limitations, and potential improvements. The in vitro tissue culturing methods employed for the production of xanthones from different species of plant are reviewed addressing differences in xanthone classes. This review sheds the light of computational approaches, viz., response surface methodology (RSM) and artificial neural networks (ANN), for optimizing the culture performance and improving xanthones production.
Phenolic compounds: Natural alternative in inflammation treatment. A Review

Abstract Inflammation is a biological defense mechanism caused by the interruption of the tissue homeostasis caused by the presence of a biological, chemical, or physical agents in the body; immune system produces a series of pro-inflammatory mediators, however their overproduction, as occurs in chronic inflammation, might lead to the occurrence of several chronic diseases. For this reason, slowing down the inflammation process becomes very important, and with this purpose non-steroid anti-inflammatory drugs are generally used with the subsequent occurrence of adverse side effects. As an alternative in inflammation treatment, folklore medicine has used several plants and herbs with minimal or null side effects, with the phenolic compounds being one of their principal components. Phenolic compounds are able to inhibit either the production or the action of pro-inflammatory mediators, resulting in anti-inflammatory capacity.
Relationship of dairy heifer reproduction with survival to first calving, milk yield and culling risk in the first lactation

Objective The aim of our study was to determine the associations of heifer reproductive performance with survival up to the first calving, first-lactation milk yield, and the probability of being culled within 50 days after first calving. Methods Data from 33 large Holstein-Friesian commercial dairy herds were gathered from the official milk recording database in Hungary. The data of heifers first inseminated between January 1, 2011 and December 31, 2014 were analyzed retrospectively, using Cox proportional hazards models, competing risks models, multivariate linear and logistic mixed-effects models. Results Heifers (n = 35,128) with younger age at conception were more likely to remain in the herd until calving, and each additional month in age at conception increased culling risk by 5.1%. Season of birth was related to first-lactation milk yield (MY1; n = 19,931), with cows born in autumn having the highest milk production (p<0.001). The highest MY1 was achieved by heifers that first calved between 22.00 and 25.99 months of age. Heifers that calved in autumn had the highest MY1, whereas calving in summer was related to the lowest milk production (p<0.001). The risk of culling within 50 days in milk in first lactation (n = 21,225) increased along with first calving age, e.g. heifers that first calved after 30 months of age were 5.52-times more likely to be culled compared to heifers that calved before 22 months of age (p<0.001). Calving difficulty was related to higher culling risk in early lactation (p<0.001). Heifers that required caesarean section were 24.01-times more likely to leave the herd within 50 days after first calving compared to heifers that needed no assistance (p<0.001). Conclusion Reproductive performance of replacement heifers is closely linked to longevity and milk production in dairy herds.
Emergence of coagulase-negative staphylococci

ABSTRACT Introduction: Compared to Staphylococcus aureus, coagulase-negative staphylococci (CoNS) are characterized by a lower capacity to cause acute, live-threatened infections. CoNS are, however, of ever increasing importance as pathogens causing infections in immunocompromised patients and after foreign-material implantation. Typically, antibiotics fail to cure foreign body-related infections and removal of the implanted device is inevitable. Areas covered: This review focuses on the emergence of CoNS species, their pathogenic potential in particular due to their ability to form therapy-refractory biofilms on biotic and abiotic surfaces and evasion strategies to resist host response and antibiotic treatment. Their medical significance and proven and novel therapy strategies are discussed. Expert opinion: CoNS contribute significantly to morbidity and socio-economic costs. The anticipated developments in modern medicine, in particular the increasing use of foreign materials and the rising numbers of immunocompromised patients, as well as the changing demographic and hospital-related factors will inevitably contribute to further emergence of CoNS infections. Increasing rates of (multi-)resistant CoNS strains will limit the therapeutic armamentarium and aggravate treatment strategies. Increased research is necessary to understand their role as resistance and virulence gene reservoir and to reduce CoNS infections by the development of innovative colonization-preventing materials and other CoNS-tailored treatment strategies.
Functional validation of nicotinic acetylcholine receptor (nAChR) α6 as a target of spinosyns in Spodoptera exigua utilizing the CRISPR/Cas9 system.

BACKGROUND The beet armyworm, Spodoptera exigua, is a serious agricultural pest that primarily controlled using chemical insecticides. Recently, resistance to the insecticide spinosad has been described in S. exigua field populations. To date, there has been no functional evidence proving the involvement of the nicotinic acetylcholine receptor (nAChR) α6 mutation in spinosad resistance in S. exigua. RESULTS In this study, using the CRISPR/Cas9 genome-editing system, a homozygous strain (Seα6-KO) with ~1760-bp deletion within Seα6 in S. exigua causing a premature truncation of Seα6 was successfully constructed. Insecticide bioassays showed that Seα6-KO exhibited 373-fold higher resistance to spinosad and 850-fold higher resistance to spinetoram compared to WH-S strain with the same genetic background but showed no significant change in susceptibility to emamectin benzoate and chlorantraniliprole. Genetic analysis revealed that Seα6-KO is inherited as an incompletely recessive trait. CONCLUSION The results clearly demonstrated the functional role of Seα6 in resistance to spinosyn insecticides and provide an example of using genome editing to verify a target premature truncation associated with resistance. This article is protected by copyright. All rights reserved.
The first comprehensive LC-MS/MS method allowing dissection of the thiamine pathway in plants.

Arabidopsis thaliana serves as a model plant for genetic research, including vitamin research. When aiming at engineering the thiamine (vitamin B1) pathway in plants, availability of tools that allow the quantitative determination of different intermediates in the biosynthesis pathway is of pivotal importance. This is a challenge, given the nature of the compounds and the minute quantities of genetically engineered material that may be available for analysis. Here, we report on the first LC-MS/MS method for the simultaneous quantification of thiamine, its mono- and diphosphate derivatives and its precursors 4-methyl-5-(2-hydroxyethyl) thiazole (HET) and 4-amino-2-methyl-5-hydroxymethylpyrimidine (HMP). This method was optimized and validated for the quantitative determination of these analytes in Arabidopsis thaliana. All analytes were chromatographically separated within less than 2.5 min during an 8 min run. No unacceptable interferences were found. The method was fully validated based on international guidelines. Accuracy (%bias) and total imprecision (%CV) were within pre-set acceptance criteria for all analytes in both QC and real samples. All analytes were stable in extracted samples when stored for 48h at 4°C (autosampler stability) and when re-analyzed after storage at -80°C and -20°C for 2 weeks (freeze/thaw stability). We demonstrated the start material should be stored at -80°C to ensure stability of all analytes during short- and long-term storage (up to 3 months). The validity and applicability of the developed procedure was demonstrated via its successful application on Arabidopsis lines, genetically engineered to enhance thiamine content.