Miracle-dz/UniFAR-FTUs huggingface dataset:
Reduction of Allergenic Potential in Bread Wheat RNAi Transgenic Lines Silenced for CM3, CM16 and 0.28 ATI Genes

Although wheat is used worldwide as a staple food, it can give rise to adverse reactions, for which the triggering factors have not been identified yet. These reactions can be caused mainly by kernel proteins, both gluten and non-gluten proteins. Among these latter proteins, α-amylase/trypsin inhibitors (ATI) are involved in baker’s asthma and realistically in Non Celiac Wheat Sensitivity (NCWS). In this paper, we report characterization of three transgenic lines obtained from the bread wheat cultivar Bobwhite silenced by RNAi in the three ATI genes CM3, CM16 and 0.28. We have obtained transgenic lines showing an effective decrease in the activity of target genes that, although showing a higher trypsin inhibition as a pleiotropic effect, generate a lower reaction when tested with sera of patients allergic to wheat, accounting for the important role of the three target proteins in wheat allergies. Finally, these lines show unintended differences in high molecular weight glutenin subunits (HMW-GS) accumulation, involved in technological performances, but do not show differences in terms of yield. The development of new genotypes accumulating a lower amount of proteins potentially or effectively involved in allergies to wheat and NCWS, not only offers the possibility to use them as a basis for the production of varieties with a lower impact on adverse reaction, but also to test if these proteins are actually implicated in those pathologies for which the triggering factor has not been established yet.
TonEBP Promotes β-Cell Survival under ER Stress by Enhancing Autophagy

The endoplasmic reticulum (ER) stress response and autophagy are important cellular responses that determine cell fate and whose dysregulation is implicated in the perturbation of homeostasis and diseases. Tonicity-responsive enhancer-binding protein (TonEBP, also called NFAT5) is a pleiotropic stress protein that mediates both protective and pathological cellular responses. Here, we examined the role of TonEBP in β-cell survival under ER stress. We found that TonEBP increases β-cell survival under ER stress by enhancing autophagy. The level of TonEBP protein increased under ER stress due to a reduction in its degradation via the ubiquitin–proteasome pathway. In response to ER stress, TonEBP increased autophagosome formations and suppressed the accumulation of protein aggregates and β-cell death. The Rel-homology domain of TonEBP interacted with FIP200, which is essential for the initiation of autophagy, and was required for autophagy and cell survival upon exposure to ER stress. Mice in which TonEBP was specifically deleted in pancreatic endocrine progenitor cells exhibited defective glucose homeostasis and a loss of islet mass. Taken together, these findings demonstrate that TonEBP protects against ER stress-induced β-cell death by enhancing autophagy.
A Phase-Coded Sequence Design Method for Active Sonar

Phase-coded sequences are widely studied as the transmitted signals of active sonars. Recently, several design methods have been developed to generate phased-coded sequences satisfying specific aperiodic or periodic autocorrelation sidelobe level metrics. In this paper, based on the majorization–minimization strategy and the squared iterative acceleration scheme, we propose a method to generate sequences with the periodic weighted integrated sidelobe level metric. Numerical simulations illustrate that the proposed method can effectively suppress the periodic autocorrelation sidelobe levels in specific time lags. Compared with other sequence design methods satisfying the periodic weighted integrated sidelobe level metric, our method improves the computational efficiency significantly. In addition, the proposed sequence demonstrates better matched filter performance in specific range intervals compared with its counterpart. The results suggest that the method could be applied as a valid and real-time design method for transmitted signals of active sonars.
Metagenomic and 14 C tracing evidence for autotrophic microbial CO2 fixation in paddy soils.

Autotrophic carbon dioxide (CO2 ) fixation by microbes is ubiquitous in the environment and potentially contributes to the soil organic carbon (SOC) pool. However, the multiple autotrophic pathways of microbial carbon assimilation and fixation in paddy soils remain poorly characterized. In this study, we combine metagenomic analysis with 14 C-labelling to investigate all known autotrophic pathways and CO2 assimilation mechanisms in five typical paddy soils from southern China. Marker genes of six autotrophic pathways are detected in all soil samples, which are dominated by the cbbL genes (67-82%) coding the ribulose-bisphosphate carboxylase large chain in the Calvin cycle. These marker genes are associated with a broad range of phototrophic and chemotrophic genera. Significant amounts of 14 C-CO2 are assimilated into SOC (74.3 to 175.8 mg 14 C kg-1 ) and microbial biomass (5.2 to 24.1 mg 14 C kg-1 ) after 45 days incubation, where more than 70% of 14 C-SOC was concentrated in the relatively stable humin fractions. These results show that paddy soil microbes contain the genetic potential for autotrophic carbon fixation spreading over broad taxonomic ranges, and can incorporate atmospheric carbon into organic components, which ultimately contribute to the stable SOC pool. This article is protected by copyright. All rights reserved.
Ultrastructure of conidiogenesis and conidia in two species of Septoria sensu lato

Conidiogenesis and conidial morphology of Septoria quercicola and S. aceris was studied with light (LM) and transmission electron microscopy (TEM) in vivo and in vitro on three media. No fun- damental differences in conidiogenesis were ob- served between these species. Ontogeny of conidia is holoblastic, and after delimitation by a transverse sep- tum, conidia are liberated schizolytically. Prolifera- tion of the conidiogenous cell can be percurrent or sympodial, and three categories of conidiogenous cells occur: (i) annellides, (ii) sympodulae, and (iii) cells proliferating both percurrently and sympodially. Conidiogenous cells of the last category were only observed in vivo, and most had a number of percur- rent and one or two terminal sympodial prolifera- tions. Annellides with close annellations had been in- terpreted as phialides with periclinal thickenings in LM. After secession, a majority of conidia of S. quer- cicola and S. aceris developed noncellular, mucoid ap- pendages on either end, visible in LM and TEM; in S. quercicola appendages were formed in vivo and in vitro, in S. aceris only in vitro. No influence of either illumination (diffuse daylight or near-UV) or medi- um (OA, CMA, 2% MEA) was observed on qualitative aspects of conidiogenesis. The data are compared with those of S. chrysanthemella and their significance to Septoria systematics is discussed. The relation with Septoriella in respect of ontogeny of mucoid append-
TLR3-Dependent Activation of TLR2 Endogenous Ligands via the MyD88 Signaling Pathway Augments the Innate Immune Response

The role of the adaptor molecule MyD88 is thought to be independent of Toll-like receptor 3 (TLR3) signaling. In this report, we demonstrate a previously unknown role of MyD88 in TLR3 signaling in inducing endogenous ligands of TLR2 to elicit innate immune responses. Of the various TLR ligands examined, the TLR3-specific ligand polyinosinic:polycytidylic acid (poly I:C), significantly induced TNF production and the upregulation of other TLR transcripts, in particular, TLR2. Accordingly, TLR3 stimulation also led to a significant upregulation of endogenous TLR2 ligands mainly, HMGB1 and Hsp60. By contrast, the silencing of TLR3 significantly downregulated MyD88 and TLR2 gene expression and pro-inflammatory IL1β, TNF, and IL8 secretion. The silencing of MyD88 similarly led to the downregulation of TLR2, IL1β, TNF and IL8, thus suggesting MyD88 to somehow act downstream of TLR3. Corroborating in vitro data, Myd88−/− knockout mice downregulated TNF, CXCL1; and phospho-p65 and phospho-IRF3 nuclear localization, upon poly I:C treatment in a mouse model of skin infection. Taken together, we identified a previously unknown role for MyD88 in the TLR3 signaling pathway, underlying the importance of TLRs and adapter protein interplay in modulating endogenous TLR ligands culminating in pro-inflammatory cytokine regulation.
A Scaffold-Free 3-D Co-Culture Mimics the Major Features of the Reverse Warburg Effect In Vitro

Most tumors consume large amounts of glucose. Concepts to explain the mechanisms that mediate the achievement of this metabolic need have proposed a switch of the tumor mass to aerobic glycolysis. Depending on whether primarily tumor or stroma cells undergo such a commutation, the terms ‘Warburg effect’ or ‘reverse Warburg effect’ were coined to describe the underlying biological phenomena. However, current in vitro systems relying on 2-D culture, single cell-type spheroids, or basal-membrane extract (BME/Matrigel)-containing 3-D structures do not thoroughly reflect these processes. Here, we aimed to establish a BME/Matrigel-free 3-D microarray cancer model to recapitulate the metabolic interplay between cancer and stromal cells that allows mechanistic analyses and drug testing. Human HT-29 colon cancer and CCD-1137Sk fibroblast cells were used in mono- and co-cultures as 2-D monolayers, spheroids, and in a cell-chip format. Metabolic patterns were studied with immunofluorescence and confocal microscopy. In chip-based co-cultures, HT-29 cells showed facilitated 3-D growth and increased levels of hexokinase-2, TP53-induced glycolysis and apoptosis regulator (TIGAR), lactate dehydrogenase, and: translocase of outer mitochondrial membrane 20 (TOMM20), when compared with HT-29 mono-cultures. Fibroblasts co-cultured with HT-29 cells expressed higher levels of mono-carboxylate transporter 4, hexokinase-2, microtubule-associated proteins 1A/1B light chain 3, and ubiquitin-binding protein p62 than in fibroblast mono-cultures, in both 2-D cultures and chips. Tetramethylrhodamin-methylester (TMRM) live-cell imaging of chip co-cultures revealed a higher mitochondrial potential in cancer cells than in fibroblasts. The findings demonstrate a crosstalk between cancer cells and fibroblasts that affects cellular growth and metabolism. Chip-based 3-D co-cultures of cancer cells and fibroblasts mimicked features of the reverse Warburg effect.
Comparison of Static and Dynamic Assays When Quantifying Thermal Plasticity of Drosophilids

Simple Summary Temperature directly affects many biological processes, from enzymatic reactions to population growth, and thermal stress tolerance is central to our understanding of the global distribution and abundance of species and populations. Given the importance of thermal stress tolerance in ecophysiology and evolutionary biology it is important to be able to measure thermal stress resistance accurately and in ecologically relevant ways. Several methods for such quantification exist in the arthropod literature and the comparability of different methods is currently being debated. Here we reconcile the two most commonly used thermal assays (dynamic ramping and static knockdown assays) for quantifying insect heat tolerance limits and plastic responses using a newly suggested modeling technique. We find that results obtained on the basis of the two assays are highly correlated and that data from one assay can therefore reasonably well predict estimates from the other. These data are of general relevance to the study of thermal biology of ectotherms. Abstract Numerous assays are used to quantify thermal tolerance of arthropods including dynamic ramping and static knockdown assays. The dynamic assay measures a critical temperature while the animal is gradually heated, whereas the static assay measures the time to knockdown at a constant temperature. Previous studies indicate that heat tolerance measured by both assays can be reconciled using the time × temperature interaction from “thermal tolerance landscapes” (TTLs) in unhardened animals. To investigate if this relationship remains true within hardened animals, we use a static assay to assess the effect of heat hardening treatments on heat tolerance in 10 Drosophila species. Using this TTL approach and data from the static heat knockdown experiments, we model the expected change in dynamic heat knockdown temperature (CTmax: temperature at which flies enter coma) and compare these predictions to empirical measurements of CTmax. We find that heat tolerance and hardening capacity are highly species specific and that the two assays report similar and consistent responses to heat hardening. Tested assays are therefore likely to measure the same underlying physiological trait and provide directly comparable estimates of heat tolerance. Regardless of this compliance, we discuss why and when static or dynamic assays may be more appropriate to investigate ectotherm heat tolerance.
A Robust Laser Stripe Extraction Method for Structured-Light Vision Sensing

Environmental sensing is a key technology for the development of unmanned cars, drones and robots. Many vision sensors cannot work normally in an environment with insufficient light, and the cost of using multiline LiDAR is relatively high. In this paper, a novel and inexpensive visual navigation sensor based on structured-light vision is proposed for environment sensing. The main research contents of this project include: First, we propose a laser-stripe-detection neural network (LSDNN) that can eliminate the interference of reflective noise and haze noise and realize the highly robust extraction of laser stripes region. Then we use a gray-gravity approach to extract the center of laser stripe and used structured-light model to reconstruct the point clouds of laser center. Then, we design a single-line structured-light sensor, select the optimal parameters for it and build a car–platform for experimental evaluation. This approach was shown to be effective in our experiments and the experimental results show that this method is more accurate and robust in complex environment.
Association of Infertility Treatment with Perception of Infant Crying, Bonding Impairment and Abusive Behavior towards One’s Infant: A Propensity-Score Matched Analysis

Background: Although previous qualitative studies suggested the link between infertility treatment and negative emotions towards infants, few empirical population-based studies have investigated the association of infertility treatment with the perception of infant crying, bonding impairment, and abusive behavior towards one’s infant. Methods: Women who participated in a four month health-checkup program in Aichi Prefecture, Japan (n = 6590) were asked to a complete a questionnaire that included infertility treatment history, perception of infant crying, maternal–infant bonding impairment assessed by the Mother to Infant Bonding Scale Japanese version, and abusive behavior towards one’s infant. Outcomes were dichotomized, and a conditional logistic regression was applied, using the propensity score match for infertility treatment exposure adjusted for known covariates. Results: A total of 690 participants (11.1%) reported infertility treatment history, and 625 cases were matched. We found that mothers with infertility treatment history were 1.36 times more likely to perceive a higher frequency of infant crying (95% confidence interval (CI):1.05–1.78), but no association with maternal–infant bonding impairment (odds ratio (OR): 1.18; 95% CI: 0.81–1.72) and abusive behavior towards the infant (OR: 0.82; 95% CI: 0.49–1.36). Conclusions: Infertility treatment may be associated with the perception of a higher frequency of infant crying, but it is not associated with bonding impairment and abusive behavior. Further longitudinal study is needed to replicate the findings.
Introduction to the Special Issue on Advances in Biological Tissue Biomechanics

Chung-Hao Lee 1,2,* and Jun Liao 3,* 1 Biomechanics and Biomaterials Design Laboratory (BBDL), School of Aerospace and Mechanical Engineering, The University of Oklahoma, Norman, OK 73019, USA 2 Institute for Biomedical Engineering, Science and Technology (IBEST), The University of Oklahoma, Norman, OK 73019, USA 3 Tissue Biomechanics and Bioengineering Laboratory (TBBL), Department of Bioengineering, University of Texas at Arlington, Arlington, TX 76010, USA * Correspondence: ch.lee@ou.edu (C.-H.L.); jun.liao@uta.edu (J.L.)
Production of Biodegradable Palm Oil-Based Polyurethane as Potential Biomaterial for Biomedical Applications

Being biodegradable and biocompatible are crucial characteristics for biomaterial used for medical and biomedical applications. Vegetable oil-based polyols are known to contribute both the biodegradability and biocompatibility of polyurethanes; however, petrochemical-based polyols were often incorporated to improve the thermal and mechanical properties of polyurethane. In this work, palm oil-based polyester polyol (PPP) derived from epoxidized palm olein and glutaric acid was reacted with isophorone diisocyanate to produce an aliphatic polyurethane, without the incorporation of any commercial petrochemical-based polyol. The effects of water content and isocyanate index were investigated. The polyurethanes produced consisted of > 90% porosity with interconnected micropores and macropores (37–1700 µm) and PU 1.0 possessed tensile strength and compression stress of 111 kPa and 64 kPa. The polyurethanes with comparable thermal stability, yet susceptible to enzymatic degradation with 7–59% of mass loss after 4 weeks of treatment. The polyurethanes demonstrated superior water uptake (up to 450%) and did not induce significant changes in pH of the medium. The chemical changes of the polyurethanes after enzymatic degradation were evaluated by FTIR and TGA analyses. The polyurethanes showed cell viability of 53.43% and 80.37% after 1 and 10 day(s) of cytotoxicity test; and cell adhesion and proliferation in cell adhesion test. The polyurethanes produced demonstrated its potential as biomaterial for soft tissue engineering applications.
Advanced Nanomaterials, Printing Processes, and Applications for Flexible Hybrid Electronics

Recent advances in nanomaterial preparation and printing technologies provide unique opportunities to develop flexible hybrid electronics (FHE) for various healthcare applications. Unlike the costly, multi-step, and error-prone cleanroom-based nano-microfabrication, the printing of nanomaterials offers advantages, including cost-effectiveness, high-throughput, reliability, and scalability. Here, this review summarizes the most up-to-date nanomaterials, methods of nanomaterial printing, and system integrations to fabricate advanced FHE in wearable and implantable applications. Detailed strategies to enhance the resolution, uniformity, flexibility, and durability of nanomaterial printing are summarized. We discuss the sensitivity, functionality, and performance of recently reported printed electronics with application areas in wearable sensors, prosthetics, and health monitoring implantable systems. Collectively, the main contribution of this paper is in the summary of the essential requirements of material properties, mechanisms for printed sensors, and electronics.
A Translational Study on Acute Traumatic Brain Injury: High Incidence of Epileptiform Activity on Human and Rat Electrocorticograms and Histological Correlates in Rats

Background: In humans, early pathological activity on invasive electrocorticograms (ECoGs) and its putative association with pathomorphology in the early period of traumatic brain injury (TBI) remains obscure. Methods: We assessed pathological activity on scalp electroencephalograms (EEGs) and ECoGs in patients with acute TBI, early electrophysiological changes after lateral fluid percussion brain injury (FPI), and electrophysiological correlates of hippocampal damage (microgliosis and neuronal loss), a week after TBI in rats. Results: Epileptiform activity on ECoGs was evident in 86% of patients during the acute period of TBI, ECoGs being more sensitive to epileptiform and periodic discharges. A “brush-like” ECoG pattern superimposed over rhythmic delta activity and periodic discharge was described for the first time in acute TBI. In rats, FPI increased high-amplitude spike incidence in the neocortex and, most expressed, in the ipsilateral hippocampus, induced hippocampal microgliosis and neuronal loss, ipsilateral dentate gyrus being most vulnerable, a week after TBI. Epileptiform spike incidence correlated with microglial cell density and neuronal loss in the ipsilateral hippocampus. Conclusion: Epileptiform activity is frequent in the acute period of TBI period and is associated with distant hippocampal damage on a microscopic level. This damage is probably involved in late consequences of TBI. The FPI model is suitable for exploring pathogenetic mechanisms of post-traumatic disorders.
Induction of Callogenesis, Organogenesis, and Embryogenesis in Non-Meristematic Explants of Bleeding Heart and Evaluation of Chemical Diversity of Key Metabolites from Callus

Lamprocapnos spectabilis (L.) Fukuhara is a perennial plant species valued in the horticultural, cosmetic, and pharmaceutical markets. To date, however, there were no studies on tissue culture systems in this species when adjusted from non-meristematic explants. The aim of this study is to induce callogenesis, organogenesis, and somatic embryogenesis in non-meristematic explants of Lamprocapnos spectabilis ‘Alba’ cultured in various media and to analyze the chemical diversity of the produced callus. Leaf, petiole, and internode explants were cultured on the modified Murashige and Skoog (MS) medium fortified with various combinations and concentrations of 6-benzyladenine (BA), indole-3-acetic acid (IAA), 1-naphthaleneacetic acid (NAA), 2,4-dichlorphenoxyacetic acid (2,4-D), and picloram (PIC). After 10 weeks of culturing, the morphogenetic response of explants was evaluated and the concentration of chlorophylls, carotenoids, anthocyanins, and polyphenols in callus was analyzed. There was no influence of explant type on the callogenesis efficiency (62.1–65.3%). The highest fresh weight of callus was produced on leaf explants in the presence of 2,4-D or PIC. In contrast, the highest share of dry weight was found in internode-derived calli and cultured on IAA-supplemented medium (up to 30.8%). Only 2.5% of all explants regenerated adventitious shoots, while rhizogenesis was reported in 4.5% of explants. Somatic embryos were produced indirectly by 0% to 100% of explants, depending on the culture medium and explant type. The highest mean number of embryos (11.4 per explant) was found on petioles cultured in the MS medium with 0.5 mg·L−1 BA and 1.0 mg·L−1 PIC. Calli cultured in media with NAA usually contained a higher content of primary and secondary metabolites. There was also a significant impact of explant type on the content of anthocyanins, polyphenols, and carotenoids in callus. Further studies should focus on the elicitation of metabolites production in callus culture systems of the bleeding heart.