Miracle-dz/UniFAR-FTUs huggingface dataset:
Identification and expression analysis of the DREB transcription factor family in pineapple (Ananas comosus (L.) Merr.)

Background Dehydration responsive element-binding (DREB) transcription factors play a crucial role in plant growth, development and stress responses. Although DREB genes have been characterized in many plant species, genome-wide identification of the DREB gene family has not yet been reported in pineapple (Ananas comosus (L.) Merr. ). Results Using comprehensive genome-wide screening, we identified 20 AcoDREB genes on 14 chromosomes. These were categorized into five subgroups. AcoDREBs within a group had similar gene structures and domain compositions. Using gene structure analysis, we showed that most AcoDREB genes (75%) lacked introns, and that the promoter regions of all 20 AcoDREB genes had at least one stress response-related cis-element. We identified four genes with high expression levels and six genes with low expression levels in all analyzed tissues. We detected expression changes under abiotic stress for eight selected AcoDREB genes. Conclusions This report presents the first genome-wide analysis of the DREB transcription factor family in pineapple. Our results provide preliminary data for future functional analysis of AcoDREB genes in pineapple, and useful information for developing new pineapple varieties with key agronomic traits such as stress tolerance.
Relative influence of habitat modification and interspecific competition on woodland bird assemblages in eastern Australia

Abstract Many of eastern Australia's woodland birds have declined in recent decades. Although historical landscape transformation ultimately underlies these declines, effective conservation action requires knowledge of the relative importance of current threats to woodland birds. Through a literature review and analysis of empirical data from seven woodland regions, we investigated the relative importance of habitat structure, site context and aggressive avian competitors (miners, Manorina spp.) for woodland birds in eastern Australia. The literature review revealed that the factor which most consistently influenced the richness, abundance and assemblage composition of woodland birds was the density or presence of Manorina honeyeaters. A positive effect of site structural complexity was also often reported, but the effects of area, isolation and grazing varied among the reviewed studies. Across the seven empirical datasets, density of Manorina honeyeaters was responsible for the great majority of the independently explained variance in all but one region. We conclude that interspecific competition with Manorina honeyeaters is one of the most important and widespread processes threatening woodland birds in eastern Australia. In regions where this threatening process is prevalent, the greatest conservation gains for woodland birds may therefore be achieved by focussing on reducing habitat suitability for aggressive Manorina honeyeaters.
Ion accumulation in the cell walls of rice plants growing under saline conditions: evidence for the Oertli hypothesis

When plants of rice (Oryza sativa L.) are subjected to mildly saline (50 mol m-3 NaCl) conditions, the leaves show symptoms of water deficit, even though ion accumulation has been more than sufficient to adjust to the decrease in external water potential. After a few days of exposure to salt, there is a negative correlation, in a population of leaves, between the leaf water concentration (g water per g dry weight) and their sodium concentration (mmol Na per g dry weight). Ion concentrations in the cell walls and the cytoplasm of cells of plants grown in low salinity were measured by X-ray microanalysis. The NaCl concentration in solution in the apoplast was calculated to be around 600 mol m-3 in leaves of plants whose roots were exposed to only 50 mol m-3 NaCl. This constitutes strong evidence that an important factor in salt damage in rice is dehydration due to the extracellular accumulation of salt as suggested in the Oertli hypothesis. The implication, that changes in tissue ion concentration and solute potentials equivalent to the external medium is not evidence of plant osmotic adjustment to salinity, is discussed.
WAVE3 upregulation in esophageal squamous cell carcinoma and its effect on the migration of human esophageal cancer cell lines in vitro

The present study aimed to investigate the role of Wiskott-Aldrich syndrome verprolin-homologous protein 3 (WAVE3) in the progression of esophageal squamous cell carcinoma (ESCC), and to explore its effect on the migration of esophageal cancer cell lines in vitro. The expression level of WAVE3 in ESCC tissues was determined via immunohistochemistry, and the relative levels of WAVE3 mRNA and micro (mi)RNA200b were assessed in the serum of patients with ESCC using reverse transcription-quantitative PCR (RT-qPCR). Following cell transfection, the levels of miRNA200b and WAVE3 protein were determined via RT-qPCR and western blot analysis, and cell migration was examined using a Transwell assay. Subsequently, the clinical parameters were used to analyze whether the expression of WAVE3 in tissues and serum was associated with the occurrence and development of ESCC. The results demonstrated that the expression of WAVE3 was increased in ESCC tissues compared with normal tissues. The results also revealed increased expression levels of WAVE3 and decreased expression levels of miRNA200b in the serum of patients with ESCC, compared with healthy volunteers. High expression of WAVE3 was significantly associated with tumor TNM stage, invasion depth and lymphatic invasion of ESCC. In cells transfected with miRNA200b mimic, the miRNA200b was overexpressed, WAVE3 protein was downregulated and cell migration ability was decreased. The results of the present study suggest that WAVE3 may serve as an oncogene in ESCC, and its inhibition via miRNA200b decreased tumor cell migration. Therefore, WAVE3 may serve as a novel biological marker and therapeutic target for ESCC.
Brain responsivity provides an individual readout for motor recovery after stroke

See Fowler and Kalaria in Brain Communications (doi: 10.1093/braincomms/fcaa067) for a joint scientific commentary on this article and ‘Structural brain networks and functional motor outcome after stroke—a prospective cohort study’ by Schlemm et al. (doi.org/10.1093/braincomms/fcaa001). Tscherpel et al. evaluate the potential of combined TMS and EEG for the assessment of motor recovery after stroke. Abnormal TMS-evoked EEG responses are related not only to the initial motor deficit but also to recovery in the chronic phase.
Non‐necrotizing granulomatous pneumonitis and chronic pleuritis in soldiers deployed to Southwest Asia

Reports of respiratory illnesses among soldiers returning from Southwest Asia have been described. During deployment to Southwest Asia, soldiers are exposed to various respiratory hazards, including dust storms, smoke from burn pits and industrial air pollutants. A few studies have reported increased rates of constrictive bronchiolitis and asthma in these patients. We sought to expand upon the pathological findings in this cohort.
In Vitro Organotypic Systems to Model Tumor Microenvironment in Human Papillomavirus (HPV)-Related Cancers

Despite the well-known role of chronic human papillomavirus (HPV) infections in causing tumors (i.e., all cervical cancers and other human malignancies from the mucosal squamous epithelia, including anogenital and oropharyngeal cavity), its persistence is not sufficient for cancer development. Other co-factors contribute to the carcinogenesis process. Recently, the critical role of the underlying stroma during the HPV life cycle and HPV-induced disease have been investigated. The tumor stroma is a key component of the tumor microenvironment (TME), which is a specialized entity. The TME is dynamic, interactive, and constantly changing—able to trigger, support, and drive tumor initiation, progression, and metastasis. In previous years, in vitro organotypic raft cultures and in vivo genetically engineered mouse models have provided researchers with important information on the interactions between HPVs and the epithelium. Further development for an in-depth understanding of the interaction between HPV-infected tissue and the surrounding microenvironment is strongly required. In this review, we critically describe the HPV-related cancers modeled in vitro from the simplified ‘raft culture’ to complex three-dimensional (3D) organotypic models, focusing on HPV-associated cervical cancer disease platforms. In addition, we review the latest knowledge in the field of in vitro culture systems of HPV-associated malignancies of other mucosal squamous epithelia (anogenital and oropharynx), as well as rare cutaneous non-melanoma associated cancer.
Impaired alcohol-induced dopamine release in the nucleus accumbens in an inflammatory pain model: behavioural implications in male rats.

Recent studies have drawn the attention to the link between Alcohol Use Disorder (AUD) and the presence of pain. Indeed, the correct management of pain in patients with a previous history of AUD has been reported to decrease the risk of relapse in alcohol drinking, suggesting that in this prone population, pain may increase the vulnerability to relapse. Previous data in male rats revealed that inflammatory pain desensitizes mu opioid receptors (MORs) in the ventral tegmental area (VTA) and increases intake of high doses of heroine. Due to the relevant role of MORs in alcohol effects, we hypothesize that pain may also alter alcohol reinforcing properties and therefore affect alcohol relapse in male rats. Our microdialysis studies show that the presence of inflammatory pain blunted the increase of extracellular dopamine levels in the Nucleus Accumbens induced by 1.5g/kg of ethanol (s.c.). Moreover, we also revealed that the administration of 52 nmol of ethanol into the VTA failed to induce place preference only in inflammatory pain-suffering animals, and a higher dose (70nmol) was necessary to reverse this effect. Finally, we evaluated the effect of inflammatory pain on the alcohol deprivation effect (ADE) in long-term ethanol-experienced male rats. After four cycles of free ethanol intake and abstinence periods, inflammatory pain induced ADE without affecting its magnitude. These intriguing data reveals the impact of pain on neurochemical and behavioral effects following alcohol administration but also underscore the necessity of finding an appropriate paradigm to determine the long-term behavioral consequences.
Plant and animal chromatin 3D organization, similar structure but different function.

Chromatin is the main carrier of genetic information and non-randomly distributed within the nucleus. Next generation sequence-based chromatin conformation capture technologies have enabled us to directly examine its 3D organization at an unprecedented scale and resolution. In the best studied mammalian models, chromatin folding can be broken down into three hierarchical levels, compartment, domains, and loops, which play important roles in transcriptional regulation. Although similar structures have now been identified in plants, they might not process identical function as the mammalian ones. Here, we review the recent plant Hi-C and ChIA-PET findings, compare plant chromatin structures with their mammalian counterparts, and also discuss the differences between plants of different genome sizes.
PERFORMANCE AND CARCASS CHARACTERISTICS OF CULL DAIRY COWS GIVEN TESTOSTERONE-ESTRADIOL IMPLANTS

Twenty-eight cull dairy cows of similar physiological age were fed an alfalfa silage, high-moisture corn ration to appetite once daily for 70 days. At the start of the trial, 14 cows were implanted with a growth promotant (Synovex H). All animals maintained a high rate of gain during the feeding period (1.19 kg/day), but there were no differences between implanted and nonimplanted cows both for feedlot performance and carcass characteristics. Key words: Cull cows, implant, growth
CRISPR–Cas12a system in fission yeast for multiplex genomic editing and CRISPR interference

Abstract The CRISPR–Cas12a is a class II, type V clustered regularly interspaced short palindromic repeat (CRISPR) system with both RNase and DNase activity. Compared to the CRISPR–Cas9 system, it recognizes T-rich PAM sequences and has the advantage of multiplex genomic editing. Here, in fission yeast Schizosaccharomyces pombe, we successfully implemented the CRISPR–Cas12a system for versatile genomic editing and manipulation. In addition to the rrk1 promoter, we used new pol II promoters from endogenous coding genes to express crRNA for Cas12a and obtained a much higher editing efficiency. This new design expands the promoter choices for potential applications in fission yeast and other organisms. In addition, we expressed a gRNA array using a strong constitutive pol II promoter. The array transcript is processed by Cas12a itself to release multiple mature crRNAs. With this construct, multiplex genomic editing of up to three loci was achieved from a single yeast transformation. We also built a CRISPR interference system using a DNase-dead Cas12a to significantly repress endogenous gene expression. Our study provides the first CRISPR-Cas12a toolkit for efficient and rapid genomic gene editing and regulation in fission yeast.
Increased risk of gastric cancer in workers with occupational dust exposure

Background/Aims Workers who are exposed to dust in the workplace tend to show a higher incidence of gastric cancer. Nevertheless, scientific evidence to support an association between dust exposure and the risk of gastric cancer is inadequate. This study aimed to investigate whether or not occupational dust exposure influences the risk of gastric cancer. Methods We collected the electronic data from the Pneumoconiosis Health Examination (PHE) program, provided by the Ministry of Employment and Labor and the Korea Workers’ Compensation and Welfare Service from 2002 to 2017. The PHE database was linked to the National Health Insurances databases. The age-standardized incidence ratio (SIR) and 95% confidence intervals (CIs) of the risk of gastric cancers were evaluated in workers with occupational dust exposure, and the results were compared to those in the general population. Results From 2004 to 2015, 1,543 cases of gastric cancer were observed in the male participants, as compared with 1,174 of expected cases, which yielded an SIR of 1.314 (95% CI, 1.249 to 1.380). Under dust exposure, the risk of gastric cancer was increased 23.9% in the male participants (95% CI, 19.9 to 27.5), and the degree of impairment of lung function was inversely related to the risk of gastric cancer. Conclusions Workers with occupational dust exposure were at higher risk of developing gastric cancer than the general population. Thus, future efforts for the prevention of gastric cancer are necessary for dust exposed workers.
Will biased ligands be the opioids of the future?

The principal opioid medications used in clinical practice act by binding to the endogenous m-opioid receptors to initiate specific cellular signaling events that result in the observed pharmacological responses. These responses are initiated by G-protein activation, which affects calcium and potassium ion channel conductance to inhibit neuronal excitability and reduce neurotransmitter release. Sustained opioid receptor activation results in recruitment of b-arrestin, which is a scaffolding protein that desensitizes G-protein signaling but also activates various kinase cascades that can potentially result in other opioid receptormediated effects. Thus, opioid receptor activation results in 2 forms of cellular signaling: an arrestin-dependent and an arrestinindependent set of responses. Recently, tremendous excitement in the analgesic drug development field has been generated by the realization that different opioid drugs might preferentially activate one pathway or another. This concept is called pharmacological “bias” or “functional receptor selectivity,” and it has been proposed that certain opioids that preferentially activate the arrestin-independent pathway might be safer analgesics. The idea that opioid-induced analgesia could be associated specifically with G-protein-dependent signaling, whereas certain adverse effects could be medicated by b-arrestin arose from the finding that b-arrestin 2 knockout mice showed enhanced morphine analgesia with less respiratory depression, tolerance, and constipation. So began decades of investment and research seeking a “biased” opioid agonist that might provide better, more sustainable, analgesia without respiratory depression or other potentially catastrophic side effects. Although respiratory depression is potentially the most catastrophic of adverse opioid outcomes, other side effects including opioid tolerance, hyperalgesia, constipation, and addiction liability seriously limit the utility of opioid drugs in the treatment of chronic pain. The premise of the recent investigations into biased opioids is that G-protein signaling is responsible for the desirable effects (analgesia), whereas the arrestin-dependent effects (respiratory depression, constipation, and euphorigenic effects) aremediated by arrestin-dependent signaling. That dichotomy has recently been challenged. However, G-biased opioid agonists have been identified, and their potential therapeutic advantages are worth exploring. We do know that the neural circuits controlling these different pharmacological responses are anatomically distinct (eg, the respiratory centers in the brainstem are distinct from the reward centers in themidbrain), but whethermuopioid receptor signaling in these different circuits use distinct signaling cascades is not yet known. Nevertheless, efforts to develop safer analgesics are certainly justified by the unmet clinical need for effective treatments for chronic pain. Here, wewill focus on the potential role for biased opioid ligands in reducing 3 important adverse opioid effects: respiratory depression, abuse potential, and analgesic tolerance.
ESTABLISHING AND MAINTAINING ROADSIDE COVER IN THE PIEDMONT PLATEAU OF GEORGIA

EROSION CONTROL CAN BE SECURED ON MOST STEEP ROADBANKS BY ESTABLISHING GOOD VEGETATIVE COVER OF ADAPTED SPECIES. MULCH AIDS THIS COVER ESTABLISHMENT AND PROVIDES TEMPORARY EROSION CONTROL UNTIL SUFFICIENT PLANT COVER DEVELOPS, ADEQUATE FERTILIZER AND LIME HASTEN PLANT GROWTH AND COVER. PROPER MOWING SCHEDULES AID SEED PRODUCTION, PLANT VIGOR, AND COVER DEVELOPMENT. /AUTHOR/
Nicotinamide mononucleotide attenuates glucocorticoid-induced osteogenic inhibition by regulating the SIRT1/PGC-1α signaling pathway

Long-term and high-dose glucocorticoid treatment is recognized as an important influencing factor for osteoporosis and osteonecrosis. Nicotinamide mononucleotide (NMN) is an intermediate of NAD+ biosynthesis, and is widely used to replenish the levels of NAD+. However, the potential role of NMN in glucocorticoid-induced osteogenic inhibition remains to be demonstrated. In the present study, the protective effects of NMN on dexamethasone (Dex)-induced osteogenic inhibition, and its underlying mechanisms, were investigated. Bone mesenchymal stem cells were treated with Dex, which decreased the levels of the osteogenic markers alkaline phosphatase, Runt-related transcription factor 2 and osteocalcin. NMN treatment attenuated Dex-induced osteogenic inhibition and promoted the expression of sirtuin 1 (SIRT1) and peroxisome proliferator-activated receptor gamma coactivator (PGC)-1α. SIRT1 knockdown reversed the protective effects of NMN and reduced the expression levels of PGC-1α. Collectively, the results of the present study reveal that NMN may be a potential therapeutic target for glucocorticoid-induced osteoporosis.
Nano-patterning of a monolayer molybdenum disulfide with sub-nanometer helium ion beam: considering its shape, size and damage

We have studied nano-patterning of a two-dimensional (2D) material with an ultrafine helium ion beam considering shape-, size- and damage-control. The study reveals that the crystalline structure plays an important role in shape-control. Instead of commonly circular-shaped nanopores, spot irradiation onto a single layer of molybdenum disulfide (MoS2) gives rise to a rhombus-shaped nanopore, which is well explained by the sub-rhombus crystalline structure of MoS2. Helium ion beams also show promising capability to precisely control size using a delivered dose. However, the size of the nanopores is not linear with the delivered dose, due to the Gaussian distributed intensity profile of the helium ion beam. The intensity profiles are further estimated by considering aperture size, those results could be taken as a significant reference for size-control. In addition, we clarify that most of the damage is a result of re-deposition, thus controlling re-deposition might be a useful way to alleviate the damage.
Omalizumab for treatment of refractory severe atopic dermatitis. A pediatric perspective

Omalizumab is a monoclonal antibody, targeting Fc receptor of IgE, approved for the treatment of allergic asthma and chronic spontaneous urticaria. Its utility in atopic dermatitis appears controversial from data in literature since the molecule is well tolerated but it seems less effective than other medications used in adult patients (eg, Dupilumab). At present, the use of Dupilumab is not approved in pediatric patients therefore there are no second level treatments available in this age group. Here we report two clinical cases of patients (15 and 16 years old) suffering from both atopic dermatitis and asthma, treated with Omalizumab. Our experience suggests that atopic eczema of young patients with allergic comorbidities can benefit from asthma treatment with Omalizumab observing improvement on both conditions.
Cytokine Receptor Common β Subunit-mediated STAT5 Activation Confers NF-κB Activation in Murine proB Cell Line Ba/F3 Cells*

The cytokine receptor common β subunit (βc) transmits intracellular signals upon binding ligand such as granulocyte-macrophage colony-stimulating factor or interleukin-3 (IL-3); however, transcriptional regulation under the control of signaling events downstream of the βc is not fully understood. Using murine Ba/F3 cells, here we demonstrate that the βc-mediated signals stimulate NF-κB-driven gene expression of not only the reporter construct but also endogenous target genes such as IL-6. Analyzing the effects of several inhibitors or mutant receptors revealed that this NF-κB activation is mediated neither by MEK/ERK/MAPK nor by the phosphatidylinositol 3-kinase pathway but by STAT5. Overexpression experiments of the wild-type or constitutive active form of STAT5 further confirmed this notion. In addition, STAT5-dependent NF-κB activation is mediated not through an inducible nuclear translocation but via up-regulation of both DNA binding activity and transactivation potential of NF-κB. Furthermore, we also show that as yet undefined humoral factor(s) may be involved in this NF-κB activation process. Taken together, we may propose that cytokine receptor-mediated STAT5 activation and expression of its target genes culminates in a unique mode of NF-κB activation and gene expression.