Miracle-dz/UniFAR-FTUs huggingface dataset:
Defeating copper tolerance: an example of how “omics” research can accelerate discovery of new wood protection compounds

Imagine if you could measure all the genes being expressed at any one time in an organism and you knew what all the genes did in a cell. The power of this knowledge would allow you to determine how organisms regulate gene activity to survive. This is the essence of how “omics” science accelerates biological understanding. From a wood protections standpoint, understanding which genes regulate copper tolerance effectively identifies metabolic chokepoints that would have the highest likelihood of interfering with copper tolerance. Thus, the search for copper co-biocides is no longer random, but instead, follows a rational process, guided by knowledge of which steps in metabolism are being differentially regulated for survival on substrates containing copper. We used this rational process to identify to potential inhibitors that might defeat copper tolerance: pyraclostrobin (a member of the strobilurin family of fungicides) and salicylhydroxamic acid (SHAM). The strobilurins and SHAM disrupt different steps in mitochondrial respiration, a metabolic pathway we found to be up-regulated with biosynethesis of oxalate in our omics analysis. Oxalate is the molecule that has a direct role in removing copper toxicity by trapping the copper in an insoluble copper oxalate crystal. In accordance with our hypothesis, the triple combination of 5000 µg/mL copper sulfate, 4 or 8 µg/mL pyraclostrobin, and 100 µg/mL SHAM completely inhibited growth compared to compounds tested alone over a 20-day observation period in agar plate studies with the copper-tolerant fungus, Fibroporia radiculosa. Results from AWPA E22 soil block tests, which uses percent compression strength loss as a measure of decay, were also promising when tested against F. radiculosa and another copper-tolerant species, Fomitopsis palustris. Using above ground retentions for copper ethanolamine, the triple combination wood treatment (copper, pyraclostrobin, and SHAM) performed much better than copper ethanolamine alone, and performed as well or better than wood treated with our reference, the above ground retention for ACQ-D. With over 900 potential targets or genes that showed differential regulation for survival on copper, it is our hope that co-biocide discovery will no longer be the bottleneck in wood preservative development.
Increased inflammatory markers correlate with liver damage and predict severe COVID-19: a systematic review and meta-analysis

Aim: This study aimed to determine whether patients with elevated CRP, TNFα, and IL-6 levels may be at increased risk for severe infection and liver damage of COVID-19. Background: The COVID-19 outbreak is a serious health problem to human beings. The evidence suggests that inflammatory markers related to liver damage increase in severe forms of COVID-19 compared to mild cases. Methods: The electronic databases ISI Web of Science, EMBASE, and Cochrane Library were comprehensively searched for articles published up to May, 2020. Data from each identified study was combined using the random effects model to estimate standardized mean difference (SMD) and 95% confidence intervals (95% CIs). Sensitivity and publication bias were also calculated. Results: Totally, 23 studies were included in this meta-analysis comprising 4313 patients with COVID-19. The random effects results demonstrated that patients with severe COVID-19 had significantly higher levels of CRP [SMD = 3.26 mg/L; (95% CI 2.5, 3.9); p<0.05; I2 = 98.02%; PHeterogeneity = 0.00], TNFα [SMD = 1.78 ng/mL; (95% CI 0.39, 3.1); p=0.012; I2 = 98.2%; PHeterogeneity = 0.00], and IL-6 [ SMD = 3.67 ng/mL; (95% CI 2.4, 4.8); p<0.05; I2 = 97.8%; PHeterogeneity = 0.00] compared with those with the mild form of the disease. Significant heterogeneity was present. No significant publication bias was observed in the meta-analysis. Sensitivity analyses showed a similar effect size while reducing the heterogeneity. Conclusion: The data suggests that enhanced inflammation may be associated with COVID-19-related liver damage, possibly involving inflammatory marker-related mechanisms.
Design Method for Compact Multifunctional Reconfigurable Filtering Power Divider on a New Tunable Three-Port Multi-Mode Topology

In this paper, a new effective approach is proposed to design compact multifunctional reconfigurable filtering power divider (FPD) based on a developed tunable multi-mode FPD topology. Different from conventional tunable FPD method by cascading tunable filter with power divider (PD), and double tunable filtering structures based on the tunable FPD method, it provides one promising solution of high operation performance, miniaturization and design flexibility enhancement etc., for industrial multi-functional modern wireless communication systems. By reformulating the traditional coupling matrix in terms of element-variable coupling coefficients for the developed tunable FPD topology, bandwidth (BW), center frequency (CF), as well as power division ratio (PDR) tuning are well accounted, which can help guide a new class of tunable FPD designs. For demonstration, a new second-order tunable FPD with only one common ring loaded coupled line tunable resonant unit is implemented as an example without losing generality. Higher-order tunable FPD case is further discussed and investigated by freely generalizing the FPD structure through the adoption of different tunable resonant units without dramatically increasing circuit complexity and size. Experimental results indicates that an improved performance (wider tuning range for CF, BW and PDR with nice isolation and matching), a very compact size and flexible design are achieved in the proposed work, which stands out from those in the literature.
Complete chloroplast genome of Prunus matuurai (Rosaceae), a wild flowering cherry endemic to Taiwan Island

Abstract Prunus matuurai is an endemic flowering cherry on Taiwan Island, China. Here, we determined the first complete chloroplast genome of P. matuurai using genome skimming approach. The cp genome was 157,928 bp long, with a large single-copy region (LSC) of 85,904 bp and a small single-copy region (SSC) of 19,104 bp separated by a pair of inverted repeats (IRs) of 26,460 bp. It encodes 129 genes, including 84 protein-coding genes, 37 tRNA genes, and 8 ribosomal RNA genes. The phylogenetic analysis indicated that P. matuurai is closely related to P. speciose.
How non-veridical perception drives actions in healthy humans - Evidence from Synaesthesia

We continually perform actions driven by our perception and it is commonly held that only objectively perceived changes within the ‘real’ world affect behaviour. Exceptions are usually only made for clinical conditions associated with hallucinations, where objectively non-existent percepts can influence behavior. Using synaesthesia as a model condition, we show that even in healthy populations irrelevant non-veridical precepts exert an effect on action. By non-veridical we refer to stimulus dimensions that are only subjectively perceived to be there. Applying electrophysiological (EEG) methods, we show that although these examined peculiarities are perceptual in nature, not primarily perceptual processes underlie the effects of irrelevant non-veridical perceptions on actions. Rather, high-order processes linking perceptions and motor control in medial frontal cortices reflect the underlying mechanism how irrelevant non-veridical perceptions modulate behaviour. Our results challenge assumptions about the determinants of healthy human behaviour but can be embedded within existing frameworks detailing perception action interactions.
A Stochastic Gordon-Shapiro Formula with Excess Volatility

It is well-known that stock prices fluctuate far more than dividends. Traditional valuation methods are not able to depict this fact. In this paper we incorporate excess volatility into a simple DCF model by considering an autoregressive cash flows process with random coefficients. We show that the model is free of arbitrage and that the transversality condition is met and we prove a valuation equation that differs from the classical Gordon-Shapiro version: Cost of capital (respectively dividend-price ratio) is stochastic and our model represents excess volatility. We discuss whether our assumptions are compatible with an equilibrium.
Testicular ste­re­o­logy of lambs supplemented with organic and inorganic zinc

N. GOODARZI, M. E. NOORIYAN SOROOR, P. RAHIMI-FEYLI & S. KAZEMI Department of Basic Science, Faculty of Veterinary Medicine, Razi University, Kermanshah, Iran; Department of Animal Science, Faculty of Agriculture, Razi University, Kermanshah, Iran; Department of Clinical Science, Faculty of Veterinary Medicine, Razi University, Kermanshah, Iran; D.V.M. Graduate, Faculty of Veterinary Medicine, Razi University, Kermanshah, Iran
First record of the Chinese fanray, Platyrhina sinensis (Elasmobranchii: Myliobatiformes: Platyrhinidae), in the seawaters of Zhujiajian, Zhoushan, China

There are several studies of the ichthyofauna of the East China Sea, however, the knowledge of fishes from this region still remains incomplete. This report confirms the occurrence of Chinese fanray, Platyrhina sinensis (Bloch et Schneider, 1801), in the seawaters of Zhoushan by analysing nine specimens of the Chinese fanray obtained in Zhujiajian from May 2017 to December 2017. The morphometric measurements and meristic counts were taken. The principal characters that are conclusive for the species were consistent with P. sinensis and were sufficient for separation of the examined specimens from other Platyrhina species. In addition, the fragment of 12S rRNA was also sequenced for the purpose of classification. The mean genetic distance within P. sinensis group was 0.71%, group mean distance between P. sinensis and other Platyrhina species ranged from 6.01% to 7.71%. Species were also separated from each other at the genetic level. Given the Chinese fanray has not been reported to exist in this region, our findings represent the first record from Zhoushan and extend the distribution range of this species into the north of the East China Sea. The reason behind the observed northward migration of some P. sinensis individuals from their southern habitat might be global warming. Collection of many additional specimens is needed to better define the geographic limits of the Chinese fanray.
Parallel Open-Circuit Fault Diagnosis Method of a Cascaded Full-Bridge NPC Inverter With Model Predictive Control

In this article, a parallel open-circuit fault diagnosis method (POFDM) is proposed for cascaded full-bridge neutral-point clamped inverters (CFNPCIs) employing the model predictive control. It can be inferred that the open-circuit fault will cause abnormal capacitor voltage changes in the submodule. Therefore, eight count variables are configured to correspond to the eight Insulated gate bipolar transistors (IGBTs) for each submodule. In the POFDM, the eight variables count all the abnormal changes, and the variables corresponding to the healthy switches are cleared to 0. Then, the switch whose corresponding variable is first added to the maximum is diagnosed as the fault device. Because the independent and parallel structure is adopted, the proposed POFDM can diagnose not only a single fault but also multiple faults in different submodules. And it can be easily extended to CFNPCIs with arbitrary submodules due to its parallel structure and modular software. Finally, the feasibility and validity of the POFDM are verified on the experimental prototype.
Living wages across the Pacific Rim: A localised replication study from China

Theoretically, a living wage is a threshold that, once crossed, may transform qualities of work life, including from wage injustice to justice, organizational disengagement to commitment, and life dissatisfaction to satisfaction. Initial studies from New Zealand, South Africa and Thailand have found a threshold-like cusp in the relationship between wages and quality-of-work-life. Our aim in this study was to explore whether we would replicate a cusp in a localized study within China, among 135 employees in Shandong Province, Northern China. Survey data used minimal assumption and exploratory techniques to probe links between levels of employees’ (1) take-home wage and (2) net household income; and (3) perceived wage justice, (4) commitment to employing organization, and (5) life satisfaction. Measures were locally aligned and statistically reliable. Consistent with living wage theory, as a participant’s wage tended to cross a pay threshold of (1) RMB 4–5000 personally per month and (2) RMB 7–8000 household monthly, workers tended to report (3) wage justice (in place of injustice), (4) presence (replacing absence) of organizational commitment, and (5) satisfaction with life (replacing dissatisfaction). Our replication aim was met, but generalizing to any kind of national living wage across China would require a larger and more representative study and sample.
Sustainable Strategic Management Model for Hotel Companies: A Multi-Stakeholder Proposal to “Walk the Talk” toward SDGs

As we reach the fifth anniversary of the Declaration of the United Nations 2030 Agenda for Sustainable Development, the tourism sector responsible for over 10% of the world’s GDP still does not have an open-source, sustainable management criteria that would enable and empower them to “walk the talk” to contribute to the Sustainable Development Goals (SDGs). The purpose of this paper is to fill the gap in the social sciences and business management literature by providing a theoretical Sustainable Strategic Management Model (SSMM) proposal for the Fourth Sector (4S), Small- and Medium-sized (SMEs) Hotel companies (4S-SM-HCs), which are committed and have the will to contribute firmly to the 2030 Agenda. Based on their corporate purpose and aligned with the SDGs, this article provides a holistic proposal with a multi-stakeholder approach, adding the SDG perspective. Through a qualitative research methodology based on two focus groups in which the main stakeholders and the management team of the 4S-SM-HC under examination took part, a theoretical SSMM is co-defined so that the hotel company can make significant contributions to the five areas of the SDGs. Basing their structure on the internationally recognized Global Sustainable Tourism Council (GSTC) Criteria and co-created through social learning, this SSMM proposes four strategic management axis and develops ten principles of ethical performance (PEP). The main contributions of this article are two: (1) to provide an ecosystemic SSMM proposal to the 4S-SM-HCs to allow them to make significant contributions to the SDGs, and (2) to facilitate a methodological framework with a multi-stakeholder approach and SDG perspective to enable them to contribute to the wellbeing of people, the community and the planet.
Differential effects of open- and closed-loop intracortical microstimulation on firing patterns of neurons in distant cortical areas

Background Intracortical microstimulation can be used successfully to modulate neuronal activity. Activity-dependent stimulation (ADS), in which action potentials recorded extracellularly from a single neuron are used to trigger stimulation at another cortical location (closed-loop), is an effective treatment for behavioral recovery after brain lesion in rodents. Neurophysiological changes in cortical communication induced by ADS, and how these changes differ from those induced by open-loop random stimulation (RS) are still not clear. Objectives We investigated the ability of ADS and RS to induce changes in firing patterns in distant populations of neurons in healthy anesthetized rats. Methods For this study we used 23 adult Long-Evan rats, recording from a total of 591 neuronal units. Stimulation was delivered to either forelimb or barrel field somatosensory cortex, using either randomly-timed stimulus pulses or ADS triggered from neuronal spikes recorded in the rostral forelimb area (RFA) of the motor cortex. Results Both RS and ADS stimulation protocols rapidly altered spike firing within RFA compared with no stimulation. Changes consisted of increases in mean firing rates and patterns of spike firing as measured by the revised Local Variation metric. ADS was more effective than RS in increasing short-latency evoked spikes during the stimulation periods, by producing a reliable, progressive increase in stimulus-related activity over time. Conclusions These results are critical for understanding the efficacy of electrical microstimulation protocols in altering activity patterns in interconnected brain networks. These data further strengthen the idea that activity-dependent microstimulation, can be used to modulate cortical state and functional connectivity.
Comparative Kinetics and Distribution to Target Tissues of Organophosphates Using Physiologically- Based Pharmacokinetic Modeling

Abstract : A physiologically-based pharmacokinetic model has been developed to examine the effects of organophosphates on the levels of acetylcholine in different tissues throughout the mammalian body. Many organophosphate-like chemical and kinetic characteristics are tested without reference to a specific chemical. Characteristics include partition coefficients, metabolic constants, the inhibition coefficient, the aging rate, and the regeneration rate. Two separate exposure scenarios are tested and compared against a baseline. The baseline consists of a direct inhalation exposure. The first exposure scenario examines the effects of bronchial scrubbing (via inhalation) and the second scenario is a study of dermal exposures and compares the levels of ACh in the different tissues with those in the inhalation (baseline) tests. Organophosphates that are absorbed directly into the bronchial tissue exhibit little variation on the levels of ACh buildup in any of the tissue groups tested when compared to the inhalation exposures. No matter what the scrubbing coefficient used, or the combination of the parameters (partition coefficients, inhibition coefficient, aging rate, and regeneration rate) values, the change in ACh was minimal. The results showed different behavior between inhalation and dermal exposures. The dermal results suggest that an individual may have additional time to don protective equipment before the levels of ACh are high enough to render the person incapable of doing so.
TP promotes malignant progression in hepatocellular carcinoma through pentose Warburg effect

Tumor progression is dependent on metabolic reprogramming. Metastasis and vasculogenic mimicry (VM) are typical tumor progression. The relationship of metastasis, VM and metabolic reprogramming is not clear. In this study, we identified the novel role of Twist1, a VM regulator, in the transcriptional regulation of the expression of thymidine phosphorylase (TP). We demonstrated that TP promoted extracellular thymidine metabolization into ATP and amino acids through pentose Warburg effect by coupling the pentose phosphate pathway and glycolysis. Moreover, Twist1 relied on TP-induced metabolic reprogramming to promote hepatocellular carcinoma (HCC) metastasis and VM formation mediated by VE-Cad, VEGFR1, and VEGFR2 in vitro and in vivo. TP inhibitor tipiracil reduced promotion effect of TP enzyme activity on HCC VM formation and metastasis. Our findings demonstrate that TP, transcriptionally activated by Twist1, promotes HCC VM formation and metastasis through pentose Warburg effect, contributing to tumor progression.
Two Lytic Bacteriophages That Depend on the Escherichia coli Multi-Drug Efflux Gene tolC and Differentially Affect Bacterial Growth and Selection

Bacterial pathogens are increasingly evolving drug resistance under natural selection from antibiotics in medicine, agriculture, and nature. Meanwhile, bacteria ubiquitously encounter bacteriophages and can rapidly evolve phage resistance. However, the role of phages in interacting with drug-resistant and drug-sensitive bacteria remains unclear. To gain insight into such relationships, we screened for and characterized phages that rely on the multi-drug efflux pump gene tolC. First, we screened a collection of 33 environmental and commercial Escherichia coli phages for their ability to infect cells that lacked tolC. Our screen revealed two phages that had reduced efficiency of plating (EOP) on the tolC knockout compared to wild type. We further characterized these phages with bacterial growth curves, transmission electron microscopy, and analysis of phage-resistant mutants. Phage U136B is a curly-tailed virus in family Siphoviridae with no ability to infect a tolC knockout, suggesting TolC is the U136B receptor. Phage 132 is a contractile-tailed virus in family Myoviridae with reduced EOP on cells lacking ompF and its positive regulators tolC and ompR. U136B and 132 differentially effect bacterial growth and lysis, and U136B-resistant mutants contain mutations of the tolC gene. Together, these results show that the tolC gene involved in drug resistance can modify bacteria-phage interactions in multiple ways, altering bacterial lysis and selection. These new phages offer utility for studying evolution, tradeoffs, and infection mechanisms. Importance Bacteria face strong selection by antibiotics in medicine and agriculture, resulting in increasing levels of drug resistance among bacterial pathogens. Slowing this process will require an understanding of the environmental contexts in which drug resistance evolutionarily increases or decreases. In this study, we investigate two newly-isolated bacteriophages that rely on a bacterial antibiotic resistance gene. These bacteriophages vary in their interactions with drug-resistant bacteria, with one of the phages selecting for phage-resistant mutants that have mutations in the antibiotic resistance gene. Further study of these new phages will be useful to understanding evolutionary tradeoffs and how phages might be applied in natural settings to reverse the problem of drug resistance.
Immune Landscape in the Inflamed Colonic Mucosa of Patients with IBD

Background: Myeloid cells, and dendritic cells (DC), play vital roles in innate immunity, and in the initiation and maintenance of adaptive immunity. While T cell-associated activation pathways and cytokines have been identified and evaluated in inflammatory bowel disease (IBD) patients [1] , the role of mononuclear phagocytes are less understood. Recent reports support the crucial role of DC subsets in the development of acute colitis models [2] and suggest they may contribute to the pathogenesis of ulcerative colitis (UC) by inducing Th1/Th2/Th17 responses [3]. Results: We performed in silico analysis and evaluated the enrichment of immune cells, with a focus on mononuclear phagocytes in IBD patient colonic biopsies. Samples were from different gut locations, with different levels of disease severity, and with treatment response to current therapies. We observe enrichment of monocytes, M1 macrophages, activated DCs (aDCs) and plasmacytoid dendritic cells (pDCs) in inflamed tissues from various gut locations. This enrichment correlates with disease severity. Additionally, the same mononuclear phagocytes subsets are among the top enriched cell types in both infliximab and vedolizumab treatment non-responder samples. We further investigated the enrichment of selected DC and monocyte subsets based on gene signatures derived from a DC-and monocyte-focused single cell RNA-seq (scRNA-seq) study [4], and verified enrichment in both inflamed tissues and those with treatment resistance. Moreover, we validated an increased mononuclear phagocyte subset abundance in a Dextran Sulphate Sodium (DSS) induced colitis model in C57Bl/6 mice representative of chronic inflammation. Conclusions: We conducted an extensive analysis of immune cell populations in IBD patient colonic samples and identified enriched subsets of monocytes, macrophages and dendritic cells in inflamed tissues. Understanding how they interact with other immune cells and other cells in the colonic microenvironment such as epithelial and stromal cells will help us to delineate disease pathogenesis.