Miracle-dz/UniFAR-FTUs huggingface dataset:
Antifungal Activity of Eugenol Derivatives against Botrytis Cinerea

Botrytis cinerea is a worldwide spread fungus that causes the grey mold disease, which is considered the most important factor in postharvest losses in fresh fruit crops. Consequently, the control of gray mold is a matter of current and relevant interest for agricultural industries. In this work, a series of phenylpropanoids derived from eugenol were synthesized and characterized. Their effects on the mycelial growth of a virulent and multi-resistant isolate of B. cinerea (PN2) have been evaluated and IC50 values for the most active compounds range between 31–95 ppm. The antifungal activity exhibited by these compounds is strongly related to their chemical structure, i.e., increasing activity has been obtained by isomerization of the double bond or introduction of a nitro group on the aromatic ring. Based on the relationship between the fungicide activities and chemical structure, a mechanism of action is proposed. Finally, the activity of these compounds is higher than that reported for the commercial fungicide BC-1000 that is currently employed to combat this disease. Thus, our results suggest that these compounds are potential candidates to be used in the design of new and effective control with inspired natural compounds of this pathogen.
Caffeine: Toward Uniformed Representation and Acceleration for Deep Convolutional Neural Networks

With the recent advancement of multilayer convolutional neural networks (CNNs) and fully connected networks (FCNs), deep learning has achieved amazing success in many areas, especially in visual content understanding and classification. To improve the performance and energy efficiency of the computation-demanding CNN, the FPGA-based acceleration emerges as one of the most attractive alternatives. In this paper, we design and implement Caffeine, a hardware/software co-designed library to efficiently accelerate the entire CNN and FCN on FPGAs. First, we propose a uniformed convolutional matrix-multiplication representation for both computation-bound convolutional layers and communication-bound FCN layers. Based on this representation, we optimize the accelerator micro-architecture and maximize the underlying FPGA computing and bandwidth resource utilization based on a revised roofline model. Moreover, we design an automation flow to directly compile high-level network definitions to the final FPGA accelerator. As a case study, we integrate Caffeine into the industry-standard software deep learning framework Caffe. We evaluate Caffeine and its integration with Caffe by implementing VGG16 and AlexNet networks on multiple FPGA platforms. Caffeine achieves a peak performance of 1460 giga fixed point operations per second on a medium-sized Xilinx KU060 FPGA board; to our knowledge, this is the best published result. It achieves more than <inline-formula> <tex-math notation="LaTeX">$100\boldsymbol {\times }$ </tex-math></inline-formula> speed-up on FCN layers over prior FPGA accelerators. An end-to-end evaluation with Caffe integration shows up to <inline-formula> <tex-math notation="LaTeX">$29\boldsymbol {\times }$ </tex-math></inline-formula> and <inline-formula> <tex-math notation="LaTeX">$150\boldsymbol {\times }$ </tex-math></inline-formula> performance and energy gains over Caffe on a 12-core Xeon server, and <inline-formula> <tex-math notation="LaTeX">$5.7\boldsymbol {\times }$ </tex-math></inline-formula> better energy efficiency over the GPU implementation. Performance projections for a system with a high-end FPGA (Virtex7 690t) show even higher gains.
Synthesis of Nitrogen-Doped Lignin/DES Carbon Quantum Dots as a Fluorescent Probe for the Detection of Fe3+ Ions

Carbon quantum dots (CQDs) as a rising star of carbon nanomaterials have extensive applications due to their excellent characteristics. In this work, we introduce a simple and green method to prepare nitrogen-doped lignin carbon quantum dots (N-L-CQDs) by using alkali lignin carbon sources and deep eutectic solvent (DES) as solution and nitrogen source. The physiochemical characterization results suggested that N-L-CQDs with diameters ranging from 4 to 12 nm were successfully synthesized. The optical properties data indicated that the as-prepared N-L-CQDs with a quantum yield of 7.95% exhibited excellent optoelectronic properties, excitation-dependent and pH stability. After that, we have investigated the N-L-CQDs used as fluorescent probes to detect iron ions, which suggested that the as-prepared N-L-CQDs exhibited excellent sensitivity and selectivity for Fe3+ with a detection limit of 0.44 μM. Besides, cytotoxicity of N-L-CQDs was also evaluated by MTT assay. These results demonstrated that the as-prepared N-L-CQDs with excellent properties have potential applications in environment and biomedicine.
Photocatalytic Dye and Cr(VI) Degradation Using a Metal-Free Polymeric g-C3N4 Synthesized from Solvent-Treated Urea

The development of visible-light-driven polymeric g-C3N4 is in response to an emerging demand for the photocatalytic dye degradation and reduction of hexavalent chromium ions. We report the synthesis of g-C3N4 from urea treated with various solvents such as methanol, ethanol, and ethylene glycol. The samples were characterized and the Williamson–Hall method was applied to investigate the lattice strain of the samples. The activity of the samples was evaluated by observing the degradation of methyl orange and K2Cr2O7 solution under light irradiation. Photocatalytic reaction kinetics were determined as pseudo-first-order and zero-order for the degradation of methyl orange and reduction of hexavalent chromium, respectively. Due to the inhibited charge separation resulting from the small lattice strain, reduced crystal imperfection, and sheet-like structure, g-C3N4 obtained from ethanol-treated urea exhibited the highest activity among the evaluated samples.
Inflection point in climatic suitability of insect pest species in Europe suggests non‐linear responses to climate change

Climate change and globalization affect the suitable conditions for agricultural crops and insect pests, threatening future food security. It remains unknown whether shifts in species’ climatic suitability will be linear or rather non‐linear, with crop exposure to pests suddenly increasing when a critical temperature threshold is crossed. Moreover, uncertainty of forecasts can arise because of the modelling approach based either on species distribution data or on physiological measurements. Here, we compared the predictions of two modelling approaches (physiological models and species distribution models) for forecasting the potential distribution of agricultural insect pests in Europe. Despite conceptual differences, we found good agreement overall between the two approaches. We further identified a potential regime change in pest pressure along a temperature gradient. With both modelling approaches, we found an inflection point in the number of pest species with suitable climatic conditions around a minimum temperature of the coldest month of −3°C. Our results could help decision‐makers anticipate the onset of rising pest pressure and provide support for intensifying surveillance measures, particularly in regions where temperatures are already beyond the inflection point.
Novel hybrid action of GABA mediates inhibitory feedback in the mammalian retina

The stream of visual information sent from photoreceptors to second-order bipolar cells is intercepted by laterally interacting horizontal cells that generate feedback to optimize and improve the efficiency of signal transmission. The mechanisms underlying the regulation of graded photoreceptor synaptic output in this nonspiking network have remained elusive. Here, we analyze with patch clamp recording the novel mechanisms by which horizontal cells control pH in the synaptic cleft to modulate photoreceptor neurotransmitter release. First, we show that mammalian horizontal cells respond to their own GABA release and that the results of this autaptic action affect cone voltage-gated Ca2+ channel (CaV channel) gating through changes in pH. As a proof-of-principle, we demonstrate that chemogenetic manipulation of horizontal cells with exogenous anion channel expression mimics GABA-mediated cone CaV channel inhibition. Activation of these GABA receptor anion channels can depolarize horizontal cells and increase cleft acidity via Na+/H+ exchanger (NHE) proton extrusion, which results in inhibition of cone CaV channels. This action is effectively counteracted when horizontal cells are sufficiently hyperpolarized by increased GABA receptor (GABAR)-mediated HCO3− efflux, alkalinizing the cleft and disinhibiting cone CaV channels. This demonstrates how hybrid actions of GABA operate in parallel to effect voltage-dependent pH changes, a novel mechanism for regulating synaptic output.
THE DISK IMAGING SURVEY OF CHEMISTRY WITH SMA. I. TAURUS PROTOPLANETARY DISK DATA

Chemistry plays an important role in the structure and evolution of protoplanetary disks, with implications for the composition of comets and planets. This is the first of a series of papers based on data from DISCS, a Submillimeter Array survey of the chemical composition of protoplanetary disks. The six Taurus sources in the program (DM Tau, AA Tau, LkCa 15, GM Aur, CQ Tau, and MWC 480) range in stellar spectral type from M1 to A4 and offer an opportunity to test the effects of stellar luminosity on the disk chemistry. The disks were observed in 10 different lines at ∼3″ resolution and an rms of ∼100 mJy beam−1 at ∼0.5 km s−1. The four brightest lines are CO 2–1, HCO+ 3–2, CN 23 3/4/2 − 12 2/3/1, and HCN 3–2, and these are detected toward all sources (except for HCN toward CQ Tau). The weaker lines of CN 22 2–11 1, DCO+ 3–2, N2H+ 3–2, H2CO 30 3–20 2, and 41 4–31 3 are detected toward two to three disks each, and DCN 3–2 only toward LkCa 15. CH3OH 42 1–31 2 and c-C3H2 are not detected. There is no obvious difference between the T Tauri and Herbig Ae sources with regard to CN and HCN intensities. In contrast, DCO+, DCN, N2H+, and H2CO are detected only toward the T Tauri stars, suggesting that the disks around Herbig Ae stars lack cold regions for long enough timescales to allow for efficient deuterium chemistry, CO freeze-out, and grain chemistry.
TRAILblazing Strategies for Cancer Treatment

In the late 1990s, tumor necrosis factor (TNF)-related apoptosis-inducing ligand (TRAIL), a member of the TNF-family, started receiving much attention for its potential in cancer therapy, due to its capacity to induce apoptosis selectively in tumour cells in vivo. TRAIL binds to its membrane-bound death receptors TRAIL-R1 (DR4) and TRAIL-R2 (DR5) inducing the formation of a death-inducing signalling complex (DISC) thereby activating the apoptotic cascade. The ability of TRAIL to also induce apoptosis independently of p53 makes TRAIL a promising anticancer agent, especially in p53-mutated tumour entities. Thus, several so-called TRAIL receptor agonists (TRAs) were developed. Unfortunately, clinical testing of these TRAs did not reveal any significant anticancer activity, presumably due to inherent or acquired TRAIL resistance of most primary tumour cells. Since the potential power of TRAIL-based therapies still lies in TRAIL’s explicit cancer cell-selectivity, a desirable approach going forward for TRAIL-based cancer therapy is the identification of substances that sensitise tumour cells for TRAIL-induced apoptosis while sparing normal cells. Numerous of such TRAIL-sensitising strategies have been identified within the last decades. However, many of these approaches have not been verified in animal models, and therefore potential toxicity of these approaches has not been taken into consideration. Here, we critically summarise and discuss the status quo of TRAIL signalling in cancer cells and strategies to force tumour cells into undergoing apoptosis triggered by TRAIL as a cancer therapeutic approach. Moreover, we provide an overview and outlook on innovative and promising future TRAIL-based therapeutic strategies.
The relation between parental involvement and school readiness: the mediating role of preschoolers’ self-regulation skills

ABSTRACT This study investigates the relations between school readiness and self-regulation skills of preschool children and parental involvement towards education of their preschool children. More specifically, we focused on the mediation role of preschoolers’ self-regulation skills on the relation between parental involvement and school readiness. The sample of the study includes 277 children, their parents (both mothers and fathers) and preschool teachers. Structural equation model was used to test the model. It is shown that the parental involvement and self-regulation skills are significantly related to children’s school readiness. We also examined if self-regulation mediated the relation between parental involvement and school readiness and observed that the indirect effect of self-regulation skills from parental involvement to school readiness was not significant.
White Matter Tract-Cognitive Relationships in Children with High-Functioning Autism Spectrum Disorder

Objective The purpose of the present study was to clarify the relationship between white matter tracts and cognitive symptoms in children with high-functioning autism spectrum disorder (ASD). Methods We examined the cognitive functions of 17 children with high-functioning ASD and 18 typically developing (TD) controls and performed diffusion tensor imaging (DTI) tractography. We compared the results between the groups and investigated the correlations between the cognitive scores and DTI parameters within each group. Results The Comprehension scores in the ASD group exhibited a positive correlation with mean diffusivity (MD) in the forceps minor (F minor). In the TD group, the Comprehension scores were positively correlated with fractional anisotropy (FA) in the right inferior fronto-occipital fasciculus (IFO) and left anterior thalamic radiation (ATR), and negatively correlated with MD in the left ATR, radial diffusivity (RD) in the right IFO, and RD in the left ATR. Additionally, a positive correlation was observed between the Matching Numbers scores and MD in the left uncinate fasciculus and F minor, and RD in the F minor. Furthermore, the Sentence Questions scores exhibited a positive correlation with RD in the right inferior longitudinal fasciculus. Relative to TD controls, the specific tract showing a strong correlation with the cognitive scores was reduced in the ASD group. Conclusion Our findings indicate that white matter tracts connecting specific brain areas may exhibit a weaker relationship with cognitive functions in children with ASD, resulting in less efficient cognitive pathways than those observed in TD children.
Functional and Structural Features of Disease-Related Protein Variants

Modern sequencing technologies provide an unprecedented amount of data of single-nucleotide variations occurring in coding regions and leading to changes in the expressed protein sequences. A significant fraction of these single-residue variations is linked to disease onset and collected in public databases. In recent years, many scientific studies have been focusing on the dissection of salient features of disease-related variations from different perspectives. In this work, we complement previous analyses by updating a dataset of disease-related variations occurring in proteins with 3D structure. Within this dataset, we describe functional and structural features that can be of interest for characterizing disease-related variations, including major chemico-physical properties, the strength of association to disease of variation types, their effect on protein stability, their location on the protein structure, and their distribution in Pfam structural/functional protein models. Our results support previous findings obtained in different data sets and introduce Pfam models as possible fingerprints of patterns of disease related single-nucleotide variations.
Prediction of VRC01 neutralization sensitivity by HIV-1 gp160 sequence features

The broadly neutralizing antibody (bnAb) VRC01 is being evaluated for its efficacy to prevent HIV-1 infection in the Antibody Mediated Prevention (AMP) trials. A secondary objective of AMP utilizes sieve analysis to investigate how VRC01 prevention efficacy (PE) varies with HIV-1 envelope (Env) amino acid (AA) sequence features. An exhaustive analysis that tests how PE depends on every AA feature with sufficient variation would have low statistical power. To design an adequately powered primary sieve analysis for AMP, we modeled VRC01 neutralization as a function of Env AA sequence features of 611 HIV-1 gp160 pseudoviruses from the CATNAP database, with objectives: (1) to develop models that best predict the neutralization readouts; and (2) to rank AA features by their predictive importance with classification and regression methods. The dataset was split in half, and machine learning algorithms were applied to each half, each analyzed separately using cross-validation and hold-out validation. We selected Super Learner, a nonparametric ensemble-based cross-validated learning method, for advancement to the primary sieve analysis. This method predicted the dichotomous resistance outcome of whether the IC50 neutralization titer of VRC01 for a given Env pseudovirus is right-censored (indicating resistance) with an average validated AUC of 0.868 across the two hold-out datasets. Quantitative log IC50 was predicted with an average validated R2 of 0.355. Features predicting neutralization sensitivity or resistance included 26 surface-accessible residues in the VRC01 and CD4 binding footprints, the length of gp120, the length of Env, the number of cysteines in gp120, the number of cysteines in Env, and 4 potential N-linked glycosylation sites; the top features will be advanced to the primary sieve analysis. This modeling framework may also inform the study of VRC01 in the treatment of HIV-infected persons.
Deubiquitinase DUB3 Regulates Cell Cycle Progression via Stabilizing Cyclin A for Proliferation of Non-Small Cell Lung Cancer Cells

The deubiquitinase DUB3 is frequently overexpressed in non-small cell lung cancer (NSCLC) and contributes to its malignant phenotype. However, the underlying molecular mechanism of DUB3 in NSCLC is largely unknown. In this study, we report that DUB3 regulates cell cycle progression by deubiquitinating cyclin A that links to proliferation of NSCLC cells. We found that knockdown of DUB3 decreases cyclin A levels, whereas overexpression of DUB3 strongly increases cyclin A levels. Mechanistically, DUB3 interacts with cyclin A, which removes the polyubiquitin chains conjugated onto cyclin A and stabilizes the cyclin A protein. Furthermore, we demonstrate that DUB3 regulates cell cycle progression by stabilizing cyclin A, because ablation of DUB3 arrests cell cycle from G0/G1 to S phase and the resulting effect can be rescued by introducing cyclin A into NSCLC cells. Functionally, we found that the effect of DUB3 on cyclin A mediates proliferation of NSCLC cells. Moreover, a significant correlation between DUB3 abundance and cyclin A expression levels were also found in NSCLC samples. Taken together, these results reveal that DUB3 functions as a novel cyclin A regulator through maintaining cyclin A stability, and that the DUB3-cyclin A signaling axis plays a critical role in cell cycle progression for proliferation of NSCLC.
Firm sustainable investment: Are female directors greener?

Are female directors greener than their male counterparts? We investigate this issue by examining the impact of female directors on firm sustainable investment. Using data of S&P 1500 indexed firms in the United States, covering the period 2004–2016, we find a positive relationship between female directors and sustainable investment. Consistent with critical mass theory, we also find that boards with two or more female directors have a pronounced impact on sustainable investment. Moreover, female independent directors have a stronger impact on sustainable investment than female executive directors. Our additional analysis shows higher value for firms with the presence of female directors and sustainable investment. Our findings are robust to alternative variable specification, estimation techniques, and different identification strategies including the two‐stage least squares, generalized method of moments, and propensity score matching. The study provides novel evidence on the role of female directors in promoting sustainable investment and adds a new dimension to the ongoing debate in sustainability literature.
Neuroanatomy of the equine brain as revealed by high-field (3Tesla) magnetic-resonance-imaging

In this study, the morphology of the horse brain (Equus caballus) is decribed in detail using high field MRI. The study includes sagittal, dorsal, and transverse T2-weighted images at 0.25 mm resolution at 3 Tesla and 3D models of the brain presenting the external morphology of the brain. Representative gallocyanin stained histological slides of the same brain are presented. The images represent a useful tool for MR image interpretation in horses and may serve as a starting point for further research aiming at in vivo analysis in this species.
Suppression of Light-Induced Retinal Degeneration by Quercetin via the AP-1 Pathway in Rats

We examined the cytoprotective effect of quercetin via activator protein (AP-1) and the heat shock protein 70 (Hsp70) pathway against light-induced retinal degeneration in rats. Quercetin was administered intraperitoneally to Sprague-Dawley rats for seven days before light exposure to intense white fluorescent light (3000 lux) for 24 h. Light-induced retinal damage was determined by the number of rows of photoreceptor cell nuclei, the microstructures of the rod outer segments and retinal pigment epithelium, and terminal deoxynucleotidyl transferase (TdT)-mediated 2′-Deoxyuridine-5′-triphosphate (dUTP) nick end labeling. To elucidate the cytoprotective mechanism of quercetin, expression levels were measured in the rat retinas of 8-hydroxy-deoxyguanosine (8-OHdG), a marker of oxidative stress; Hsp70; and transcription factor AP-1 transcription activity. Pretreatment with quercetin inhibited light-induced photoreceptor cellular apoptosis and subsequent retinal degeneration in rats. 8-OHdG and Hsp70 protein expressions were up-regulated markedly by light exposure and suppressed by quercetin pretreatment. The results of an electrophoretic mobility shift assay showed that AP-1-binding activity was activated by light exposure, and binding of c-Fos and c-Jun, but not JunB, mediated the binding activity. Intraperitoneal administration of quercetin decreases photooxidative damage in the retina and mediates cytoprotection against light-induced photoreceptor cell degeneration in rats. Suppression of the heterodimeric combination of c-Jun and c-Fos proteins at the AP-1 binding site is highly involved in quercetin-mediated cytoprotection.