Miracle-dz/UniFAR-FTUs huggingface dataset:
Genome-wide Network-assisted Association and Enrichment Study of Amyloid Imaging Phenotype in Alzheimer's Disease.

BACKGROUND The etiology of Alzheimer's disease remains poorly understood at the mechanistic level, and genome-wide network-based genetics have the potential to provide new clues of the disease mechanisms. OBJECTIVE To explore the collective effects of multiple genetic association signals on an AV-45 PET measure, which is a well-known Alzheimer's disease biomarker, by employing a network-assisted strategy. METHOD First, we took advantage of dense module search algorithm to identify modules enriched by genetic association signals in a protein-protein interaction network. Next, we performed statistical evaluations to the modules identified by dense module search, including a normalization process to adjust the topological bias in the network, a replication test to ensure the modules were not found by chance, and a permutation test to evaluate unbiased associations between the modules and amyloid imaging phenotype. Finally, topological analysis, module similarity tests and functional enrichment analysis were performed for the identified modules. RESULTS We identified 24 consensus modules enriched by robust genetic signals in a genome-wide association analysis. The results not only validated several previously reported AD genes (APOE, APP, TOMM40, DDAH1, PARK2, ATP5C1, PVRL2, ELAVL1, ACTN1 and NRF1), but also nominated a few novel genes (ABL1, ABLIM2) that have not been studied in Alzheimer's disease but have shown associations with other neurodegenerative diseases. CONCLUSION The identified genes, consensus modules and enriched pathways may provide important clues to future research on the neurobiology of Alzheimer's disease and suggest potential therapeutic targets.
Plasmonic sensors with an ultra-high figure of merit

We propose and numerically demonstrate a high-quality hybridized resonant platform, composed of a one-dimensional metal grating and a dielectric cavity. Under a moderate oblique illumination, an ultra-high spectral quality (Q) factor of 1375 is achieved, which shows orders of magnitude larger than that of the system under normal excitation. The high-Q mode results from the strong coupling effect between the surface plasmon polariton of the metal grating and the photonic mode of the dielectric cavity. Based on this hybridized plasmonic resonator, a high-performance sensing scheme with the spectral sensitivity (S) up to 800 nm/RIU (refractive index unit, RIU) is further introduced. Moreover, the figure of merit reaches 1337, indicating a new record for both the localized or propagating surface plasmons based sensors. These features could find applications in sensing and detecting devices, plasmonic switches, and light flow modulators.
Identification of Novel Adenylyl Cyclase 5 (AC5) Signaling Networks in D1 and D2 Medium Spiny Neurons using Bimolecular Fluorescence Complementation Screening

Adenylyl cyclase type 5 (AC5), as the principal isoform expressed in striatal medium spiny neurons (MSNs), is essential for the integration of both stimulatory and inhibitory midbrain signals that initiate from dopaminergic G protein-coupled receptor (GPCR) activation. The spatial and temporal control of cAMP signaling is dependent upon the composition of local regulatory protein networks. However, there is little understanding of how adenylyl cyclase protein interaction networks adapt to the multifarious pressures of integrating acute versus chronic and inhibitory vs. stimulatory receptor signaling in striatal MSNs. Here, we presented the development of a novel bimolecular fluorescence complementation (BiFC)-based protein-protein interaction screening methodology to further identify and characterize elements important for homeostatic control of dopamine-modulated AC5 signaling in a neuronal model cell line and striatal MSNs. We identified two novel AC5 modulators: the protein phosphatase 2A (PP2A) catalytic subunit (PPP2CB) and the intracellular trafficking associated protein—NSF (N-ethylmaleimide-sensitive factor) attachment protein alpha (NAPA). The effects of genetic knockdown (KD) of each gene were evaluated in several cellular models, including D1- and D2-dopamine receptor-expressing MSNs from CAMPER mice. The knockdown of PPP2CB was associated with a reduction in acute and sensitized adenylyl cyclase activity, implicating PP2A is an important and persistent regulator of adenylyl cyclase activity. In contrast, the effects of NAPA knockdown were more nuanced and appeared to involve an activity-dependent protein interaction network. Taken together, these data represent a novel screening method and workflow for the identification and validation of adenylyl cyclase protein-protein interaction networks under diverse cAMP signaling paradigms.
A Robust Fully-Integrated Digital-Output Inductive CMOS-MEMS Accelerometer with Improved Inductor Quality Factor

This paper presents the design, fabrication, and characterization of an inductive complementary metal oxide semiconductor micro-electromechanical systems (CMOS-MEMS) accelerometer with on-chip digital output based on LC oscillators. While most MEMS accelerometers employ capacitive detection schemes, the proposed inductive detection scheme is less susceptible to the stress-induced structural curling and deformation that are commonly seen in CMOS-MEMS devices. Oscillator-based frequency readout does not need analog to digital conversion and thus can simplify the overall system design. In this paper, a high-Q CMOS inductor was connected in series with the low-Q MEMS sensing inductor to improve its quality factor. Measurement results showed the proposed device had an offset frequency of 85.5 MHz, sensitivity of 41.6 kHz/g, noise floor of 8.2 mg/√Hz, bias instability of 0.94 kHz (11 ppm) at an average time of 2.16 s, and nonlinearity of 1.5% full-scale.
Draft Genome Sequence of the Plant Growth-Promoting Streptomyces sp. Strain 6-11-2

A genome sequence of Streptomyces sp. strain 6-2-11, a bacterium capable of promoting plant growth, was determined using the Illumina NovaSeq and MinION sequencers. An 8.9-Mb genome sequence composed of 3 contigs was successfully assembled, where 7,980 gene-coding regions, 6 rrn operons, and 86 tRNA genes were located. ABSTRACT A genome sequence of Streptomyces sp. strain 6-2-11, a bacterium capable of promoting plant growth, was determined using the Illumina NovaSeq and MinION sequencers. An 8.9-Mb genome sequence composed of 3 contigs was successfully assembled, where 7,980 gene-coding regions, 6 rrn operons, and 86 tRNA genes were located.
Antioxidant System and Biomolecules Alteration in Pisum sativum under Heavy Metal Stress and Possible Alleviation by 5-Aminolevulinic Acid

Environmental pollution is the most serious problem that affects crop productivity worldwide. Pisum sativum is a leguminous plant that is cultivated on a large scale in the Nile Delta of Egypt as a winter crop, and many of the cultivated fields irrigated with drainage water that contained many pollutants including heavy metals. The present research aimed to investigate the impact of Cd and Ni on the biochemical and physiological processes in P. sativum and evaluate the potential alleviation of their toxicity by 5-aminolevulinic acid (ALA). Seedlings of P. sativum were grown in Hoagland solution treated with CdCl2 or NiCl2 for 72 h in the growth chamber. Hydrogen peroxide, lipid peroxidation, protein carbonylation, reduced glutathione, oxidized glutathione, proline, phenolics, antioxidant enzymes, as well as Cd and Ni concentrations were measured at 0, 12, 24, 36, 48, 72 h. An experiment of alleviation was conducted where ALA was added to the growth solution at a concentration of 200 µM coupled with 100 µM of either CdCl2 or NiCl2. Hydrogen peroxide, lipid peroxidation, protein carbonylation, reduced glutathione, oxidized glutathione, proline, and phenolics were induced due to the toxicity of Cd and Ni. The activities of antioxidant enzymes [NADH-oxidase (EC: 1.6.3.1), ascorbate peroxidase (EC: 1.11.1.11), glutathione reductase (EC: 1.6.4.2), superoxide dismutase (EC: 1.15.1.1), and catalase (EC: 1.11.1.6)] were induced under the treatments of both metals. On the other hand, the soluble protein decreased gradually depending upon the time of exposure to the heavy metals. The concentration of Cd and Ni in the leaves treated plants increased in time of exposure dependent manner, while their contents remained within the acceptable limits. The addition of ALA decreased the oxidative stress in treated P. sativum plants. The results revealed the significance of using ALA in the cultivation of P. sativum might improve its tolerance against heavy metal stress.
Atorvastatin and Vitamin E Accelerates NASH Resolution by Dietary Intervention in a Preclinical Guinea Pig Model

Despite affecting millions of patients worldwide, no pharmacological treatment has yet proved effective against non-alcoholic steatohepatitis (NASH) induced liver fibrosis. Current guidelines recommend lifestyle modifications including reductions in dietary energy intake. Recently, therapy with atorvastatin and vitamin E (vitE) has been recommended, although clinical studies on the resolution of hepatic fibrosis are inconclusive. Targeting NASH-induced hepatic end-points, this study evaluated the effects of atorvastatin and vitE alone or in combination with a dietary intervention in the guinea pig NASH model. Guinea pigs (n = 72) received 20 weeks of high fat feeding before allocating to four groups: continued HF feeding (HF), HF diet with atorvastatin and vitE (HF+), low-fat diet (LF) and low-fat with atorvastatin and vitE (LF+), for four or eight weeks of intervention. Both LF and LF+ decreased liver weight, cholesterol and plasma dyslipidemia. LF+ further improved hepatic histopathological hallmarks (p < 0.05), liver injury markers aspartate aminotransferase (AST) and alanine aminotransferase (ALT) (p < 0.05) and reduced the expression of target genes of hepatic inflammation and fibrosis (p < 0.05), underlining an increased effect on NASH resolution in this group. Collectively, the data support an overall beneficial effect of diet change, and indicate that atorvastatin and vitE therapy combined with a diet change act synergistically in improving NASH-induced endpoints.
One-Pot Synthesis of 5-Acyl-1,2,3-Thiadiazoles from Enaminones, Tosylhydrazine and Elemental Sulfur under Transition Metal-Free Conditions.

I2/DMSO-mediated C-S, S-N and C-N bond cross-coupling cyclization reaction for the synthesis of 5-acyl-1,2,3-thiadiazoles from enaminones, tosylhydrazine, and elemental sulfur has been developed under transition metal-free conditions. This strategy is operationally simple, compatible with a wide range of functional groups, and provides the desired products in moderate to excellent yields.
On the Aperture Problem of Binocular 3D Motion Perception

Like many predators, humans have forward-facing eyes that are set a short distance apart so that an extensive region of the visual field is seen from two different points of view. The human visual system can establish a three-dimensional (3D) percept from the projection of images into the left and right eye. How the visual system integrates local motion and binocular depth in order to accomplish 3D motion perception is still under investigation. Here, we propose a geometric-statistical model that combines noisy velocity constraints with a spherical motion prior to solve the aperture problem in 3D. In two psychophysical experiments, it is shown that instantiations of this model can explain how human observers disambiguate 3D line motion direction behind a circular aperture. We discuss the implications of our results for the processing of motion and dynamic depth in the visual system. Dataset: osf.io/2j6sq.
Effects of Climate and Host Age on Flight Activity, Infestation Percentage, and Intensity by Coptoborus ochromactonus (Coleoptera: Curculionidae: Scolytinae) in Commercial Balsa Plantations of Ecuador

Abstract Coptoborus ochromactonus (Smith and Cognato) is one of the most common and important pests of balsa, Ochroma pyramidale (Cav. Ex Lam. Urb.), an economic pillar of the wood industry in Ecuador. Commercial balsa plantations have been expanded from humid to dry climate areas to limit insect damage, but basic knowledge is still lacking on the interaction of C. ochromactonus activity with variation in climate and plantation age. We investigated the effects of climate and host age on the seasonal flight activity of C. ochromactonus and its infestation rate and intensity, as well as the effect of age and individual infestation intensity on balsa dieback. Experiments were conducted in 1-, 2-, and 3-yr-old commercial balsa plantations located in areas of humid or dry climates. Seasonal flight activity (monitored with baited traps) differed between study sites and seasons. Increased flight activity was significantly correlated with higher relative humidity, higher mean temperature, and reduced precipitation during the dry season in the humid site and with increased mean and minimum temperature and increased precipitation during the rainy season in the dry site. Infestation rates by C. ochromactonus significantly increased with plantation age, especially in the humid site. Intensity of individual infestations (measured as number of successful insect entry holes per tree) was significantly influenced by both climate and plantation age, and it was particularly severe on 3-yr-old trees in the dry site. Percentage of foliage loss significantly increased with infestation intensity. Overall, our results can be relevant for devising preventive measures and suitable management strategies for this emerging pest in Ecuadorian wood plantations.
Observer-Based Impulsive Synchronization for Neural Networks With Uncertain Exchanging Information

This article investigates synchronization for a group of discrete-time neural networks (NNs) with the uncertain exchanging information, which is caused by the uncertain connection weights among the NNs nodes, and they are transformed into a norm-bounded uncertain Laplacian matrix. Distributed impulsive observers, which possess the advantage of reducing the communication load among NNs nodes, are designed to observe the NNs state. The impulsive controller is proposed to improve the efficiency of the controller. An impulsive augmented error system (IAES) is obtained based on the matrix Kronecker product. A sufficient condition is established to ensure synchronization of the group of NNs by proving the stability of the IAES. An iterative algorithm is given to obtain a suboptimal allowed interval of the impulsive signal, and the corresponding gains of the observer and the controller are derived. The developed result is illustrated by a numerical example.
Impact of Support (MCF, ZrO2, ZSM-5) on the Efficiency of Ni Catalyst in High-Temperature Conversion of Lignocellulosic Biomass to Hydrogen-Rich Gas

The main objective of this work was to evaluate an impact of a support on the efficiency of nickel catalysts in the high-temperature conversion of lignocellulosic biomass to hydrogen-rich gas. The most important parameters influencing catalytic performance of the catalysts were identified. The properties of three materials (ZSM-5, ZrO2, and MCF (mesostructured cellular foam)) used as a support differing in surface acidity, surface area, pore structure, ability to interact with an active phase, and resistance to coking, have been studied. The results revealed that Ni/MCF, characterized by large pore size and pore volume, low acidity, small NiO crystallites size, and moderate interaction with the active phase, is the most efficient among studied catalysts, while an application of Ni on ZSM-5 support with high-acidity was not beneficial. The results suggest that structure of the support, in particular larger pore size and a better contact between an active phase and reaction intermediates, play an important role in the formation of gaseous products during thermal decomposition of lignocellulosic feedstock. On the other hand, high acidity of the support did not increase the formation of large amounts of hydrogen-rich gaseous products.
Cunninghamia lanceolata PSK Peptide Hormone Genes Promote Primary Root Growth and Adventitious Root Formation

Phytosulfokine-α (PSK-α) is a newly discovered short peptide that acts as a phytohormone in various plants. Previous studies have shown that PSK-α is critical for many biological processes in plants, such as cell division and differentiation, somatic embryogenesis, pollen germination and plant resistance. In this study, we cloned two PSK homolog genes from Cunninghamia lanceolata (Lamb.) Hook (Chinese fir), ClPSK1 and ClPSK2, and characterized their function in root development. Quantitative RT-PCR analyses showed that both ClPSK1 and ClPSK2 were expressed in vegetative organs, mainly in roots. Transgenic Arabidopsis plants overexpressing ClPSK1 or ClPSK2 showed a higher frequency of adventitious root formation and increased root length. The expression of genes in Arabidopsis that are involved in stem cell activity (PLT1, PLT2 and WOX5), radial organization of the root (SHR and SCR) and cell cycle (CYCB1;1, CYCD4;1, CDKB1;1 and RBR) were significantly up-regulated, which may contribute to the elongation of the primary root and the formation of adventitious root in transgenic lines. Our results suggest that ClPSKs play an important role during root growth and development.
S-nitrosylation of Connexin43 hemichannels elicits cardiac stress induced arrhythmias in Duchenne Muscular Dystrophy mice.

Patients with Duchene Muscular Dystrophy (DMD) commonly present severe ventricular arrhythmias that contribute to heart failure. Arrhythmias and lethality are also consistently observed in adult Dmdmdx mice, a mouse model of DMD, after acute β-adrenergic stimulation. These pathological features were previously linked to aberrant expression and remodeling of the cardiac gap junction protein connexin 43 (Cx43). Here, we report that remodeled Cx43 protein forms Cx43 hemichannels in the lateral membrane of Dmdmdx cardiomyocytes and that the β -adrenergic agonist isoproterenol (Iso) aberrantly activates these hemichannels. Block of Cx43 hemichannels or a reduction in Cx43 levels (using Dmdmdx:Cx43+/- mice) prevents the abnormal increase in membrane permeability, plasma membrane depolarization and Iso-evoked electrical activity in these cells. Additionally, Iso treatment promotes nitric oxide (NO) production and S-nitrosylation of Cx43 hemichannels in Dmdmdx heart. Importantly, inhibition of NO production prevents arrhythmias evoked by Iso. We found that NO directly activates Cx43 hemichannels by S-nitrosylation of cysteine at the position 271. Our results demonstrate that opening of remodeled and S-nitrosylated Cx43 hemichannels play a key role in the development of arrhythmias in DMD mice and may serve as therapeutic targets to prevent fatal arrhythmias in DMD patients.
DNA-Templated Fluorescent Nanoclusters for Metal Ions Detection

DNA-templated fluorescent nanoclusters (NCs) have attracted increasing research interest on account of their prominent features, such as DNA sequence-dependent fluorescence, easy functionalization, wide availability, water solubility, and excellent biocompatibility. Coupling DNA templates with complementary DNA, aptamers, G-quadruplex, and so on has generated a large number of sensors. Additionally, the preparation and applications of DNA-templated fluorescent NCs in these sensing have been widely studied. This review firstly focuses on the properties of DNA-templated fluorescent NCs, and the synthesis of DNA-templated fluorescent NCs with different metals is then discussed. In the third part, we mainly introduce the applications of DNA-templated fluorescent NCs for sensing metal ions. At last, we further discuss the future perspectives of DNA-templated fluorescent NCs in the synthesis and sensing metal ions in the environmental and biological fields.
The Effect of Various Doses of Phenylalanine Supplementation on Blood Phenylalanine and Tyrosine Concentrations in Tyrosinemia Type 1 Patients

Tyrosinemia type 1 (TT1) treatment with 2-(2-nitro-4-trifluormethyl-benzyl)-1,3-cyclohexanedione (NTBC) and a phenylalanine-tyrosine restricted diet is associated with low phenylalanine concentrations. Phenylalanine supplementation is prescribed without comprehensive consideration about its effect on metabolic control. We investigated the effect of phenylalanine supplementation on bloodspot phenylalanine, tyrosine, NTBC and succinylacetone. Eleven TT1 patients received 0, 20 and 40 mg/kg/day phenylalanine supplementation with the phenylalanine-tyrosine free L-amino acid supplements. Bloodspots were collected before breakfast, midday and evening meal. Differences between study periods, sample times and days within a study period were studied using (generalized) linear mixed model analyses. Twenty and 40 mg/kg/day phenylalanine supplementation prevented daytime phenylalanine decreases (p = 0.05) and most low phenylalanine concentrations, while tyrosine concentrations increased (p < 0.001). Furthermore, NTBC and succinylacetone concentrations did not differ between study periods. To conclude, 20 mg/kg/day phenylalanine supplementation can prevent most low phenylalanine concentrations without increasing tyrosine to concentrations above the target range or influencing NTBC and succinylacetone concentrations, while 40 mg/kg/day increased tyrosine concentrations to values above the targeted range. Additionally, this study showed that the effect of phenylalanine supplementation, and a possible phenylalanine deficiency, should be assessed using pre-midday meal blood samples that could be combined with an overnight fasted sample when in doubt.
The Steroidogenesis Inhibitor Finasteride Reduces the Response to Both Stressful and Rewarding Stimuli

Finasteride (FIN) is the prototypical inhibitor of steroid 5α-reductase (5αR), the enzyme that catalyzes the rate-limiting step of the conversion of progesterone and testosterone into their main neuroactive metabolites. FIN is clinically approved for the treatment of benign prostatic hyperplasia and male baldness; while often well-tolerated, FIN has also been shown to cause or exacerbate psychological problems in vulnerable subjects. Evidence on the psychological effects of FIN, however, remains controversial, in view of inconsistent clinical reports. Here, we tested the effects of FIN in a battery of tests aimed at capturing complementary aspects of mood regulation and stress reactivity in rats. FIN reduced exploratory, incentive, prosocial, and risk-taking behavior; furthermore, it decreased stress coping, as revealed by increased immobility in the forced-swim test (FST). This last effect was also observed in female and orchiectomized male rats, suggesting that the mechanism of action of FIN does not primarily reflect changes in gonadal steroids. The effects of FIN on FST responses were associated with a dramatic decrease in corticotropin release hormone (CRH) mRNA and adrenocorticotropic hormone (ACTH) levels. These results suggest that FIN impairs stress reactivity and reduces behavioral activation and impulsive behavior by altering the function of the hypothalamus–pituitary–adrenal (HPA) axis.