Miracle-dz/UniFAR-FTUs huggingface dataset:
Best practices for generating and analyzing 16S rRNA amplicon data to track coral microbiome dynamics

Over the past two decades, researchers have searched for methods to better understand the relationship between coral hosts and their microbiomes. Data on how coral-associated bacteria are involved in their host’s responses to stressors that cause bleaching, disease, and other deleterious effects can elucidate how they may mediate, ameliorate, and exacerbate interactions between the coral and the surrounding environment. At the same time tracking coral bacteria dynamics can reveal previously undiscovered mechanisms of coral resilience, acclimatization, and evolutionary adaptation. Although modern techniques have reduced the cost of conducting high-throughput sequencing of coral microbes, to explore the composition, function, and dynamics of coral-associated bacteria, it is necessary that the entire procedure, from collection to sequencing, and subsequent analysis be carried out in an objective and effective way. Corals represent a difficult host with which to work, and unique steps in the process of microbiome assessment are necessary to avoid inaccuracies or unusable data in microbiome libraries, such as off-target amplification of host sequences. Here, we review, compare and contrast, and recommend methods for sample collection, preservation, and processing (e.g., DNA extraction) pipelines to best generate 16S amplicon libraries with the aim of tracking coral microbiome dynamics. We also discuss some basic quality assurance and general bioinformatic methods to analyze the diversity, composition, and taxonomic profiles of the microbiomes. This review aims to be a generalizable guide for researchers interested in starting and modifying the molecular biology aspects of coral microbiome research, highlighting best practices and tricks of the trade.
Instability of anomalous viscosity disks around young stellar objects

Abstract An accretion disk with vertical structure around a young stellar object is investigated, considering anomalous magnetic viscosity. It was found that the I-mode was unstable in the outer disk, and sometimes turned stable in the inner disk, for the standard α model. However, we find that the I-mode is always unstable in the inner disk, owing to the anomalous magnetic viscosity.
Microstrip Magnetic Dipole Yagi Array Antenna With Endfire Radiation and Vertical Polarization

A new microstrip Yagi array antenna with endfire radiation and vertical polarization is proposed. The Yagi antenna has a low profile, a wide bandwidth and a high gain. Each element of the Yagi array is based on a new microstrip antenna that has one edge opened and the other three edges shorted, working as a “magnetic dipole antenna”. As opposed to previous microstrip Yagi array antennas, the proposed Yagi antenna could produce a beam radiating at exactly endfire for infinite ground plane, with vertical polarization in the horizontal plane. A coupling microstrip line is introduced between the driven element and the first director element to strengthen the coupling between them, and therefore the front-to-back ratio and bandwidth of the array can be improved. The endfire gain can be enhanced as the number of the director elements increases, in either case where the array has an infinite or a finite ground plane.
Singularity Hypotheses: An Overview Introduction to: Singularity Hypotheses: A Scientific and Philosophical Assessment

Bill Joy in a widely read but controversial article claimed that the most powerful 21st century technologies are threatening to make humans an endangered species (Joy 2000). Indeed, a growing number of scientists, philosophers and forecasters insist that the accelerating progress in disruptive technologies such as artificial intelligence, robotics, genetic engineering, and nanotechnology may lead to what they refer to as the technological singularity: an event or phase that will radically change human civilization, and perhaps even human nature itself, before the middle of the 21st century (Paul and Cox 1996; Broderick 2001; Garreau 2005, Kurzweil 2005). Singularity hypotheses refer to either one of two distinct and very different scenarios. The first (Vinge 1993; Bostrom to appear) postulates the emergence of artificial superintelligent agents—software-based synthetic minds—as the ‘singular’ outcome of accelerating progress in computing technology. This singularity results
Sildenafil Blunts Lung Inflammation and Oxidative Stress in a Rat Model of Cholestasis

Background: Cholestasis is a multifaceted disease that influences not only the function of the liver but also affects many other organs. In this context, cholestasis-induced lung injury is a significant clinical complication. Unfortunately, there is no precise therapeutic option against cholestasis-associated lung injury. It has been revealed that oxidative stress and inflammatory response play a role in cholestasis-induced pulmonary damage. Sildenafil is a phosphodiesterase enzyme inhibitor used in the management of erectile dysfunction. Meanwhile, several experiments revealed the effects of sildenafil on oxidative stress and inflammation. This study aimed to evaluate the effect of sildenafil on cholestasis-induced oxidative stress and inflammation in cholestasis-induced lung injury. Methods: Rats underwent bile duct ligation (BDL) to induce cholestasis. Bronchoalveolar lavage fluid (BALF) levels of inflammatory cells, cytokine, and immunoglobulin were monitored at (3, 7, and 14 days after BDL surgery). Moreover, lung tissue histopathological alterations and biomarkers of oxidative stress were evaluated. Results: A significant increase in BALF inflammatory cells, TNF-α, and immunoglobulin G (IgG) was evident in BDL animals. Moreover, the infiltration of inflammatory cells, vascular congestion, and hemorrhage were detected in the lung of BDL rats. Increased markers of oxidative stress were also evident in the lung of BDL animals. Sildenafil (10 and 20 mg/kg) significantly blunted inflammatory response, oxidative stress, and histopathological alterations in the lung of cholestatic animals. Conclusion: The effects of sildenafil on inflammatory response and oxidative stress biomarkers seems to play a crucial role in its protective properties in the lung of cholestatic animals.
Migraine and thyroid dysfunction: Co‐occurrence, shared genes and biological mechanisms

Migraine and thyroid dysfunction, particularly hypothyroidism, are common medical conditions and are known to have high heritability. Thyroid function measures, thyroid stimulating hormone (TSH) and free thyroxine (fT4), are also known to be genetically influenced. Although observational epidemiological studies report an increased co‐occurrence of migraine and thyroid dysfunction, a clear and combined interpretation of the findings is currently lacking. A narrative review is provided of the epidemiological and genetic association evidence linking migraine, hypothyroidism, hyperthyroidism and thyroid hormones TSH and fT4.
An Improved Score for the Evaluation of Mucosal Healing in Inflammatory Bowel Disease—A Pilot Study

Inflammatory bowel diseases are chronic conditions characterized by periods of remission, alternating with episodes of exacerbation, in which the primary therapeutic target is mucosal healing. Although colonoscopy is currently considered the gold standard for assessing disease activity, it presents a significant number of disadvantages. Over time, various inflammatory biomarkers have been proposed to detect disease activation, but current biomarkers have many limitations. Our study aimed to analyze the most commonly used biomarkers for patient monitoring and follow-up both independently and taken together as a group, in order to propose an improved activity score that more accurately reflects the changes occurring at the intestinal level, in order to limit the number of colonoscopic interventions. By applying logistic regression as a method of statistical analysis to the retrospectively collected data, we obtained an easy-to-calculate improved score that quantifies the chance that a given patient may be in remission or in a period of endoscopic activity. To achieve a widely accessible score that is easily accessible in clinical practice, we have included only the most commonly used clinical and biological parameters.
Label-Free Imaging and Histo-Optical Evaluation of Head and Neck Cancers with Multiphoton Autofluorescence Microscopy

Simple Summary Efforts to identify lesions of head and neck cancers with high malignant potential are important to improve patient outcomes, as 5-year survival rates remain low due to late detection. Optical imaging approaches that provide direct cellular and structural atypia could be helpful in detection and pathology guidance. This study evaluates the method of multiphoton autofluorescence microscopy (MPAM) for its ability to reveal atypia associated with neoplasia in resected tumor samples without the need for exogenous dyes or tissue sectioning, showing a correlation with the corresponding histology. Abstract Depth-resolved label-free optical imaging by the method of multiphoton autofluorescence microscopy (MPAM) may offer new ways to examine cellular and extracellular atypia associated with epithelial squamous cell carcinoma (SCC). MPAM was evaluated for its ability to identify cellular and microstructural atypia in head and neck tissues from resected discarded tumor tissue. Three-dimensional image volumes were obtained from tissues from the floor of the mouth, tongue, and larynx, and were then processed for histology. MPAM micrographs were evaluated for qualitative metrics of cell atypia and quantitative measures associated with nuclear pleomorphism. Statistical analyses correlated MPAM endpoints with histological grade from each imaged site. Cellular overcrowding, discohesion, anisonucleosis, and multinucleated cells, as observed through MPAM, were found to be statistically associated with dysplasia and SCC grading, but not in histologically benign regions. A quantitative measure of the coefficient of variance in nuclear size in SCC and dysplasia was statistically elevated above histologically benign regions. MPAM also allowed for the identification of cellular heterogeneity across transitional areas and other features, such as inflammatory infiltrates. In the future, MPAM could be evaluated for the non-invasive detection of neoplasia, possibly as an adjunct to traditional conventional examination and biopsy.
Multilayered Composites with Carbon Nanotubes for Electromagnetic Shielding Application

Bulk polylactic acid (PLA)/multiwall carbon nanotube (MWCNT) composites were prepared and investigated in wide frequency ranges (20 Hz–1 MHz and 24–40 GHz). It was determined that the percolation threshold in bulk PLA/MWCNT composites is close to 0.2 vol.% MWCNT. However, the best microwave dielectric properties and absorption were observed in composites with 3.0–5.0 vol.% MWCNT. Therefore, for future investigations, we selected layered (laminate) polymeric structures with gradual changes in MWCNT concentration from 0.2 to 8.0 vol.% MWCNT. Two approaches to laminate structure designs were examined and compared: a five-layer composite and a nine-layer composite that included four pure PLA middle layers. The addition of MWCNT enhanced the elastic modulus by up to 1.4-fold and tensile strength by up to 1.2-fold, with the best performance achieved at 5.0 vol.% loading. High microwave shielding was observed for these layered PLA/MWCNT structures with a gradient change in MWCNT concentration (up to 26 dB in both transmission and absorption coefficients) in the broad frequency range (from 24 to 40 GHz). Obtained structures are highly anisotropic, and the absorption coefficient is 2–5 dB higher in the direction of MWCNT concentration increase; however, the transmission coefficient is the same in both directions. The properties of microwave absorption are mainly unaffected by the additional polymeric layers. The absorption of the layered structure is greater than the absorption of single-layer composites with an optimal MWCNT concentration of the same thickness. The proposed laminate structure design is promising in the field of efficient electromagnetic shielding.
Computational Exploration of Dirhodium Complex-Catalyzed Selective Intermolecular Amination of Tertiary vs. Benzylic C−H Bonds

The mechanism and origins of site-selectivity of Rh2(S-tfpttl)4-catalyzed C(sp3)–H bond aminations were studied using density functional theory (DFT) calculations. The synergistic combination of the dirhodium complex Rh2(S-tfpttl)4 with tert-butylphenol sulfamate TBPhsNH2 composes a pocket that can access both tertiary and benzylic C–H bonds. The nonactivated tertiary C–H bond was selectively aminated in the presence of an electronically activated benzylic C–H bond. Both singlet and triplet energy surfaces were investigated in this study. The computational results suggest that the triplet stepwise pathway is more favorable than the singlet concerted pathway. In the hydrogen atom abstraction by Rh–nitrene species, which is the rate- and site-selectivity-determining step, there is an attractive π–π stacking interaction between the phenyl group of the substrate and the phthalimido group of the ligand in the tertiary C–H activation transition structure. By contrast, such attractive interaction is absent in the benzylic C–H amination transition structure. Therefore, the DFT computational results clearly demonstrate how the synergistic combination of the dirhodium complex with sulfamate overrides the intrinsic preference for benzylic C–H amination to achieve the amination of the nonactivated tertiary C–H bond.
Bifurcation Phenomena in Open-Loop DCM-Operated DC–DC Switching Converters Feeding Constant Power Loads

Constant power loading is an effect that appears in multiple-stage energy conversion systems with individually regulated switching power converters. In a two-stage system, an upstream or source converter drives one or more downstream or load converters. The downstream converters in a two-stage power conversion system are designed to provide the fastest transient response in stand-alone operation. Consequently, they behave as a constant power load (CPL) to the upstream converter within their control bandwidth. In the past, open-loop power converters feeding CPLs and operating in discontinuous conduction mode (DCM) were considered to be stable. In this paper, it is shown that these systems can undergo instabilities, which have been so far overlooked. First, numerical simulations from the switched model of an open-loop boost converter under DCM operation and loaded with a tightly regulated buck converter and the same converter loaded by an ideal CPL are presented to show that they exhibit similar nonlinear behavior and bifurcation phenomena. Then, the three elementary open-loop DC–DC converters operating in the DCM were considered and their bifurcation phenomena were revealed. It is shown that the period-doubling route to chaos in the DC–DC boost converter is interrupted by a sudden appearance of dangerous destructive dynamics due to the excessively unlimited load current in the CPL. For the buck converter, only the first period-doubling bifurcation is observed before the destructive behavior appears. The open-loop buck–boost converter under DCM and feeding a CPL is always unstable and exhibits no periodic orbit. Based on the observed phenomena, approximate discrete-time models were derived, which despite their simplicity, were seen to display the most-important and -essential features of the corresponding switching converters before destructive dynamics occurs.
Multi‐feature subspace representation network for person re‐identification via bird's‐eye view image

Person re‐identification (Re‐ID) is one of the most remarkable research topics that widely applied in our daily lives. For person Re‐ID in bird's eye scenes, traditional computer vision‐based methods used multiple features, for example, texture and color, of a pedestrian's head and shoulders. Those methods are difficult to cope with environments of variety and the change the appearance of different people due to the instability of feature detection. On the other hand, although recent advanced deep learning‐based methods are powerful to extract discriminative features, the requirement of a large amount of annotated training data restricts the appliable tasks. To overcome this problem, in this article, we propose a novel method fusing multiple heterogeneous features through a multi‐feature subspace representation network (MFSRN) to maximize the classification performance while keeping the disparity among features as small as possible, that is, common‐subspace constraints. We conducted comparative experiments with state‐of‐the‐art models on the bird's‐eye view person dataset, and extensive experimental results demonstrated that our proposed MFSRN could achieve better recognition performance. Furthermore, the validity and stability of the method are confirmed.
Internet gaming disorder and tobacco use disorder share neural connectivity patterns between the subcortical and the motor network

Internet gaming disorder (IGD) and tobacco use disorder (TUD) are globally common, non‐substance‐related disorders and substance‐related disorders worldwide, respectively. Recognizing the commonalities between IGD and TUD will deepen understanding of the underlying mechanisms of addictive behavior and excessive online gaming. Using node strength, 141 resting‐state data were collected in this study to compute network homogeneity. The participants included participants with IGD (PIGD: n = 34, male = 29, age: 15–25 years), participants with TUD (PTUD: n = 33, male = 33, age: 19–42 years), and matched healthy controls (control‐for‐IGD: n = 41, male = 38, age: 17–32 years; control‐for‐TUD: n = 33, age: 21–27 years). PIGD and PTUD exhibited common enhanced node strength between the subcortical and motor networks. Additionally, a common enhanced resting‐state functional connectivity (RSFC) was found between the right thalamus and right postcentral gyrus in PIGD and PTUD. Node strength and RSFC were used to distinguish PIGD and PTUD from their respective healthy controls. Interestingly, models trained on PIGD versus controls could classify PTUD versus controls and vice versa, suggesting that these disorders share common neurological patterns. Enhanced connectivity may indicate a greater association between rewards and behaviors, inducing addiction behaviors without flexible and complex regulation. This study discovered that the connectivity between the subcortical and motor networks is a potential biological target for developing addiction treatment in the future.
Micro-Raman spectroscopy study of ALVAC virus infected chicken embryo cells

Micro- Raman spectroscopic investigation of ALVAC virus and of normal chicken embryo fibroblast cells and the cells infected with ALVAC virus labeled with green fluorescence protein (GFP) were performed with a 785 nm laser. Good quality Micro-Raman spectra of the Alvac II virus were obtained. These spectra show that the ALVAC II virus contains buried tyrosine residues and the coat protein of the virus has α-helical structure. A comparison of Raman spectra of normal and virus infected chicken embryo fibroblast cells revealed that the virus infected cells show additional bands at 535, 928, and 1091 cm-1, respectively, corresponding to δ(C-O-C) glycosidic ring, protein α-helix, and DNA (O-P-O) modes. In addition, the tyrosine resonance double (833 and 855 cm-1) shows reversal in the intensity of the higher-frequency band as compared to the normal cells that can be used to identify the infected cells. In the C-H stretching region, the infected cells show bands with higher intensity as compared to that of the corresponding bands in the normal cells. We also found that the presence of GFP does not affect the Raman spectra of samples when using a 785 nm micro-Raman system because the green fluorescence wavelength of GFP is well below the Stokes-Raman shifted spectral region.
Elucidating Flavonoid and Antioxidant Activity in Edible and Medicinal Herbs Woodwardia japonica (L.f.) Sm. Based on HPLC-ESI-TOF-MS and Artificial Neural Network Model: Response to Climatic Factors

Woodwardia japonica is a kind of great potential edible and medicinal fern. In a previous study, it was found that flavonoid and antioxidant activity of W. japonica from different sites were different. However, the cause of the differences has still been unclear, which has restricted the utilization of W. japonica. In this paper, flavonoid and antioxidant activity of W. japonica from nine different regions were determined with the method of a colorimetric assay with UV-VIS spectrophotometry and HPLC-ESI-TOF-MS, and the effects of climate factors on flavonoids and antioxidant activities were evaluated by mathematical modeling and statistical methods. The results showed: (1) total flavonoid content (TFC) of W. japonica from Wuyi Mountain (Jiangxi) was the highest, which might be related to the low temperature; (2) the differences of antioxidant activities of W. japonica might be related to precipitation; (3) five flavonols, two flavones and one isoflavone were tentatively identified in W. japonica; (4) flavonol and isoflavone might be affected by sunshine duration, and flavones were probably related to temperature. In conclusion, the effects of climate factors on flavonoids and antioxidants are significant, which would provide an important basis for further exploring the mechanism of climate affecting secondary metabolites.
A new vibration theory for sonoelasticity imaging

Sonoelasticity is a new imaging technique for detection of hard tumors in tissues. In this novel diagnostic technique, a low frequency vibration at audio range is externally applied to excite internal vibrations within the tissue under inspection. Regions of different stiffness respond with different displacement. The low frequency vibration can be detected using Doppler ultrasound. By employing a properly designed scanning and detection algorithm, a real-time vibration image can be made. A theory for vibrations, or shear wave propagation in inhomogeneous elastic tissue has been developed. A tumor is modeled as an elastic inhomogeneity inside a lossy homogeneous elastic medium. The solutions take into account varying parameters such as tumor size, tumor stiffness, shape of vibration source, lossy factor of the material and vibration frequency. Computer simulations show that the vibrations around the tumor exhibit unique patterns which distinguish it from the surrounding tissue. Therefore examination of the vibration image can reveal the hard tumor inclusions. The problem of the lowest detectable change in stiffness is addressed using the theory, answering one of the most critical questions in this diagnostic technique