Miracle-dz/UniFAR-FTUs huggingface dataset:
Computer-Aided Drug Design: Integration of Structure-Based and Ligand-Based Approaches in Drug Design

In silico high throughput screens provide an efficient (time and money) and effective (with comparable or better accuracy) alternatives in comparison to their experimental counterparts, and hence is of enormous interest to drug discovery research. However the assessment of a variety of virtual screening techniques ranging from simple fingerprint based similarity searching to the sophisticated docking algorithms reveals the inverse proportionality of the speed and accuracy of these algorithms, thus presenting a significant challenge, in enabling the use of computational tools to drug research. Some of the advantages and disadvantages of the structure-based (direct) and ligand-based (indirect) drug design techniques are typically discussed in terms of their requirements vis-a-vis the accuracy and time required for the analysis. The various integration strategies conceptualized to circumvent the above problems in the recent years are summarized with their merits and demerits.
COVID-19 and Health-Related Quality of Life: A Community-Based Online Survey in Hong Kong

The COVID-19 pandemic itself and related public health measurements have had substantial impacts on individual social lives and psychological and mental health, all to the detriment of health-related quality of life (HRQoL). There have been extensive studies investigating the mental health of people in different populations during the COVID-19 pandemic. However, few studies have explored the impact of COVID-19 and its association with HRQoL. To fill this research gap and provide further empirical evidence, this study examined the impact of COVID-19 on Hong Kong people and evaluated its association with HRQoL. A total of 500 participants were randomly recruited to complete an online questionnaire on their concerns related to COVID-19. This entailed responding to the World Health Organization Quality of Life-BREF instrument. Data were collected between 24 April and 3 May 2020. Independent t-tests and multiple linear regressions were used to examine the association between the impact of COVID-19 and HRQoL. Overall, 69.6% of participants were worried about contracting COVID-19, and 41.4% frequently suspected themselves of being infected. Furthermore, 29.0% were concerned by the lack of disinfectants. All of these findings were associated with poorer HRQoL in the physical and psychological health, social relationships, and environment domains. On the other hand, 47.4% of participants were concerned that they may lose their job because of the pandemic, while 39.4% were bothered by the insufficient supply of surgical masks. These two factors were associated with poorer HRQoL in the physical and psychological health and environment domains. The adverse impact of COVID-19 on individuals is multifactorial, affecting all aspects of HRQoL. In addition to enhancing anti-epidemic efforts, it is equally important to implement public health and social welfare measures, thereby diminishing the adverse impact of COVID-19 on overall well-being.
Optical Monitoring of Microplastics Filtrated from Wastewater Sludge and Suspended in Ethanol

The abundance of microplastics (MPs) in the atmosphere, on land, and especially in water bodies is well acknowledged. In this study, we establish an optical method based on three different techniques, namely, specular reflection to probe the medium, transmission spectroscopy measurements for the detection and identification, and a speckle pattern for monitoring the sedimentation of MPs filtrated from wastewater sludge and suspended in ethanol. We used first Raman measurements to estimate the presence and types of different MPs in wastewater sludge samples. We also used microscopy to identify the shapes of the main MPs. This allowed us to create a teaching set of samples to be characterized with our optical method. With the developed method, we clearly show that MPs from common plastics, such as polypropylene (PP), polyethylene terephthalate (PET), polystyrene (PS), and polyethylene (PE), are present in wastewater sludge and can be identified. Additionally, the results also indicate that the density of the plastics, which influences the sedimentation, is an essential parameter to consider in optical detection of microplastics in complex natural environments. All of the methods are in good agreement, thus validating the optics-based solution.
Interactions of COMT and ALDH2 Genetic Polymorphisms on Symptoms of Parkinson’s Disease

(1) Background: Monoamine neurotransmitters play essential roles in the normal functioning of our nervous system. However, the metabolism of monoamine neurotransmitters is accompanied by the production of neurotoxic metabolites, and inefficient removal of the metabolites has been suggested to cause neurodegeneration. (2) Methods: To examine the effect of reduced activity of catechol-O-methyltransferase (COMT) and aldehyde dehydrogenase 2 (ALDH2) conferred by single nucleotide polymorphisms COMT rs4680(A) and ALDH2 rs671(A) on the symptoms of patients with Parkinson’s disease (PD), a total of 114 PD patients were recruited cross-sectionally and received genotyping for rs4680 and rs671 along with MDS-UPDRS evaluation. (3) Results: We found that patients carrying rs4680(A) had more severe bradykinesia in the upper extremity and rest tremor. Besides, patients carrying rs671(A) had more difficulty maintaining personal hygiene, while patients with genotype rs671(GG) had higher scores in the item “depressed mood. ” More importantly, we found the effect of rs4680 to be moderated by rs671 SNP for the symptom of “hand movements. ” The detrimental impact of rs4680(A) is more pronounced in the presence of genotype rs671(GG). (4) Conclusions: This study facilitates a deeper understanding of the detrimental effect of reduced activity of COMT and ALDH2 conferred by genetic variation and provides novel insight into the interactions between enzymes metabolizing monoamine neurotransmitters in the pathogenesis of PD.
Modeling of Nonlinear Optical Phenomena in Host-Guest Systems Using Bond Fluctuation Monte Carlo Model: A Review

We review the results of Monte Carlo studies of chosen nonlinear optical effects in host-guest systems, using methods based on the bond-fluctuation model (BFM) for a polymer matrix. In particular, we simulate the inscription of various types of diffraction gratings in degenerate two wave mixing (DTWM) experiments (surface relief gratings (SRG), gratings in polymers doped with azo-dye molecules and gratings in biopolymers), poling effects (electric field poling of dipolar molecules and all-optical poling) and photomechanical effect. All these processes are characterized in terms of parameters measured in experiments, such as diffraction efficiency, nonlinear susceptibilities, density profiles or loading parameters. Local free volume in the BFM matrix, characterized by probabilistic distributions and correlation functions, displays a complex mosaic-like structure of scale-free clusters, which are thought to be responsible for heterogeneous dynamics of nonlinear optical processes. The photoinduced dynamics of single azopolymer chains, studied in two and three dimensions, displays complex sub-diffusive, diffusive and super-diffusive dynamical regimes. A directly related mathematical model of SRG inscription, based on the continuous time random walk (CTRW) formalism, is formulated and studied. Theoretical part of the review is devoted to the justification of the a priori assumptions made in the BFM modeling of photoinduced motion of the azo-polymer chains.
Direct Metal-Free Transformation of Alkynes to Nitriles: Computational Evidence for the Precise Reaction Mechanism

Density functional theory calculations elucidated the precise reaction mechanism for the conversion of diphenylacetylenes into benzonitriles involving the cleavage of the triple C≡C bond, with N-iodosuccinimide (NIS) as an oxidant and trimethylsilyl azide (TMSN3) as a nitrogen donor. The reaction requires six steps with the activation barrier ΔG‡ = 33.5 kcal mol−1 and a highly exergonic reaction free-energy ΔGR = −191.9 kcal mol−1 in MeCN. Reaction profiles agree with several experimental observations, offering evidence for the formation of molecular I2, interpreting the necessity to increase the temperature to finalize the reaction, and revealing thermodynamic aspects allowing higher yields for alkynes with para-electron-donating groups. In addition, the proposed mechanism indicates usefulness of this concept for both internal and terminal alkynes, eliminates the option to replace NIS by its Cl- or Br-analogues, and strongly promotes NaN3 as an alternative to TMSN3. Lastly, our results advise increasing the solvent polarity as another route to advance this metal-free strategy towards more efficient processes.
Circadian Misalignment Induced by Chronic Night Shift Work Promotes Endoplasmic Reticulum Stress Activation Impacting Directly on Human Metabolism

Simple Summary The demands of modern society have made shift work a necessity. Night work is associated with an increased risk of metabolic problems such as obesity and diabetes, which is mainly due to the misalignment of circadian rhythms that play a crucial role in many biological processes. This study performed clinical, anthropometric, and molecular analyses on 40 hospital workers who work day or night. We demonstrated that night workers had increased glucose levels, triglycerides, waist circumference, and blood pressure compared to day workers. Surprisingly, we report that night workers have significant changes in the expression of circadian clock genes and an up-regulation of genes related to endoplasmic reticulum stress (ERS). These findings provide new insights into the effects of night shift work on the expression of circadian cycle genes and ERS activation, leading to metabolic stress and the development of metabolic diseases associated with night work. Abstract Night work has become necessary in our modern society. However, sleep deprivation induces a circadian misalignment that effectively contributes to the development of diseases associated with metabolic syndrome, such as obesity and diabetes. Here, we evaluated the pattern of circadian clock genes and endoplasmic reticulum stress (ERS) genes in addition to metabolic and anthropometric measures in subjects that work during a nocturnal period compared with day workers. We study 20 night workers (NW) and 20 day workers (DW) submitted to a work schedule of 12 h of work for 36 h of rest for at least 5 years in a hospital. The present report shows that NW have increased fasting blood glucose, glycated hemoglobin (HbA1c), triglycerides, and low-density lipoprotein (LDL)-cholesterol levels, and lower high-density lipoprotein (HDL)-cholesterol levels compared to DW. In addition, we observed that waist circumference (WC), waist–hip ratio (WHR), and systemic blood pressure are also increased in NW. Interestingly, gene expression analysis showed changes in CLOCK gene expression in peripheral blood mononuclear cells (PBMC) samples of NW compared to the DW, evidencing a peripheral circadian misalignment. This metabolic adaptation was accompanied by the up-regulation of many genes of ERS in NW. These findings support the hypothesis that night shift work results in disturbed glycemic and lipid control and affects the circadian cycle through the deregulation of peripheral CLOCK genes, which is possibly due to the activation of ERS. Thus, night work induces important metabolic changes that increase the risk of developing metabolic syndrome.
Assessment of Health-Promoting Lifestyle among Dental Students in Zagreb, Croatia

As future healthcare professionals, dental medicine students are expected to exhibit healthy lifestyle behaviors. This study aims to assess the health-promoting behaviors among undergraduate dental medicine students of all six academic study years at the University of Zagreb, and determine their predictors. Students were invited to complete a two-part survey, consisting of a self-reported sociodemographic questionnaire and the Health-Promoting Lifestyle Profile II (HPLP II). Three hundred and forty-nine students completed the survey; the response rate was 60.3%. The total mean HPLP II score was 2.64 ± 0.34. Students in the second academic study year scored the lowest (2.50 ± 0.33), and students in the sixth academic study year scored the highest (2.77 ± 0.32). Health responsibility was the overall lowest scored subcategory, while interpersonal relations was scored the highest. Female students reported lower spiritual growth and stress management than male students. Higher body mass index (BMI) was related to lower health responsibility. Smoking, place of residence and the age of participants did not seem to have an impact on health-promoting behaviors. Dental students at our faculty exhibit moderate health-promoting behaviors, even in the absence of a formal health-promoting course in the existing curriculum.
Characterization and Vector Competence Studies of Chikungunya Virus Lacking Repetitive Motifs in the 3′ Untranslated Region of the Genome

Using reverse genetics, we analyzed a chikungunya virus (CHIKV) isolate of the Indian Ocean lineage lacking direct repeat (DR) elements in the 3′ untranslated region, namely DR1a and DR2a. While this deletion mutant CHIKV-∆DR exhibited growth characteristics comparable to the wild-type virus in Baby Hamster Kidney cells, replication of the mutant was reduced in Aedes albopictus C6/36 and Ae. aegypti Aag2 cells. Using oral and intrathoracic infection of mosquitoes, viral infectivity, dissemination, and transmission of CHIKV-∆DR could be shown for the well-known CHIKV vectors Ae. aegypti and Ae. albopictus. Oral infection of Ae. vexans and Culex pipiens mosquitoes with mutant or wild-type CHIKV showed very limited infectivity. Dissemination, transmission, and transmission efficiencies as determined via viral RNA in the saliva were slightly higher in Ae. vexans for the wild-type virus than for CHIKV-∆DR. However, both Ae. vexans and Cx. pipiens allowed efficient viral replication after intrathoracic injection confirming that the midgut barrier is an important determinant for the compromised infectivity after oral infection. Transmission efficiencies were neither significantly different between Ae. vexans and Cx. pipiens nor between wild-type and CHIKV-∆DR. With a combined transmission efficiency of 6%, both Ae. vexans and Cx. pipiens might serve as potential vectors in temperate regions.
Strategies to Apply Water-Deficit Stress: Similarities and Disparities at the Whole Plant Metabolism Level in Medicago truncatula

Water-deficit stresses such as drought and salinity are the most important factors limiting crop productivity. Hence, understanding the plant responses to these stresses is key for the improvement of their tolerance and yield. In this study M. truncatula plants were subjected to 250 mM NaCl as well as reduced irrigation (No-W) and 250 g/L polyethylene glycol (PEG)-6000 to induce salinity and drought stress, respectively, provoking a drop to −1.7 MPa in leaf water potential. The whole plant physiology and metabolism was explored by characterizing the stress responses at root, phloem sap and leaf organ level. PEG treatment led to some typical responses of plants to drought stress, but in addition to PEG uptake, an important impairment of nutrient uptake and a different regulation of carbon metabolism could be observed compared to No-W plants. No-W plants showed an important redistribution of antioxidants and assimilates to the root tissue, with a distinctive increase in root proline degradation and alkaline invertase activity. On the contrary, salinity provoked an increase in leaf starch and isocitrate dehydrogenase activity, suggesting key roles in the plant response to this stress. Overall, results suggest higher protection of salt-stressed shoots and non-irrigated roots through different mechanisms, including the regulation of proline and carbon metabolism, while discarding PEG as safe mimicker of drought. This raises the need to understand the effect at the whole plant level of the different strategies employed to apply water-deficit stress.
Salivary Characteristics, Individual Casual Parameters, and Their Relationships with the Significant Caries Index among Korean Children Aged 12 Years

This study aimed to investigate the salivary characteristics and individual daily living patterns in Korean children aged 12 years and evaluate their relationships according to the significant caries (SiC) index. The study sample consisted of 52 healthy Korean children. The subjects were allocated into a low caries-affected (low CA) group and a high caries-affected (high CA) group, according to the SiC index. Children underwent a standardized oral examination, and parents completed the questionnaires. Stimulated salivary samples were collected to evaluate the salivary pH, salivary flow rate, and salivary levels of Mutans streptococci (MS) and Lactobacilli (LB). The low CA group did not significantly differ from the high CA group for salivary flow rate and salivary pH. However, there were significant differences in salivary MS levels between the two groups (p < 0.05). Among the individual casual parameters, the prevalence of a sugar-associated primary energy source between meals was significantly higher in the high CA group than in the low CA group (p < 0.05). Within the limitations of this study, different levels of salivary MS and the consumption of different foods were observed in the low CA and high CA groups. The implications of these findings should be considered for caries susceptibility.
On the Development of Selective Chelators for Cadmium: Synthesis, Structure and Chelating Properties of 3-((5-(trifluoromethyl)-1,3,4-thiadiazol-2-yl)amino)benzo[d]isothiazole 1,1-dioxide, a Novel Thiadiazolyl Saccharinate

Aquatic contamination by heavy metals is a major concern for the serious negative consequences it has for plants, animals, and humans. Among the most toxic metals, Cd(II) stands out since selective and truly efficient methodologies for its removal are not known. We report a novel multidentate chelating agent comprising the heterocycles thiadiazole and benzisothiazole. 3-((5-(trifluoromethyl)-1,3,4-thiadiazol-2-yl)amino)benzo[d]isothiazole 1,1-dioxide (AL14) was synthesized from cheap saccharin and characterized by different techniques, including single crystal X-ray crystallography. Our studies revealed the efficiency and selectivity of AL14 for the chelation of dissolved Cd(II) (as compared to Cu(II) and Fe(II)). Different spectral changes were observed upon the addition of Cd(II) and Cu(II) during UV-Vis titrations, suggesting different complexation interactions with both metals.
Vertical Transmission of SARS-CoV-2 in Second Trimester Associated with Severe Neonatal Pathology

The effects of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infection in women on the gestation course and the health of the fetus, particularly in the first and second trimesters, remain very poorly explored. This report describes a case in which the normal development of pregnancy was complicated immediately after the patient had experienced Coronavirus disease 2019 (COVID-19) at the 21st week of gestation. Specific conditions included critical blood flow in the fetal umbilical artery, fetal growth restriction (1st percentile), right ventricular hypertrophy, hydropericardium, echo-characteristics of hypoxic-ischemic brain injury (leukomalacia in periventricular area) and intraventricular hemorrhage at the 25th week of gestation. Premature male neonate delivered at the 26th week of gestation died after 1 day 18 h due to asystole. The results of independent polymerase chain reaction (PCR), mass spectrometry and immunohistochemistry analyses of placenta tissue, umbilical cord blood and child blood jointly indicated vertical transmission of SARS–CoV-2 from mother to the fetus, which we conclude to be the major cause for the development of maternal vascular malperfusion in the studied case.
Housing, Husbandry and Welfare of a “Classic” Fish Model, the Paradise Fish (Macropodus opercularis)

Simple Summary Paradise fish (Macropodus opercularis) has been a favored subject of behavioral research during the last decades of the 20th century. Lately, however, with a massively expanding genetic toolkit and a well annotated, fully sequenced genome, zebrafish (Danio rerio) became a central model of recent behavioral research. But, as the zebrafish behavioral repertoire is less complex than that of the paradise fish, the focus on zebrafish is a compromise. With the advent of novel methodologies, we think it is time to bring back paradise fish and develop it into a modern model of behavioral and evolutionary developmental biology (evo-devo) studies. The first step is to define the housing and husbandry conditions that can make a paradise fish a relevant and trustworthy model. Here, we define the relevant welfare parameters for keeping a healthy population of paradise fish and provide a detailed description of our recent experience in raising and successfully breeding this species under laboratory conditions. Abstract Thanks to its small size, external fertilization and fecundity, over the past four decades, zebrafish (Danio rerio) has become the dominant fish model species in biological and biomedical research. Multiple lines of evidence, however, suggest that the reliance on only a handful of genetic model organisms is problematic, as their unique evolutionary histories makes them less than ideal to study biological questions unrelated to their historically contingent adaptations. Therefore, a need has emerged to develop novel model species, better suited for studying particular problems. The paradise fish (Macropodus opercularis) has a much more complex behavioral repertoire than zebrafish and has been a favored model animal in ethological research during the last decades of the previous century. We believe that with currently available, easily adaptable genetic toolkits, this species could be easily developed into a popular model of behavioral genetics. Despite its earlier popularity, however, the description of a detailed housing and husbandry protocol for this species is still missing from scientific literature. We present here a detailed description of how to raise and breed paradise fish successfully under laboratory conditions, and also discuss some of the challenges we faced while creating a stable breeding population for this species in our facility.
Thermal Traits of MNPs under High-Frequency Magnetic Fields: Disentangling the Effect of Size and Coating

We investigated the heating abilities of magnetic nanoparticles (MNPs) in a high-frequency magnetic field (MF) as a function of surface coating and size. The cobalt ferrite MNPs were obtained by a hydrothermal method in a water–oleic acid–ethanol system, yielding MNPs with mean diameter of about 5 nm, functionalized with the oleic acid. By applying another cycle of hydrothermal synthesis, we obtained MNPs with about one nm larger diameter. In the next step, the oleic acid was exchanged for 11-maleimidoundecanoic acid or 11-(furfurylureido)undecanoic acid. For the heating experiments, all samples were dispersed in the same solvent (dichloroethane) in the same concentration and the heating performance was studied in a broad interval of MF frequencies (346–782 kHz). The obtained results enabled us to disentangle the impact of the hydrodynamic, structural, and magnetic parameters on the overall heating capabilities. We also demonstrated that the specific power absorption does not show a monotonous trend within the series in the investigated interval of temperatures, pointing to temperature-dependent competition of the Brownian and Néel contributions in heat release.