Miracle-dz/UniFAR-FTUs huggingface dataset:
Exploring the Binding Mechanism and Accessible Angle of SARS-CoV-2 Spike and ACE2 by Molecular Dynamics Simulation and Free Energy Calculation

The SARS-CoV-2 has caused more than 2,000 deaths as of 20 February 2020 worldwide but there is no approved effective drug. The SARS-CoV-2 spike (S) glycoprotein is a key drug target due to its indispensable function for viral infection and fusion with ACE2 as a receptor. To facilitate the drug discovery and development with S protein as drug target, various computational techniques were used in this study to evaluate the binding mechanisms between S protein and its acceptor ACE2. Impressively, SARS-CoV-2 S protein has higher affinity binding to ACE2 at two different “up” angles of RBD than SARS-CoV S protein to ACE2 at the same angles. The energy decomposition analysis showed that more interactions formed between SARS-CoV-2 S protein and ACE2, which may partially account for its higher infectiousness than SARS-CoV. In addition, we found that 52.2° is a starting accessible “up” angle of the BRD of SARS-CoV-2 S protein to bind ACE2, demonstrating that BRD is not necessary to be fully opened in order to bind ACE2. We hope that this work will be helpful for the design of effective SARS-CoV-2 S protein inhibitors to address the ongoing public health crisis.
Effect of dietary supplementation of fermented garlic by Leuconostoc mesenteroides KCCM35046, on growth performance, blood constituents, nutrient digestibility, fecal microflora, and fecal scores in sows and their piglets

Eighteen lactating sows (Landrace × Yorkshire) were used in an experiment to determine the effects of fermented garlic by Leuconostoc mesenteroides KCCM35046 on growth performance, blood constituents, nutrient digestibility, fecal microflora, and fecal scores in sows and their piglets. The experiment was started before farrowing 30 d to weaning, and sows were randomly assigned to the following dietary treatments: control basal diet (CON) and the CON + 0.1% or 0.2% fermented garlic (FG). During the lactation period, sows had free access to feed and water. At farrowing day and weaning (day 28), body weight (BW) loss of sows reduced linearly (P = 0.042; P = 0.006, respectively) in FG diets. There was a linear improvement in piglets’ BW with increasing dietary FG levels at weaning (P = 0.033). Piglets fed the diets with the FG linearly increased the average daily gain (ADG) at the 3rd and 4th weeks (P = 0.041; P = 0.002, respectively). Overall, the ADG of piglets linearly increased when lactating sows fed the diets with FG supplementation (P = 0.004). Red blood cell concentrations linearly decreased (P = 0.004) in sows fed dietary FG supplementation at the weaning day. Dietary inclusion of the FG tended to increase the fecal Lactobacillus population and decrease Escherichia coli population of piglets at weanling day (P = 0.075; P = 0.051, respectively). In conclusion, the results of this study indicated that dietary supplementation of FG (0.1% and 0.2%) improved growth performance in sows and their piglets.
The Effect of Internal Minor Stress on Marital Satisfaction in Indonesian Intercultural Couples

Intercultural couples face cultural conflicts in their marriage, resulting in internal minor stress. Stress as a dyadic phenomenon – commonly found in marriage – affects both individuals involved in the relationship. As a result, couples experience low levels of marital satisfaction. Forty-five intercultural couples from Jakarta, Bogor, Depok, Tangerang, Bekasi Bandung, and Pekanbaru completed this study. The highlight of this study was the use of the Actor-Partner Interdependence Model in the data analysis, using the APIM_SEM application. The result from this study implied that internal minor stress affected marital satisfaction at an individual level, however, no significant effects were found in the partner-effect.
Exploring the Relationship Between Children’s Vocabulary and their Understanding of Cardinality: A Methodological Approach

Is there a relationship between vocabulary and children’s understanding of cardinality? Does the way in which we classify cardinality data as tested by the Give-a-Number task affect finding such a relationship? This thesis explored these questions using a methodological approach, by testing the relationship between children’s receptive vocabulary scores and Give-a-Number scores classified in two different ways, the traditional knower-level assessment, as well as by calculating the proportion of trials answered correctly. A significant correlation was found between participants’ receptive vocabulary scores and Give-a-Number scores using both manners of classification, independent of the children’s ages. The results were compared with those of past studies to examine what discrepancies exist regarding the relationship, and what factors may be contributing to the discrepancies. Though it was not reflected in our dataset, after comparing the results of several studies, we determined that the manner of classification (i.e., knower-level vs. proportion-correct), as well as age, may have an effect on the existence and strength of the relationship between children’s vocabulary and understanding of cardinality.
Micronutrient Spray Effects on Growth, Yield and Quality of Papaya (Carica papaya L.) Cv. Madhu Bindu

The investigation was undertaken with a view to determine the “Effect of foliar spray of various micronutrients on growth, yield and quality of papaya (Carica papaya L.) cv. Madhu Bindu” and results revealed that the individual application of ZnSO 4 0.5% and borax 0.3% exerted great influence on plant height, stem girth and number of leaves as well as earlier initiation of flower bud and minimum days taken from fruit setting to first harvest. The yield characters i.e. average weight of fruit, number of fruit and yield of fruits per plant with maximum yield per hectare was also recorded maximum with ZnSO4 0.5% and borax 0.3% when the plants sprayed at 30, 60 and 90 days after transplanting. In quality point of view, different levels of ZnSO4 and borax had markedly influenced the quality of papaya fruits i.e., ascorbic acid (mg/100g), total soluble solids (%), reducing sugar (%), non-reducing sugar and total sugar (%).
Combinatorial BRD4 and AURKA inhibition is synergistic against preclinical models of Ewing sarcoma

Ewing sarcoma (ES), a bone cancer affecting children, adolescents, and young adults, is driven by the EWS‐FLI1 fusion protein in the majority of cases, but the mechanisms of tumorigenesis are still being elucidated. Consequentially, therapeutic advances have been limited in the last 25 years. Two therapeutic targets have been recently examined. Aurora kinase A (AURKA) promotes cell cycling and posttranslational stabilization of the oncoprotein MYC, while bromodomain‐containing protein 4 (BRD4) promotes gene expression epigenetically. Studies of AURKA and BRD4 inhibitors showed some impairment of tumorigenesis in ES preclinical models, but this efficacy was limited in single‐agent use. AURKA and BRD4 activate common oncogenic pathways through different mechanisms, so we hypothesized dual inhibition would be synergistic against tumorigenesis.
Extraction and Purification of Protease from Nigella sativa for Its Potential Use in Celiac Disease

Celiac disease (CD) is a disease of the digestive system resulting from the intolerance of autoimmune system against gluten and gliadin proteins in wheat, barley, rye and some varieties of oats. In this work protease was isolated and partially purified from Nigella Sativa using ammonium sulphate, acetone and trichloroacetic acid. The purified protease was evaluated further for its possible use in celiac disease by its ability to hydrolyse both, gluten and gliadin. Data indicate that the highest purity of digestive protease enzymes was obtained by acetone 80% and 0.2M trichloroacetic acid (TCA). The enzyme purified by acetone exhibited the high value of Vmax (166.66 mg/min) and the low value of Km (0.133 mg/ml). When the obtained enzyme was tested to hydrolyse gluten and gliadin at two increasing concentrations of 1 and 2 mg/ml, almost similar efficacy was observed (28.46% and 32.02%; for gluten) and (22.7% and 16.84%; for gliadin), whereas Digestin, a positive control which contain Papain and Sanzyme 3500 and works by helping in the breakdown of proteins, produced higher efficacy at 2 mg/ml to hydrolyse gluten (38.67%) with 1 mg/ml (25.68%) whereas similar results were observed against gliadin at both concentrations (22.06% and 22.5%). This study show the efficacy of protease obtained from Nigella Sativa as a natural and economical source for the hydrolysis of gluten and gliadin, which is considered the primary reason for celiac disease.
Compromised word-level neural tracking in the high-gamma band for children with attention deficit hyperactivity disorder

Children with attention deficit hyperactivity disorder (ADHD) exhibit pervasive difficulties in speech perception. Given that speech processing involves both acoustic and linguistic stages, it remains unclear which stage of speech processing is impaired in children with ADHD. To investigate this issue, we measured neural tracking of speech at syllable and word levels using electroencephalography (EEG), and evaluated the relationship between neural responses and ADHD symptoms in 6–8 years old children. Twenty-three children participated in the current study, and their ADHD symptoms were assessed with SNAP-IV questionnaires. In the experiment, the children listened to hierarchical speech sequences in which syllables and words were, respectively, repeated at 2.5 and 1.25 Hz. Using frequency domain analyses, reliable neural tracking of syllables and words was observed in both the low-frequency band (<4 Hz) and the high-gamma band (70–160 Hz). However, the neural tracking of words in the high-gamma band showed an anti-correlation with the ADHD symptom scores of the children. These results indicate that ADHD prominently impairs cortical encoding of linguistic information (e.g., words) in speech perception.
Bio-inspired design for engineering applications: empirical and finite element studies of biomechanically adapted porous bone architectures

ii ACKNOWLEDGEMENTS . iv 1.1 Professional Acknowledgements . iv 1.2 Personal Acknowledgements . vi Chapter 1: Introduction: Trabecular architecture in large mass animals . 1 1.1 Trabecular bone . 1 1.2 Trabecular bone architectural indices . 2 1.3 Allometric scaling . 3 1.4 Mechanics of cellular solids . 6 1.5 Finite element modeling and trabecular bone risk assessment . 7 1.6 Dinosaurs and their bones . 9 1.7 Motivation for research . 10 1.8 Hypotheses . 11 Chapter 2: Strong and light weight structures from dinosaur trabecular architecture . 12 2.1 Methods . 12 2.1.1 Species analyzed in study . 12 2.1.2 Fossilized bone verification through optical microscopy and energy dispersive x-ray spectroscopy . 14 2.1.3 Computed tomography scanning . 14 2.1.4 Finite element model generation . 16 2.1.5 Finite element modeling . 17 2.1.6 Apparent and Specific Apparent Modulus . 19 2.1.7 Risk of failure assessment . 19 2.1.8 Allometric scaling . 20 2.1. 9 Statistical analyses . 21 2.2 Results . 22 2.2.1 Fossilized bone verification . 22 2.2.2 CT scan segmentation . 24 2.2.3 Trabecular indices and allometric scaling . 26 2.2. 4 Finite element modeling . 30 2.3 Discussion . 34
Student Perceptions of Mathematics Readiness from a University Preparatory Program to Undergraduate Studies.

For many mature-aged students, there can be a considerable gap between finishing formal study and beginning university. They are often required to draw on qualifications and skills, including mathematics, which are dated, but necessary for success. Most universities offer several pathways that prospective students can take to enter university: from school; from vocational education; based on prior learning; or via a university preparatory program. Even with extra preparation from a preparatory program, success is not guaranteed, as the assumed skills can be quite specific to particular degrees. Mathematics prerequisites for entry into undergraduate programs are not enforced in many Australian universities. Students are only advised of the level of senior mathematics that is ‘assumed’ or ‘recommended knowledge’ for their degree and are often uncertain if their current mathematical skills are enough to understand the content of a particular course. A survey to investigate students’ perceptions of how well their pre-university studies prepared them for first year undergraduate courses that required quantitative skills was conducted at one regional university in Australia. As part of this survey, the perceptions of mathematical preparedness of students who had qualified for entrance to undergraduate studies via the university’s tertiary preparation program were investigated. Most respondents who transitioned through the preparatory program felt well prepared for their undergraduate mathematics. However, a greater proportion of these students either withdrew from the undergraduate quantitative course that they had enrolled in or achieved lower grades when compared to other survey respondents who had entered university through more traditional pathways.
Emotional Dissonance and the IT Professional – A Replication

: This study is a conceptual replication of the Rutner, Hardgrave, and McKnight (2008) model of emotional dissonance analyzed as an antecedent of work exhaustion and job satisfaction extending the original Moore (2000a) model of turnover intention. Using a sample of IT workers from a Fortune 500 company, we tested the model of emotional dissonance and turnover intention. Our sample size is 303, nearly double the sample size (N=161) used in the original study. We successfully replicated five of the seven hypotheses tested in original paper. These results strengthen theories in information systems exploring job satisfaction and turnover intention among IT workers. Future research might consider new stressors or issues facing IT workers that could be investigated with emotional dissonance.
Empyema thoracis of odontogenic origin: experience from a maxillofacial unit

Introduction: Cervicofacial infections of odontogenic origin continue to cause various complications despite improvements in clinical services, especially the use of potent antibiotics. Empyema thoracis is a life-threatening and extremely rare complication of odontogenic infections. Objectives: The aim of this report is to discuss the pattern of presentation of empyema thoracis as complication of odontogenic cervicofacial infections observed in a maxillofacial unit. Material and methods: A retrospective review of cases of descending cervicofacial infection with chest cavity involvement seen at the oral and maxillofacial clinic and co-managed with the cardiothoracic unit between January 2016 and January 2020. Results: Five male patients presented with empyema thoracis from odontogenic infections, aged between 21 and 29 years (median, 27; mean age, 25.4 years). Coexisting systemic conditions were diabetes mellitus (1 patient), malnutrition (1 case), and mental illness (1 patient). In all cases, plain radiographs revealed pneumothorax, lung collapse, and pleural effusion. Treatment included systemic intravenous antibiotic therapy, control of diabetes, nutritional supplementation, and chest tube insertion. There was favorable outcome in four cases, while one patient died. Patients were discharged home after removal of chest tube. Conclusions: Cervicofacial odontogenic infections are complicated by empyema thoracis, which could be fatal in various patients.
Communication With a Magnetic Dipole: Near-Field Propagation From Air to Undersea

In this article, the famous Sommerfeld integrals (SIs) have been revisited by assuming that the approximation of $\gamma _{0}\approx {\mathrm{ i}}\lambda $ is valid for the near-field propagation of low frequencies over a plane conducting ground. A deduction from that is proposed and adopted in the present study, which is defined by $|\gamma _{0}\gamma _{1}|\gg k_{0}^{2}$ , extending to cover a magnetic dipole source in air-to-undersea communications. The focus is on deriving complete and effective solutions in air and seawater regions under the cylindrical coordinates for the electromagnetic near-field, which is generated by a vertical magnetic dipole above sea surface. The resulting formulas can be given by a few summands in closed form as the well-known Fourier–Bessel integrals. It is believed to go a step further by relaxing the reliance on various distance conditions and replacing the integrands by simple, exact integrated terms which are usable at the frequencies of interest for any distance from the source. Computations and discussions are carried out by comparing with related works and late experiments, including the field components and Poynting vectors. It is verified that the derived formulas can be degenerated into some simplified forms which are in accord with those obtained by a “quasi-static” treatment.
A Primase-Induced Conformational Switch Controls the Stability of the Bacterial Replisome

Recent studies of bacterial DNA replication have led to a picture of the replisome as an entity that freely exchanges DNA polymerases and displays intermittent coupling between the helicase and polymerase(s). Challenging the textbook model of the polymerase holoenzyme acting as a stable complex coordinating the replisome, these observations suggest a role of the helicase as the central organizing hub. We show here that the molecular origin of this newly-found plasticity lies in the >400-fold increase in strength of the interaction between the polymerase holoenzyme and the replicative helicase upon association of the primase with the replisome. By combining in vitro ensemble-averaged and single-molecule assays, we demonstrate that this conformational switch operates during replication and promotes recruitment of multiple holoenzymes at the fork. Our observations provide a molecular mechanism for polymerase exchange and offer a revised model for the replication reaction that emphasizes its stochasticity.
Preparation of human amniotic membrane for transplantation in different application areas

The human amniotic membrane (hAM) is the inner layer of the placenta and plays protective and nutritional roles for the fetus during pregnancy. It contains multiple growth factors and proteins that mediate unique regenerative properties and enhance wound healing in tissue regeneration. Due to these characteristics hAM has been successfully utilized in ophthalmology for many decades. This material has also found application in a variety of additional therapeutic areas. Particularly noteworthy are the extraordinary effects in the healing of chronic wounds and in the treatment of burns. But hAM has also been used successfully in gynecology, oral medicine, and plastic surgery and as a scaffold for in vitro cell culture approaches. This review aims to summarize the different graft preparation, preservation and storage techniques that are used and to present advantages and disadvantages of these methods. It shows the characteristics of the hAM according to the processing and storage methods used. The paper provides an overview of the currently mainly used application areas and raises new application possibilities. In addition, further preparation types like extracts, homogenates, and the resulting treatment alternatives are described.
WOOD AND CHARCOAL ANATOMY OF FOUR MYRTACEAE SPECIES

Qualitative and quantitative changes in anatomical characteristics of charcoal from Campomanesia xanthocarpa, Eugenia pyriformis, Myrcia retorta and Plinia peruviana were described to provide its correct discrimination and information’s to contribute to evaluations in illegal logging. The material came from Planalto Catarinense region, southern Brazil. For each species, three discs at diameter at breast height were collected from three randomly selected trees. All the disks were sectioned to obtain samples in different positions of the trunk (bark, intermediate and pith). Samples were wrapped in aluminum foil and carbonized in a muffl e furnace, with a fi nal temperature of 450 °C and a heating rate of 1.66 °C.min-1. In species analyzed, growth rings are few distinct, delimitated by fi ber regions; solitary vessel and axial parenchyma diffuse or diffuse-in-aggregate is predominant. The wood to charcoal conversion caused variation in the following characteristics: vessel diameters decreased varying from 21.1% in Myrcia retorta to 33.4% in Eugenia pyriformis, while the vessel frequency increased with values from 50.7% to 92.3% related to the same species; height and width of the rays showed reduction, however, Myrcia retorta presented ruptures in ray cells and dimensions increased; ray frequency increased from 3.9% in Eugenia pyriformis to 54.1% in Campomanesia xantocharpa. Qualitative characteristics of wood from studied species remained in charcoal after carbonization at 450 oC, being possible to discriminate the material based on wood anatomy. In charcoal, vessels dimensions and frequency, after ray characteristics can be applied as fi rst step in this Myrtaceae species distinction at forest control. v.24 n.3 2018
Efforful verb recollection drives beta suppression in mesial frontal regions involved in action initiation

Whether the motor cortex activation accompanying concrete verbs comprehension is necessary for verbs conceptual processing is still a hotly debated topic in the literature. Answering this question, we examined to what extent the more difficult access to verb semantics requires an additional engagement of cortical motor system in verb generation task. Using power suppression of MEG beta oscillations (15-30 Hz) as an index of sensorimotor activation, we presented to our participants the noun cues which either were strongly associated with a single verb and prompted the fast and effortless verb retrieval, or were weakly associated with multiple verbs and were more difficult to respond to. A whole-brain analysis of beta suppression revealed that the only cortical regions sensitive to the difficulty of semantic access were the higher order motor areas on the medial and lateral surfaces of the frontal lobe. This differential activation of cortical motor system accompanied effortful verb retrieval and preceded the preparation of vocal response for more than 500 milliseconds. Since the mid-frontal frontal brain areas are involved in maintaining abstract representations of actions during their initiating and planning, we argue that our finding supports the view that motor associations contribute to retrieval of verb semantics.
Occurrence of Listeria monocytogenes and Salmonella Typhimurium in Fruit Juices from Local Stalls and Restaurant in Kuching, Sarawak

Listeria spp. and Salmonella spp. are capable of causing food-borne outbreaks and diseases in humans. This study aimed to quantify and detect the occurrence of Listeria monocytogenes and Salmonella Typhimurium in fruit juices by utilizing Most Probable Number (MPN) in combination with Polymerase Chain Reaction (PCR). In this study, a total of 50 fruit juice samples, consisting of orange, papaya, watermelon, honeydew and apple were collected from Kota Samarahan and Kuching. Specific Polymerase Chain Reaction (PCR) assay targeting the virulence gene, hlyA gene in L. monocytogenes and fliC gene in S. Typhimurium was performed, with the expected size of 730 bp and 559 bp, respectively. MPN analysis showed that the estimated microbial loads of Listeria spp. and Salmonella spp. in all samples were more than 1100 MPN/g. However, based on the PCR analysis, none of the samples (0%) were positive for L. monocytogenes or S. Typhimurium. This study presented as a preliminary food safety screening for the occurrence of Listeria spp. and Salmonella spp. from retailed fruit juices. Hygienic practices and food safety measures should be adhered by all food vendors and restaurants in order to avoid foodborne disease outbreaks in the future. Keywords: fliC, hlyA, Listeria, PCR, Salmonella