Cluster Analysis on Dengue Incidence and Weather Data Using K-Medoids and Fuzzy C-Means Clustering Algorithms (Case Study: Spread of Dengue in the DKI Jakarta Province)

In Indonesia, Dengue incidence tends to increase every year but has been fluctuating in recent years. The potential for Dengue outbreaks in DKI Jakarta, the capital city, deserves serious attention. Weather factors are suspected of being associated with the incidence of Dengue in Indonesia. This research used weather and Dengue incidence data for five regions of DKI Jakarta, Indonesia, from December 30, 2008, to January 2, 2017. The study used a clustering approach on time-series and non-time-series data using K-Medoids and Fuzzy C-Means Clustering. The clustering results for the non-time-series data showed a positive correlation between the number of Dengue incidents and both average relative humidity and amount of rainfall. However, Dengue incidence and average temperature were negatively correlated. Moreover, the clustering implementation on the time-series data showed that rainfall patterns most closely resembled those of Dengue incidence. Therefore, rainfall can be used to estimate Dengue incidence. Both results suggest that the government could utilize weather data to predict possible spikes in DHF incidence, especially when entering the rainy season and alert the public to greater probability of a Dengue outbreak.

Pharmacophore Modeling, Docking, and Molecular Dynamics Simulation of Flavonoids as Inhibitors of Urokinase-type Plasminogen Activator

The urokinase-type plasminogen activator (uPA) system plays a significant role in the invasion and metastasis of cancer cells. The present study was conducted to investigate natural product compounds as inhibitors and hit molecules of uPA using in-silico analysis. A pharmacophore model was built to screen the Indonesian Herbal Database (HerbalDB) to obtain inhibitors of different scaffolds. Based on the molecular docking score, four ligands were selected as potential uPA inhibitors. Subsequently, the stability of the ligand-uPA complex was analyzed using molecular dynamics (MD) simulation. An RMSD graph of the backbone protein and the RMSF values of the amino acid residues were also determined. In addition, the MM-PBSA method was applied to calculate the free binding energy. According to the results, Model_3, characterized by aromatic rings 23 (F1 and F2), cationic H-bond donor (F3), and metal ligator (F4) features, had an adequate goodness-of-hit score (GH). The four top-ranked ligands, isorhamnetin, rhamnetin, quercetin, and kaempferol, showed higher docking scores compared to the others. This study confirmed that isorhamnetin, rhamnetin, and kaempferol build stable complexes with uPA with lower binding energy than quercetin.

Properties of the Environment of Galaxies in Clusters of Galaxies CL 0024+1654 and RX J0152.7−1357

We report the results of combined analyses of X-ray and optical data of two galaxy clusters, CL 0024+1654 and RX J0152.7−1357 at redshift z = 0.395 and z = 0.830, respectively, offering a holistic physical description of the two clusters. Our X-ray analysis yielded temperature and density profiles of the gas in the intra-cluster medium (ICM). Using optical photometric and spectroscopic data, complemented with mass distribution from a gravitational lensing study, we investigated any possible correlation between the physical properties of the galaxy members, i.e. their color, morphology, and star formation rate (SFR), and their environments. We quantified the properties of the environment around each galaxy by galaxy number density, ICM temperature, and mass density. Although our results show that the two clusters exhibit a weaker correlation compared to relaxed clusters, it still confirms the significant effect of the ICM on the SFR in the galaxies. The close relation between the physical properties of galaxies and the condition of their immediate environment found in this work indicates the locality of galaxy evolution, even within a larger bound system such as a cluster. Various physical mechanisms are suggested to explain the relation between the properties of galaxies and their environment.

Role of Hypoxia on Growth and Differentiation of Human Adipose Derived Stem Cells Grown on Silk Fibroin Scaffold Induced by Platelet Rich Plasma

Previous research has proven that 10% platelet-rich plasma (PRP) can enhance growth and differentiation of human adipose derived stem cells (hADSC) grown on silk fibroin scaffold into chondrocytes. A low oxygen concentration (hypoxia) condition is an important factor that potentially affects the ability of hADSC to grow and differentiate. The objective of this research was to analyze the difference in growth and differentiation capacity of hADSC grown on salt leached silk fibroin scaffold supplemented by 10% PRP under normoxic and hypoxic conditions. The growth capacity of the hADSC was determined by MTT assay and differentiation was tested using glycosaminoglycan (GAG) content analysis, while chondrocyte markers were visualized with the immunocytochemistry (ICC) method. This research observed hADSC proliferation under normoxic and hypoxic conditions for 21 days. Visualization of type 2 collagen showed that it was more abundant under hypoxia compared to normoxia. HIF-1α was only detected in the hADSC cultured in hypoxic conditions. In conclusion, culture under hypoxic conditions increases the capacity of hADSC to grow and differentiate into chondrocytes. This is the first study that has shown that hypoxia is able to enhance the proliferation and differentiation of hADSC grown on 3D salt leached silk fibroin scaffold supplemented by 10% PRP.

Inherent Irreversibility of Mixed Convection within Concentric Pipes in a Porous Medium with Thermal Radiation

This work investigated the thermal putrefaction and inherent irreversibility in a steady flow of an incompressible inconstant viscosity radiating fluid within two concentric pipes filled with a porous medium. Following the Brinkmann-Darcy-Forchheimer approach, the nonlinear differential equations governing the model were obtained. The model boundary value problem was addressed numerically via a shooting quadrature with the Runge-Kutta-Fehlberg integration scheme. The effects of diverse emerging parameters on the fluid velocity, temperature, skin friction, Nusselt number, entropy generation rate and the Bejan number are provided in graphs and discussed in this paper.

Designing Aquifer Model for the Banks of the Serayu River, Sokawera, Somagede, Banyumas, Indonesia by Means of 1D-Electrical Resistivity Data

A geoelectric survey using the 1D-electrical resistivity method was applied to design a groundwater aquifer model for the banks of the Serayu River in Sokawera Village, Somagede District, Banyumas Regency, Indonesia. The aim of this research was to identify the characteristics of aquifers in the research area based on resistivity log data. Acquisition, modeling, and interpretation of resistivity data were carried out and the results were lithological logs at seven sounding points. Correlation between the lithological logs resulted in a hydrostratigraphic model. This model is composed of several hydrological units, i.e. shallow aquifer, aquitard, and deep aquifer. The shallow aquifers are composed of sandy clay (10.81-18.21 Wm) and clayey sand (3.04-7.43 Wm) with a depth of groundwater from the water table to 27.51 m. The deep aquifers are composed of sandstone with variation of porosity (2.24-12.04 Wm) at a depth of more than 54.98 m. Based on this model, potential shallow aquifers were estimated to be at sounding points Sch-5, Sch-6, and Sch-7. This hydrostratigraphic model shows that the two types of aquifers are separated by an aquitard layer, allowing groundwater infiltration from the shallow aquifer to the deep aquifer and vice versa. Moreover, the Serayu riverbanks in this research area are estimated to be a groundwater discharge area.

Purely Data-driven Exploration of COVID-19 Pandemic After Three Months of the Outbreak

Many research studies have been carried out to understand the epidemiological characteristics of the COVID-19 pandemic in its early phase. The current study is yet another contribution to better understand the disease properties by parameter estimation based on mathematical SIR epidemic modeling. The authors used Johns Hopkins University’s dataset to estimate the basic reproduction number of COVID-19 for five representative countries (Japan, Germany, Italy, France, and the Netherlands) that were selected using cluster analysis. As byproducts, the authors estimated the transmission, recovery, and death rates for each selected country and carried out statistical tests to see if there were any significant differences.

Optimal Control in a Mathematical Model of Smoking

This paper presents a dynamic model of smoking with optimal control. The mathematical model is divided into 5 sub-classes, namely, non-smokers, occasional smokers, active smokers, individuals who have temporarily stopped smoking, and individuals who have stopped smoking permanently. Four optimal controls, i.e., anti-smoking education campaign, anti-smoking gum, anti-nicotine drug, and government prohibition of smoking in public spaces are considered in the model. The existence of the controls is also presented. The Pontryagin maximum principle (PMP) was used to solve the optimal control problem. The fourth-order Runge-Kutta was employed to gain the numerical solutions.

Slater-Pauling-like Behavior of Spin Hall Conductivity in Pt-based Superlattices

The intrinsic spin Hall effect in the bulk systems of late transition metals (Os, Ir, Pt, and Au) as well as the Pt-based superlattices were investigated by using first-principle calculations. By comparing the computed spin Hall conductivities of Pt−M superlattices (M=Os, Ir, and Au) with different compositions and those obtained from atomic bulk composition, we saw that the spin Hall conductivities (SHCs) follow the behavior described by the Slater-Pauling curve, the maximum of which is at pure Pt bulk. From the examination of the band structures of the considered systems, we found that the origin of this behavior comes from the variation of the band structures as a direct consequence of the change of the number of electrons and hybridization effects.

Fibroin and Spidroin Thin Film to Support the Attachment and Spread of Human Dermal Fibroblast: The Potency of Skin Tissue Engineering

This study aimed to determine the characteristics of scaffolds made of fibroin from Bombyx mori and spidroin from Argiope appensa in supporting the attachment and proliferation of HDF cells on the scaffolds. Thin-film scaffolds were made using the solvent casting technique, where the scaffold is an amalgamation of fibroin, spidroin, PVA, and glycerol. HDF cells were grown on DMEM medium with 10% FBS and 1% antibiotic-antimicotic. Characterization of the scaffolds was performed by using ATR-FTIR, swelling test, contact angle measurement, tensile test, biodegradation, MTT and SEM. The results of the ATR-FTIR analysis showed that the scaffolds contained fibroin, spidroin, PVA, and glycerol. Swelling and contact angle tests showed that all scaffold combinations were hydrophilic. Mechanical properties and in vitro biodegradation tests showed no significant difference among the scaffold combinations. MTT testing showed that all scaffolds could facilitate the attachment of fibroblasts and showed increased viability from day 1, 3, and 5. Scanning electron microscopy showed that the cells in the 70% fibroin and 10% spidroin scaffold had the best cell morphology and the best combination for potential application in skin tissue engineering.