Miracle-dz/UniFAR-FTUs huggingface dataset:
The Role of Entrepreneurial Orientation in Improving Small Medium Enterprise (SME) Performance

The purpose of this study is to examine and analyse the effect of entrepreneurial orientation on market orientation, technological capability and performance of SMEs. The study was conducted on 120 SMEs in the field of leather craft in the Special Province of Yogyakarta, Indonesia. The sample selection uses area proportionate random sampling from 4 districts and 1 city in Yogyakarta. Data was analysed using SEM with the WarpPLS approach. The results of the study show that entrepreneurial orientation significantly influences market orientation, technological capability and SME’s performance. Market orientation has a significant effect on technological capability and SMEs’ performance. The technological capability has a significant effect on SMEs’ performance. Based on the results of this study, SMEs’ performance can be improved through strategic orientation, entrepreneurial orientation, market orientation and firm capability, as well as technological capabilities.
A Real Business Cycle Model for Panel Data: An Application for the Central European Transition Economies

This paper has two objectives — a real business cycle model is analyzed for panel data over a short time period and the Central European transition experience is explained by RBC theory. In particular, the catch-up process of transition economies to the Western European level of development is described. The main contribution of the paper is a rigorous proof that transition data is consistent both with the standard stylized facts about macroeconomic fluctuations and with predictions from the proposed real business cycle model.
Synthesis of Unequally Spaced Linear Micro Strip Rectangular Patch Antenna Array Using Improved Local Search Particle Swarm Optimization

Antenna array systems with low side lobe levels are essential for today wireless communication systems. This paper presents the synthesis of unequally spaced linear rectangular micro strip antenna array with minimum side lobe levels using the novel evolutionary algorithm known as improved local search particle swarm optimization (ILSPSO). ILSPSO is a modified version of particle swarm optimization (PSO), in which Gaussian distribution is used to enhance the local search of the PSO. In this paper, ILPSO is applied to optimize the positions of the micro strip antenna elements to suppress the peak side lobe level (PSLL) along with PSO and differential evolution (DE) algorithms. The steps involved in problem formulation along with design examples illustrating the performance of the ILPSO in minimizing the side lobe levels are demonstrated. A 20 and 32 element linear micro strip rectangular patch antenna (MSRPA) element are considered to show the effectiveness of the proposed method. The optimized micro strip antenna array is simulated using high frequency structure simulator (HFSS). The synthesis results demonstrate that the ILSPSO outperforms PSO and DE in terms of producing lower PSLL and convergence rate. The flexibility and ease of implementation of the ILSPSO algorithm is obvious from this paper, showing the algorithms usefulness in other array synthesis problems.
Recognition of G-quadruplex topology through hybrid binding with implications in cancer theranostics

The selective recognition and imaging of oncogene specific G-quadruplex (GQ) structures holds great promise in the development of diagnostic therapy (theranostics) for cancer and has been challenging due to their structural dynamics and diversity. We report selective recognition of GQ by a small molecule through unique hybrid loop stacking and groove binding mode with turn on far-red fluorescence response and anticancer activity demonstrating the potential implications for GQ-targeted cancer theranostics. Methods: Biophysical investigation reveal the turn on far-red emission property of TGP18 for selective recognition of GQ. In cellulo studies including DNA damage and oxidative stress evaluation guided us to perform in vitro (3D spheroid) and in vivo (xenograft mice model) anti-cancer activity, and tumor tissue imaging to assess the theranostic potential of TGP18. Results: Neocuproine-based far-red turn on fluorescence probe TGP18 shows GQ-to-duplex selectivity and specifically recognizes BCL-2 GQ with high affinity through a unique hybrid binding mode involving loop-stacking and groove interactions. Our study reveals that the selective recognition originating from the distinct loop structure of GQ that alters the overall probe interaction and binding affinity. TGP18 binding to anti-apoptotic BCL-2 GQ ablates the pro-survival function and elicit anti-cancer activity by inducing apoptosis in cancer cells. We deciphered that inhibition of BCL-2 transcription synergized with signaling cascade of nucleolar stress, DNA damage and oxidative stress in triggering apoptosis signaling pathway. Conclusion: Intervention of GQ mediated lethality by TGP18 has translated into anti-cancer activity in both in vitro 3D spheroid culture and in vivo xenograft models of lung and breast cancer with superior efficacy for the former. In vivo therapeutic efficacy supplemented with tumor 3D spheroid and tissue imaging potential define the role of TGP18 in GQ-targeted cancer theranostics.
A Dynamic Component and Aspect-Oriented Platform

Component-based software development (CBSD) represents a significant advance towards assembling systems by plugging in independent and (re)usable components. On the other hand, aspect-oriented software development (AOSD) is presently considered as a possible technology to improve the modularity and adaptability of complex and large-scale distributed systems. Both are complementary technologies, so it would be helpful to have models that combine them to take advantage of all their mutual benefits. Thus recent research has tried to combine CBSD and AOSD by considering aspects as reusable parts that can be woven and then attached to the individual components. Our contribution to the integration of these technologies is CAM, a new component and aspect model that defines components and aspects as first-order entities, together with a non-intrusive composition mechanism to plug aspects into components. The underlying infrastructure supporting CAM is the dynamic aspect-oriented platform (DAOP), a component and aspect platform that provides the usual services of distributed applications, as well as a composition mechanism to perform the plugging of software aspects into components at runtime.
Filter paper for preservation, storage, and distribution of insect and pathogen DNA samples.

Proper DNA storage is critical for studies involving genetic analysis of insects and for molecular diagnostics of pathogens carried by them. Molecular surveillance of pathogens carried by insects can involve screening of thousands of insect DNA samples. Problems with storage and degradation of these samples can arise. In this study, a simple filter paper-based method for storage and preservation of insect DNA was evaluated using polymerase chain reaction (PCR). DNA was isolated from individual house fly, Musca domestica L. , adults by using a cell lysis technique. From 50 house flies known to carry Campylobacter spp. , a portion of the DNA sample was stored frozen and another portion was pipetted onto filter paper. At monthly intervals for 7 mo, PCR was conducted using 1 μl of the frozen DNA sample and a 2.0-mm disk from the filter paper samples as the PCR template. Two markers were used, a 450-bp region of the insect mitochondrial DNA (mtDNA) ND5 gene and a 857-bp region of the Campylobacter spp. mtDNA 16S rDNA gene. PCR amplification was successful for all of the samples regardless of the storage method. The filter paper method is a simple and economical way to store, preserve, and distribute DNA samples for PCR analysis.
Gut microbiota of obese and diabetic Thai subjects and interplay with dietary habits and blood profiles

Obesity and type 2 diabetes mellitus (T2DM) have become major public health issues globally. Recent research indicates that intestinal microbiota play roles in metabolic disorders. Though there are numerous studies focusing on gut microbiota of health and obesity states, those are primarily focused on Western countries. Comparatively, only a few investigations exist on gut microbiota of people from Asian countries. In this study, the fecal microbiota of 30 adult volunteers living in Chiang Rai Province, Thailand were examined using next-generation sequencing (NGS) in association with blood profiles and dietary habits. Subjects were categorized by body mass index (BMI) and health status as follows; lean (L) = 8, overweight (OV) = 8, obese (OB) = 7 and diagnosed T2DM = 7. Members of T2DM group showed differences in dietary consumption and fasting glucose level compared to BMI groups. A low level of high-density cholesterol (HDL) was observed in the OB group. Principal coordinate analysis (PCoA) revealed that microbial communities of T2DM subjects were clearly distinct from those of OB. An analogous pattern was additionally illustrated by multiple factor analysis (MFA) based on dietary habits, blood profiles, and fecal gut microbiota in BMI and T2DM groups. In all four groups, Bacteroidetes and Firmicutes were the predominant phyla. Abundance of Faecalibacterium prausnitzii, a butyrate-producing bacterium, was significantly higher in OB than that in other groups. This study is the first to examine the gut microbiota of adult Thais in association with dietary intake and blood profiles and will provide the platform for future investigations.
Factors Influencing Retinal Pigment Epithelium-Atrophy Progression Rate in Stargardt Disease

Purpose To evaluate demographic, clinical, imaging, and genetic factors associated with retinal pigment epithelium enlargement in Stargardt disease (STGD1) and to measure the agreement between short-wavelength fundus autofluorescence (SW-FAF) and near-infrared fundus autofluorescence (NIR-FAF). Methods Retrospective cohort study of patients with STGD1 with ≥2 gradable SW-FAF images. RPE-atrophy areas were measured on SW-FAF and NIR-FAF at each visit and regressed against time to obtain the rate of RPE-atrophy enlargement. Agreement between SW-FAF and NIR-FAF with regards to baseline atrophic areas and rates of enlargement was evaluated. Baseline factors predictive of faster SW-FAF RPE-atrophy enlargement were investigated with linear mixed models. Results Fifty-four eyes of 28 patients (median age: 45 years; 13 males) were included. SW-FAF and NIR-FAF agreed well for slow rates of RPE-atrophy progression, but agreement decreased as the rate increased. Median (interquartile range [IQR]) rate of RPE-atrophy expansion was 0.18 (0.10–0.85) mm2/year on SW-FAF and 0.24 (0.08–0.33) mm2/year on NIR-FAF. Larger baseline RPE-atrophy area (estimate: 0.057 mm2/year, P < 0.001), worse visual acuity (0.305 mm2/year, P = 0.005), multifocal disease (0.401 mm2/year, P = 0.02), and SW-FAF pattern (0.534 mm2/year, P =0 .03) were associated with a faster rate of progression (predictive R2: 0.65). Conclusions SW-FAF and NIR-FAF are not interchangeable in the evaluation of RPE-atrophy enlargement, and both imaging modalities may be required for optimal detection of disease progression. A multivariable model based on baseline clinical and imaging information may identify patients at higher risk of fast disease progression. Translational Relevance The knowledge of the agreement of different FAF modalities, the estimated rates of RPE-atrophy enlargement, and factors predictive of faster anatomic decay in STGD1 may allow tailored clinical management and better clinical trials design.
Classification of genomic components and prediction of genes of Begomovirus based on subsequence natural vector and support vector machine

Background Begomoviruses are widely distributed and causing devastating diseases in many crops. According to the number of genomic components, a begomovirus is known as either monopartite or bipartite begomovirus. Both the monopartite and bipartite begomoviruses have the DNA-A component which encodes all essential proteins for virus functions, while the bipartite begomoviruses still contain the DNA-B component. The satellite molecules, known as betasatellites, alphasatellites or deltasatellites, sometimes exist in the begomoviruses. So, the genomic components of begomoviruses are complex and varied. Different genomic components have different gene structures and functions. Classifying the components of begomoviruses is important for studying the virus origin and pathogenic mechanism. Methods We propose a model combining Subsequence Natural Vector (SNV) method with Support Vector Machine (SVM) algorithm, to classify the genomic components of begomoviruses and predict the genes of begomoviruses. First, the genome sequence is represented as a vector numerically by the SNV method. Then SVM is applied on the datasets to build the classification model. At last, recursive feature elimination (RFE) is used to select essential features of the subsequence natural vectors based on the importance of features. Results In the investigation, DNA-A, DNA-B, and different satellite DNAs are selected to build the model. To evaluate our model, the homology-based method BLAST and two machine learning algorithms Random Forest and Naive Bayes method are used to compare with our model. According to the results, our classification model can classify DNA-A, DNA-B, and different satellites with high accuracy. Especially, we can distinguish whether a DNA-A component is from a monopartite or a bipartite begomovirus. Then, based on the results of classification, we can also predict the genes of different genomic components. According to the selected features, we find that the content of four nucleotides in the second and tenth segments (approximately 150-350 bp and 1,450–1,650 bp) are the most different between DNA-A components of monopartite and bipartite begomoviruses, which may be related to the pre-coat protein (AV2) and the transcriptional activator protein (AC2) genes. Our results advance the understanding of the unique structures of the genomic components of begomoviruses.
OBAMA: OBAMA for Bayesian amino-acid model averaging

Background Bayesian analyses offer many benefits for phylogenetic, and have been popular for analysis of amino acid alignments. It is necessary to specify a substitution and site model for such analyses, and often an ad hoc, or likelihood based method is employed for choosing these models that are typically of no interest to the analysis overall. Methods We present a method called OBAMA that averages over substitution models and site models, thus letting the data inform model choices and taking model uncertainty into account. It uses trans-dimensional Markov Chain Monte Carlo (MCMC) proposals to switch between various empirical substitution models for amino acids such as Dayhoff, WAG, and JTT. Furthermore, it switches base frequencies from these substitution models or use base frequencies estimated based on the alignment. Finally, it switches between using gamma rate heterogeneity or not, and between using a proportion of invariable sites or not. Results We show that the model performs well in a simulation study. By using appropriate priors, we demonstrate both proportion of invariable sites and the shape parameter for gamma rate heterogeneity can be estimated. The OBAMA method allows taking in account model uncertainty, thus reducing bias in phylogenetic estimates. The method is implemented in the OBAMA package in BEAST 2, which is open source licensed under LGPL and allows joint tree inference under a wide range of models.
Taxonomic recognition of some species-level lineages circumscribed in nominal Rhizoplaca subdiscrepans s. lat. (Lecanoraceae, Ascomycota)

Background Rhizoplaca subdiscrepans (Nyl.) R. Sant. , a saxicolous, placodioid lichen, is considered to have a worldwide distribution in warm-temperate to boreal-arctic areas in Asia, Europe and North America. However, recent studies have revealed that this species includes five unrecognized species-level lineages—‘subd A, B, C, D and E’. During research focused on the diversity of saxicolous lichens in mountainous areas of southern Poland, some interesting representatives of the genus Rhizoplaca were found. The main aim of our study was to determine the taxonomic status of the collected specimens by means of molecular tools and a comparative analysis of similar herbarium materials. Methods Detailed morphological, anatomical and chemical examinations of reference material from Asia, Europe and North and South America focused primarily on a selected group of lecanoroid taxa with a placodioid thallus. In addition, 21 new generated sequences representing Lecanora pseudomellea, Protoparmeliopsis muralis, Rhizoplaca opiniconensis, R. subdiscrepans s. lat. and R. phaedrophthalma were selected for molecular study using the internal transcribed spacer region (ITS rDNA), together with 95 available GenBank sequences mainly from the genus Rhizoplaca. Results Polish specimens that clustered with members of a potential species-level lineage ‘subd E’ of Rhizoplaca subdiscrepans complex were recovered. Comprehensive analyses of the lichen group led us to the conclusion that lineage ‘subd E’ represents R. subdiscrepans s. str. and that the taxon appears to have a limited geographical distribution and specific habitat preferences. Furthermore, some of the recently defined species candidates within R. subdiscrepans s. lat. —‘subd D’ and ‘subd A’—should be assigned to two previously known species of Rhizoplaca, namely R. opiniconensis (Brodo) Leavitt, Zhao Xin & Lumbsch and R. phaedrophthalma (Poelt) Leavitt, Zhao Xin & Lumbsch, respectively. These two species are characterized by phenotypic features observed as well in analyzed specimens representing lineages ’subd D’ and ’subd A’. Moreover, the representatives of these lineages demonstrate some differences in occupied habitat and geographical range that also correspond with the indicated species. Additionally, it was found that Lecanora pseudomellea B.D. Ryan is a strongly supported monophyletic lineage within Rhizoplaca, and therefore an appropriate new combination for the species is proposed.
Clinical Features at Onset and Genetic Characterization of Pediatric and Adult Patients with TNF-α Receptor—Associated Periodic Syndrome (TRAPS): A Series of 80 Cases from the AIDA Network

This study explores demographic, clinical, and therapeutic features of tumor necrosis factor receptor-associated periodic syndrome (TRAPS) in a cohort of 80 patients recruited from 19 Italian referral Centers. Patients' data were collected retrospectively and then analyzed according to age groups (disease onset before or after 16 years) and genotype (high penetrance (HP) and low penetrance (LP) TNFRSF1A gene variants). Pediatric- and adult-onset were reported, respectively, in 44 and 36 patients; HP and LP variants were found, respectively, in 32 and 44 cases. A positive family history for recurrent fever was reported more frequently in the pediatric group than in the adult group (p < 0.05). With reference to clinical features during attacks, pericarditis and myalgia were reported more frequently in the context of adult-onset disease than in the pediatric age (with p < 0.01 and p < 0.05, respectively), while abdominal pain was present in 84% of children and in 25% of adults (p < 0.01). Abdominal pain was significantly associated also to the presence of HP mutations (p < 0.01), while oral aphthosis was more frequently found in the LP variant group (p < 0.05). Systemic amyloidosis occurred in 25% of subjects carrying HP variants. As concerns laboratory features, HP mutations were significantly associated to higher ESR values (p < 0.01) and to the persistence of steadily elevated inflammatory markers during asymptomatic periods (p < 0.05). The presence of mutations involving a cysteine residue, abdominal pain, and lymphadenopathy during flares significantly correlated with the risk of developing amyloidosis and renal impairment. Conversely, the administration of colchicine negatively correlated to the development of pathologic proteinuria (p < 0.05). Both NSAIDs and colchicine were used as monotherapy more frequently in the LP group compared to the HP group (p < 0.01). Biologic agents were prescribed to 49 (61%) patients; R92Q subjects were more frequently on NSAIDs monotherapy than other patients (p < 0.01); nevertheless, they required biologic therapy in 53.1% of cases. At disease onset, the latest classification criteria for TRAPS were fulfilled by 64/80 (80%) patients (clinical plus genetic items) and 46/80 (57.5%) patients (clinical items only). No statistically significant differences were found in the sensitivity of the classification criteria according to age at onset and according to genotype (p < 0.05). This study describes one of the widest cohorts of TRAPS patients in the literature, suggesting that the clinical expression of this syndrome is more influenced by the penetrance of the mutation rather than by the age at onset itself. Given the high phenotypic heterogeneity of the disease, a definite diagnosis should rely on both accurate working clinical assessment and complementary genotype.
Reliability and Recommended Settings for Pediatric Circumpapillary Retinal Nerve Fiber Layer Imaging Using Hand-Held Optical Coherence Tomography

Purpose To investigate feasibility and reliability of 3-dimensional full circumpapillary retinal nerve fiber layer (cpRNFL) analysis in children, with and without glaucoma, without the use of sedation and to recommend a protocol for hand-held optical coherence tomography use. Methods A cohort of pediatric glaucoma patients and normal children were imaged with hand-held optical coherence tomography to assess the feasibility of obtaining full cpRNFL. Two consecutive scans were acquired in a smaller sample to investigate test–retest repeatability and interassessor reproducibility. The cpRNFL thickness was assessed in four quadrants, at several visual angles from the optic nerve center. Results Scanning was attempted in both eyes of 90 children with pediatric glaucoma and 180 controls to investigate feasibility (mean age, 6.98 ± 4.42 years). Scanning was not possible in 68 eyes of glaucoma children mainly owing to nystagmus, unclear optical media, or high refractive errors. Where three-dimensional imaging was possible, success at obtaining full cpRNFL was 67% in children with glaucoma and 89% for controls. Seventeen children with pediatric glaucoma and 34 controls contributed to reliability analysis (mean age, 6.3 ± 3.63 years). For repeatability intraclass correlation coefficients across quadrants ranged from 0.63 to 0.82 at 4° and improved to 0.88 to 0.94 at 6°. Intraclass correlation coefficients for reproducibility were also highest at 6° (>0.97 across all quadrants). Conclusions We demonstrate that acquisition and measurement of cpRNFL thickness values using 3-dimensional hand-held optical coherence tomography volumes in awake children is both feasible and reliable and is optimal at 6° from optic nerve center. Translational Relevance Our recommended protocol provides guidance on how pediatric optic nerve pathologies are managed by clinicians.