Miracle-dz/UniFAR-FTUs huggingface dataset:
The Design and Implementation of a Modeling Tool for Regular Expressions

Model-based testing has been widely studied to generate test cases from the Finite State Machine (FSM). Due to the limitation of the modeling theory of FSM, it is hard to build a right model for software concurrent behaviors by FSM. Recently, we proposed a theory of test modeling based on regular expressions to construct test models for concurrent systems. To realize and put this theory into practice, we develop a lightweight modeling tool named as Regular-Finite State Machine (RFSM) to support visual modeling with regular expressions. It supports the production of seven operators for describing software behaviors and two methods for constructing the expression model, including the RFSM code editor and the toolbar editor. An algorithm for transforming the model into the extended regular expressions is also introduced.
Application of Inductive Logic Programming to Produce Emergent Behavior in an Artificial Society

Artificial society is a discipline to study mechanisms of social system and phenomena which the mechanisms make. Emergence is global phenomena occurred by local mechanisms, such as, by collective behavior of autonomous agents. Understanding of emergence phenomena is a challenging subject. In this paper we use the framework of inductive logic programming (ILP) for artificial society and emergence behavior study. ILP is a branch of machine learning based on logic programming and inductive inference. We investigate the possibility of ILP in artificial society study. ILP and logic programming technique are applied to representation of an artificial society model, called Sugarscape, and to rule learning for agent behavior. Although classical ILP algorithms target classification problems, the proposed algorithm grows behavior rule for an evaluation measurement. Phenomena which this paper treate is limited but we showed that ILP technique can be applied to study in the field of artificial society.
Fragment Screening by Native State Mass Spectrometry

Native state mass spectrometry (MS) has been recognised as a rapid, sensitive, and high throughput method to directly investigate protein-ligand interactions for some time, however there are few examples reporting this approach as a screening method to identify relevant protein–fragment interactions in fragment-based drug discovery (FBDD). In this paper an overview of native state MS will be presented, highlighting the attractive properties of this method within the context of fragment screening applications. A summary of published examples using MS for fragment screening will be described and reflection on the outlook for the future adoption and implementation of native state MS as a complementary fragment screening method will be presented.
Changes in the connections of the main olfactory bulb after mitral cell selective neurodegeneration

The connections of the main olfactory bulb (OB) of the mouse were studied with iontophoretic injections of biotinylated dextran amine. To sort efferences from mitral cells and tufted cells, the Purkinje cell degeneration (PCD) mouse was used. This mutant animal undergoes a specific neurodegeneration of mitral cells, whereas tufted cells do not degenerate. The unilateral tracer injections used were small and confined largely to the OB of both PCD and control mice at P120. Seven days after tracer injection, the efferences from the OB and the centrifugal afferences from secondary olfactory structures to it were studied. Although there is a large overlap of their target fields, mitral cell axons innervated more caudal regions of the olfactory cortex than tufted cell axons, thus providing definitive evidence of the differential projections of olfactory output neurons. Additionally, an important increase in retrogradely‐labeled neurons was detected in the ipsilateral anterior olfactory nucleus of the mutant animals. This was not observed in any other secondary olfactory structure, suggesting a strengthening of the centrifugal input to the OB from that central area after mitral cell loss. Moreover, we recorded a complete loss of bilaterality in the olfactory connections of the PCD mice due to degeneration of the anterior commissure. These results point to an important reorganization of this essential olfactory circuit between the anterior olfactory nucleus and the OB, and hint at a transsynaptic level of plasticity not considered previously in literature. © 2007 Wiley‐Liss, Inc.
The Immediate Early Gene Egr3 Is Required for Hippocampal Induction of Bdnf by Electroconvulsive Stimulation

Early growth response 3 (Egr3) is an immediate early gene (IEG) that is regulated downstream of a cascade of genes associated with risk for psychiatric disorders, and dysfunction of Egr3 itself has been implicated in schizophrenia, bipolar disorder, and depression. As an activity-dependent transcription factor, EGR3 is poised to regulate the neuronal expression of target genes in response to environmental events. In the current study, we sought to identify a downstream target of EGR3 with the goal of further elucidating genes in this biological pathway relevant for psychiatric illness risk. We used electroconvulsive stimulation (ECS) to induce high-level expression of IEGs in the brain, and conducted expression microarray to identify genes differentially regulated in the hippocampus of Egr3-deficient (-/-) mice compared to their wildtype (WT) littermates. Our results replicated previous work showing that ECS induces high-level expression of the brain-derived neurotrophic factor (Bdnf) in the hippocampus of WT mice. However, we found that this induction is absent in Egr3-/- mice. Quantitative real-time PCR (qRT-PCR) validated the microarray results (performed in males) and replicated the findings in two separate cohorts of female mice. Follow-up studies of activity-dependent Bdnf exons demonstrated that ECS-induced expression of both exons IV and VI requires Egr3. In situ hybridization demonstrated high-level cellular expression of Bdnf in the hippocampal dentate gyrus following ECS in WT, but not Egr3-/-, mice. Bdnf promoter analysis revealed eight putative EGR3 binding sites in the Bdnf promoter, suggesting a mechanism through which EGR3 may directly regulate Bdnf gene expression. These findings do not appear to result from a defect in the development of hippocampal neurons in Egr3-/- mice, as cell counts in tissue sections stained with anti-NeuN antibodies, a neuron-specific marker, did not differ between Egr3-/- and WT mice. In addition, Sholl analysis and counts of dendritic spines in golgi-stained hippocampal sections revealed no difference in dendritic morphology or synaptic spine density in Egr3-/-, compared to WT, mice. These findings indicate that Egr3 is required for ECS-induced expression of Bdnf in the hippocampus and suggest that Bdnf may be a downstream gene in our previously identified biologically pathway for psychiatric illness susceptibility.
Psycho-visual evaluation of image quality attributes in digital pathology slides viewed on a medical color LCD display

We investigate the effects of common types of image manipulation and image degradation on the perceived image quality (IQ) of digital pathology slides. The reference images in our study were digital images of animal pathology samples (gastric fundic glands of a dog and liver of a foal) stained with haematoxylin and eosin. The following 5 types of artificial manipulations were applied to the images, each very subtle (though visually discernible) and always one at a time: blurring, gamma modification, adding noise, change in color saturation, and JPG compression. Three groups of subjects: pathology experts (PE), pathology students (PS) and imaging experts (IE), assessed 6 IQ attributes in 72 single-stimulus trials. The following perceptual IQ attribute ratings were collected: overall IQ, blur disturbance, quality of contrast, noise disturbance, and quality of color saturation. Our results indicate that IQ ratings vary quite significantly with expertise, especially, PE and IE tend to judge IQ according to different criteria. In particular, IE seem notably more sensitive to noise than PE who, on the other side, tend to be sensitive to manipulations in color and gamma parameters. It remains an important question for future research to examine the impact of IQ on the diagnostic performance of PE. That should support our present findings in suggesting directions for further development of the numerical IQ metrics for digital pathology data.
Perceived School Support in Inclusive Education

Bu arastirmanin amaci Kaynastirma Egitiminde Algilanan Okul Destegi Olcegini (KEAODO) (Ahmmed, 2013) Turkce ’ye uyarlamaktir. Arastirma kapsaminda uyarlanan olcek 221 ogretmene uygulanmistir. Dogrulayici faktor analizinde 8 maddeden olusan tek boyutlu modelin iyi uyum verdigi gozlemlenmistir. Olcegin psikometrik ozelliklerini inceleyebilmek amaciyla ic tutarlilik, madde ve faktor analizi calismalari yapilmistir. Olcegin ic tutarlilik analizleri sonucu . 85 bulunulmus olup, yapilan analiz ile guvenirlik icin gerekli olan orana ulasildigi gorulmustur. KEAODO'nin orijinal tek faktorlu yapisinin, madde ayirt ediciligi ve dogrulayici faktor analizinden alinan sonuclar dogrultusunda Turk orneklemine uygunlugu belirlenmistir. (x2= 97.57, sd= 20, RMSEA= .133, NFI=.92, NNFI= .91, CFI = .93, IFI=.93,SRMR=066, GFI= .90). Bu durumda olcegin Turk orneklem grubu icin egitim surecinde ogretmenlerin "Kaynastirma Egitiminde Algilanan Okul Destegi" duzeylerinin belirlenmesi icin uygulanabilecegi dusunulmektedir
Structural Transition and Antibody Binding of EBOV GP and ZIKV E Proteins from Pre-Fusion to Fusion-Initiation State

Membrane fusion proteins are responsible for viral entry into host cells– a crucial first step in viral infection. These proteins undergo large conformational changes from pre-fusion to fusion initiation structures, and, despite differences in viral genomes and disease etiology, many fusion proteins are arranged as trimers. Structural information for both pre-fusion and fusion initiation states is critical for understanding virus neutralization by the host immune system. In the case of Ebola glycoprotein (GP) and Zika envelope protein (Zika E), pre-fusion state structures have been identified experimentally, but only partial structures of fusion initiation states have been described. While the fusion initiation structure is in an energetically unfavorable state that is difficult to solve experimentally, the existing structural information combined with computational approaches enabled the modeling of fusion initiation state structures of both proteins. These structural models provide an improved understanding of four different neutralizing antibodies in the prevention of viral host entry.
Application of surface mapping to visualize wall shear stress and particles deposition in a realistic human nasal cavity

Nasal cavity is an important component of respiration system for the various physiological functions (Elad et al., 2008; Lee, 2010). By using a commercial CFD software Ansys-Fluent and a surface mapping software Unfold3D, wall shear stress (WSS) distribution and particle deposition patterns on the nasal cavity wall were simulated and transformed into a normalized UV domain (where U and V denote coordinate axes of a 2D space) to present a complete view of an entire wrapped surface, therefore to be analyzed with better precision and to allow direct comparisons between left and right cavities. In this paper, applications of surface mapping methods on a nasal cavity are demonstrated, and results for WSS distribution and time dependent particle deposition on UV domain during steady inhalation are analyzed.
DC link capacitor optimization for integrated modular motor drives

In this paper, selection of optimum DC link capacitor for Integrated Modular Motor Drives (IMMD) is presented. First, a review of IMMD technologies is given and current research and future prospects are studied. Inverter topologies and gate drive techniques are evaluated in terms of DC link performance. The urge for volume reduction in IMMD poses a challenge for the selection of optimum DC link capacitor. DC Link capacitor types are discussed and critical aspects in selecting the DC links capacitor are listed. Analytical modeling of DC link capacitor parameters is performed and it is verified by simulations conducted using MATLAB/Simulink. Optimum selection of DC link capacitor is achieved based on the electrical, thermal and economical model.
Influence of Ionic Strength on the pH-sensitive in vitro Ibuprofen Release from Dextran-poly(acrylic acid) Copolymer

The effects of cations and pH on the in vitro ibuprofen release from dextran-poly(acrylic acid) copolymer were investigated at varying pH and Na+ or Ca2+ concentrations. These results revealed that ibuprofen release was strongly depended on the acidic and basic environments, in which, the cumulative amount released in 24 h reached up to 87 % at pH 2.0 but only 32 % at pH 7.4, respectively, demonstrating a good pH-dependency. However, cations in release solution exerted a remarkable influence on ibuprofen release, especially in the acidic media. Meanwhile, ibuprofen release rate decreased with increasing strength of Na+, Ca2+ and NaCl concentration. The zeta potential profiles and particle distributions at different ionic strengths indicated that cations strongly influence ibuprofen release performance, through surface charge, hydrogen bonding, and electrostatic interactions in and between the polymer and ibuprofen. These results suggested that Na+ and Ca2+ strength exerted a profound influence on the pH-sensitive in vitro ibuprofen release from the dextran-poly(acrylic acid) copolymer.
Comparative Evaluation of Marginal Integrity and Microleakage in Nanoionomer and Low Shrinkage Posterior Composite Restorative Materials: An In Vitro Study

Contributors: 1Senior Lecturer, Department of Pedodontics, St. Joseph Dental College, Eluru, Andhra Pradesh, India; 2Professor and Head, Department of Pedodontics, Kamineni Institute of Dental and Medical Sciences, Nalgonda, Telangana, India; 3Reader, Department of Pedodontics, Saraswathi Dhanwantari Dental College, Parbhani, Maharashtra, India; 4Professor and Head, Department of Pedodontics, St. Joseph Dental College, Eluru, Andhra Pradesh, India; 5Reader, Department of Pedodontics, St. Joseph Dental College, Eluru, Andhra Pradesh, India; 6Private Practitioner, Hyderabad, Telangana, India. Correspondence: Dr. Velagapudi NJ. Department of Pedodontics, St. Joseph Dental College and Hospital, Eluru 534003, Andhra Pradesh, India. Phone: +91-7093322538. Email: jyovelagapudi@gmail.com How to cite the article: Velagapudi NJ, Reddy ER, Aduri R, Prasad MG, Sahana S, Vaila A. Comparitive evaluation of marginal integrity and microleakage in nanoionomer and low shrinkage posterior composite restorative materials: An in vitro study. J Int Oral Health 2016;8(2):261-266. Abstract: Background: Restorative dentistry had shown considerable progress, leading to the development of improved tooth-colored restorative materials. The main concern regarding these refers to the durability and integrity of marginal sealing. The aim of this study was to evaluate and correlate microleakage and marginal integrity of silorane based low shrinkage posterior composite with nano-filled resin modified glass ionomer cement (RMGIC). Materials and Methods: In this in vitro study, Class V cavity preparations were made and the specimens were divided into two equal groups. Specimens in Group I were restored with silorane based (Filtek P90)TM and Group II with nano filled RMGIC (Ketac N 100). TM Specimens were subjected to thermocycling and later sectioned using hard tissue microtome. Microleakage was evaluated under a stereomicroscope and later scanning electron microscope is used to assess the marginal adaptation. The obtained values were tabulated and subjected to statistical analysis. Results: Silorane based composite demonstrated least microleakage with a mean score of 0.25 and the interface gap of 2.46 compared with nanoionomer with mean microleakage score of 0.44 and interface gap of 14.73, respectively. Conclusion: Silorane based low shrinkage posterior composite (Filtek P90) exhibited adequate resistance to microleakage and better interface gap than nano-filled RMGICs. Considering the limitations of the in-vitro studies, it can be clinically correlated that Filtek P90 has better marginal properties than Ketac N 100.
T cell receptor binding affinity governs the functional profile of cancer-specific CD8+ T cells

Antigen‐specific T cell receptor (TCR) gene transfer via patient‐derived T cells is an attractive approach to cancer therapy, with the potential to circumvent immune regulatory networks. However, high‐affinity tumour‐specific TCR clonotypes are typically deleted from the available repertoire during thymic selection because the vast majority of targeted epitopes are derived from autologous proteins. This process places intrinsic constraints on the efficacy of T cell‐based cancer vaccines and therapeutic strategies that employ naturally generated tumour‐specific TCRs. In this study, we used altered peptide ligands and lentivirus‐mediated transduction of affinity‐enhanced TCRs selected by phage display to study the functional properties of CD8+ T cells specific for three different tumour‐associated peptide antigens across a range of binding parameters. The key findings were: (i) TCR affinity controls T cell antigen sensitivity and polyfunctionality; (ii) supraphysiological affinity thresholds exist, above which T cell function cannot be improved; and (iii) T cells transduced with very high‐affinity TCRs exhibit cross‐reactivity with self‐derived peptides presented by the restricting human leucocyte antigen. Optimal system‐defined affinity windows above the range established for natural tumour‐specific TCRs therefore allow the enhancement of T cell effector function without off‐target effects. These findings have major implications for the rational design of novel TCR‐based biologics underpinned by rigorous preclinical evaluation.
EQUILIBRIUM MOLECULAR DYNAMICS STUDY OF PHONON THERMAL TRANSPORT IN NANOMATERIALS

In this work, the thermal conductivity of nanofilms, nanowires, and nanoparticles are studied using molecular dynamics simulation. It is found that their thermal conductivity depends significantly on the characteristic size until it reaches a large value. Comparison with results of the lattice Boltzmann method reflects strong effects of surface structure, especially when the film thickness is comparable to the mean free path of phonons. Study of the phonon thermal transport in nanowires and nanoparticles reveals much stronger boundary-scattering effect on thermal transport than in nanofilms, which is attributed to the more confined phonon movements in these two- and one-dimensional nanomaterials.
Field evaluation of vaccine efficacy.

This paper describes the epidemiological techniques available for measuring vaccine efficacy and recommends a practical approach to their use. The efficacy of vaccines in clinical use can be determined by a variety of means, including screening, outbreak investigations, secondary attack rates in families or clusters, vaccine coverage assessment, and case-control studies. They all offer a means of monitoring vaccine programs under conditions of day-to-day vaccine use. A table summarizes the different techniques for measuring efficacy. The screening technique is the most useful and rapid means of determining whether there is a problem with a vaccine. All that is required is a reliable estimate of the proportion of cases occurring in vaccinated individuals and an estimate of the vaccine coverage in the population at risk. If the estimated efficacy is within expected limits, more detailed studies are not warranted. If the results suggest low efficacy, more rigorous methods are necessary to assess the efficacy more accurately. Of the more accurate methods available, outbreak investigation offers the simplest means of measuring vaccine efficacy and is the preferred technique if the situation permits. The biases inherent in the method can be minimized, particularly if the disease incidence rate is high during the outbreak and accurate records exist. In large populations, the underlying immunization status prior to the outbreak can be estimated using the same cluster sampling method used in coverage assessments. Calculation of secondary attack rates in families is also an excellent and accurate means of measuring vaccine efficacy and is an acceptable alternative to the outbreak investigation. Vaccine coverage methods in endemic areas are best suited to urban areas where the measles incidence rate is high after age 11 months and low before 12 months, and maternal histories of disease are thought to be accurate. Case-control studies are best suited to areas where reliable personal immunization records may be difficult to find but other information, such as clinic records, may be available. No epidemiological method is perfect because it cannot exactly duplicate the experimental conditions of a prospective randomized clinical trial. The most accurate results will be obtained when biases are anticipated and corrective measures are taken whenever possible. Clinical vaccine efficacy determinations are carried out in order to assess whether the observed pattern of illness is consistent with the proper use of a highly effective vaccine. The components of a vaccine efficacy evaluation -- case definition, case ascertainment, and vaccination status determination -- apply to studies on all vaccines.
Lycopene Is Enriched in Tomato Fruit by CRISPR/Cas9-Mediated Multiplex Genome Editing

Numerous studies have been focusing on breeding tomato plants with enhanced lycopene accumulation, considering its positive effects of fruits on the visual and functional properties. In this study, we used a bidirectional strategy: promoting the biosynthesis of lycopene, while inhibiting the conversion from lycopene to β- and α-carotene. The accumulation of lycopene was promoted by knocking down some genes associated with the carotenoid metabolic pathway. Finally, five genes were selected to be edited in genome by CRISPR/Cas9 system using Agrobacterium tumefaciens-mediated transformation. Our findings indicated that CRISPR/Cas9 is a site-specific genome editing technology that allows highly efficient target mutagenesis in multiple genes of interest. Surprisingly, the lycopene content in tomato fruit subjected to genome editing was successfully increased to about 5.1-fold. The homozygous mutations were stably transmitted to subsequent generations. Taken together, our results suggest that CRISPR/Cas9 system can be used for significantly improving lycopene content in tomato fruit with advantages such as high efficiency, rare off-target mutations, and stable heredity.
Efficient Shortest Paths in Scale-Free Networks with Underlying Hyperbolic Geometry

A standard approach to accelerating shortest path algorithms on networks is the bidirectional search, which explores the graph from the start and the destination, simultaneously. In practice this strategy performs particularly well on scale-free real-world networks. Such networks typically have a heterogeneous degree distribution (e.g., a power-law distribution) and high clustering (i.e., vertices with a common neighbor are likely to be connected themselves). These two properties can be obtained by assuming an underlying hyperbolic geometry. To explain the observed behavior of the bidirectional search, we analyze its running time on hyperbolic random graphs and prove that it is Õ(n2 - 1/α + n1/(2α) + δ max) with high probability, where α ∈ (1/2, 1) controls the power-law exponent of the degree distribution, and δmax is the maximum degree. This bound is sublinear, improving the obvious worst-case linear bound. Although our analysis depends on the underlying geometry, the algorithm itself is oblivious to it.