Miracle-dz/UniFAR-FTUs huggingface dataset:
Chapter 17 Lipopolysaccharides and Plant Innate Immunity

Plants posses an innate immune system that has many parallels with those found in mammals and insects. A range of molecules of microbial origin called Microbe Associated Molecular Patterns (MAMPs) act to trigger basal defense responses in plants. These elicitors include lipopolysaccharides (LPS) from diverse Gram-negative bacteria. Both core oligosaccharide and the lipid A moieties of LPS as well as synthetic O-antigen oligosaccharides have activity in inducing defense responses in the model plant Arabidopsis thaliana. Very little is known of the mechanism of LPS perception by plants, although plant receptors for other MAMPs such as flagellin have been described. Recent work has implicated the Arabidopsis syntaxin PEN1 as a potential actor in LPS induction of plant defenses, which may suggest a role for vesicle trafficking in the signalling process.
Inducible Nitric Oxide Synthase Contributes to Immune Dysfunction Following Trauma

ABSTRACT Trauma results in a persistent depression in adaptive immunity, which contributes to patient morbidity and mortality. This state of immune paralysis following trauma is characterized by a change in cell-mediated immunity, specifically a depression in T-cell function and a shift toward TH2 T-cell phenotype. Upregulation of inducible nitric oxide synthase (iNOS) is well recognized after injury and contributes to the inflammatory response and organ damage early after trauma. However, it is unknown whether iNOS plays a role in adaptive immune dysfunction after trauma. This study utilized a murine model of severe peripheral tissue injury to show that iNOS is rapidly upregulated in macrophages and a (Gr-1hi–CD11bhi) myeloid-derived suppressor cell subpopulation in the spleen. Through the use of iNOS knockout mice, a specific iNOS inhibitor, and a nitric oxide (NO) scavenger, this study demonstrates that iNOS-derived NO is required for the depression in T-lymphocyte proliferation, interferon &ggr;, and interleukin 2 production within the spleen at 48 h after trauma. These findings support the hypothesis that iNOS regulates immune suppression following trauma and suggest that targeting the sustained production of NO by iNOS may attenuate posttraumatic immune depression.
Fixational saccadic eye movements are altered in anisometropic amblyopia.

PURPOSE Amblyopia develops during a critical period in early visual development and is characterized by reduced visual sensory functions and structural reorganization of the brain. However, little is known about oculomotor functions in amblyopes despite the special role of eye movements in visual perception, task execution and fixation. Therefore, we studied the relationship of visual deficits in anisometropic amblyopia and fixational saccadic eye movements. METHODS We recruited twenty-eight anisometropic amblyopes and twenty-eight age-matched control subjects. Using a high-speed eye-tracker, fixational eye-movements of both eyes were recorded. A computerized fixational saccadic component analysis of eye-movement waveforms was developed to quantify the parameters of fixational saccades (FSs) and a simulation model was developed to help explain the FS performances. RESULTS Amblyopic eyes, but not control eyes, showed fewer FSs, but these had increased amplitudes, increased peak velocities, and longer inter-saccadic intervals. The reduced FSs occurred mainly in the 0- to 0.6-degree amplitude range, and the probability of FSs with larger amplitudes and longer inter-saccadic intervals was significantly higher than in controls. A new simulation model analysis suggests that an excitatory-inhibitory activity imbalance in superior colliculus may explain these FSs changes. CONCLUSIONS We propose that the abnormal visual processing and circuitry reorganization in anisometropic amblyopia has an impact on the fixational saccade generation. We see two possible interpretations: (i) altered FSs may be an attempt of the visual system to adapt to the deficit, trying to capture more information from a broader spatial domain of the visual world so as to enhance the contrast sensitivity to low spatial frequencies viewed by the amblyopic eye, or (ii) it may be the cause of amblyopia or a contributing factor to the original deficit that aggravates the early deprivation.
Design and simulation of the embedded system

Abstract This paper is focused on the design, modelling, and simulation of an embedded systems using UML. UML is de facto the standard for modelling of software systems. However, UML should be extended to allow the modelling of real-time and embedded systems. The UML profile MARTE (Modelling and Analysis of Real Time and Embedded systems) was developed by consortium OMG to address the modelling of this kind of systems where time and allocation of both hardware and software resources are very important metrics of the system. The MARTE profile allows the modelling the system using different views on this system. The automatic source code generation and simulations are mentioned in connection with MARTE. There is presented the first proposal of a new simulation and verification tool which is being developed at our university.
Fetal Tricuspid Valve Size and Growth as Predictors of Outcome in Pulmonary Atresia With Intact Ventricular Septum

OBJECTIVE. Pulmonary atresia with intact ventricular septum is a complex congenital cardiovascular anomaly that frequently requires single ventricle palliation. Fetal diagnosis of pulmonary atresia with intact ventricular septum is common, but the natural history of pulmonary atresia with intact ventricular septum diagnosed in midgestation, predictors of neonatal anatomy, and predictors of biventricular repair have not been determined. The objective of this study was to determine whether the size and rate of growth of the fetal tricuspid valve predict neonatal anatomy and biventricular repair. DESIGN AND RESULTS. Twenty-three fetuses diagnosed with pulmonary atresia with intact ventricular septum between 1990 and 2004 were studied. Of 13 fetuses with a midgestation fetal tricuspid valve z score ≤−3, 1 achieved biventricular repair, compared with 5 of 5 with a tricuspid valve z score >−3. Of 13 fetuses with a midgestation fetal tricuspid valve z score ≤−3, 8 were diagnosed postnatally with a right ventricular dependent coronary circulation, compared with none with a tricuspid valve z score >−3. Midgestation and late gestation fetal tricuspid valve z scores correlated with neonatal tricuspid valve z score. The average rate of tricuspid valve growth between mid- and late fetal echocardiograms was significantly lower in patients who did not achieve biventricular repair than in those who did (0.012 ± 0.008 cm per week vs 0.028 ± 0.014 cm per week). CONCLUSIONS. Fetal tricuspid valve z score and rate of growth predict postnatal outcome in pulmonary atresia with intact ventricular septum. These findings may have important implications for prenatal counseling and selection of patients for fetal pulmonary valve dilation.
Theoretical study on frontier orbitals of dehydrogenated tetrahydrocurcumin in gas phase

In this present work, we calculated two frontier orbital energies - singly occupied molecular orbital (SOMO) and lowest unoccupied molecular orbital (LUMO) - of dehydrogenated tetrahydrocurumin (THC) using density-functional theory (DFT) in gas phase. We used the energy difference of SOMO and LUMO to assess the stability of dehydrogenated THC after performing a hydrogen atom transfer toward reactive oxygen species (ROS). We began by optimizing dehydrogenated THC at six hydrogen abstraction sites. Two hydrogen abstraction sites are at O-H groups and four hydrogen abstraction sites are at C-H groups. Then, we compared the value of SOMO and LUMO energy difference in each site. Our calculations showed that dehydrogenated THC at O-H groups are more stable than dehydrogenated THC at C-H groups.
Pemodelan Pola Spasial Demam Berdarah Dengue di Kabupaten Semarang Menggunakan Fungsi Moran's I

This study aims to model the spread of dengue disease by vectors and density Incidence Rate (IR) in Semarang regency. This study is divided into three stages, the first stage of the preparation of preliminary data, both architectural design and modeling and modeling and visualization of all three. The research data derived from data Angka Bebas Jentik (ABJ) and House Index (HI) as a measure of vector density and Incidence Rate (IR) sub district level in Semarang regency period 2005-2009. Processing the data using the method of Moran’s I to describe the pattern of incidenc of the Angka Bebas Jentik (ABJ), House Index (HI) and Incidence Rate (IR). Final output of the spatial patterns are visualized using the Moran Scatterplot and LISA maps. The results showed that the variable ABJ, HI and IR can be modeled by the method of spatial Moran’s I. Modeling results of ABJ, HI and IR variables can be used as an indicator of the spread of dengue fever in Semarang regency.
Advanced material appearance modeling

For many years appearance models in computer graphics focused on general models for reflectance functions coupled with texture maps. Recently it has been recognized that even very common materials such as hair, skin, fabric, and rusting metal require more sophisticated models to appear realistic. We will begin by briefly reviewing basic reflectance models and the use of texture maps. We then describe common themes in advanced material models that include combining the effects of layers, groups of particles and/or fibers. We will survey the detailed models necessary needed to model materials such as (but not limited to) skin (including pigmentation, pores, subsurface scattering), plants (including internal structure) and automotive paints (including color flop and sparkle). We will then treat the modeling of complex appearance due to aging and weathering processes. A general taxonomy of effects will be presented, as well as methods to simulate and to capture these effects.
Investigation of positioning of FBG sensors for smart monitoring of oil and gas subsea structures

Condition monitoring of offshore structures is an indispensable task in the oil and gas industry. Fibre Bragg Grating (FBG) is the key technology used down-hole in order to sense different physical parameters such as strain, vibration, etc. This paper investigates the effect of FBG sensor positions on its reflected signal, in order to optimise the sensor positioning plan in structural health monitoring of subsea structures. Theoretical and experimental study was carried out on FBG sensors, to evaluate its strain sensitivities with varying positions. In addition, micro-displacement based strain analysis of FBG was carried out using a cantilever setup, in order to identify the effects of tensile and compressive strain under various load conditions. Furthermore, the effect of different grating parameters on FBG sensing signal were also analyzed. Theoretical modeling and simulation of FBG was conducted in MATLAB using the coupled mode theory.
Ionizing radiation induces up-regulation of functional β 1-integrin in human lung tumour cell lines in vitro

Purpose : Cell-matrix interactions are in part mediated through the β 1-integrin pathway regulating cell survival, proliferation, adhesion and migration. This study was performed to elucidate alterations of expression of the β 1-integrin and its co-localized protein kinase, integrin-linked kinase (ILK), after exposure to ionizing radiation in two lung carcinoma cell lines in the presence or absence of different β 1-integrin-dependent matrix proteins. Materials and methods : Exponentially growing A549 and SKMES1 cells grown on fibronectin, laminin, BSA or plastic were exposed to 2 Gy or 6 Gy. Besides colony formation assays (0.5-8 Gy) and immediate plating experiments, flow cytometry (for β 1-integrin) and immunoblotting (for β 1-integrin and ILK) were carried out to analyze the protein expression. The localization of both proteins plus filamentous (f-) actin was further examined by immunofluorescence staining and laser confocal scanning microscopy. Functionality of the β 1 receptor subunit after irradiation was investigated in adhesion assays. Results : A549 and SKMES1 cells grown on fibronectin or laminin demonstrated a significant increase in cell survival after irradiation compared to cells grown on BSA or plastic. Immediate plating of cells after irradiation on fibronectin did not show an improved survival. Flow cytometric and Western blot data showed a dose- and matrix-dependent induction of β 1-integrin and ILK expression after irradiation within 48 h. Adhesion to fibronectin or laminin compared to BSA or plastic was increased by 10-fold after irradiation, demonstrating these specific cell surface receptors to be functional. The staining of β 1-integrin and ILK in A549 cells confirmed the radiation-induced up-regulation of both proteins. Additionally, β 1-integrin and ILK co-localized with accumulated actin fibers at the cytoplasmic face of the cell membrane at confined areas. Conclusions : Ionizing radiation strongly induced the expression of functional β 1-integrin and ILK in the two lung cancer cell lines, A549 and SKMES1, dependent on different matrices used. Additionally, the subcellular localization of both proteins was altered by irradiation, and the individual cellular radiosensitivity was reduced in the presence of an extracellular matrix. On the one hand, this may result in aggravated therapeutic approaches and on the other hand, cells could adhere more strongly in their environment by the increase in functional surface receptor density preventing metastasis. Concerning intravascular located tumour cells, β 1-integrin up-regulation might enable these cells to adhere to the endothelium, which represents a prerequisite for metastatic disease. Identification of such mechanisms will provide considerable insights into the understanding of tumorigenicity and metastatic phenotypes, possibly leading to new, optimized radiochemotherapeutic regimens.
Moleküler Markörlerin Bitki Islahında Kullanımı

Konvansiyonel bitki islahi zaman alicidir ve cevresel sartlara baglidir. Yeni bir cesidin islahi uzun yillar surebildigi gibi gelistirilen cesidin piyasaya cikarilmasi garanti edilemeyebilir. Bu nedenle arastirmacilar islah surecinde daha etkili kullanilabilecek yeni yontemlerle ilgilenmislerdir. Molekuler markor teknolojisi bitki islahinda seleksiyon stratejilerini gelistirmek icin genis kapsamli yeni uygulamalarin benimsenmesini saglamistir. Materyal degerlendirmede daha deneyimli olan klasik bitki islahcilarinin molekuler genetik ya da hucre biyolojisi konusunda calisma yapmasi, elde edilen yeni bitkilerin yaygin kullanimi ya da materyalin degerlendirilmesi acisindan gerekli gorulmektedir. Bitki islahcilari DNA uzerindeki arastirmalardan cok azini kullanma firsati bulmustur. Ozellikle bitki molekuler genetigi ile ilgili olarak son yillarda elde edilen bilgiler, bitki islahi calismalarina yansiyabilecek niteliktedir. Bu nedenle, yeni gelistirilen ya da degistirilmis bitki islahi yontemleri, bitki molekuler biyolojisi calismalarindan elde edilen bilgilere dayanilarak kullanilmalidir. Bu derlemede genel olarak bitkilerde yaygin olarak kullanilan baslica molekuler markorlerin tipleri, avantajlari/dezavantajlari ve bitki islahinda kullanim alanlari ile ilgili calismalar ele alinmistir
Factors affecting adherence to evidence-based guidelines in the treatment of URI, sinusitis, and pharyngitis

Introduction Sinus infections, sore throats, and upper respiratory tract infections (URI) are common reasons patients seek medical care. Well-established treatment guidelines exist for prescribing antibiotics in these clinical scenarios, but are not often followed. Objective The objective of this study is to determine practice patterns related to prescribing antibiotics for sinusitis, URI, and pharyngitis. The main hypothesis is that attending physicians improve their adherence to antibiotic guidelines with a learner present. Methods A retrospective cohort study was performed on patients treated for URI, sinusitis, and pharyngitis at an ambulatory faculty practice. The use of relevant ICD-9 codes from January 1, 2008 to January 30, 2012 resulted in 1,548 patient encounters which were reviewed for guideline adherence. Univariate analysis and multivariate logistic regression was performed for each outcome variable to determine if they influence antibiotic adherence. Variables studied were physician, presence of a learner, BMI, age, gender, day of the week, month, diabetes, immunosuppression, and COPD. Results Multivariate analysis showed the statistically significant variables were age (p=0.038) for pharyngitis and provider (p=0.013) for URI. There were no significant findings for sinusitis. Guideline adherence was 24% in patients with pharyngitis, 42% in acute sinusitis, 79% in URI, and 57% overall. Conclusion Guideline adherence varies depending on the treating physician and decreases when treating younger patients with pharyngitis. The presence of a learner did not improve prescribing habits. The reason for these findings remain unclear, but considerations for improvement could include following antibiotic adherence as a quality measure, giving patients handouts educating them about the impact of overprescribing antibiotics, and further education amongst faculty and residents about adhering to nationally recognized guidelines.
Outcome of thyroid function in Graves' patients treated with radioiodine: role of thyroid-stimulating and thyrotropin-blocking antibodies and of radioiodine-induced thyroid damage.

UNLABELLED We investigated the interrelationship and the influence of thyroid-stimulating antibodies (TSAb), TSH-blocking antibodies (TSHBAb), and of radioiodine (131I)-induced thyroid damage in the early (within 1 yr) outcome of thyroid function in hyperthyroid patients with Graves' disease (GD) treated with 131I. TSAb, TSHBAb, and ultrasound thyroid volume (as an index of thyroid damage) were simultaneously measured before and at 1, 3, 6, and 12 months after 131I in 31 GD patients. One year after radioiodine, 9.7% of patients were hyperthyroid (Hyper-group), requiring methimazole; 12.9% were euthyroid (Eu-group); and 77.4% were hypothyroid (Hypo-group). Pretreatment thyroid volume in the Eu-group and Hyper-group was significantly greater (P = 0.009) than in the Hypo-group. Pre-131I TSAb levels were higher in the Hyper-group vs. the Hypo-group (P = 0.01) or the Eu-group (P = 0.03). A significant post-131I increase in TSAb levels occurred in 66% of patients developing hypothyroidism but not in those remaining hyperthyroid. After 131I, TSHBAb appeared in 7 patients, in all but one associated with high levels of TSAb. One year after radioiodine: 1) the mean percent reduction in thyroid volume was greater in the Hypo-group (80.7%) or the Eu-group (83.5%) than in the Hyper-group (35.7%) (P = 0.007 and 0.0033 respectively); 2) hypothyroid patients had smaller (P = 0.0058) post-131I thyroids than hyperthyroid patients; and 3) TSAb were still elevated in 75% hypothyroid patients, but all of them had a thyroid volume < or = 8 mL, indicating major postradioiodine gland damage. IN CONCLUSION 1) the early outcome of thyroid function after 131I for GD is mainly related to pretreatment thyroid volume and to the degree of its reduction after therapy; 2) high TSAb levels before 131I are associated with a relative resistance to therapy; 3) a postradioiodine increase in TSAb levels is related to the development of hypothyroidism; and 4) the concomitant appearance of TSHBAb and disappearance of TSAb are not frequent after 131I and play a role in the development of early postradioiodine hypothyroidism only in a minority of patients.
A preliminary study of users' experiences of meditation in virtual reality

This poster describes a between-groups study (n=24) exploring the use of virtual reality (VR) for facilitating focused meditation. Half of the participants were exposed to a meditation session combing the sound of a guiding voice and a visual environment including virtual objects for the participants to focus on. The other half of the participants were only exposed to the auditory guide. The participants' experience of the sessions was assessed using self-reported measures of perceived concentration, temporal duration, stress reduction, and comfort. Interestingly, no statistically significant differences were found between the two conditions. This finding may be revealing in regards to the usefulness of VR-based meditation.
Energy Monitoring System Based on Internet of Things Toward Smart Campus in Institut Teknologi Sumatera

The critical subject to provide energy consumption graphs from a building is an energy monitoring system. With the rapid Internet of Things (IoT) development, it is possible to develop a better energy monitoring system based on IoT. This system presents the real-time energy consumption data. Hence, this paper proposes the development of an energy monitoring system prototype based on IoT for buildings in Institut Teknologi Sumatera campus area. The current and voltage are measured in real-time for each wiring phase on the building electrical panel. The data is collected in the cloud server and displayed in a web-based system using custom web panel. Finally, the prototype is implemented in the building during 24/7 for one week achieving about 97% of the accuracy.
Vertex Types in Book-Embeddings

A new measure of the complexity of a book-embedding of a simple undirected graph, the number of vertex types in the embedding, is studied. The type of a vertex $v $ in a p-page book-embedding is the $p \times 2$ matrix of nonnegative integers \[ \tau (v ) = \begin{pmatrix} L_1 & & R_1 \\ L_2 & & R_2 \\ & \vdots & \\ L_P & & {R_P } \end{pmatrix}, \] where $L_i $; (respectively, $R_i $) is the number of edges incident to $v $ that connect on page i to vertices lying to the left (respectively, to the right) of $v $. The number of types in a book-embedding relates to the amount of logic necessary to realize fault-tolerant arrays of processors using one specific design methodology. Three sorts of issues regarding vertex types in book-embeddings are studied. A number of techniques for bounding the type-numbers of a variety of graphs are developed; the relationships between typenumber and other graph properties, such as book thickness, are investigated; and the problem of minimizing the typenumber of a graph is .
PPAR g Induces the Insulin-dependent Glucose Transporter GLUT 4 in the Absence of C / EBP a During the Conversion of 3 T 3 Fibroblasts Into Adipocytes

To define the molecular mechanisms that control GLUT4 expression during adipogenesis, NIH-3T3 fibroblasts ectopically expressing different adipogenic transcription factors (C/EBP b , C/EBP d , C/EBP a , and PPAR g ) under the control of a tetracycline-responsive inducible (C/EBPs) or a constitutive retroviral (PPAR g ) expression system were used. Enhanced production of C/EBP b ( b 2 cell line), C/EBP b together with C/EBP d ( b / d 39 cell line), C/EBP a ( a 1 cell line), or PPAR g (P g 2 cell line) in cells exposed to dexamethasone and the PPAR g ligand ciglitazone (a thiazolidinedione) resulted in expression of GLUT4 mRNA as well as other members of the adipogenic gene program, including aP2 and adipsin. Focusing our studies on the b / d 39 cells, we have demonstrated that C/EBP b along with C/EBP d in the presence of dexamethasone induces PPAR g , adipsin, and aP2 mRNA production; however, GLUT4 mRNA is only expressed in cells exposed to ciglitazone. In addition, enhanced expression of a ligand-activated form of PPAR g in the b / d 39 fibroblasts stimulates synthesis of GLUT4 protein and gives rise to a population of adipocytic cells that take up glucose in direct response to insulin. C/EBP a is not expressed in the b / d 39 cells under conditions that stimulate the adipogenic program. This observation suggests that PPAR g alone or in combination with C/EBP b and C/EBP d is capable of activating GLUT4 gene expression. ( J. Clin. Invest. 1998. 101:22–32.)