Miracle-dz/UniFAR-FTUs huggingface dataset:
Impact of technological processing conditions on optical properties of inorganic-organic hybrid polymers

Nanostructured materials are intensively investigated due to their wide range of physical and chemical properties which result in a large variety of applications. From an industrial point of view, emphasis has not only to be on materials performance and on control of their properties, but also on cost reduction either for the materials, the processes, or for both. Materials are searched for which enable different processing technologies, feature sizes and shapes as well as an integration up to a centimeter scale. The combination of low-cost materials with tunable material parameters such as low optical absorption, tunable refractive index, good processability as well as high chemical, thermal and mechanical stability, is very attractive for integrated optical applications. A particular class of low-cost nanoscale materials which fulfills these requirements is the class of inorganic-organic hybrid polymers (ORMOCER(R)s1) which are synthesized by catalytically controlled hydrolysis/ polycondensation reactions, resulting in storage-stable, photo-sensitive resins. The material properties, for example refractive index or optical absorption, can be widely varied by choice of alkoxysilane precursors or synthesis conditions such as catalysts or solvents. In addition, the material properties can also be significantly influenced by the technological processing conditions. For example, the degree of organic cross-linking can be adjusted by variation of UV initiator kind and concentration, or by various exposure doses. This, consequently, is directly correlated to the refractive index. The impact of processing conditions on the refractive index was investigated by FTIR spectroscopy and refractive index measurements. The refractive indices are correlated to the material's degree of organic cross-linking, and application examples will be given.
Computational Aspects of Efficient Estimation of Harmonically Related Sine-Waves

This paper proposes an actual implementation of a well-known method [1] for spectral analysis of signals composed of harmonically related sine waves. The method itself requires computations which carried out directly according to the theoretical formulas do not yield computationally efficient implementation. Thus, utilizing matrix factorizations and mathematical “shortcuts”, several algorithms have been developed, which perform computations efficiently and make the method suitable for large-scale applications. Implementation details are clearly explained both theoretically and from computational point of view, and the achieved improvements have been proven by extensive simulations. Particular calculations applied will be equally efficient in all similar problems, which renders the proposed routines into widely useful building blocks.
Lossless Compression of Color Map Images by Context Tree Modeling

Significant lossless compression results of color map images have been obtained by dividing the color maps into layers and by compressing the binary layers separately using an optimized context tree model that exploits interlayer dependencies. Even though the use of a binary alphabet simplifies the context tree construction and exploits spatial dependencies efficiently, it is expected that an equivalent or better result would be obtained by operating directly on the color image without layer separation. In this paper, we extend the previous context-tree-based method to operate on color values instead of binary layers. We first generate an n-ary context tree by constructing a complete tree up to a predefined depth, and then prune out nodes that do not provide compression improvements. Experiments show that the proposed method outperforms existing methods for a large set of different color map images
From (p)ppGpp to (pp)pGpp: Characterization of Regulatory Effects of pGpp Synthesized by the Small Alarmone Synthetase of Enterococcus faecalis

ABSTRACT The bacterial stringent response (SR) is a conserved stress tolerance mechanism that orchestrates physiological alterations to enhance cell survival. This response is mediated by the intracellular accumulation of the alarmones pppGpp and ppGpp, collectively called (p)ppGpp. In Enterococcus faecalis, (p)ppGpp metabolism is carried out by the bifunctional synthetase/hydrolase E. faecalis Rel (RelEf) and the small alarmone synthetase (SAS) RelQEf. Although Rel is the main enzyme responsible for SR activation in Firmicutes, there is emerging evidence that SASs can make important contributions to bacterial homeostasis. Here, we showed that RelQEf synthesizes ppGpp more efficiently than pppGpp without the need for ribosomes, tRNA, or mRNA. In addition to (p)ppGpp synthesis from GDP and GTP, RelQEf also efficiently utilized GMP to form GMP 3′-diphosphate (pGpp). Based on this observation, we sought to determine if pGpp exerts regulatory effects on cellular processes affected by (p)ppGpp. We found that pGpp, like (p)ppGpp, strongly inhibits the activity of E. faecalis enzymes involved in GTP biosynthesis and, to a lesser extent, transcription of rrnB by Escherichia coli RNA polymerase. Activation of E. coli RelA synthetase activity was observed in the presence of both pGpp and ppGpp, while RelQEf was activated only by ppGpp. Furthermore, enzymatic activity of RelQEf is insensitive to relacin, a (p)ppGpp analog developed as an inhibitor of “long” RelA/SpoT homolog (RSH) enzymes. We conclude that pGpp can likely function as a bacterial alarmone with target-specific regulatory effects that are similar to what has been observed for (p)ppGpp. IMPORTANCE Accumulation of the nucleotide second messengers (p)ppGpp in bacteria is an important signal regulating genetic and physiological networks contributing to stress tolerance, antibiotic persistence, and virulence. Understanding the function and regulation of the enzymes involved in (p)ppGpp turnover is therefore critical for designing strategies to eliminate the protective effects of this molecule. While characterizing the (p)ppGpp synthetase RelQ of Enterococcus faecalis (RelQEf), we found that, in addition to (p)ppGpp, RelQEf is an efficient producer of pGpp (GMP 3′-diphosphate). In vitro analysis revealed that pGpp exerts complex, target-specific effects on processes known to be modulated by (p)ppGpp. These findings provide a new regulatory feature of RelQEf and suggest that pGpp may represent a new member of the (pp)pGpp family of alarmones.
A Named Entity Recognizer for Filipino Texts

In this paper, we define the task of named entity recognition, look at existing systems for named entity recognition, and discuss the design, implementation, and evaluation of a system that performs named entity recognition on Filipino texts. We also compare the results of the system with an existing named entity recognizer designed for English texts using a Filipino corpus.
Predicting Biotransformation Potential from Molecular Structure

The program PASS-BioTransfo is presented, which is capable of predicting many classes of biotransformation for chemical compounds. A particular class of biotransformation is defined by the chemical transformation type and may additionally include the name of the enzyme involved in a transformation. An evaluation of the approach is presented, using biotransformations taken from the databases Metabolite (MDL) and Metabolism (Accelrys), respectively. When trained with biotransformations from Metabolite, PASS-BioTransfo predicts 1927 classes of biotransformation; the average accuracy estimated in LOO cross-validation is about 88%. After training with the biotransformations from the Metabolism database, 178 classes of biotransformation are predicted with an average accuracy of about 85%. The results of cross-prediction with several training and evaluation sets are presented and discussed.
Viruses' Life History: Towards a Mechanistic Basis of a Trade-Off between Survival and Reproduction among Phages

Life history theory accounts for variations in many traits involved in the reproduction and survival of living organisms, by determining the constraints leading to trade-offs among these different traits. The main life history traits of phages—viruses that infect bacteria—are the multiplication rate in the host, the survivorship of virions in the external environment, and their mode of transmission. By comparing life history traits of 16 phages infecting the bacteria Escherichia coli, we show that their mortality rate is constant with time and negatively correlated to their multiplication rate in the bacterial host. Even though these viruses do not age, this result is in line with the trade-off between survival and reproduction previously observed in numerous aging organisms. Furthermore, a multiple regression shows that the combined effects of two physical parameters, namely, the capsid thickness and the density of the packaged genome, account for 82% of the variation in the mortality rate. The correlations between life history traits and physical characteristics of virions may provide a mechanistic explanation of this trade-off. The fact that this trade-off is present in this very simple biological situation suggests that it might be a fundamental property of evolving entities produced under constraints. Moreover, such a positive correlation between mortality and multiplication reveals an underexplored trade-off in host–parasite interactions.
Evidence that IgE molecules mediate a spectrum of effects on mast cell survival and activation via aggregation of the FcεRI

We demonstrate that binding of different IgE molecules (IgEs) to their receptor, FcεRI, induces a spectrum of activation events in the absence of a specific antigen and provide evidence that such activation reflects aggregation of FcεRI. Highly cytokinergic IgEs can efficiently induce production of cytokines and render mast cells resistant to apoptosis in an autocrine fashion, whereas poorly cytokinergic IgEs induce these effects inefficiently. Highly cytokinergic IgEs seem to induce more extensive FcεRI aggregation than do poorly cytokinergic IgEs, which leads to stronger mast cell activation and survival effects. These effects of both types of IgEs require Syk tyrosine kinase and can be inhibited by FcεRI disaggregation with monovalent hapten. In hybridoma-transplanted mice, mucosal mast cell numbers correlate with serum IgE levels. Therefore, survival effects of IgE could contribute to the pathogenesis of allergic disease.
Are boxes better for classification?

The design of a classifier usually has the important step of attribute or feature selection. A computationally tractable scheme almost always relies on a subset of attributes that optimize a certain criterion is chosen, resulting in a good suboptimal solution. We show that it is possible to directly define the region for each class in terms of an n-dimensional box, using all numeric attributes (discrete or continuous). Several shapes are used for the modeling of classes. Shapes are tested and results compared. As with our previous algorithm, this classifier is transparent. The approach compares favorably with previous approaches in both accuracy and efficiency. It has the added advantage of being able to classify when one class is entirely within another class
Heterogeneous Expression of Interleukin-18 and Its Receptor in B-Cell Lymphoproliferative Disorders Deriving from Naive, Germinal Center, and Memory B Lymphocytes

Purpose: Dysregulated cytokine/cytokine receptor expression may occur in B-cell lymphoproliferative disorders. Little information is available on interleukin-18 receptor (IL-18R) and IL-18 expression in normal and malignant B cells. Our purpose was to investigate this issue in human naive, germinal center (GC) and memory B cells, and in their neoplastic counterparts. Experimental Design: We have evaluated IL-18 expression and production in tonsil naive, GC, and memory B cells and in their presumed neoplastic counterparts by reverse transcription-PCR and ELISA. Moreover, IL-18Rα and β expression was investigated in the same cells by reverse transcription-PCR, flow cytometry, and immunohistochemistry. Results: We found that: (a) IL-18 mRNA was expressed in tonsil naive, GC, and memory B cells. Bioactive IL-18 was secreted by naive and GC, but not by memory B cells; (b) IL-18Rα and β transcripts were expressed in the three B-cell subsets. IL-18Rα was detected on the surface of naive, GC, and memory B lymphocytes, and IL-18Rβ was detected on GC and memory, but not naive, B cells; (c) mantle zone, follicular, marginal zone, Burkitt lymphoma (BL), and B-cell chronic lymphocytic leukemia (B-CLL) cells expressed IL-18 mRNA. B-CLL and BL cells did not produce bioactive IL-18; and (d) lymphoma B cells displayed heterogeneous expression of either or both IL-18R chain mRNA. In contrast, B-CLL cells expressed both IL-18R chains at the mRNA and protein levels. Conclusions: Dysregulated expression of IL-18 and/or IL-18R in chronic B-cell lymphoproliferative disorders may sometimes contribute to tumor escape from the host immune system.
New method for side pumping of double-clad fiber lasers using planar grating written into the inner cladding

A new side pumping method based on the diffractive properties of a planar grating which is directly written into the inner cladding of a double-clad fiber (DCF) is proposed. This technique assumes that the inner cladding of the DCF is highly photosensitive and its diameter is large enough. Then a planar grating with a proper thickness can be written into the inner cladding. The principles, characteristics and coupling efficiencies of the proposed scheme are described and simulated by coupled wave theory. The simulating results show that the coupling efficiencies can achieve over 98% for TE-, TM- and un-polarized incident pump lights simultaneously. And the average coupling efficiencies can still achieve 80% regardless of TE or TM polarization even when the pump wavelength ranges from 974 to 978nm and the incident angle ranges from −0.8° to 0.8°. The fabrication tolerances of the planar grating and the leakage of pump powers for multi-point side-pumping are also analyzed. The advantages of the proposed scheme include: (1) no risk of damaging the DCF; (2) no index-matching optical adhesive; (3) high temperature sustainability; (4) simple, stable and compact. It provides an effective way to scale the output power of DCF lasers or amplifiers to a high level.
Clinical and genetic characterization of a large Dutch family with primary focal dystonia

We describe a large family with a primary focal dystonia from a small Dutch village on a former island. Twenty‐four individuals spanning three generations were examined by two movement‐disorder neurologists. Two other movement‐disorder neurologists evaluated the videos independently. Subjects were classified as “affected,” “possibly affected,” or “not affected. ” A diagnosis was defined if all the neurologists agreed on the definition. Eight definitely affected and four possibly affected subjects were detected. Clinical presentation consisted of mild cranio‐cervical‐brachial dystonia. Mean age at onset was 45.5 years (range, 39–56). Mean BFMDRS motor score was 4.4 (range, 1–8). Mean TWSTRS score (part I) was 11.3 (range, 8–23). Mutations in DYT1 gene and in the ε‐sarcoglycan (SGCE) genes were not detected. We could not find linkage to the dominant DYT6, DYT7, DYT13, or the recessive DYT16 loci. The identification and accurate clinical evaluation of large dystonia families not linked to known genes is crucial for further advancement in molecular genetic characterization of focal dystonia. © 2008 Movement Disorder Society
Inflammatory Infiltrates and Neovessels Are Relevant Sources of MMPs in Abdominal Aortic Aneurysm Wall

Objectives: Abdominal aortic aneurysm (AAA) wall is characterized by degradation of extracellular matrix through matrix metalloproteinases (MMPs), chronic inflammatory cell infiltration and extensive neovascularization. So far, MMP expression within AAA wall in association with infiltrates and neovascularization has not yet been studied. Methods: Vessel walls of 15 AAA patients and 8 organ donors were analyzed by immunohistochemistry for expression of various MMPs (MMP-1, -2, -3, -7, -8, -9, -12 and -13) in all cells located within the AAAs and correlated with infiltrates and neovascularization. Results: Luminal endothelial cells (ECs) were positive for MMP-1, -3 and -9, ECs of mature neovessels were furthermore positive for MMP-2. Immature neovessels expressed all MMPs tested except for MMP-13. Aortic medial smooth muscle cells (SMCs) expressed MMP-1, -2, -3 and -9, SMCs of mature neovessels, only MMP-1, -3 and -9. Inflammatory infiltrates expressed all MMPs tested except for MMP-2, macrophages expressed all MMPs. Infiltrates were composed mainly of B cells (58.5 ± 10.9%) and T lymphocytes (26.3 ± 9.5%). Furthermore, significant inverse correlations were found between the amounts of inflammatory cells, neovessels and collagen/elastin content of the aortic vessel wall (r = +0.806/p < 0.001, r = –0.650/p = 0.012, r = –0.63/p < 0.015; respectively). Conclusion: Inflammatory infiltrates and invading neovessels are relevant sources of MMPs in the AAA wall and may substantially contribute to aneurysm wall instability.
Managed care and physician/hospital integration.

This paper examines the extent to which hospitals and physicians use new organizational structures designed to facilitate contracting with managed care firms and the extent to which this use is associated with managed care revenue. The data come from a nationally representative sample of 1,495 U.S. community hospitals responding to a 1993 survey about different organizational structures. The results indicate that only 23.3 percent of hospitals participate in at least one form. Hospitals with more than 15 percent of revenues from managed care are twice as likely to participate and favor forms that provide tighter linkages with physicians.
Using fMRI to dissociate sensory encoding from cognitive evaluation of heat pain intensity

Neuroimaging studies of painful stimuli in humans have identified a network of brain regions that is more extensive than identified previously in electrophysiological and anatomical studies of nociceptive pathways. This extensive network has been described as a pain matrix of brain regions that mediate the many interrelated aspects of conscious processing of nociceptive input such as perception, evaluation, affective response, and emotional memory. We used functional magnetic resonance imaging in healthy human subjects to distinguish brain regions required for pain sensory encoding from those required for cognitive evaluation of pain intensity. The results suggest that conscious cognitive evaluation of pain intensity in the absence of any sensory stimulation activates a network that includes bilateral anterior insular cortex/frontal operculum, dorsal lateral prefrontal cortex, bilateral medial prefrontal cortex/anterior cingulate cortex, right superior parietal cortex, inferior parietal lobule, orbital prefrontal cortex, and left occipital cortex. Increased activity common to both encoding and evaluation was observed in bilateral anterior insula/frontal operculum and medial prefrontal cortex/anterior cingulate cortex. We hypothesize that these two regions play a crucial role in bridging the encoding of pain sensation and the cognitive processing of sensory input. Hum Brain Mapp, 2005. © 2005 Wiley‐Liss, Inc.
Comparative Sequence Analysis of a Multidrug-Resistant Plasmid from Aeromonas hydrophila

ABSTRACT Aeromonas hydrophila is a pathogenic bacterium that has been implicated in fish, animal, and human disease. Recently, a multidrug resistance (MDR) plasmid, pR148, was isolated from A. hydrophila obtained from a tilapia (Oreochromis niloticus) farm in Thailand. pR148 is a 165,906-bp circular plasmid containing 147 coding regions showing highest similarity to pNDM-1_Dok1, an MDR plasmid isolated from a human pathogen. pR148 was also very similar to other IncA/C plasmids isolated from humans, animals, food, and fish. pR148 contains a mercuric resistance operon and encodes the complete set of genes for the type 4 secretion system. pR148 encodes a Tn21 type transposon. This transposon contains the drug resistance genes qacH, blaOXA-10, aadA1, and sul1 in a class 1 integron; tetA and tetR in transposon Tn1721; and catA2 and a duplicate sul1 in a locus showing 100% similarity to IncU plasmids isolated from fish. The blaOXA-10 and aadA1 genes showed 100% similarity to those from the Acinetobacter baumannii AYE genome. The similarity of pR148 to a human pathogen-derived plasmid indicates that the plasmids were either transferred between different genera or that they are derived from a common origin. Previous studies have shown that IncA/C plasmids retain a conserved backbone, while the accessory region points to lateral gene transfer. These observations point out the dangers of indiscriminate use of antibiotics in humans and in animals and the necessity of understanding how drug resistance determinants are disseminated and transferred.
Scalable Parallel Approach for High-Fidelity Steady-State Aeroelastic Analysis and Adjoint Derivative Computations

Aeroelastic systems achieve the best performance when the aerodynamic shape and structural sizing are optimized concurrently, but such an optimization is challenging when high-fidelity aerodynamic and structural models are required. This paper addresses this challenge through several significant improvements. Fully coupled Newton–Krylov methods are presented for the solution of aerostructural systems and for the corresponding adjoint systems. The coupled adjoint method presented can compute gradients with respect to thousands of multidisciplinary design variables accurately and efficiently. This is enabled by several improvements in the computation of the multidisciplinary terms in the coupled adjoint. The parallel scalability of the methods is demonstrated for a full aircraft configuration using an Euler computational fluid dynamics model with more than 8×106 state variables and a detailed structural finite element model of the wing with more than 1×106 degrees of freedom. The coupled Newton–Krylov metho.
Lifestyle Counseling for Type 2 Diabetes Risk Reduction in Dutch Primary Care

OBJECTIVE To study the overall effect of the Active Prevention in High-Risk Individuals of Diabetes Type 2 in and Around Eindhoven (APHRODITE) lifestyle intervention on type 2 diabetes risk reduction in Dutch primary care after 0.5 and 1.5 years and to evaluate the variability between general practices. RESEARCH DESIGN AND METHODS Individuals at high risk for type 2 diabetes (Finnish Diabetes Risk Score ≥13) were randomly assigned into an intervention group (n = 479) or a usual-care group (n = 446). Comparisons were made between study groups and between general practices regarding changes in clinical and lifestyle measures over 1.5 years. Participant, general practitioner, and nurse practitioner characteristics were compared between individuals who lost weight or maintained a stable weight and individuals who gained weight. RESULTS Both groups showed modest changes in glucose values, weight measures, physical activity, energy intake, and fiber intake. Differences between groups were significant only for total physical activity, saturated fat intake, and fiber intake. Differences between general practices were significant for BMI and 2-h glucose but not for energy intake and physical activity. In the intervention group, the nurse practitioners’ mean years of work experience was significantly longer in individuals who were successful at losing weight or maintaining a stable weight compared with unsuccessful individuals. Furthermore, successful individuals more often had a partner. CONCLUSIONS Risk factors for type 2 diabetes could be significantly reduced by lifestyle counseling in Dutch primary care. The small differences in changes over time between the two study groups suggest that additional intervention effects are modest. In particular, the level of experience of the nurse practitioner and the availability of partner support seem to facilitate intervention success.