Miracle-dz/UniFAR-FTUs huggingface dataset:
Fish peptone development using enzymatic hydrolysis of silver carp by-products as a nitrogen source in Staphylococcus aureus media

Fish peptone was produced using enzymatic hydrolysis of silver carp filleting by-products by alcalase and trypsin. Also, the efficiency of the hydrolysates as a nitrogen source in Staphylococcus aureus medium was compared with commercial TSB. The results indicated that the protein hydrolysate from alcalase and trypsin had high protein content (92.92%, 91.53 respectively), and degree of hydrolysis (4.94%, 4.6% respectively). The results showed that silver carp filleting waste can be an efficient source for fish peptone production as a nitrogen source for S. aureus medium. However, the type of the used proteolytic enzyme considerably affected the performance of the resulting peptone despite the same DH. Fish peptone produced by alcalese performed significantly (P < 0.05) better than commercial TSB as a media for the bacteria while the performance of the trypsin peptone was not as good as the commercial medium.
Targeting orphan G protein‐coupled receptors for the treatment of diabetes and its complications: C‐peptide and GPR146

G protein‐coupled receptors (GPCRs) are the most abundant receptor family encoded by the human genome and are the targets of a high percentage of drugs currently in use or in clinical trials for the treatment of diseases such as diabetes and its associated complications. Thus, orphan GPCRs, for which the ligand is unknown, represent an important untapped source of therapeutic potential for the treatment of many diseases. We have identified the previously orphan GPCR, GPR146, as the putative receptor of proinsulin C‐peptide, which may prove to be an effective treatment for diabetes‐associated complications. For example, we have found a potential role of C‐peptide and GPR146 in regulating the function of the retinal pigment epithelium, a monolayer of cells in the retina that serves as part of the blood–retinal barrier and is disrupted in diabetic macular oedema. However, C‐peptide signalling in this cell type appears to depend at least in part on extracellular glucose concentration and its interaction with insulin. In this review, we discuss the therapeutic potential of orphan GPCRs with a special focus on C‐peptide and GPR146, including past and current strategies used to ‘deorphanize’ this diverse family of receptors, past successes and the inherent difficulties of this process.
Anthracobunids from the Middle Eocene of India and Pakistan Are Stem Perissodactyls

Anthracobunidae is an Eocene family of large mammals from south Asia that is commonly considered to be part of the radiation that gave rise to elephants (proboscideans) and sea cows (sirenians). We describe a new collection of anthracobunid fossils from Middle Eocene rocks of Indo-Pakistan that more than doubles the number of known anthracobunid fossils and challenges their putative relationships, instead implying that they are stem perissodactyls. Cranial, dental, and postcranial elements allow a revision of species and the recognition of a new anthracobunid genus. Analyses of stable isotopes and long bone geometry together suggest that most anthracobunids fed on land, but spent a considerable amount of time near water. This new evidence expands our understanding of stem perissodactyl diversity and sheds new light on perissodactyl origins.
Crack‐healing and mechanical behaviour of Al2O3/SiC composites at elevated temperature

Alumina/silicon carbide (Al 2 O 3 /SiC) composite ceramics with large self-crack-healing ability, high strength and high heat-resistance limit temperature for strength were developed and subjected to three-point bending. A semicircular surface crack 100 μm in diameter was made on each sample. Crack-healing behaviour was systematically studied, as functions of crack-healing temperature and healing time, and the fatigue strengths of the crack-healed sample at room temperature and 1373 K were investigated. Four main conclusions were drawn from the present study. (1) Al 2 O 3 /SiC composite ceramics have the ability to heal after cracking from 1273to 1673 K in air. (2) The heat-resistance limit temperature for strength of the crack-healed sample is ≅ 1573 K, and ≅68% of the samples fractured from outside the crack-healed zone in the testing-temperature range 873-1573 K. (3) The crack-healed sample exhibited very high fatigue limit at room temperature and also 1373 K. (4) The large self-crack-healing ability is a desirable technique for the high structural integrity of ceramic component.
NANOPOROUS AAO: A PLATFORM FOR REGULAR HETEROGENEOUS NANOSTRUCTURES AND ENERGY STORAGE DEVICES

Title of Document: NANOPOROUS AAO: A PLATFORM FOR REGULAR HETEROGENEOUS NANOSTRUCTURES AND ENERGY STORAGE DEVICES Israel Perez, Doctor of Philosophy, 2009 Directed By: Professor Gary W. Rubloff Department of Materials Science and Engineering and the Institute for Systems Research Nanoporous anodic aluminum oxide (AAO) has vast implications as a tool for nanoscience research and as a nanostructure in which nanoscale devices can be fabricated because of its regular and ordered nanopores. Self-assembly plays a critical role in pore ordering, causing nanopores to grow parallel with one another in high density. The mild electrochemical conditions in which porous AAO grows along with its relatively cheap starting materials makes this nanomaterial a cost effective alternative to advanced photolithography techniques for forming high surface area nanostructures over large areas. In this research, atomic layer deposition (ALD) was used to deposit conformal films within in nanoporous AAO with hopes to 1) develop methodologies to characterize ALD depositions within its high aspect ratio nanopores and 2) to better understand how to use nanoporous AAO templates as a scaffold for energy devices, specifically Metal-Insulator-Metal (MIM) capacitors. Using the nanotube template synthesis method, ALD films were deposited onto nanoporous AAO, later removing the films deposited within the templates nanopores for characterization in TEM. This nanotube metrology characterization involves first obtaining images of full length ALD-AAO nanotubes, and then measuring wall thickness as a function of depth within the nanopore. MIM nanocapacitors were also constructed in vertical AAO nanopores by deposition of multilayer ALD films. MIM stacks were patterned into micro-scale capacitors for electrical characterization. NANOPOROUS AAO: A PLATFORM FOR REGULAR HETEROGENEOUS NANOSTRUCTURES AND ENERGY STORAGE DEVICES
Nurses experience of using scientific knowledge in clinical practice: a grounded theory study.

BACKGROUND Guidelines recommend the use of evidence-based practice in nursing. Nurses are expected to give patients care and treatment based on the best knowledge available. They may have knowledge and positive attitudes, but this does not mean that they are basing their work on evidence-based practice. Knowledge is still lacking about what is needed to successfully implement evidence-based practice. AIM The aim of this study was to gain more knowledge about what nurses perceive as the most important challenge in implementing evidence-based practice and to explain how they act to face and overcome this challenge. METHOD We used classical grounded theory methodology and collected data through four focus groups and one individual interview in different geographical locations in one large hospital trust in Norway. Fourteen registered clinical practice nurses participated. We analysed the data in accordance with grounded theory, using the constant comparative method. RESULTS Contextual balancing of knowledge emerged as the core category and explains how the nurses dealt with their main concern, how to determine what types of knowledge they could trust. The nurses' main strategies were an inquiring approach, examining knowledge and maintaining control while taking care of patients. They combined their own experienced-based knowledge and the guidelines of evidence-based practice with a sense of control in the actual situation. CONCLUSION The grounded theory contextual balancing of knowledge may help us to understand how nurses detect what types of knowledge they can trust in clinical practice. The nurses needed to rely on what they did, and they seemed to rely on their own experience rather than on research.
Image Denoising Based on Wavelet for IR Images Corrupted by Gaussian, Poisson & Impulse Noises

Summery Image denoising has remained a fundamental problem in various applications of image processing. This paper proposes a new denoising algorithm on Cohen-Daubechies-Feauveau wavelets (CDF 9/7) wavelet transform. We first applied the lifting structure to improve the drawbacks of the wavelet transform where conventional wavelet transforms and other classical decompositions seem to be restricted or limited to handle. Our proposed algorithm in this paper is very efficient in estimating and reducing noises for the contaminated images by the most popular noises such as Gaussian noise, Poisson noise and impulse (salt& pepper) noise. In this algorithm, the noisy image is first decomposed into many levels obtained from different frequency bands and then to be found the best decomposition level for the noise removal. Experimental results on several conditions are investigated for infrared images as study cases under our proposed algorithm. They are very impressive, for example under the noise with σ = 0.2 and density = 20%, for mean square error (MSE) our method decreasing 83%; peak signal to noise ratio (PSNR) increasing 98% and mean of structural similarity (MSSIM) increasing 95%, multi-scale structural similarity (MSSSIM) enhancing 93%, Feature similarity (FSIM) index growing 98.8%, Riesz-transform based Feature Similarity index (RFSIM) increasing 83.4% with the same conditions in other methods. Obviously, the experimental results shown for our proposed algorithm are significantly superior to other related methods.
Immuno and Affinity Cytochemical Analysis of Cell Wall Composition in the Moss Physcomitrella patens

In contrast to homeohydric vascular plants, mosses employ a poikilohydric strategy for surviving in the dry aerial environment. A detailed understanding of the structure, composition, and development of moss cell walls can contribute to our understanding of not only the evolution of overall cell wall complexity, but also the differences that have evolved in response to selection for different survival strategies. The model moss species Physcomitrella patens has a predominantly haploid lifecycle consisting of protonemal filaments that regenerate from protoplasts and enlarge by tip growth, and leafy gametophores composed of cells that enlarge by diffuse growth and differentiate into several different types. Advantages for genetic studies include methods for efficient targeted gene modification and extensive genomic resources. Immuno and affinity cytochemical labeling were used to examine the distribution of polysaccharides and proteins in regenerated protoplasts, protonemal filaments, rhizoids, and sectioned gametophores of P. patens. The cell wall composition of regenerated protoplasts was also characterized by flow cytometry. Crystalline cellulose was abundant in the cell walls of regenerating protoplasts and protonemal cells that developed on media of high osmolarity, whereas homogalactuonan was detected in the walls of protonemal cells that developed on low osmolarity media and not in regenerating protoplasts. Mannan was the major hemicellulose detected in all tissues tested. Arabinogalactan proteins were detected in different cell types by different probes, consistent with structural heterogneity. The results reveal developmental and cell type specific differences in cell wall composition and provide a basis for analyzing cell wall phenotypes in knockout mutants.
T Cell-Induced Mast Cell Activation: A Role for Microparticles Released from Activated T Cells

Close physical proximity between mast cells and T cells has been demonstrated in several T cell-mediated inflammatory processes. However, the way by which mast cells are activated in these T cell-mediated immune responses has not been fully elucidated. We previously identified and characterized a novel mast cell activation pathway initiated by physical contact with activated T cells and showed that this pathway is associated with degranulation and cytokine release. In this study, we provide evidence that mast cells may also be activated by microparticles released from activated T cells that are considered miniature versions of a cell. Microparticles were isolated from supernatants of activated T cells by Centricon filtration or by high-speed centrifugation and identified by electron microscopy, flow cytometry (Annexin stain), and expression of the integrin LFA-1. Stimulated T cells were found to generate microparticles that induce degranulation and cytokine (IL-8 and oncostatin M) release from human mast cells. Mast cell activation by T cell microparticles involved the MAPK signaling pathway. The results were similar when mast cells were stimulated by activated fixed T cells or by whole membranes of the latter. This suggests that microparticles carry mast cell-activating factors similar to cells from which they originate. By releasing microparticles, T cells might convey surface molecules similar to those involved in the activation of mast cells by cellular contact. By extension, microparticles might affect the activity of mast cells, which are usually not in direct contact with T cells at the inflammatory site.
(Not) yet another matcher

Discovering correspondences between schema elements is a crucial task for data integration. Most schema matching tools are semi-automatic, e.g. an expert must tune some parameters (thresholds, weights, etc.). They mainly use several methods to combine and aggregate similarity measures. However, their quality results often decrease when one requires to integrate a new similarity measure or when matching particular domain schemas. This paper describes YAM (Yet Another Matcher), which is a schema matcher factory. Indeed, it enables the generation of a dedicated matcher for a given schema matching scenario, according to user inputs. Our approach is based on machine learning since schema matchers can be seen as classifiers. Several bunches of experiments run against matchers generated by YAM and traditional matching tools show how our approach is able to generate the best matcher for a given scenario.
Trajbase: searching trajectories in multi-region

The recent years witnessed popular use of smart phones and wearable devices. Such mobile devices are widely equipped with GPS sensors to record their geographical positions, generating massive spatial trajectory data. Many real applications, such as urban computing and intelligent transportation systems, search the trajectory data. To process such queries, it is important to meet two objectives including fast running time and low space cost. Previous work frequently only meets one objective but compromises another. In this work, we design a compact data structure TrajBase to index trajectory data. The novelty of such an indexing structure is a carefully designed encoding approach. The approach can achieve comparable compression ratio compared with the state of the art approach and fast building time. Extensive evaluation with two real trajectory datasets can successfully verify that TrajBase outperforms previous works in terms of query processing time and indexing space cost.
Combination of innate and adaptive immune alterations increased the likelihood of fibrostenosis in Crohn's disease†

Background: Mutations in the nucleotide oligomerization domain‐2 (NOD2) gene and positive antibodies to microbial antigens have been found to be associated with the Crohn's disease (CD) phenotype, fibrostenosis. The aim of this study was to confirm these relationships in a large cohort of CD patients and to determine the correlation between the presence of NOD2 variants and antibodies to oligomannan, CBir, outer membrane porin‐C (OmpC), and I2 in CD patients with fibrostenosis. Methods: Sera and DNA from 731 unrelated CD patients were tested for NOD2 variants (SNP 8, 12, and 13) and the antibodies. The results were correlated with CD phenotypes, fibrostenosis, internal penetrating, perianal penetrating, and ulcerative colitis (UC)‐like as well as other clinical features. Results: The presence of NOD2 allelic variants was primarily associated with fibrostenosis, secondarily with small bowel disease and small bowel surgery, and was inversely associated with UC‐like disease. This association was present in patients with a fibrostenosis only (Vienna B2) and those with both stricturing and penetrating disease. The presence and level of antibodies to microbial antigens was also associated with the fibrostenosis phenotype. In the 316 patients with fibrostenosis the prevalence of NOD2 variants was significantly correlated with the antibody titer by quartile sum score. Further, when these patients with fibrostenosis were clustered by quartile sum score, the odds ratio for fibrostenosis was significantly higher in the patients with NOD2 variant alleles within each cluster, indicating synergy. Conclusions: Defects of innate (NOD2 variants) and adaptive (antibodies to microbial antigens) immunity act synergistically to increase the risk of the fibrostenosis phenotype. (Inflamm Bowel Dis 2009;)
Investigation of molecular serum profiles associated with predisposition to antipsychotic-induced weight gain

Abstract Objectives. Metabolic disturbances are major adverse side effects in the treatment of schizophrenia patients with antipsychotics. A substantial proportion of patients discontinue treatment with second-generation antipsychotics due to weight gain. The objective of this study was to investigate molecular factors predisposing patients to the development of such metabolic disturbances. Methods. We investigated whether serum molecules measured before treatment initiation were associated with subsequent weight gain following a 6-week treatment with antipsychotics. The concentrations of 191 molecules were measured longitudinally in serum from 77 schizophrenia patients using multiplex immunoassays. Results. This showed that the levels of 10 serum molecules at T0 were significantly associated with ΔBMI, which included interleukin-6 receptor, epidermal growth factor and thyroid stimulating hormone. Conclusions. Our results suggest that patients who experience antipsychotic-induced weight gain have specific molecular alterations already prior to treatment. Further studies are required to validate and evaluate current findings in the context of response and side-effect development. This may ultimately lead to molecular tests that can aid in the selection of antipsychotic treatments.
Multiframe demosaicing and super-resolution of color images

In the last two decades, two related categories of problems have been studied independently in image restoration literature: super-resolution and demosaicing. A closer look at these problems reveals the relation between them, and, as conventional color digital cameras suffer from both low-spatial resolution and color-filtering, it is reasonable to address them in a unified context. In this paper, we propose a fast and robust hybrid method of super-resolution and demosaicing, based on a maximum a posteriori estimation technique by minimizing a multiterm cost function. The L/sub 1/ norm is used for measuring the difference between the projected estimate of the high-resolution image and each low-resolution image, removing outliers in the data and errors due to possibly inaccurate motion estimation. Bilateral regularization is used for spatially regularizing the luminance component, resulting in sharp edges and forcing interpolation along the edges and not across them. Simultaneously, Tikhonov regularization is used to smooth the chrominance components. Finally, an additional regularization term is used to force similar edge location and orientation in different color channels. We show that the minimization of the total cost function is relatively easy and fast. Experimental results on synthetic and real data sets confirm the effectiveness of our method.
Computational Analyses of Ancient Polyploidy

Whole genome duplication has played a major role in the evolution of many eukaryotic lineages. Polyploidy has long been postulated as a powerful mechanism for evolutionary innovation, and recent analyses have provided convincing evidence that independent ancient genome duplications occurred in the ancestors of yeast, plants, vertebrates and fish. It is the growing availability of whole genome sequences that has facilitated the detection and analysis of these polyploidizations. However, because polyploidy is often followed by massive gene loss and chromosomal rearrangements, identifying such events is not always easy. Here is presented a review of a wide array of computational methods of ever-increasing sophistication developed to identify the obscured traces of ancient polyploidy events in genomic sequences. These methods use a variety of analytical approaches, including comparative genomics, phylogenetics and molecular clock analyses. We have also reviewed recent research on the long-term evolution of genes and genomes duplicated by polyploidization. This has emerged as a fruitful field, utilizing genome-wide functional information and genomic sequence data to further our understanding of the impact of polyploidy on organismal biology and evolution.
Theta Phase Synchrony and Conscious Target Perception: Impact of Intensive Mental Training

The information processing capacity of the human mind is limited, as is evidenced by the attentional blink—a deficit in identifying the second of two targets (T1 and T2) presented in close succession. This deficit is thought to result from an overinvestment of limited resources in T1 processing. We previously reported that intensive mental training in a style of meditation aimed at reducing elaborate object processing, reduced brain resource allocation to T1, and improved T2 accuracy [Slagter, H. A. , Lutz, A. , Greischar, L. L. , Francis, A. D. , Nieuwenhuis, S. , Davis, J., et al. Mental training affects distribution of limited brain resources. PloS Biology, 5, e138, 2007]. Here we report EEG spectral analyses to examine the possibility that this reduction in elaborate T1 processing rendered the system more available to process new target information, as indexed by T2-locked phase variability. Intensive mental training was associated with decreased cross-trial variability in the phase of oscillatory theta activity after successfully detected T2s, in particular, for those individuals who showed the greatest reduction in brain resource allocation to T1. These data implicate theta phase locking in conscious target perception, and suggest that after mental training the cognitive system is more rapidly available to process new target information. Mental training was not associated with changes in the amplitude of T2-induced responses or oscillatory activity before task onset. In combination, these findings illustrate the usefulness of systematic mental training in the study of the human mind by revealing the neural mechanisms that enable the brain to successfully represent target information.