Miracle-dz/UniFAR-FTUs huggingface dataset:
Increased Lipid Absorption and Transport in the Small Intestine of Zucker Obese Rats

The aim of this study was to compare the potency of intestinal lipid absorption in Zucker obese rats compared with Sprague-Dawley (SD) rats. Six male Zucker obese (fa/fa) and six male SD rats baring intestinal lymph fistulae were used in this study. After 24 h recovery, rats were infused inraduodenally with a lipid emulsion containing 40 µmol triolein (labeled with glycerol tri[3H-oleate]), 7.8 µmol phosphatidyl choline in 3 ml phosphate buffered saline at a rate of 3 ml/h for 8 h. Lymph samples were collected and the radioactive lipid content determined. Apolipoprotein B (apo B) level in the lymph was evaluated. The Zucker obese rats transported more radioactive lipid into the lymph compared with the SD rats, particularly in the early phase of lipid absorption. Lymph apo B levels in the intestinal mucosa were significantly increased compared with the SD rats. In conclusion, this study indicated that lipid absorption and transport in Zucker obese rats is concomitant with increased apo B levels in the mesenteric lymph, indicating that the increase in lipid absorption may be responsible, at least in part, for obesity progression and hyperlipidemia.
Sparse Template-Based variational Image Segmentation

We introduce a variational approach to image segmentation based on sparse coverings of image domains by shape templates. The objective function combines a data term that achieves robustness by tolerating overlapping templates with a regularizer enforcing sparsity. A suitable convex relaxation leads to the variational approach that is amenable to large-scale convex programming. Our approach takes implicitly into account prior knowledge about the shape of objects and their parts, without resorting to combinatorially difficult problems of variational inference. We illustrate our approach by numerical examples and indicate how prior knowledge acquisition may be achieved by learning from examples.
Smallest enclosing ball for probabilistic data

This paper deals with computing the smallest enclosing ball of a set of points subject to probabilistic data. In our setting, any of the n points may not or may occur at one of finitely many locations, following its own discrete probability distribution. The objective is therefore considered to be a random variable and we aim at finding a center minimizing the expected maximum distance to the points according to their distributions. Our main contribution presented in this paper is the first polynomial time (1 + ϵ)-approximation algorithm for the probabilistic smallest enclosing ball problem with extensions to the streaming setting.
Intravitreal triamcinolone for intraocular inflammation and associated macular edema

Triamcinolone acetonide (TA) is a corticosteroid that has many uses in the treatment of ocular diseases because of its potent anti-inflammatory and anti-permeability actions. Intraocular inflammation broadly referred to as uveitis can result from several causes, including the immune system and after ophthalmic surgery. One of the most common reasons for vision loss with uveitis is macular edema. TA has been used for many years as an intravitreal injection for the treatment of ocular diseases. Several case control studies have been reported showing the efficacy of TA in the treatment of intraocular inflammation and associated macular edema caused by Behcet’s disease, Vogt-Koyanagi-Harada syndrome, sympathetic ophthalmia and white dot syndromes. It has also been shown efficacious in cases of pars planitis and idiopathic posterior uveitis. Some authors have reported its use in postoperative cystoid macular edema. Many of the studies on the use of TA in controlling intraocular inflammation and concomitant macular edema showed its effect to be transient in many patients requiring reinjection. Complications can arise from intravitreal injection of TA including elevated intraocular pressure and cataract. Rarely, it can be associated with infectious and non-infectious endophthalmitis. TA may be useful as an adjuvant in the treatment of uveitis and its associated macular edema, especially in patients resistant or intolerant to standard treatment.
Search--based approaches to the component selection and prioritization problem

This poster paper addresses the problem of choosing sets of software components to combine in component--based software engineering. It formulates both ranking and selection problems as feature subset selection problems to which search based software engineering can be applied. We will consider selection and ranking of elements from a set of software components from the component base of a large telecommunications organisation.
Mesangial cell signaling cascades in response to mechanical strain and glucose.

BACKGROUND Elevated glucose levels and glomerular hypertension (Pgc) are considered to contribute to the elaboration of matrix protein by mesangial cells (MCs) in diabetic glomeruli. MCs grown in 30 mM of glucose produce excessive matrix protein, as do MCs exposed to cyclic strain, and the combination of the two exacerbates this. Tight glucose control or reduction in Pgc clinically delays progression of diabetic nephropathy. MC c-fos is induced in response to either application of strain or high ambient glucose, inducing increases in activated protein-1 transactivational activity and extracellular matrix production. Stimuli that lead to c-fos induction pass through the three mitogen-activated protein (MAP) kinase pathways: p44/42, SAPK/JNK, and p38/HOG. We studied MAP kinase activation in MCs exposed to mechanical strain and a high glucose. METHODS MCs (passage 5 through 10) cultured for 96 hours on type 1 collagen-coated flexible-bottom plates in either 5.6 or 30 mM glucose were exposed to 5, 10, or 30 minutes of cyclic strain (60 cycles per min) by computer-driven generation of vacuums of -14 kPa, inducing 20% elongation in the diameter of the surface. Control MCs were grown on both coated rigid and flexible-bottom plates. Protein levels (by Western blot) and activity assays for all three kinase cascades were performed at baseline and after 5, 10, and 30 minutes. All experiments were performed in triplicate. RESULTS MAP kinase signaling was seen in response to stretch, and high ambient glucose affected the pattern of activation. Both p44/42 and p38HOG kinase activities showed small increases to a maximum of 2.5- to 3.5-fold greater than static MCs at 10 minutes. Activity in both kinase cascades was slightly suppressed by 30 mM glucose. In contrast, SAPK/JNK activity was present at a very low level in static MCs and increased markedly by 10 minutes of stretch. Thirty micromolars of glucose augmented this effect by a factor of six over MCs cultured in 5.6 mM glucose after 10 minutes of stretch. Neither glucose concentration nor mechanical strain had any effect on the protein expression of any of the kinases by Western blot. CONCLUSIONS MAP kinase cascade signaling is seen when physical force is applied to MCs, and glucose affects the pattern of activity. Thirty micromolars of glucose markedly increase the level of SAPK/JNK activation. This may have implications in diabetic signal transduction and matrix protein production.
Knee pain and knee osteoarthritis severity in self-reported task specific disability: the Johnston County Osteoarthritis Project.

OBJECTIVE To evaluate the contributions of radiographic knee osteoarthritis (OA) and knee pain severity to self-reported disability performing upper and lower extremity tasks in a rural, population based sample. METHODS Data from 1192 African-American and Caucasian participants in the Johnston County Osteoarthritis Project were analyzed with multiple logistic regression to examine the roles of Kellgren-Lawrence radiographic knee OA grade and knee pain severity in self-reported difficulty performing 20 activities of the Health Assessment Questionnaire. Potential confounders included age, sex, race, marital status, education, and body mass index. RESULTS Forty-three percent reported difficulty performing at least one task. Mild knee pain was independently associated with difficulty performing 16 upper and lower extremity tasks, and moderate/severe knee pain with all 20 tasks, with little change after adjustment (p < 0.0001). In contrast, mild radiographic knee OA was associated with difficulty in only 4 mobility and transfer tasks: climbing 5 steps, taking a tub bath, getting in/out of a car, and performing chores. Moderate/severe radiographic knee OA was associated with difficulty in 17 of 20 tasks (in 10 of 17, p < 0.0001), except lifting a cup, opening car doors, and turning faucets. However, no associations between radiographic knee OA and difficulty were statistically significant after adjustment for knee pain and the above factors. CONCLUSION Knee pain severity was the strongest risk factor for self-reported difficulty performing tasks of upper and lower extremity function. Future studies of disability should include data on knee pain severity.
Closed-form design of maximally flat IIR half-band filters

In this paper, a new closed-form expression for the transfer function of the maximally flat (MF) IIR half-band (HB) filters is presented. The filter coefficients are directly obtained by solving a linear system of Vandermonde equations that are derived from the maximal flatness conditions. The proposed IIR half-band filters are more general than the existing half-band filters, because they include the conventional FIR half-band filters with exactly linear phase, the generalized FIR half-band filters with approximately linear phase; and the allpass-based IIR half-band filters, as special cases. Furthermore, the IIR HB filters with exactly linear phase and the causal stable IIR HB filters can be realized also. Finally, some design examples are presented to demonstrate the effectiveness of the proposed IIR HB filters.
Verification of a new test of endolymphatic hydrops

Abstract A new objective test of endolymphatic hydrops has been described previously. The test uses auditory brainstem response (ABR) techniques to estimate the basilar membrane travelling wave velocity (TWV). The underlying hypothesis is that raised pressure in the scala media will lead to an increase in the stiffness of the basilar membrane and that this will give rise to a travelling wave velocity that is greater than normal. It was considered that verification of the technique could be obtained by carrying out the new test before and during a glycerol dehydration procedure. Patients who required this procedure for verification of the diagnosis or as a prognostic indicator for sacculotomy, underwent the following tests. Prior to dehydration an audiogram, the ABR TWV test and a blood sample (for plasma osmolality) were taken. The patient was then given the appropriate amount of glycerol mixed with lemon juice and laid on a bed in a test room. The audiogram and a blood sample were repeated every hour and the ABR TWV test was repeatedly carried out every twenty minutes between the other tests. Six of these procedures have been carried out. In five of them the 0.5 and 1kHz average threshold improved by at least 10dB and in all those cases the ABR TWV test showed an abnormal pre-dehydration result which moved towards the normal value following dehydration. One patient gave ABR TWV results that were within normal limits before and during the procedure and gave an audiometric change of only 5dB. These data indicate that the ABR TWV test does detect endolymphatic hydrops. The additional hardware to carry out this test has been constructed and parallel clinical trials at IHR Southampton, Addenbrooke's Hospital, Cambridge, and Queen's Medical Centre, Nottingham, are in hand.
Data structures and compression algorithms for genomic sequence data

MOTIVATION The continuing exponential accumulation of full genome data, including full diploid human genomes, creates new challenges not only for understanding genomic structure, function and evolution, but also for the storage, navigation and privacy of genomic data. Here, we develop data structures and algorithms for the efficient storage of genomic and other sequence data that may also facilitate querying and protecting the data. RESULTS The general idea is to encode only the differences between a genome sequence and a reference sequence, using absolute or relative coordinates for the location of the differences. These locations and the corresponding differential variants can be encoded into binary strings using various entropy coding methods, from fixed codes such as Golomb and Elias codes, to variables codes, such as Huffman codes. We demonstrate the approach and various tradeoffs using highly variables human mitochondrial genome sequences as a testbed. With only a partial level of optimization, 3615 genome sequences occupying 56 MB in GenBank are compressed down to only 167 KB, achieving a 345-fold compression rate, using the revised Cambridge Reference Sequence as the reference sequence. Using the consensus sequence as the reference sequence, the data can be stored using only 133 KB, corresponding to a 433-fold level of compression, roughly a 23% improvement. Extensions to nuclear genomes and high-throughput sequencing data are discussed. AVAILABILITY Data are publicly available from GenBank, the HapMap web site, and the MITOMAP database. Supplementary materials with additional results, statistics, and software implementations are available from http://mammag.web. uci.edu/bin/view/Mitowiki/ProjectDNACompression.
AUTOMATED LASCO CME CATALOG FOR SOLAR CYCLE 23: ARE CMEs SCALE INVARIANT?

In this paper, we present the first automatically constructed LASCO coronal mass ejection (CME) catalog, a result of the application of the Computer Aided CME Tracking software (CACTus) on the LASCO archive during the interval 1997 September–2007 January. We have studied the CME characteristics and have compared them with similar results obtained by manual detection (CDAW CME catalog). On average, CACTus detects less than two events per day during solar minimum, up to eight events during maximum, nearly half of them being narrow (<20°). Assuming a correction factor, we find that the CACTus CME rate is surprisingly consistent with CME rates found during the past 30 years. The CACTus statistics show that small-scale outflow is ubiquitously observed in the outer corona. The majority of CACTus-only events are narrow transients related to previous CME activity or to intensity variations in the slow solar wind, reflecting its turbulent nature. A significant fraction (about 15%) of CACTus-only events were identified as independent events, thus not related to other CME activity. The CACTus CME width distribution is essentially scale invariant in angular span over a range of scales from 20° to 120° while previous catalogs present a broad maximum around 30°. The possibility that the size of coronal mass outflows follow a power-law distribution could indicate that no typical CME size exists, i.e., that the narrow transients are not different from the larger well defined CMEs.
A canonical representation of input-balanced realizations for discrete-time systems

In this paper, based on a matrix factorization a novel structure is proposed for digital system implementation and adaptive filtering applications. The equivalent state-space realization of such a structure is an input-balanced realization. Like the normalized lattice structure, it contains a series of Givens rotations. This proposed structure is simpler than the normalized structure and can be implemented very efficiently using the Coordinate Rotation Digital Computer (CORDIC) techniques. This canonical parametrization is particularly important for ensuring the bounded input bounded output (BIBO) stability when used for adaptive filtering. Numerical examples show that the proposed structure outperforms the traditional direct-form II (DFII) structures as well as the normalized lattice structure in terms of minimizing parameter sensitivity and hence roundoff noise.
Convergence analysis of the least squares constant modulus algorithm

This paper examines the convergence behavior of the least squares constant modulus algorithm in an adaptive beamforming application. The improvement in output SIR with each iteration of the algorithm is predicted for several different signal environments. Deterministic results are presented for an environment containing two tones. Probabilistic results are presented for a constant modulus desired signal with a constant modulus interferer and with a gaussian interferer. The asymptotic improvement in output SIR as the output SIR becomes high is also derived.
The Oxide Defect of C70250 Alloy

The oxide skin defect during hot rolling process for Cu-Ni-Si alloy strip was investigated. Oxide skin defects were analyzed by means of alloy elements detection and microstructures characterization. The characterization and test results showed that high temperature oxidation and silicon segregation are the main causes of the oxide skin defect. Pilot scale tests indicated that hot processing temperature for C70250 alloy should be lower than 950°C. Reducing atmosphere is recommended during the thermal treatment of Cu-Ni-Si alloys.
Consistent privacy preferences (CPP): model, semantics, and properties

The Platform for Privacy Preferences (P3P) is a W3C specification that can be used to build useful protocols and services for protecting user privacy on the semantic Web. An outstanding issue is the need for a simple and efficient representation and management of consistent sets of rules for user privacy preferences. Thus we describe a model for privacy preference representation and management that has a number of desirable properties which are lacking in privacy preference models proposed thus far. We detail semantics and properties of matching preference rules with requests. We specify the properties of a consistent set of privacy preferences, and propose maintenance operations. Finally, we describe an implementation of our proposal that uses OWL (Web Ontology Language) and the Jena reasoning engine to illustrate the practicality of managing consistent user preferences in privacy rule-sets. An important advantage of our approach is that the user is encouraged to clarify privacy preferences as he/she modifies them as part of a back-end management task, as opposed to mainly at website interaction times.
MiRNA-Directed Regulation of VEGF and Other Angiogenic Factors under Hypoxia

MicroRNAs (miRNAs) are a class of 20–24 nt non-coding RNAs that regulate gene expression primarily through post-transcriptional repression or mRNA degradation in a sequence-specific manner. The roles of miRNAs are just beginning to be understood, but the study of miRNA function has been limited by poor understanding of the general principles of gene regulation by miRNAs. Here we used CNE cells from a human nasopharyngeal carcinoma cell line as a cellular system to investigate miRNA-directed regulation of VEGF and other angiogenic factors under hypoxia, and to explore the principles of gene regulation by miRNAs. Through computational analysis, 96 miRNAs were predicted as putative regulators of VEGF. But when we analyzed the miRNA expression profile of CNE and four other VEGF-expressing cell lines, we found that only some of these miRNAs could be involved in VEGF regulation, and that VEGF may be regulated by different miRNAs that were differentially chosen from 96 putative regulatory miRNAs of VEGF in different cells. Some of these miRNAs also co-regulate other angiogenic factors (differential regulation and co-regulation principle). We also found that VEGF was regulated by multiple miRNAs using different combinations, including both coordinate and competitive interactions. The coordinate principle states that miRNAs with independent binding sites in a gene can produce coordinate action to increase the repressive effect of miRNAs on this gene. By contrast, the competitive principle states when multiple miRNAs compete with each other for a common binding site, or when a functional miRNA competes with a false positive miRNA for the same binding site, the repressive effects of miRNAs may be decreased. Through the competitive principle, false positive miRNAs, which cannot directly repress gene expression, can sometimes play a role in miRNA-mediated gene regulation. The competitive principle, differential regulation, multi-miRNA binding sites, and false positive miRNAs might be useful strategies in the avoidance of unwanted cross-action among genes targeted by miRNAs with multiple targets.
Computational Modeling of Spatiotemporal Ca2+ Signal Propagation Along Hepatocyte Cords

Objective: The purpose of this study is to model the dynamics of lobular Ca2+ wave propagation induced by an extracellular stimulus, and to analyze the effect of spatially systematic variations in cell-intrinsic signaling parameters on sinusoidal Ca2+ response. Methods: We developed a computational model of lobular scale Ca2+ signaling that accounts for receptor- mediated initiation of cell-intrinsic Ca2+ signal in hepatocytes and its propagation to neighboring hepatocytes through gap junction-mediated molecular exchange. Results: Analysis of the simulations showed that a pericentral-to-periportal spatial gradient in hormone sensitivity and/or rates of IP3 synthesis underlies the Ca2+ wave propagation. We simulated specific cases corresponding to localized disruptions in the graded pattern of these parameters along a hepatic sinusoid. Simulations incorporating locally altered parameters exhibited Ca2+ waves that do not propagate throughout the hepatic plate. Increased gap junction coupling restored normal Ca2+ wave propagation when hepatocytes with low Ca2+ signaling ability were localized in the midlobular or the pericentral region. Conclusion: Multiple spatial patterns in intracellular signaling parameters can lead to Ca2+ wave propagation that is consistent with the experimentally observed spatial patterns of Ca2+ dynamics. Based on simulations and analysis, we predict that increased gap junction-mediated intercellular coupling can induce robust Ca2+ signals in otherwise poorly responsive hepatocytes, at least partly restoring the sinusoidally oriented Ca 2+ waves. Significance: Our bottom-up model of agonist-evoked spatial Ca2+ patterns can be integrated with detailed descriptions of liver histology to study Ca2+ regulation at the tissue level.