Miracle-dz/UniFAR-FTUs huggingface dataset:
Effect of ischemic pretreatment on heat shock protein 72, neurologic outcome, and histopathologic outcome in a rabbit model of spinal cord ischemia.

OBJECTIVE In the present study, we investigated the effect of ischemic pretreatment on heat shock protein 72 concentration and neurologic and histopathologic outcome after transient spinal cord ischemia. METHODS In 28 New Zealand White rabbits, an aortic occlusion device was placed infrarenally. The animals were randomly assigned to 2 groups: ischemic pretreatment (n = 14 animals) and control (n = 14 animals). The duration of ischemic pretreatment was 6 minutes. After 24 hours, the aorta was occluded for 26 minutes in both groups of animals. Neurologic function was assessed 24 and 48 hours after the definite ischemic insult. At 48 hours, the animals were killed for histopathologic evaluation of the spinal cord. In a separate set of animals, heat shock protein 72 levels were determined in the lumbar spinal cord after both a 6- and 10-minute ischemic period, with the use of a Western blot analysis. RESULTS No significant difference in neurologic outcome between the groups was observed at 24 and 48 hours. The incidence of paraplegia and severe paresis at 48 hours was 79% in the control group and 92% in the ischemic pretreatment group. There was no difference in histopathologic scores between the groups. Heat shock protein 72 could be clearly detected 1 and 2 days after 6- or 10-minute periods of spinal cord ischemia. CONCLUSIONS In the present rabbit study, ischemic pretreatment could not induce tolerance against a moderately severe spinal cord ischemic insult, despite increased heat shock protein 72 levels after the preconditioning stimulus.
A Novel Random Walk and Scale Control Method for Event Recommendation

Recently, social event recommendation, which is to recommend a list of upcoming events to a user, has attracted a lot of research interests. In this paper, we first construct a heterogeneous graph to express the interactions among different types of entities in event-based social network. Based on the constructed graph, we propose a novel recommendation algorithm called reverse random walk with restart to obtain the recommended events for each user. Since the participant capacity of an event may be constrained to a limited number of users, we further propose a scale control algorithm to coordinate unbalanced user arrangements among events. Experiment results on Meetup dataset show that the proposed method outperforms the state-of-art algorithms in terms of higher recommendation precision, larger recommendation coverage.
SATB1 Mediates Long-Range Chromatin Interactions: A Dual Regulator of Anti-Apoptotic BCL2 and Pro-Apoptotic NOXA Genes

Aberrant expression of special AT-rich binding protein 1 (SATB1), a global genomic organizer, has been associated with various cancers, which raises the question of how higher-order chromatin structure contributes to carcinogenesis. Disruption of apoptosis is one of the hallmarks of cancer. We previously demonstrated that SATB1 mediated specific long-range chromosomal interactions between the mbr enhancer located within 3’-UTR of the BCL2 gene and the promoter to regulate BCL2 expression during early apoptosis. In the present study, we used chromosome conformation capture (3C) assays and molecular analyses to further investigate the function of the SATB1-mediated higher-order chromatin structure in co-regulation of the anti-apoptotic BCL2 gene and the pro-apoptotic NOXA gene located 3.4Mb downstream on Chromosome 18. We demonstrated that the mbr enhancer spatially juxtaposed the promoters of BCL2 and NOXA genes through SATB1-mediated chromatin-loop in Jurkat cells. Decreased SATB1 levels switched the mbr-BCL2 loop to mbr-NOXA loop, and thus changed expression of these two genes. The SATB1-mediated dynamic switch of the chromatin loop structures was essential for the cooperative expression of the BCL2 and NOXA genes in apoptosis. Notably, the role of SATB1 was specific, since inhibition of SATB1 degradation by caspase-6 inhibitor or caspase-6-resistant SATB1 mutant reversed expression of BCL-2 and NOXA in response to apoptotic stimulation. This study reveals the critical role of SATB1-organized higher-order chromatin structure in regulating the dynamic equilibrium of apoptosis-controlling genes with antagonistic functions and suggests that aberrant SATB1 expression might contribute to cancer development by disrupting the co-regulated genes in apoptosis pathways.
The Involvement of Amino Acid Side Chains in Shielding the Nickel Coordination Site: An NMR Study

Coordination of proteins and peptides to metal ions is known to affect their properties, often by a change in their structural organization. Side chains of the residues directly involved in metal binding or very close to the coordination centre may arrange themselves around it, in such a way that they can, for instance, disrupt the protein functions or stabilize a metal complex by shielding it from the attack of water or other small molecules. The conformation of these side chains may be crucial to different biological or toxic processes. In our research we have encountered such behaviour in several cases, leading to interesting results for our purposes. Here we give an overview on the structural changes involving peptide side chains induced by Ni(II) coordination. In this paper we deal with a number of peptides, deriving from proteins containing one or more metal coordinating sites, which have been studied through a series of NMR experiments in their structural changes caused by Ni(II) complexation. Several peptides have been included in the study: short sequences from serum albumin (HSA), Des-Angiotensinogen, the 30-amino acid tail of histone H4, some fragments from histone H2A and H2B, the initial fragment of human protamine HP2 and selected fragments from prion and Cap43 proteins. NMR was the election technique for gathering structural information. Experiments performed for this purpose included 1D 1H and 13C, and 2D HSQC, COSY, TOCSY, NOESY and ROESY acquisitions, which allowed the calculation of the Ni(II) complexes structural models.
A Hole-Filling Approach Based on Morphological Operation for Stereoscopic Image Generation

Apply the stereoscopic image generation from 2D to 3D conversion depth image based rendering (DIBR) technique it is 2D view to multi-angle virtual view by the single depth image. We develop a stereoscopic image generation method from one-view color image and its corresponding depth information. The DIBR firstly does the preprocessing of the depth image by using the smooth filter, which sharpens the discontinuous depth changes as well as to smooth the neighboring depth of similar color and also detain noises from appearing on the warped images. The occlusion regions are applied the morphological operations on the depth image with the background depth levels to keep the depth structure. With depth-guided exemplar-based image inpainting combines the color gradient to preserve the image structure in the restored regions.
Measurement of absolute hadronic branching fractions of D mesons and e+e-→DD̄ cross sections at the ψ(3770)

Using 281 pb -1 of e + e - collisions recorded at the (ψ(3770) resonance with the CLEO-c detector at CESR (Cornell Electron Storage Ring), we determine absolute hadronic branching fractions of charged and neutral D mesons using a double tag technique. Among measurements for three D° and six D + modes, we obtain reference branching fractions B(D° → B K - π + ) = (3.891 ± 0.035 ± 0.059 ± 0.035)% and B(D+ → /K- π + π + ) = (9.14 ± 0.10 ± 0.16 ± 0.07)%, where the first uncertainty is statistical, the second is all systematic errors other than final-state radiation (FSR), and the third is the systematic uncertainty due to FSR. We include FSR in these branching fractions by allowing for additional unobserved photons in the final state. Using an independent determination of the integrated luminosity, we also extract the cross sections σ(e + e - → D 0 D 0 ) = (3.66 ± 0.03 ± 0.06) nb and σ(e + e - → D+D - ) = (2.91 ± 0.03 ± 0.05) nb at a center-of-mass energy, E cm = 3774 ± 1 MeV.
Regulation of the human tyrosinase gene in retinal pigment epithelium cells: the significance of transcription factor orthodenticle homeobox 2 and its polymorphic binding site

Purpose Tyrosinase is the rate-limiting enzyme responsible for melanin biosynthesis in the retinal pigment epithelium (RPE) of the eye. Melanin has an important role in retinal development, function, and protection against light-induced oxidative stress, and melanin levels are associated with age-related macular degeneration (AMD). Because the levels of and protection afforded by melanin seem to decline with increasing age, proper regulation of the human tyrosinase gene (TYR) in the RPE is an important but insufficiently understood process. Our purpose was to obtain detailed information on regulation of the TYR gene promoter in the human RPE and to specify the role of orthodenticle homeobox 2 (OTX2) and microphthalmia-associated transcription factor (MITF). Methods We used luciferase reporter constructs to study regulation of the human TYR gene promoter in cultured human RPE cells. We further studied the role of OTX2 and MITF, their binding sites, and endogenous expression by using mutagenesis, electrophoretic mobility shift assay, yeast two-hybrid assay, RNA interference, and gene expression analyses. Results In the RPE, OTX2 activated the human TYR gene promoter via direct trans-activation of novel OTX2 binding elements. In addition, we found that indirect activation by OTX2 via more proximal MITF binding sites, even in the absence of OTX2 sites, took place. These results are consistent with the physical interaction observed between OTX2 and MITF. Overexpression or knockdown of OTX2 in RPE cells resulted in corresponding changes in tyrosinase mRNA expression. Finally, we found that a single nucleotide polymorphism (SNP rs4547091) at the most proximal OTX2 binding site is associated with altered nuclear protein binding and a remarkable decrease in TYR promoter activity in RPE cells. This single nucleotide polymorphism (SNP) is more common in the European population in which AMD is also more prevalent. Conclusions In the RPE, OTX2 activates the human TYR gene promoter by direct DNA binding and by interaction with MITF. Such synergistic interaction highlights the role of OTX2 as a potential coregulator of numerous MITF target genes in the eye. Genetic differences in OTX2 binding sites affect tyrosinase regulation. Collectively, these findings emphasize the role of OTX2 in regulating the human TYR gene, with implications for inter-individual differences in melanin synthesis, retinal development, and function as well as susceptibility to retinal degeneration associated with aging.
Electroporation-mediated gene transfer of the Na+,K+ -ATPase rescues endotoxin-induced lung injury.

RATIONALE Acute lung injury and acute respiratory distress syndrome are common clinical syndromes resulting largely from the accumulation of and inability to clear pulmonary edema, due to injury to the alveolar epithelium. Gene therapy may represent an important alternative for the treatment and prevention of these diseases by restoring alveolar epithelial function. We have recently developed an electroporation strategy to transfer genes to the lungs of mice, with high efficiency and low inflammation. OBJECTIVES We asked whether electroporation-mediated transfer of genes encoding subunits of the Na+,K+ -ATPase could protect from LPS-induced lung injury or be used to treat already injured lungs by up-regulating mechanisms of pulmonary edema clearance. METHODS Plasmids were delivered to the lungs of mice using transthoracic electroporation. Lung injury was induced by intratracheal administration of LPS (4 mg/kg body weight). Biochemical, cellular, and physiologic measurements were taken to assess gene transfer and lung injury. MEASUREMENTS AND MAIN RESULTS Improvements in wet-to-dry ratios, pulmonary effusions, bronchoalveolar lavage protein levels and cellularity, alveolar fluid clearance, and respiratory mechanics were seen after delivery of plasmids expressing Na+,K+ -ATPase subunits, but not control plasmids, in LPS-injured lungs. Delivery of plasmids expressing Na+,K+ -ATPase subunits both protected from subsequent lung injury and partially reversed existing lung injury by these measures. CONCLUSIONS These results demonstrate that electroporation can be used effectively in healthy and injured lungs to facilitate gene delivery and expression. To our knowledge, this is the first successful use of gene delivery to treat existing lung injury, and may have future clinical potential.
BER Analysis Using Log-Map Decoding Algorithm for Turbo Codes Channel

Turbo codes are a new class of forward error correcting codes that have proved to give a performance close to the channel capacity as proposed by C. Shannon. A turbo code encoder is formed by the parallel concatenation of two identical recursive convolutional encoders separated by an interleaver. The turbo code decoder utilizes two cascaded decoding blocks where each block in turn shares a priori information produced by the other. The decoding scheme has the benefit to work iteratively such that the overall performance can be improved. In this paper, a performance analysis of turbo codes is carried out. Log maximum a posteriori probability (Log-MAP) algorithm is used in the performance analysis. The effect of using different decoding schemes is studied on both punctured and unpunctured codes. Simulations are carried out with the help of MATLAB tools.
Application of Open-Source Enterprise Information System Modules: An Empirical Study.

by Sang-Heui Lee A DISSERTATION Presented to the Faculty of The Graduate College at the University of Nebraska In Partial Fulfillment of Requirements For the Degree of Doctor of Philosophy Major: Interdepartmental Area of Business (Management) Under the Supervision of Professor Sang M. Lee Lincoln, Nebraska July 2010
TrES-3: A Nearby, Massive, Transiting Hot Jupiter in a 31 Hour Orbit

We describe the discovery of a massive transiting hot Jupiter with a very short orbital period (1.30619 days), which we name TrES-3. From spectroscopy of the host star GSC 03089-00929, we measure Teff = 5720 ± 150 K, log g = 4.6 ± 0.3, and v sin i < 2 km s-1 and derive a stellar mass of 0.90 ± 0.15 M☉. We estimate a planetary mass of 1.92 ± 0.23 MJup, based on the sinusoidal variation of our high-precision radial velocity measurements. This variation has a period and phase consistent with our transit photometry. Our spectra show no evidence of line bisector variations that would indicate a blended eclipsing binary star. From detailed modeling of our B and z photometry of the 2.5% deep transits, we determine a stellar radius 0.802 ± 0.046 R☉ and a planetary radius 1.295 ± 0.081 RJup. TrES-3 has one of the shortest orbital periods of the known transiting exoplanets, facilitating studies of orbital decay and mass loss due to evaporation, and making it an excellent target for future studies of infrared emission and reflected starlight.
Resources for health: a primary-care-based diet and physical activity intervention targeting urban Latinos with multiple chronic conditions.

OBJECTIVE The Resources for Health trial evaluates a social-ecologically based lifestyle (physical activity and diet) intervention targeting low-income, largely Spanish-speaking patients with multiple chronic conditions. DESIGN A randomized controlled trial was conducted with 200 patients recruited from an urban community health center and assigned to intervention and usual care conditions. Intervention involved 2 face-to-face, self-management support and community linkage sessions with a health educator, 3 follow-up phone calls, and 3 tailored newsletters. MAIN OUTCOME MEASURES Primary outcomes measured at 6-months were changes in dietary behavior and physical activity. Changes in multilevel support for healthy living were evaluated as a secondary outcome. RESULTS After adjustment for age, sex, language, and number of chronic conditions, significant intervention effects were observed for dietary behavior and multilevel support for healthy lifestyles but not for physical activity. CONCLUSION The Resources for Health intervention provides an effective and practical model for improving health behavior among low-income, Spanish-speaking patients with multiple chronic conditions.
Your wish is my command! The influence of symbolic modelling on preschool children’s delay of gratification

The ability of children to delay gratification is correlated with a range of positive outcomes in adulthood, showing the potential impact of helping young children increase their competence in this area. This study investigated the influence of symbolic models on the self-control of 3-year old children. Eighty-three children were randomly assigned to one of three modelling conditions: personal storytelling, impersonal storytelling, and control. Children were tested on the delay-of-gratification maintenance paradigm both before and after being exposed to a symbolic model or control condition. Repeated measures ANOVA revealed no significant differences between the two storytelling groups and the control group, indicating that the symbolic models did not influence children’s ability to delay gratification. A serendipitous finding showed a positive relationship between the ability of children to wait and their production and accurate use of temporal terms, which was more pronounced in girls than boys. This finding may be an indication that a higher temporal vocabulary is linked to a continuous representation of the self in time, facilitating a child’s representation of the future-self receiving a larger reward than what the present-self could receive.
Optimizing Overlapped Memory Accesses in User-directed Vectorization

Current processors incorporate wide and powerful vector units whose optimal exploitation is crucial to reach peak performance. However, present autovectorizing compilers fall short of that goal. Exploiting some vector instructions requires aggressive approaches that are not affordable in production compilers. Thus, advanced programmers pursuing the best performance from their applications are compelled to manually vectorize them using low-level SIMD intrinsics. We propose a user-directed code optimization that targets overlapped vector loads, i.e., vector loads that read scalar elements redundantly from memory. Instead, our optimization loads these elements once and combines them using advanced register-to-register vector instructions.This code is potentially more efficient and it uses advanced vector instructions that compilers do not widely exploit automatically. We also extend the OpenMP* SIMD directives with a new clause called overlap that allows users to easily enable and tune this optimization on demand. We implement our proposal for the Intel® Xeon Phi™ coprocessor. Our evaluation shows up to 29% speed-up over five highly-optimized stencil kernels and workloads from real-world applications. Results also demonstrate how important user hints are to maximize performance.
Stochastic Generation of Discrete-Event Simulation Models

We present a stochastic model generator for creating discrete event simulation models. The size, structure, layout and behavior of the generated model can be parameterized. By using stochastic techniques in all sections of the generation process a huge number of different models can be created. These models are to be used to test and validate new methods in automatic model abstraction and simulation visualization. We illustrate thefunctionality of the generator by describing detailed algorithms, which can be used to generate models for common discrete event simulation tools. In the end of the paper we present results of an implementation in the simulation tool d3FACT insight which demonstrates the applicability of the generator.
Instantiation and adaptation of CRISP-DM to Bioinformatics computational processes

Among the many contributions made by information technologies to Bioinformatics, the techniques of intelligent data analysis combined with optimization techniques are the main application field nowadays. Many researches focused on DNA microarray field have proposed different approaches trying to obtain new undiscovered knowledge of diseases such cancer. All these researches can be represented as a standard unique process. Thus, this paper presents an overview of a common biological and computational process of DNA microarray data analysis that include these types of researches, based on the known CRISP-DM model.
The automatic detection of scientific terms in patient information

Despite the legislative efforts to improve the readability of patient information, different surveys have shown that respondents still feel distressed by reading the information, or even consider it as fully incomprehensible. This paper deals with one of the sources of distress: the use of scientific terminology in patient information. In order to assess the scale of the problem, we collected a Dutch-English parallel corpus of European Public Assessment Reports (EPARs) which was annotated by 2 annotators. This corpus was used for evaluating and training an automatic approach to scientific term detection. We investigated the use of a lexicon-based and a learningbased approach which only relies on text-internal clues. Finally, both approaches were combined in an optimized hybrid learning-based term extraction experiment. We show that whereas the lexicon-based approach yields high precision scores on the detection of scientific terms, its coverage remains limited. The learning-based approach on the other hand demonstrates an Fscore of 80% and remains quite robust despite the highly skewed data set.
Evaluating a Collaborative Constraint-based Tutor for UML Class Diagrams

COLLECT-UML is a collaborative constraint-based tutor for teaching object-oriented analysis and design using Unified Modelling Language. It is the first system in the family of constraint-based tutors to represent a higher-level skill such as collaboration using constraints. We present the full evaluation study carried out at the University of Canterbury to assess the effectiveness of the system in teaching UML class diagrams and good collaboration. The results show that COLLECT-UML is an effective educational tool. In addition to improved problem-solving skills, the participants both acquired declarative knowledge about good collaboration and did collaborate more effectively. The participants have enjoyed working with the system and found it a valuable asset to their learning.
Multiresolution Methods in Face Recognition

Wavelets have been a prominent image analysis tool over the past decade. Face recognition researchers use it for varied reasons – pre-processing, compression and feature extraction. We refer the reader to [1] for a good review on the theory and applications of wavelets in face recognition. In this chapter we will concentrate on some new transforms that have emerged from the limitations in wavelets. First, we will outline the limitations of wavelets and show how the new image analysis tools overcome them. Next, we review some of the existing work in face recognition that has benefited from using these tools. Finally, we show how these new tools fit into the larger, newly developing arena of signal processing known as Compressive Sampling or Compressed Sensing (CS). We outline how CS can be used for face recognition which certainly will be a new direction in the field of face recognition.