Miracle-dz/UniFAR-FTUs huggingface dataset:
Neonatal brain MRI normalization with 3-D cerebral sulci registration

MR image registration (IR) has been used in brain function analysis, voxel-based-morphometry, etc. The conventional IR methods mainly use MR signal based likelihood. However, they cannot prevent miss registration of different gyri because they do not evaluate correspondence of sulci. Also, we cannot directly apply methods for adult brain to neonatal brain because there are large differences in MR signal and sulcal width. This paper focuses on neonatal brain MR images, and introduces a new feature called sulcal-distribution index (SDI), which is calculated from MR signal around the cerebral surface. Next, this paper proposes a non-rigid 3-D IR method based on a flattening with SDI. The likelihood used is mutual information of SDI. The new method evaluates the correspondence of cerebral sulci. And, the method will be effective for neonatal brain in which the accurate delineation of cerebral surface is difficult because the method evaluates the MR signal around the cerebral surface. Results in 3 neonates (modified age; 3-5 weeks) showed that the method registered one brain with the other brain successfully.
Quantitative Analysis of the Proteome Response to the Histone Deacetylase Inhibitor (HDACi) Vorinostat in Niemann-Pick Type C1 disease*

Niemann-Pick type C (NPC) disease is an inherited, progressive neurodegenerative disorder principally caused by mutations in the NPC1 gene. NPC disease is characterized by the accumulation of unesterified cholesterol in the late endosomes (LE) and lysosomes (Ly) (LE/Ly). Vorinostat, a histone deacetylase inhibitor (HDACi), restores cholesterol homeostasis in fibroblasts derived from NPC patients; however, the exact mechanism by which Vorinostat restores cholesterol level is not known yet. In this study, we performed comparative proteomic profiling of the response of NPC1I1061T fibroblasts to Vorinostat. After stringent statistical criteria to filter identified proteins, we observed 202 proteins that are differentially expressed in Vorinostat-treated fibroblasts. These proteins are members of diverse cellular pathways including the endomembrane dependent protein folding-stability-degradation-trafficking axis, energy metabolism, and lipid metabolism. Our study shows that treatment of NPC1I1061T fibroblasts with Vorinostat not only enhances pathways promoting the folding, stabilization and trafficking of NPC1 (I1061T) mutant to the LE/Ly, but alters the expression of lysosomal proteins, specifically the lysosomal acid lipase (LIPA) involved in the LIPA->NPC2->NPC1 based flow of cholesterol from the LE/Ly lumen to the LE/Ly membrane. We posit that the Vorinostat may modulate numerous pathways that operate in an integrated fashion through epigenetic and post-translational modifications reflecting acetylation/deacetylation balance to help manage the defective NPC1 fold, the function of the LE/Ly system and/or additional cholesterol metabolism/distribution pathways, that could globally contribute to improved mitigation of NPC1 disease in the clinic based on as yet uncharacterized principles of cellular metabolism dictating cholesterol homeostasis.
New CT index to quantify arterial obstruction in pulmonary embolism: comparison with angiographic index and echocardiography.

OBJECTIVE This study was designed to define and evaluate a specific index to quantify arterial obstruction with helical CT in acute pulmonary embolism. MATERIALS AND METHODS Fifty-four patients (mean age, 56 years) with proven pulmonary emboli among 158 consecutive patients, who had undergone both CT and pulmonary angiography for clinically suspected pulmonary embolism, were eligible for the study. The CT obstruction index was defined as (n. d) (n, value of the proximal clot site, equal to the number of segmental branches arising distally; d, degree of obstruction scored as partial obstruction [value of 1] or total obstruction [value of 2]). We compared the CT obstruction index with pulmonary arterial obstruction on angiography (assessed by the Miller index), using linear regression, and correlated it with findings on echocardiography. Interobserver variability was determined for both CT and pulmonary angiography indexes. RESULTS The CT obstruction index (29% +/- 17%) and the Miller index (43% +/- 25%) were well correlated (r = 0.867, p < 0.0001) with an excellent concordance between investigators for both the CT index (r = 0.944, p < 0.0001) and the Miller index (r = 0.904, p < 0.0001). A CT obstruction index greater than 40% identified more than 90% of patients with right ventricular dilatation. CONCLUSION The degree of arterial obstruction in pulmonary embolism may be quantified by a specific CT index that appears reproducible and highly correlated to the previously described index with pulmonary angiography. Further evaluations are needed to investigate the usefulness of the CT obstruction index for stratification of patient risk and determining therapeutic options.
Design of a digital phantom population for myocardial perfusion SPECT imaging research

Digital phantoms and Monte Carlo (MC) simulations have become important tools for optimizing and evaluating instrumentation, acquisition and processing methods for myocardial perfusion SPECT (MPS). In this work, we designed a new adult digital phantom population and generated corresponding Tc-99m and Tl-201 projections for use in MPS research. The population is based on the three-dimensional XCAT phantom with organ parameters sampled from the Emory PET Torso Model Database. Phantoms included three variations each in body size, heart size, and subcutaneous adipose tissue level, for a total of 27 phantoms of each gender. The SimSET MC code and angular response functions were used to model interactions in the body and the collimator-detector system, respectively. We divided each phantom into seven organs, each simulated separately, allowing use of post-simulation summing to efficiently model uptake variations. Also, we adapted and used a criterion based on the relative Poisson effective count level to determine the required number of simulated photons for each simulated organ. This technique provided a quantitative estimate of the true noise in the simulated projection data, including residual MC simulation noise. Projections were generated in 1 keV wide energy windows from 48–184 keV assuming perfect energy resolution to permit study of the effects of window width, energy resolution, and crosstalk in the context of dual isotope MPS. We have developed a comprehensive method for efficiently simulating realistic projections for a realistic population of phantoms in the context of MPS imaging. The new phantom population and realistic database of simulated projections will be useful in performing mathematical and human observer studies to evaluate various acquisition and processing methods such as optimizing the energy window width, investigating the effect of energy resolution on image quality and evaluating compensation methods for degrading factors such as crosstalk in the context of single and dual isotope MPS.
Linear auto disturbance rejection controller for vector-controlled PMSM drive system

A high-performance robust controller of permanent-magnet synchronous motor (PMSM) drive with cascade linear auto disturbance rejection controller (LADRC) is proposed. The robust controller combines the simplicity of linear controller and the merit of the auto disturbance rejection controller (ADRC). First, a systematic mathematical model is derived according to the required specifications for the PMSM drive system. Then, for the model, this paper designs the controller that includes three first-order LADRCs. The controller does not rely on the accurate mathematical model of motor. The controller can estimate and compensate the disturbances that include load disturbance and systematic parameters changes by the linear extended state observer (LESO). Simulation results show that compared with conventional PI controller, the proposed approach has strong robustness. In the same load disturbance, the speed fluctuation of the LADRCs accounts for 30% of PI controller.
Change in Efficiency Level in Achieving Human Development: Inter-Temporal Comparison of Indian States

In India, research on human development has received considerable importance from both the academic and policy point of view. However, all the previous studies on human development mainly focused on the equity aspects of development without considering the resource base. Therefore, the current study seeks to analyse the change in the effi ciency level of the states in achieving the various dimensions of human development through Panel Data Envelopment estimation of effi ciency by using the Malmquist index for the periods 1981, 1991, 2001 and 2011. It has been found that the technical effi ciency change is signifi cant but technological change is not at all prominent in achieving human development from 1981 to 2011. This indicates that the states are basically attempting to catch up with the production frontier by changing their input levels rather than through new technological improvements. One of the major fi ndings is that Uttar Pradesh faced a negative factor productivity in the health and education sectors, and in terms of the standard of living, which implies that the levels of outcome are extremely poor and still provide no scope for improvement by using the current level of inputs. This is a cause for serious concern and it must be addressed by increasing input allocation and the effi cient utilization of such inputs. The public sector also needs to be strengthened in such states.
Tissue Inhibitor of Metalloproteinase-3 is Associated with Neuronal Death in Reperfusion Injury

Programmed cell death occurs in ischemia when cell surface death receptors (DRs) are stimulated by death-inducing ligands (DILs). Matrix metalloproteinases are extracellular matrix-degrading enzymes involved in the shedding of DRs and DILs from the cell surface. Tissue inhibitor of metalloproteinase-3 (TIMP-3), which is bound to the extracellular matrix, has been shown to promote apoptosis in cancer cell lines by inhibiting cell surface sheddases. Since apoptosis is an important mechanism of cell death in ischemia, the authors hypothesized that TIMP-3 would be expressed in ischemic neurons that are undergoing programmed cell death. Spontaneously hypertensive rats had a 90-minute middle cerebral artery occlusion with reperfusion. Transcription of TIMP-3 mRNA was measured by quantitative reverse transcription–polymerase chain reaction at 2, 6, 24 and 48 hours after reperfusion. Western blots were used to measure TIMP-3 protein expression. Spatial distribution and production of TIMP-3 was studied by immunohistochemistry at 3, 24, and 48 hours, 5 days, and 3 weeks. DNA fragmentation in cells dying by necrosis and apoptosis was identified with terminal deoxynucleotidyl transferase-mediated 2′-deoxyuridine 5′-triphosphate-biotin nick end labeling (TUNEL). After 2 hours of reperfusion, TIMP-3 mRNA increased significantly in both ischemic and nonischemic hemispheres. Western blot analysis confirmed the identity of the TIMP-3, which appeared to be increased on the ischemic side. After 3 hours of reperfusion, TIMP-3 immunostaining was increased in neurons on the ischemic side, and by 24 hours the majority of the ischemic neurons were TIMP-3–positive. Dual-fluorescence staining for TUNEL and TIMP-3 showed that they were coexpressed in many neurons. The results suggest that ischemic neurons express TIMP-3, which may be inhibiting sheddases. The authors propose that TIMP-3 facilitates cell death in ischemic neurons. Further studies are needed to identify the sheddases inhibited by the TIMP-3, and on the effect of inhibition of matrix metalloproteinases on cell death mechanisms.
Identification of platelet proteins separated by two‐dimensional gel electrophoresis and analyzed by matrix assisted laser desorption/ionization‐time of flight‐mass spectrometry and detection of tyrosine‐phosphorylated proteins

Different search programs were compared to judge their particular efficiency in protein identification. We established a human blood platelet protein map and identified tyrosine‐phosphorylated proteins. The cytosolic fraction of human blood platelets was separated by two‐dimensional polyacrylamide gel electrophoresis (2‐D PAGE) and phosphorylated proteins were detected by Western blotting using anti‐phosphotyrosine antibodies. Visualized protein spots were excisted, digested with trypsin and analyzed by matrix assisted laser desorption/ionization‐time of flight‐mass spectrometry (MALDI‐TOF‐MS). The obtained mass fingerprint data sets have been analyzed using ProFound, MS‐Fit and Mascot. For those protein spots with no significant search results MALDI post source decay (PSD) spectra have been acquired on the same sample. For automatic interpretation of these fragment ion spectra, the SEQUEST and Mascot algorithm were applied. Another approach for the identification of phosphorylated proteins is immunoprecipitation using an anti‐phosphotyrosine antibody. A method for immunoprecipitation of tyrosine‐phosphorylated peptides was optimized.
Cloning of the gene encoding TROP‐2, a cell‐surface glycoprotein expressed by human carcinomas

We have cloned by expression the cDNA encoding Trop‐2, a cell‐surface glycoprotein expressed by most human carcinomas. Formal proof of the identity of the clone is the hybridization to DNA and RNA from genomic TROP2 transfectants. TROP2 is a single‐copy gene in human cells, hybridizes to a single 1.8‐kb mRNA from expressing sources and encodes a 35,709 Da type‐1 transmembrane protein with a single transmembrane domain. TROP2 is essentially identical to GA733‐1. Thus, we have proven that GA733‐1, for which a protein product had not been identified, is a functional gene. TROP2 is also homologous to TROPI/KSA/GA733‐2, confirming the serological similarities between the 2 molecules. The homology between the Trop‐1 and Trop‐2 peptides is clustered in 2 extracytoplasmic domains and in the transmembrane/cytoplasmic region. Twelve cysteines and a potential cytoplasmic tyrosine phosphorylation site are also conserved. Trop‐1 and Trop‐2 are homologous to serum IGF‐11‐binding proteins and appear as signal transducers. Thus, they likely represent novel cell‐surface receptors and may play a role in regulating the growth of carcinoma cells. On the other hand, we have found no evidence for a role of Trop‐2 and Trop‐1 as homophilic adhesion molecules. © 1995 Wiley‐Liss, Inc.
Social Trust: Evaluating Node Influential Capability in Social Networks

Social networking sites are platforms that facilitate large-scale information sharing activities in recent years. Many organizations analyze social networking traffic to gain market insights in order to observe the latest market trends. These analyses also allow organizations to identify key promoters who have strong influences on these social networking platforms to promote their products or services. It is hypothesized that social trust plays an important role in influential propagation, and it is able to increase the rate of success in influencing other social nodes in a social network. This research performs large-scale experimental simulation to study the influential outcome with and without the presence of social trust in the social nodes. strength and the acceptance results obtained from this research. These applications include distance weighted trust and trust value down the lane.
Integrating philosophy of education and the goals of education in education practice at Kenyan high schools

vi KEY TERMS.vii ABBREVIATIONS AND ACRONYMS.viii TABLE OF CONTENTS.xi CHAPTER ONE: INTRODUCTION 1.1 Background of the Study.1 1.2 Motivation for the Study.8 1.3 Formulation of the Problem . 14 1.4 Aims and Objectives of the Research.15 1.4. 1 Aims.16 1.4. 2 Objectives.16 1.5 Contribution of Research.17 1.6 Phenomenology.19 1.7 Research Methods and Design.20 1.7. 1 Research Methods.22 1.7. 1.1 Literature Review.22 1.7. 1.2 Interviews.22 1.7. 2 Research Design.23 1.8 Delimitations and Limitations of the Research.24 1.8. 1 Delimitations of the Research.24 1.8. 2 Limitations of the Research.26 1.9 Explication of Key Concepts.27 1.9. 1 Integrating.27
Communicating evidence-based information on cancer prevention to state-level policy makers.

BACKGROUND Opportunities exist to disseminate evidence-based cancer control strategies to state-level policy makers in both the legislative and executive branches. We explored factors that influence the likelihood that state-level policy makers will find a policy brief understandable, credible, and useful. METHODS A systematic approach was used to develop four types of policy briefs on the topic of mammography screening to reduce breast cancer mortality: data-focused brief with state-level data, data-focused brief with local-level data, story-focused brief with state-level data, and story-focused brief with local-level data. Participants were recruited from three groups of state-level policy makers-legislative staff, legislators, and executive branch administrators- in six states that were randomly chosen after stratifying all 50 states by population size and dominant political party in state legislature. Participants from each of the three policy groups were randomly assigned to receive one of the four types of policy briefs and completed a questionnaire that included a series of Likert scale items. Primary outcomes-whether the brief was understandable, credible, likely to be used, and likely to be shared-were measured by a 5-point Likert scale according to the degree of agreement (1 = strongly disagree, 5 = strongly agree). Data were analyzed with analysis of variance and with classification trees. All statistical tests were two-sided. RESULTS Data on response to the policy briefs (n = 291) were collected from February through December 2009 (overall response rate = 35%). All three policy groups found the briefs to be understandable and credible, with mean ratings that ranged from 4.3 to 4.5. The likelihood of using the brief (the dependent variable) differed statistically significantly by study condition for staffers (P = .041) and for legislators (P = .018). Staffers found the story-focused brief containing state-level data most useful, whereas legislators found the data-focused brief containing state-level data most useful. Exploratory classification trees showed distinctive patterns for brief usefulness across the three policy groups. CONCLUSION Our results suggest that taking a "one-size-fits-all" approach when delivering information to policy makers may be less effective than communicating information based on the type of policy maker.
Single and Multiple Ability Estimation in the SEM Framework: A Noninformative Bayesian Estimation Approach

Latent variable models with many categorical items and multiple latent constructs result in many dimensions of numerical integration, and the traditional frequentist estimation approach, such as maximum likelihood (ML), tends to fail due to model complexity. In such cases, Bayesian estimation with diffuse priors can be used as a viable alternative to ML estimation. This study compares the performance of Bayesian estimation with ML estimation in estimating single or multiple ability factors across 2 types of measurement models in the structural equation modeling framework: a multidimensional item response theory (MIRT) model and a multiple-indicator multiple-cause (MIMIC) model. A Monte Carlo simulation study demonstrates that Bayesian estimation with diffuse priors, under various conditions, produces results quite comparable with ML estimation in the single- and multilevel MIRT and MIMIC models. Additionally, an empirical example utilizing the Multistate Bar Examination is provided to compare the practical utility of the MIRT and MIMIC models. Structural relationships among the ability factors, covariates, and a binary outcome variable are investigated through the single- and multilevel measurement models. The article concludes with a summary of the relative advantages of Bayesian estimation over ML estimation in MIRT and MIMIC models and suggests strategies for implementing these methods.
Gα12 facilitates shortening in human airway smooth muscle by modulating phosphoinositide 3‐kinase‐mediated activation in a RhoA‐dependent manner

PI3K‐dependent activation of Rho kinase (ROCK) is necessary for agonist‐induced human airway smooth muscle cell (HASMC) contraction, and inhibition of PI3K promotes bronchodilation of human small airways. The mechanisms driving agonist‐mediated PI3K/ROCK axis activation, however, remain unclear. Given that G12 family proteins activate ROCK pathways in other cell types, their role in M3 muscarinic acetylcholine receptor‐stimulated PI3K/ROCK activation and contraction was examined.
Adeno-Associated Virus Type 2 Protein Interactions: Formation of Pre-Encapsidation Complexes

ABSTRACT The nonstructural adeno-associated virus type 2 Rep proteins are known to control viral replication and thus provide the single-stranded DNA genomes required for packaging into preformed capsids. In addition, complexes between Rep proteins and capsids have previously been observed in the course of productive infections. Such complexes have been interpreted as genome-linked Rep molecules associated with the capsid upon successful DNA encapsidation. Here we demonstrate via coimmunoprecipitation, cosedimentation, and yeast two-hybrid analyses that the Rep-VP association also occurs in the absence of packageable genomes, suggesting that such complexes could be involved in the preparation of empty capsids for subsequent encapsidation steps. The Rep domain responsible for the observed Rep-VP interactions is situated within amino acids 322 to 482. In the presence of all Rep proteins, Rep52 and, to a lesser extent, Rep78 are most abundantly recovered with capsids, whereas Rep68 and Rep40 vary in association depending on their expression levels. Rep78 and Rep52 are bound to capsids to roughly the same extent as the minor capsid protein VP2. Complexes of Rep78 and Rep52 with capsids differ in their respective detergent stabilities, indicating that they result from different types of interactions. Rep-VP interaction studies suggest that Rep proteins become stably associated with the capsid during the assembly process. Rep-capsid complexes can reach even higher complexity through additional Rep-Rep interactions, which are particularly detergent labile. Coimmunoprecipitation and yeast two-hybrid data demonstrate the interaction of Rep78 with Rep68, of Rep68 with Rep52, and weak interactions of Rep40 with Rep52 and Rep78. We propose that the large complexes arising from these interactions represent intermediates in the DNA packaging pathway.