Miracle-dz/UniFAR-FTUs huggingface dataset:
Size-Independent Quantification of Ligand Binding Site Depth in Receptor Proteins

We have developed a web server that implements two complementary methods to quantify the depth of ligand binding site (LBS) in protein-ligand complexes: the "secant plane" (SP) and "tangent sphere" (TS) methods. The protein molecular centroid (global centroid, GC), and the LBS centroid (local centroid, LC) are first determined. The SP is the plane passing through the LC and normal to the line passing through the LC and the GC. The "exterior side" of the SP is the side opposite GC. The TS is the sphere with center at GC and tangent to the SP at LC. The percentage of protein atoms inside the TS (TS index) and on the exterior side of the SP (SP index), are complementary measures of LBS depth. The SPi is directly proportional to LBS depth while the TSi is inversely proportional. We tested the two methods using a test set of 67 well-characterized protein-ligand structures (Laskowski, et al. 1996), as well as that of an artificial protein in the form of a grid of points in the overall shape of a sphere and in which LBS of any depth can be specified. Results from both the SP and TS methods agree well with reported data (ibid.), and results from the artificial case confirm that both methods are suitable measures of LBS depth. The web server may be used in two modes. In the "ligand mode", user inputs the protein PDB coordinates as well as those of the ligand. The "LBS mode" is the same as the former, except that the ligand coordinates are assumed to be unavailable; hence the user inputs what s/he believes to be the coordinates of the LBS amino acid residues. In both cases, the web server outputs the SP and TS indices. LBS depth is usually directly related to the amount of conformational change a protein undergoes upon ligand binding - ability to quantify it could allows meaningful comparison of protein flexibility and dynamics. The URL of our web server will be announced publicly in due course.
Use of portfolios to correct alternative conceptions and enhance learning

Forty first-year primary school student teachers at a Teacher Training College in Masvingo Province, Zimbabwe, participated in an action research study, employing the science student portfolio, during February to July, 2008 . They used the portfolio to record their prior knowledge about the lesson topic, new information learnt during the lesson, and how the new information related to their prior knowledge. Comments on lessons, monthly tests and assignment scores, reflections and a page-long conclusion were also recorded in the portfolio. The monthly test scores improved as the study progressed. Interviews revealed that alternative conceptions emanated from teachers, peers, textbooks, and the failure of students to understand teachers’ explanations. Students’ and administration’s comments revealed stakeholders’ satisfaction with the portfolio’s effectiveness.
Effectiveness of graduate programs in administrative and instructional leadership

Purpose – The purpose of this paper is twofold: to assess the effectiveness of the school building and school district leadership programs within the School of Education at a large private university and to find areas for improvement in these programs. Design/methodology/approach – This study utilized a qualitative grounded theory research strategy using a case study approach of two campuses of the university. Each case study utilized the same data collection methods and data analysis procedures in order to increase validity. Findings – The key findings revealed that the graduates emphasized the importance of professional support via a cohort structure, a sound program philosophy, and a comprehensive and coherent curriculum. Recruitment and administrative internships were two effectiveness criteria not emphasized by the participants. Thus, the findings suggest the program could be enhanced by the creation of leadership portfolios and quality administrative internships. These findings are also consistent w.
Dependence modelling in multivariate claims run-off triangles

Abstract A central issue in claims reserving is the modelling of appropriate dependence structures. Most classical models cannot cope with this task. We define a multivariate log-normal model that allows to model both, dependence between different sub-portfolios and dependence within sub-portfolios such as claims inflation. In this model we derive closed form solutions for claims reserves and the corresponding prediction uncertainty.
Employee reactions to gainsharing under seniority pay systems: The mediating effect of distributive, procedural, and interactional justice

This study examines the effects of gainsharing under seniority-based pay systems on employee attitudes in Korea. It is hypothesized that gainsharing, which emphasizes performance, employee participation, and cooperation enhances employee perceptions of distributive, procedural, and interactional justice, and that this, in turn, produces positive employee attitudes. The participants were a sample of individuals from five firms that combined seniority-based pay and gainsharing incentives and five comparable firms that used only seniority-based pay. The results supported the partial mediation model whereby distributive and interactional justice partially mediated the effects of gainsharing on employee attitudes, but procedural justice did not. The practical implications of this international compensation research include careful consideration of the integration of gainsharing with the total rewards mix in an organization. © 2008 Wiley Periodicals, Inc.
A Crystalline Singlet Phosphinonitrene: A Nitrogen Atom–Transfer Agent

N on P Nitrogen atoms form strong, relatively unreactive triple bonds with themselves (in N2) and with carbon (in cyanide and nitriles). In contrast, binding to transition metals often leaves an otherwise naked nitrogen center more prone to reactivity. Dielmann et al. (p. 1526) prepared a compound with nitrogen bound to divalent phosphorus, which acted more like a metal than a light element. Although the compound, formally a nitrene, was sufficiently stable to isolate at room temperature and characterize by x-ray diffraction, it transferred the nitrogen efficiently to unsaturated carbon compounds. A phosphorus fragment supports an otherwise uncoordinated nitrogen atom in a stable motif previously seen only with metals. A variety of transition metal–nitrido complexes (metallonitrenes) have been isolated and studied in the context of modeling intermediates in biological nitrogen fixation by the nitrogenase enzymes and the industrial Haber-Bosch hydrogenation of nitrogen gas into ammonia. In contrast, nonmetallic nitrenes have so far only been spectroscopically observed at low temperatures, despite their intermediacy in a range of organic reactions. Here, we report the synthesis of a bis(imidazolidin-2-iminato)phosphinonitrene, which is stable at room temperature in solution and can even be isolated in the solid state. The bonding between phosphorus and nitrogen is analogous to that observed for metallonitrenes. We also show that this nitrido phosphorus derivative can be used to transfer a nitrogen atom to organic fragments, a difficult task for transition metal–nitrido complexes.
Customer Portfolio Development: Modeling Destination Adopters, Inactives, and Rejecters

This study identifies factors associated with and discriminating among destination adopters, inactives, and rejecters. The setting is the state of New Mexico. The empirical findings are based on a sample of more than 900 out-of-state residents. The approach demonstrates how destination image, destination experience, and demographic character istics combine to influence segment membership. Moreover, the results also indicate that adopters and inactives can be separated by their image of the destination and by demo graphic characteristics. Managerial implications are outlined.
Seeds of Reform: Lessons from Vietnam about Informality and Institutional Change

Ordinary North Korean citizens have been coping with economic hardship by eking out livelihoods for themselves. Grassroots markets and local petty economies have become commonplace. A point of conjecture amongst scholars and policymakers is whether these developments may be the start of significant economic system change towards a market economy. This article reviews lessons learned from the transition economies about the informal and social processes required to effectively realize major economic transitions in order to discuss the preliminary evidence we have about North Korea's current informal civilian economic activity. Applying a social cognition theory of institutional change focuses our attention onto the discretionary behavior of local government, the social structure and networks that form firms and exemplars, and the social trust needed to move to new economic paradigms. It also discusses what the operations of hwa-gyo entrepreneurs, ethnic Chinese living in North Korea, pose to the existing state of the literature.
Preoperative diagnosis of primary aldosteronism, including a comparison of operative findings and preoperative tumor localization by adrenal phlebography.

The combination of aldosterone overproduction, subnormal plasma renin activity, and normal urinary 17-hydroxycorticosteroids is diagnostic of primary aldosteronism, whether hypokalemia is present or absent. Congenital aldosteronism may be a rare exception. Of 68 surgically proven cases these diagnostic criteria were fully satisfied in 64, and almost so in four. In the last 19 patients whose diagnosis was clear by these criteria, adrenal phlebography was added for tumor localization. To date, 13 patients have undergone surgery and all had tumors (12 solitary). Phlebography visualized the tumor in nine of 12 tumorous glands successfully injected. Of six patients awaiting surgery, four manifest phlebographic evidence of tumor. Adrenal phlebography is important for tumor localization and for further research on minimal diagnostic criteria in primary aldosteronism.
Mucosal remodeling in long‐standing ulcerative colitis with colorectal neoplasia: Significant alterations of NCAM+ or α‐SMA+ subepithelial myofibroblasts and interstitial cells

Evidence has been provided in ulcerative colitis (UC) that early genomic instability of both epithelial and stromal cells is important for colorectal tumorigenesis, as well as remodeling and morphological alterations of mucosal crypts. To clarify roles of stromal cells in tumor development in UC, the present study focused on heterogeneous phenotypes of subepithelial myofibroblasts and interstitial cells, in association with mucosal remodeling. To clarify the relationship of alterations to tumorigenesis, mucosa of resected rectae from patients with UC (n= 49) and sporadic cancer (n= 10) were analyzed on immunohistochemistry and also on immunoelectron microscopy. Heterogeneous phenotypes of neural cell adhesion molecule (NCAM)+ and/or α‐smooth muscle actin (α‐SMA)+ subepithelial myofibroblasts and interstitial cells were demonstrated, corresponding to colonic stellate cells. Decrease of NCAM+ subepithelial myofibroblasts and interstitial cells, and increase of α‐SMA+ interstitial cells were significant in UC with neoplasia as compared to without neoplasia. α‐SMA+ muscularis mucosae was significantly more thickened in tumor cases. Deposits of Masson's trichrome+ and type III and I collagen in the muscularis mucosae and lamina propria appeared to increase in relation to the numbers of α‐SMA+ interstitial cells. Mucosal remodeling with alterations of NCAM+ or α‐SMA+ subepithelial and interstitial cells may play a critical role in UC‐associated tumorigenesis.
Polyclonal Adaptive Regulatory CD4 Cells That Can Reverse Type I Diabetes Become Oligoclonal Long-Term Protective Memory Cells1

Type 1 diabetes is a CD4 cell-dependent disease that results from destruction of insulin-producing β cells in pancreatic islets. An ideal therapy would reverse diabetes shortly after onset when islet function in not yet fully ablated, and also prevent re-emergence of disease through the generation of memory cells that control the autoimmune response. In this study, we show that adaptive/induced polyclonal regulatory (TR) cells, which contain islet-reactive cells, fulfill these criteria in the NOD mouse model. CD4 cells induced to express FoxP3, IL-10, and TGF-β1 in response to TCR signaling and TGF-β1 can reverse diabetes with clinical restoration of prediabetic serum levels of IL-10. Unlike naturally occurring TR cells, these adaptive TR cells persist indefinitely (>1 year) as FoxP3+, CD25− memory cells that self-renew. Establishment of memory is accompanied by narrowing of the T cell repertoire to usage of a single TCR β-chain, Vβ11, implying selection by Ag. With islet-specific adaptive TR cells, we show that memory is functionally stable and transferable. Therefore, adaptive TR cells, which can be readily generated from normal CD4 populations and become focused by Ag with induction of memory, may provide a treatment and a vaccine for the long-term cure of diabetes making them attractive as immunotherapeutic agents.
Myocardial structural protein expression in umbilical cord blood mesenchymal stem cells after myogenic induction

To assess the effects of three methods of inducing myogenic cells differentiation, umbilical blood mesenchymal stem cells (UCMSCs) from nearly full‐term pregnancy mongrel dogs were purified and cultured. Fourth‐passage UCMSCs were used to detect surface antigens, including CD11a, CD11b, CD29, CD34 and CD71. The cells were induced by 5‐azacytidine (5‐aza), myocardial lysates and myocardial induced fluid. Positive expression of Nkx2.5, α‐actin, desmin, β‐MHC and troponin‐I (TN I) were detected after 3 weeks. The immunohistochemical results were CD11a (−), CD11b (−), CD34 (−), CD29 (+) and CD71 (+). Nkx2.5 was detected in 5‐aza group, myocardial lysates group and myocardial induced fluid group. Semi‐quantitative analysis showed Nkx2.5 expression significantly higher in myocardial lysates group than in the 5‐aza group or myocardial‐induced fluid group (P < 0.05), but there was no significant difference between the 5‐aza and myocardial‐induced fluid groups for Nkx2.5 expression (P > 0.05). MSCs did not express myocardial structural proteins before differentiation, but α‐actin, desmin, β‐MHC and troponin‐I were present after differentiation. The positive expression of four proteins differed with the differentiation conditions. The UCMSCs can be differentiated into myogenic cells by three methods, but the degrees of differentiation are inconsistent. Our results show that the effects of 5‐aza and myocardial lysates are better than that of myocardial induced fluid.
Kidney transplant classification with gene expression profiles using L1 feature selection ensemble classifier based on data clustering

Gene expression profiles can be extracted from DNA in order to obtain relevant information related to kidney transplant. Successful kidney transplant from donor to patient depends on the fitness of both kidneys, so more and more study should be conducted particularly in kidney transplant classification. The common problem of kidney transplant classification is large amount of genes data from various samples. In this research, we demonstrate L1 Feature Selection Ensemble Classifier based on Data Clustering to select informative genes in order to classify gene expression profiles. After classification on data clustering, ensemble classifier produces 97% overall accuracy with precision, recall, F-Test and Kappa Coefficient reaches 95.7%, 91.3%, 93.5%, 90.3% respectively.
Control Premiums, Minority Discounts, and Optimal Judicial Valuation*

This article characterizes controlling and minority share prices and optimal appraisal remedy valuation rules in a rational expectations equilibrium. The model identifies a set of optimal judicial valuation policies that would motivate shareholders to make optimal investment and freeze‐out choices and identifies consequences of judicial valuation error. The model suggests that the share appraisal rule, under which minority shares are assessed a minority discount in freeze‐out appraisals, would be more optimal than Delaware’s pro rata doctrine, which forbids discounting of minority shares. In accordance with the share appraisal rule and in contradiction with their own pro rata doctrine, Delaware courts frequently allow implicit discounts to minority shares in freeze‐out appraisals. In summary, the model articulates why courts should not equate minority share value with market price. Consistent with this implication, Delaware courts have always uniformly rejected the notion that market price should be the sole determinant of appraisal value.
VALUE FOR MONEY IN PFI PROPOSALS: A COMMENTARY ON THE UK TREASURY GUIDELINES FOR PUBLIC SECTOR COMPARATORS

The Private Finance Initiative (PFI), introduced to Britain in 1992, has become a major means of procuring public sector infrastructure. It involves long-term contracts whereby private sector suppliers construct and own capital assets and provide services for which they are paid on the basis of availability or use. This paper focuses on the early stages of a PFI procurement, the decision to use the PFI rather than any other form of procurement. In 2004 and 2006, the UK Treasury issued new Guidance as to how this should be done. There are two stages to this Guidance: qualitative and quantitative assessments. This paper comments on some of the key issues in the quantitative assessments: the treatment of risk, of residual and life-time costs, of tax, of rates of return and of the appropriate use of discounted flow techniques when finance is a constraint for an investing agency.
Taking nonprofits at their word: The role of conflict over mission in organizational change and response to environmental pressures

Central to any nonprofit is a mission; a defining purpose and set of values that provide its exempt purpose, differentiate it and motivate action by the organization and others on its behalf. Even the most formal and established mission is subject to redefinition, interpretation and different ideas over achieving it. This dissertation addresses the question of what role these interpretations of mission play in the processes by which nonprofits change, not just mission but also leadership, strategy and structure. Two distinct theoretical models are examined for fit with empirical results: (1) change processes as a response to external pressure moderated by organizational characteristics, from organization theory and nonprofit management research, and (2) change processes as internal contests over ideas, adapted from global and national level advocacy and policy process theories. Mixed methods are used to address this research question and evaluate the two models. Logistic regression of panel data on 152 internationally active nonprofits over 14 years is used to identify factors correlated with various changes. Through process tracing, narratives of change for a series of four case studies on similar nonprofits are developed. Comparisons within cases, across the four, between the qualitative and quantitative elements, and with theory are used to explore the fit between results and the two models of change. This dissertation proposes and finds evidence of two new concepts: (1) personal mission conceptions, the different interpretations of mission held by individuals or groups within a nonprofit; and (2) dominant mission conceptions, the consensus interpretation at a particular time. Evidence from both forms of analysis provide little support for the organization theory model of change, while the case studies establish support for a potential model of internal
FPGA-based predictive current control of a three-phase active front end rectifier

A predictive current controller for a active front end rectifier is presented in this paper. The predictive algorithm is implemented on a FPGA platform, using a state machine and taking advantages of the parallel processing provided by these devices. The next step model calculations and cost function evaluation required by the predictive controller are executed, for all the possible witching states, in only one clock cycle each one. The optimization procedure is implemented using a three step algorithm based on successive comparisons. Using these approaches, the execution time is drastically improved compared to a sequential predictive algorithm implementation. Simulations results using a current control of an active front end rectifier shows that the algorithm performs a very small execution time. Therefore, it is possible to increase the sampling frequency, improving the harmonic content of the input currents.
Chapter 19: Web-based tools-montage: An astronomical image mosaic engine

Montage (http://montage.ipac.caltech.edu) is a toolkit for aggregating astronomical images into mosaics. Its scientific value derives from three features of its design: • It preserves the calibration and astrometric fidelity of the input images to deliver mosaics that meet user-specified parameters of projection, coordinates, and spatial scale. It supports all projections and coordinate systems in use in astronomy. • It contains independent modules for analyzing the geometry of images on the sky, and for creating and managing mosaics; these modules are powerful tools in their own right and have applicability outside mosaic production, in areas such as data validation. It can take advantage of SIAP services to discover input images that meet the specifications of the sky coverage of the output mosaic. • It is written in ANSI-compliant C, and is portable and scaleable – the same engine runs on desktop, cluster or supercomputer environments running common Unix-based operating systems such as Linux, Solaris, Mac OS X and AIX.
GAN-D: Generative adversarial networks for image deconvolution

We propose new generative adversarial networks for generalized image deconvolution, GAN-D. Most of the previous researches concentrate to specific sub-topic of image deconvolution or generative image deconvolution models with a strong assumption. However, our network restores visual data from distorted images applied multiple dominant degradation problems such as noise, blur, saturation, compression without any prior information. As a generator, we leverage convolutional neural networks based ODCNN [12] which perform generalized image deconvolution with a decent performance, and we use VGGNet [11] to distinguish true/fake of an input image as a discriminator. We devise the loss function of the generator of GAN-D which combines mean square error (MSE) of network output and ground-truth images to traditional adversarial loss of GAN. This loss function and the presence of discriminator reinforces the generator to produce more high-quality images than the original model structured with a single convolutional neural network. During experiments with four datasets, we find that our network has higher PSNR/SSIM values and qualitative results than ODCNN.