Miracle-dz/UniFAR-FTUs huggingface dataset:
Minimal ensembles of side chain conformers for modeling protein–protein interactions

The goal of this article is to reduce the complexity of the side chain search within docking problems. We apply six methods of generating side chain conformers to unbound protein structures and determine their ability of obtaining the bound conformation in small ensembles of conformers. Methods are evaluated in terms of the positions of side chain end groups. Results for 68 protein complexes yield two important observations. First, the end‐group positions change less than 1 Å on association for over 60% of interface side chains. Thus, the unbound protein structure carries substantial information about the side chains in the bound state, and the inclusion of the unbound conformation into the ensemble of conformers is very beneficial. Second, considering each surface side chain separately in its protein environment, small ensembles of low‐energy states include the bound conformation for a large fraction of side chains. In particular, the ensemble consisting of the unbound conformation and the two highest probability predicted conformers includes the bound conformer with an accuracy of 1 Å for 78% of interface side chains. As more than 60% of the interface side chains have only one conformer and many others only a few, these ensembles of low‐energy states substantially reduce the complexity of side chain search in docking problems. This approach was already used for finding pockets in protein–protein interfaces that can bind small molecules to potentially disrupt protein–protein interactions. Side‐chain search with the reduced search space will also be incorporated into protein docking algorithms. Proteins 2012. © 2011 Wiley Periodicals, Inc.
Purchasing Power Parity as a Long-Run Relation

Dickey-Fuller and Stock-Watson tests of purchasing power parity (PPP) as a long-run proposition are provided within the cointegration framework proposed by Granger. Since different countries use different weights to construct price indices, the traditional constraint that the coefficients on the price indices should be unity in the log-linear PPP relations is relaxed. The absence of a general PPP relation cannot be rejected. At most, a PPP relation is indicated in five out of fifteen country pairs that are examined. Even if a long-run PPP relation exists, it is not found to be useful in predicting future nominal exchange rates, which is consistent with efficient speculative markets. Copyright 1990 by John Wiley & Sons, Ltd.
Continuous Vagus Nerve Monitoring during Carotid Endarterectomy

Backgrounds: Injury to the vagus nerve or one of its branches during carotid endarterectomy can result in vocal fold paralysis but the exact mechanism of injury responsible for vocal fold paralysis after carotid endarterectomy is unclear. Aims: This study was performed to identify potential predictors of vagus nerve injury and obtain feedback by application of intraoperative continuous vagus nerve monitoring. Materials and Methods: Seventy-four patients undergoing carotid endarterectomy were enrolled. A new vagus nerve electrode was designed for less invasive continuous vagus nerve stimulation and monitoring of the vocal fold electromyogram without disturbing the surgical procedure. The device was rectangular (13 mm × 9 mm), with two small round electrodes set on a flexible silicon plate and tube. The electrode was fully implantable during carotid endarterectomy and was positioned at the most distal site of the vagus nerve by suturing to the connective tissue without nerve dissection. All patients underwent laryngoscopy to assess postoperative vocal fold and pharyngeal wall palsy at one week after carotid endarterectomy. Results: Sudden loss of the vocal fold electromyogram was noted in two patients (during plaque removal and during arterial wall suture in one each). In these two patients, incomplete vocal fold and pharyngeal palsy was confirmed by laryngoscopy. The cause of vagus nerve injury may have been traction at the time of distal internal carotid artery manipulation. The vocal fold electromyogram remained normal during the operation in the other 72 patients. However laryngoscopy revealed postoperative vocal fold and pharyngeal palsy in six patients. These findings suggested that delayed vagus nerve injury can occur after carotid endarterectomy. Conclusion: The continuous vagus nerve monitoring may be worthwhile for elucidating the mechanism of vagus nerve injury related to carotid endarterectomy.
Student Achievement beyond the Classroom: Engaging Families and Communities.

Family and community involvement is consistently recognized as an important factor in cultivating success for all students. Indeed, decades of research have consistently demonstrated that family engagement in a child’s education is strongly associated with positive student outcomes (Harvard Family Research Project, 2010; Desforges & Abouchaar, 2003; Henderson & Mapp, 2002; Au, 1993). Moreover, a recent analysis of Programme for International Student Assessment (PISA) data demonstrated that this is true even across cultures and countries regardless of socio-economic circumstances (Organization for Economic Cooperation and Development [OECD], 2011). In other words, research suggests that whether students are Korean or Portuguese, of high socio-economic status or low, they will see greater academic success if they have adults at home who are engaged in their education (OECD, 2011).
Automatic Categorization of Image Databases Using Web Folksonomies

Traditional image classification techniques are based on the analysis of low-level visual features or on textual information. In this paper, we describe a novel solution which tries to improve image analysis and processing algorithms by incorporating keywords and textual annotation produced by humans in a folksonomy environment, namely Flickr. The obtained experimental results demonstrate that the proposed categorization process achieves quite good performances in terms of efficiency and effectiveness.
An application of stakeholder theory to advance community participation in tourism planning: the case for engaging immigrants as fringe stakeholders

Community participation has long been viewed as an important tenet of tourism planning, and there is general consensus among researchers that engaging all stakeholder groups contributes to tourism sustainability. However, there are gaps in the literature, and challenges in practice, that call for further research. Among these are the dynamics of heterogeneous community groups and that not all community subgroups have equal opportunity to participate in tourism planning. This paper attempts to advance community participation by drawing on progressive approaches to stakeholder theory in the management field and by exploring, for the first time, the engagement of immigrants in tourism planning as fringe stakeholders, representative of present and future community dynamics. Bringing first generation immigrants as an important but less studied segment within the broader host community into focus moves tourism planning toward a more inclusive approach to community engagement, reflecting increased diversity and change in host communities.
Are health care functions stable? An application to the Canadian and US economies

The paper examines the stability of the long-run health care expenditure function for the Canadian and US economies. The use of Hansen, and Gregory and Hansen statistics leads to rejection of the stability of both functions. When the instability problems are solved through the inclusion of some dummy variables, it is found that the estimation of income elasticity significantly diminishes, especially for the Canadian economy, in such a way that one can no longer accept health care spending to be a luxury good in this economy.
Conservation Medicine and a New Agenda for Emerging Diseases

Abstract: The last three decades have seen an alarming number of high‐profile outbreaks of new viruses and other pathogens, many of them emerging from wildlife. Recent outbreaks of SARS, avian influenza, and others highlight emerging zoonotic diseases as one of the key threats to global health. Similar emerging diseases have been reported in wildlife populations, resulting in mass mortalities, population declines, and even extinctions. In this paper, we highlight three examples of emerging pathogens: Nipah and Hendra virus, which emerged in Malaysia and Australia in the 1990s respectively, with recent outbreaks caused by similar viruses in India in 2000 and Bangladesh in 2004; West Nile virus, which emerged in the New World in 1999; and amphibian chytridiomycosis, which has emerged globally as a threat to amphibian populations and a major cause of amphibian population declines. We discuss a new, conservation medicine approach to emerging diseases that integrates veterinary, medical, ecologic, and other sciences in interdisciplinary teams. These teams investigate the causes of emergence, analyze the underlying drivers, and attempt to define common rules governing emergence for human, wildlife, and plant EIDs. The ultimate goal is a risk analysis that allows us to predict future emergence of known and unknown pathogens.
Private Equity and Financial Stability

In the mid-2000s, there was a dramatic increase in acquisitions of UK companies by private equity funds. The leverage on these buyouts, especially the larger ones, was high. The resulting increase in indebtedness makes those companies more susceptible to default, exposing their lenders to potential losses. This risk is compounded by the need for companies to refinance a cluster of buyout debt maturing over the next few years in an environment of much tighter credit conditions. From a macroprudential policy perspective it will be important to monitor the use of debt in acquisitions in future episodes of exuberance. But there is also a potential role for private equity to play in promoting recovery in a downswing, in particular at the current juncture, by restructuring companies in difficulty.
Essays on long memory time series and fractional cointegration

The dissertation considers an indirect approach for the estimation of the cointegrating parameters, in the sense that the estimators are jointly constructed along with estimating other nuisance parameters. This approach was proposed by Robinson (2008) where a bivariate local Whittle estimator was developed to jointly estimate a cointegrating parameter along with the memory parameters and the phase parameters (discussed in chapter 2). The main contributions of this dissertation is to establish, similar to Robinson (2008), a joint estimation of the memory, cointegrating and phase parameters in stationary and nonstationary fractionally cointegrated models in a multivariate framework. In order to accomplish such task, a general shape of the spectral density matrix, first noted in Davidson and Hashimzade (2008), is utilised to cover multivariate jointly dependent stationary long memory time series allowing more than one cointegrating relation (discussed in chapter 3). Consequently, the notion of the extended discrete Fourier transform is adopted based on the work of Phillips (1999) to allow for the multivariate estimation to cover the non stationary region (explained in chapter 4). Overall, the estimation methods adopted in this dissertation follows the semiparametric approach, in that the spectral density is only specified in a neighbourhood of zero frequency. The dissertation is organised in four self-contained chapters that are connected to each other, in additional to this introductory chapter: • Chapter 1 discusses the univariate long memory time series analysis covering different definitions, models and estimation methods. Consequently, parametric and semiparametric estimation methods were applied to a univariate series of the daily Egyptian stock returns to examine the presence of long memory properties. The results show strong and significant evidence of long memory in the Egyptian stock market which refutes the hypothesis of market efficiency. • Chapter 2 expands the analysis in the first chapter using a bivariate framework first introduced by Robinson (2008) for long memory time series in stationary system. The bivariate model presents four unknown parameters, including two memory parameters, a phase parameter and a cointegration parameter, which are jointly estimated. The estimation analysis is applied to a bivariate framework includes the US and Canada inflation rates where a linear combination between the US and Canada inflation rates that has a long memory less than the two individual series has been detected. • Chapter 3 introduces a semiparametric local Whittle (LW) estimator for a general multivariate stationary fractional cointegration using a general shape of the spectral density matrix first introduced by Davidson and Hashimzade (2008). The proposed estimator is used to jointly estimate the memory parameters along with the cointegrating and phase parameters. The consistency and asymptotic normality of the proposed estimator is proved. In addition, a Monte Carlo study is conducted to examine the…
The Determinants of NLRB Decision-Making Revisited

The authors develop a model of NLRB decision-making that, unlike the models employed in previous studies, distinguishes between decision-making in more important, complex cases and less important, simpler cases. Using a representative sample of Board decisions over 1957–86, they find that in deciding the minority (20%) of disputes that were particularly important or complex, Board members were influenced by their personal preferences and those of Presidents who appointed them—a finding consistent with the results of previous studies. In the remaining cases (about 80%), however, Board members were influenced in their decisions by little more than the recommendations of regional offices and administrative law judges. Another finding that substantially modifies the conclusions of earlier studies is that Board members appear to have been highly influenced by their accountability to the public when deciding more important, complex cases.
Generation and characterization of Col10a1‐mcherry reporter mice

We report here on the generation of a new fluorescent protein reporter transgenic mouse line, Col10a1‐mCherry, which can be used as a tool to study chondrocyte biology and pathology. Collagen, Type X, alpha 1 (Col10a1) is highly expressed in hypertrophic chondrocytes and commonly used as a gene marker for this cell population. The Col10a1‐mCherry reporter line was generated using a bacterial recombination strategy with the mouse BAC clone RP23‐192A7. To aid in the characterization of this animal model, we intercrossed Col10a1‐mCherry mice with Collagen, Type II, alpha 1 (Col2a1) enhanced cyan fluorescent protein (ECFP) reporter mice and characterized the expression of both chondrocyte reporters during embryonic skeletal development from days E10.5 to E17.5. Additionally, at postnatal day 0, Col10a1‐mCherry reporter expression was compared to endogenous Col10a1 mRNA expression in long bones and revealed that mCherry fluorescence extended past the Col10a1 expression domain. However, in situ hybridization for mCherry was consistent with the zone of Col10a1 mRNA expression, indicating that the persistent detection of mCherry fluorescence was a result of the long protein half life of mCherry in conjunction with a very rapid phase of skeletal growth and not due to aberrant transcriptional regulation. Taking advantage of the continued fluorescence of hypertrophic chondrocytes at the chondro‐osseus junction, we intercrossed Col10a1‐mCherry mice with two different Collagen, Type 1, alpha 1, (Col1a1) osteoblast reporter mice, pOBCol3.6‐Topaz and pOBCol2.3‐Emerald to investigate the possibility that hypertrophic chondrocytes transdifferentiate into osteoblasts. Evaluation of long bones at birth suggests that residual hypertrophic chondrocytes and osteoblasts in the trabecular zone exist as two completely distinct cell populations. genesis 49:410–418, 2011. © 2011 Wiley–Liss, Inc.
Evaluation of Novelty Complexity in Human-Machine Systems : Application to Cockpit Certification

This paper presents an approach to analyzing user-perceived complexity of new artifacts in interactive systems, or novelty complexity for short. The original goal of this research effort was to define user-perceived complexity criteria and related methods that would enable a human-centered design team to better anticipate the impact of novelty complexity on efficiency, safety and comfort. People perceive complexity as they are acting or need to act in their environment, especially when this environment changes. A major distinction is made between technologycentered internal complexity, and user-perceived complexity. They are analyzed along a maturity axis. A number of complexity-related concepts have been elicited from experts using appropriate knowledge acquisition methods. Results were synthesized into empirical criteria and methods for novelty complexity analysis useful during the whole life-cycle of a design process. A discussion is started on human-centered design based with respect to complexity and maturity issues.
Electricity Consumption-Economic Growth Nexus: The Ghanaian Case

Research into the electricity-economic growth nexus has important implications for energy conservation measures and environmental policy. However, results from the energy-economic growth nexus have been mixed in the literature on Ghana. This posses serious problems for the country’s energy policy. Much research is thus, required to establish the direction of causality between energy and economic growth. Nonetheless, less evidence is available for Ghana. It is against this background that this study seeks to investigate the direction of causality between a type of energy, electricity, and economic growth to add to the existing argument in the literature. The Toda and Yomamoto Granger Causality Test was used to carry out the test of causality between electricity consumption and economic growth from 1971 to 2008. The results obtained herein revealed that there exists a unidirectional causality running from economic growth to electricity consumption. Thus, data on Ghana supports the Growth-led-Energy Hypothesis. The results imply that electricity conservation measures are a viable option for Ghana. Keywords : Ghana; Real GDP per capita; Electricity consumption; Toda and Yomamoto; Granger Causality Test; Bounds cointegration JEL Classifications: Q400; Q430
Reordering the French election calendar: Forecasting the consequences for 2002

French politicians sometimes change election rules for political advantage. In the Spring of 2001, the ruling Socialists pushed through the inversion of the 2002 election calendar despite stiff opposition. What were the consequences of scheduling the presidential election before the legislature elections? Employing new techniques for French election forecasting, we show that the inversion brought great vote gains to the Socialist-led coalition in both the legislative and presidential arenas. One advantage of this forecasting methodology is that it allows counterfactual comparisons in advance of the actual election contest. Comparing the scenarios ‘inversion’ versus ‘no inversion’, the Socialist leadership appeared highly strategic and successful.
Trade Credit and Informational Asymmetry

Commonly used trade credit terms implicitly define a high interest rate that operates as an efficient screening device where information about buyer default risk is asymmetrically held. By offering trade credit, a seller can identify prospective defaults more quickl y than if financial institutions were the sole providers of short-ter m financing. The information is valuable in cases where a seller has made nonsalvageable investments in buyers since it enables the seller to take actions to protect such investments. Copyright 1987 by American Finance Association.
Direct detection of the magnetic fields of neuronal impulses using MRI

The neuronal (ionic) current caused by nerve firing induces subtle and transient magnetic flux density changes that potentially modulate the MR signal over successive gradient echo planar image frames. Frequency spectra derived from Fourier transformation of experimental data down these time frames show evidence of a strobe stimulus localized to regions containing the optic nerve and visual cortex, which suggests that direct detection of the magnetic fields emanating from these regions has been achieved.
Hydrolytic degradation of composites of poly(L-lactide-co-ɛ-caprolactone) 70/30 and β-tricalcium phosphate

There is an increasing need for synthetic bone substitute materials that decrease the need for allografts and autografts. In this study, composites of β-tricalcium phosphate and a biodegradable poly(L-lactide-co-ɛ-caprolactone) were manufactured using extrusion to form biodegradable composites with high β-tricalcium phosphate contents for osteoconductivity. The hydrolytic degradation of the composites containing 0, 10, 20, 35 and 50% of β-tricalcium phosphate was studied in vitro for 52 weeks. During the study, it was observed that β-tricalcium phosphate did not have an effect on the degradation rate of the polymer matrix. However, the crystallinity of the materials increased throughout the test series and changes in glass transition temperatures were also observed as the comonomer ratio of the polymer matrix changed as the degradation proceeded. The results show that the materials have desirable degradation properties and, thus, possess great potential as bioabsorbable and osteoconductive bone filling materials.
The Resurgence of Regional Economies, Ten Years Later

Since the early 1980s, social scientists have increas ingly focused upon the significance of the region to the organization of economic life. This article considers three main lines of analysis which have emerged. These concentrate respectively on insti tutions, industrial organization and transactions, and technological change and learning. Each has made strong claims about the role of the region. I argue here, however, that none has yet developed a wholly convincing explanation for the resurgence of regional economies. To do this it is necessary to understand the region as a locus of untraded interdependencies. This has implications for how we think about regional and industrial policies. I illustrate these points with some remarks on regional policies in contemporary Europe.