Miracle-dz/UniFAR-FTUs huggingface dataset:
Combining Unsupervised and Supervised Learning for Discovering Disease Subclasses

Diseases are often umbrella terms for many subcategories of disease. The identification of these subcategories is vital if we are to develop personalised treatments that are better focussed on individual patients. In this short paper, we explore the use of a combination of unsupervised learning to identify potential subclasses, and supervised learning to build models for better predicting a number of different health outcomes for patients that suffer from systemic sclerosis, a rare chronic connective tissue disorder - but one that shares many characteristics with other diseases. We explore a number of different algorithms for constructing models that simultaneously predict health outcomes and identify subcategories.
Effects of income inequality on population health: new evidence from the european community household panel

This study provides new evidence in order to explore the relationship between income inequality and health in the European Union countries using new data from the European Community Household Panel (ECHP). A variety of different specifications were tried using diverse dependent variables such as life expectancy at birth and child mortality. The results show new support to the influence of income inequality on health indicators using aggregate data and panel techniques.
Further Mapping of the Idd 5 . 1 Locus for Autoimmune Diabetes in NOD Mice

The Idd5 locus for autoimmune diabetes in nonobese diabetic (NOD) mice has been mapped to the proximal half of chromosome 1 and appears to include two loci, Idd5.1 and Idd5.2, Idd5.1 being a candidate homolog of the human IDDM12 locus. Using new recombinant congenic lines, we have reduced the Idd5.1 interval to 5 cM at most, between D1Mit279 and D1Mit19 (not included). This interval now excludes the Casp8 and Cflar (Flip) candidate genes. It still retains Cd28 and Ctla4 and also includes Icos (inducible costimulator). The previously reported differential expression of Ctla4, which is induced at a lower level in NOD than in B6-activated T-cells, was found independent of Idd5.1 itself because Ctla4 expression was induced at a low level in T-cells from Idd5.1-congenic mice. The Idd5.1 locus protected against both spontaneous and cyclophosphamide-induced diabetes, but it did not prevent inflammatory infiltration of the islets of Langerhans. Furthermore, diabetogenic precursor spleen cells from prediabetic NOD and Idd5.1-congenic mice were equally capable of transferring diabetes to immunodeficient NOD.scid/scid recipient mice. The Idd5.1 locus might affect a late event of disease development, subsequent to the onset of insulitis and possibly taking place in the islets of Langerhans. Diabetes 50:2874–2878, 2001
Factors Associated with Emergency Department Visits in Asthma Exacerbation

Objectives Despite quality improvement initiatives to prevent asthma-related emergency department (ED) visits, rates have not declined. We sought to determine factors associated with ED visits in an underserved population. Methods We performed a case–control analysis of asthma patients at three ambulatory care centers serving low-income populations. Cases consisted of asthmatic patients aged 18 to 45 years with ≥1 ED visit for an asthma exacerbation between August 1, 2008 and July 31, 2010. Controls were patients with asthma aged 18 to 45 years with ≥1 outpatient visit during the same period but with no asthma-related ED visit. Data were collected by chart review and included demographics, past referral for asthma education or to a pulmonologist, recent tobacco use, influenza vaccination, and asthma medication prescriptions in the year before the index visit. Results Among 244 cases and 475 controls, there were no significant differences in age, sex, or ethnicity. Cases were more likely than controls to have ever been referred for asthma education (odds ratio [OR] 4.09, 95% confidence interval [CI] 2.57–6.50) or to a pulmonologist (OR 2.31, 95% CI 1.15–4.66). In the year before the index visit, cases were more likely than controls to receive other medications in addition to inhaled corticosteroids (ICS; OR 1.74, 95% CI 1.14–2.66) but less likely to receive influenza vaccination (OR 0.49, 95% CI 0.34–0.71), a short-acting &bgr;-agonist (OR 0.43, 95% CI 0.24–0.78), or ICS alone (OR 0.53, 95% CI 0.34–0.84). Conclusions Markers of severe disease were associated with ED visits, as well as a lack of an influenza vaccination and failure to prescribe either ICS or short-acting &bgr;-agonists.
Interest Rate Pass-Through: Empirical Results for the Euro Area

Abstract This paper empirically examines the interest rate pass-through at the euro area level. The focus is on the pass-through of official interest rates, approximated by the overnight interest rate, to longer-term market interest rates, which, in turn, are a proxy for the marginal costs for banks to attract deposits or grant loans, and therefore passed through to retail bank interest rates. Empirical results, on the basis of a (vector) error-correction and vector autoregressive model, suggest that the pass-through of official interest to market interest rates is complete for money market interest rates up to three months, but not for market interest rates with longer maturities. Furthermore, the immediate pass-through of changes in market interest rates to bank deposit and lending rates is found to be at most 50%, whereas the final pass-through is typically found to be close to 100%, in particular for lending rates. Empirical results for a sub-sample starting in January 1999 show qualitatively similar findings and are supportive of a quicker interest rate pass-through since the introduction of the euro. It is shown that the difference between the adjustment speed of bank deposit and lending rates (typically around one versus three months since the common monetary policy) can to a large extent significantly be explained by credit risk considerations.
Enhancing the enzymatic hydrolysis of lignocellulosic biomass by increasing the carboxylic acid content of the associated lignin

To assess the effects that the physical and chemical properties of lignin might have on the enzymatic hydrolysis of pretreated lignocellulosic substrates, protease treated lignin (PTL) and cellulolytic enzyme lignin (CEL) fractions, isolated from steam and organosolv pretreated corn stover, poplar, and lodgepole pine, were prepared and characterized. The adsorption of cellulases to the isolated lignin preparations corresponded to a Langmuir adsorption isotherm. It was apparent that, rather than the physical properties of the isolated lignin, the carboxylic acid functionality of the isolated lignin, as determined by FTIR and NMR spectroscopy, had much more of an influence when lignin was added to typical hydrolysis of pure cellulose (Avicel). An increase in the carboxylic content of the lignin preparation resulted in an increased hydrolysis yield. These results suggested that the carboxylic acids within the lignin partially alleviate non‐productive binding of cellulases to lignin. To try to confirm this possible mechanism, dehydrogenative polymers (DHP) of monolignols were synthesized from coniferyl alcohol (CA) and ferulic acid (FA), and these model compounds were added to a typical enzymatic hydrolysis of Avicel. The DHP from FA, which was enriched in carboxylic acid groups compared with the DHP from CA, adsorbed a lower mount of cellulases and did not decrease hydrolysis yields when compared to the DHP from CA, which decreased the hydrolysis of Avicel by 8.4%. Thus, increasing the carboxylic acid content of the lignin seemed to significantly decrease the non‐productive binding of cellulases and consequently increased the enzymatic hydrolysis of the cellulose. Biotechnol. Bioeng. 2011; 108:538–548. © 2010 Wiley Periodicals, Inc.
A Note on the Comparison of Logit and Discriminant Models of Consumer Credit Behavior

Since the early work of Durand (1941), there has been considerable interest in using quantitative models of consumer credit behavior for credit-granting decisions. Most models are based on the concept of “scoring” by use of weights usually determined as statistically significant coefficients of some linear statistical model, frequently the linear discriminant model. It is the purpose of this note, however, to propose maximum likelihood estimation of the logit model as an alternative, and to compare the two models in a “scoring experiment. ”
CoopTFD: a repository for predicted yeast cooperative transcription factor pairs

In eukaryotic cells, transcriptional regulation of gene expression is usually accomplished by cooperative Transcription Factors (TFs). Therefore, knowing cooperative TFs is helpful for uncovering the mechanisms of transcriptional regulation. In yeast, many cooperative TF pairs have been predicted by various algorithms in the literature. However, until now, there is still no database which collects the predicted yeast cooperative TFs from existing algorithms. This prompts us to construct Cooperative Transcription Factors Database (CoopTFD), which has a comprehensive collection of 2622 predicted cooperative TF pairs (PCTFPs) in yeast from 17 existing algorithms. For each PCTFP, our database also provides five types of validation information: (i) the algorithms which predict this PCTFP, (ii) the publications which experimentally show that this PCTFP has physical or genetic interactions, (iii) the publications which experimentally study the biological roles of both TFs of this PCTFP, (iv) the common Gene Ontology (GO) terms of this PCTFP and (v) the common target genes of this PCTFP. Based on the provided validation information, users can judge the biological plausibility of a PCTFP of interest. We believe that CoopTFD will be a valuable resource for yeast biologists to study the combinatorial regulation of gene expression controlled by cooperative TFs. Database URL: http://cosbi.ee. ncku.edu. tw/CoopTFD/ or http://cosbi2.ee. ncku.edu. tw/CoopTFD/
From Needs to Goals and Representations: Foundations for a Unified Theory of Motivation, Personality, and Development

Drawing on both classic and current approaches, I propose a theory that integrates motivation, personality, and development within one framework, using a common set of principles and mechanisms. The theory begins by specifying basic needs and by suggesting how, as people pursue need-fulfilling goals, they build mental representations of their experiences (beliefs, representations of emotions, and representations of action tendencies). I then show how these needs, goals, and representations can serve as the basis of both motivation and personality, and can help to integrate disparate views of personality. The article builds on this framework to provide a new perspective on development, particularly on the forces that propel development and the roles of nature and nurture. I argue throughout that the focus on representations provides an important entry point for change and growth.
Determinants of Exports in Developing Countries

I. INTRODUCTION According to the orthodox classical economist as well to the modern liberal view trade is equivalent to an engine of economic growth. Exports promotion strategy is often in accordance with the principle of comparative advantage, when a country specialises in a product, which it can produce competitively. The goods become available to the community of the world at cheaper prices. The markets are extended. The internal and external economies are attained. Income and employment levels expand. Consequently process of economic development is facilitated. In a nutshell, putting more emphasis on the promotion of exports would permit the optimal allocation of world resources and, therefore, returns from trade sector depend upon accelerating growth of exports. The proposition of FDI led exports growth is controversial in empirical literature. But the role of domestic investment is believed to be much important for export expansion strategies. In any case the importance of FDI, if any, cannot diminish the role of productive investment from the domestic economy. While private domestic investment can be regarded as a permanent and reliable channel to enhance production capacity, investment in public sector has been considered important, for example in roads, communication and other public goods and services that are essential to stimulate private investment. Furthermore, government has a decisive role through support for research and contract with foreign buyers as well as in facilitating access to credit to both directly and indirectly exporting terms. Funke and Holly (1992) argue that the majority of the previous approaches have emphasised demand factors. Such models have generally been rather unsuccessful in explaining long run trends in export performance.
IDPicker 2.0: Improved protein assembly with high discrimination peptide identification filtering.

Tandem mass spectrometry-based shotgun proteomics has become a widespread technology for analyzing complex protein mixtures. A number of database searching algorithms have been developed to assign peptide sequences to tandem mass spectra. Assembling the peptide identifications to proteins, however, is a challenging issue because many peptides are shared among multiple proteins. IDPicker is an open-source protein assembly tool that derives a minimum protein list from peptide identifications filtered to a specified False Discovery Rate. Here, we update IDPicker to increase confident peptide identifications by combining multiple scores produced by database search tools. By segregating peptide identifications for thresholding using both the precursor charge state and the number of tryptic termini, IDPicker retrieves more peptides for protein assembly. The new version is more robust against false positive proteins, especially in searches using multispecies databases, by requiring additional novel peptides in the parsimony process. IDPicker has been designed for incorporation in many identification workflows by the addition of a graphical user interface and the ability to read identifications from the pepXML format. These advances position IDPicker for high peptide discrimination and reliable protein assembly in large-scale proteomics studies. The source code and binaries for the latest version of IDPicker are available from http://fenchurch.mc. vanderbilt.edu/ .
Modularity in KIBS: The Case of Third-Party Logistics Service Providers

This paper investigates service modularity and inter-organizational coupling in knowledge-intensive business services (KIBS). While KIBS literature traditionally emphasizes tight client–provider interactions with service customization, modularity literature emphasizes inter-organizational decoupling with service standardization. We disentangle this tension by exploring how KIBS firms utilize service modularity and shape their client–provider relationships in terms of information and knowledge sharing. Conducting two in-depth case studies of third-party logistics (TPLs), we show that TPLs extensively rely on service modularity with standard procedures as their constitutive element. We also demonstrate that service modularity and inter-organizational decoupling are aligned for knowledge sharing but not for information sharing, which remains high regardless of the service architecture. Overall, we suggest that modularity in KIBS differs in many aspects from modularity in products and that these differences significantly impact the organizational design consequences of service modularity. Theoretical and managerial implications are drawn.
Effect of anesthesia and thyroid surgery on the plasma level of PBI 131.

MANIPULATION of the thyroid gland during surgery, with the consequent release into the circulation of significant amounts of preformed thyroid hormone, has been suggested as a possible factor in the genesis of postoperative “storm” (1–4). In addition, it has been postulated that a definite correlation exists between the magnitude of this phenomenon and the severity of the postoperative reaction (1, 5). Reports of data obtained prior to the use of radioactive iodide in the assessment of thyroid function are conflicting in regard to changes in serum proteinbound iodine levels under these circumstances (1, 5–9). Measurements of the renal excretion of stable iodide have demonstrated a significant increase immediately following both thyroid (7, 10) and non-thyroid surgery (11, 12). That elevations of protein-bound iodine concentration can occur in response to therapeutic doses of radioiodide (13) and irradiation of the thyroid gland with radium or x-rays (5, 14) seems well documented.
Social outsourcing as a development tool: The impact of outsourcing IT services to women's social enterprises in Kerala

Social outsourcing means the contracting out of goods or services to social enterprises. When used by government, it can be seen as a hybrid of the workfare outsourcing found in wage employment schemes, and the commercial outsourcing of government activities to the private sector. This paper focuses on a social outsourcing initiative operated by the government of Kerala State, India. Part of this outsources information technology (IT) services to dozens of cooperatives of women from below-poverty-line families. Interview and case study research was undertaken to assess the impacts of this initiative on five areas of livelihood assets-financial, human, physical, social and political capital. This scheme has Keralan specificities and research shows that social outsourcing may introduce vulnerabilities and questions of sustainability. Overall, though, this paper suggests that social outsourcing has the potential to deliver developmental benefits to marginalised groups. It is therefore worthy of greater attention from international development agencies and governments in developing countries. Copyright © 2009 John Wiley & Sons, Ltd.
Evaluating Company's Strategic Choices: Strategic Choices Set Model

The crux of strategic management is evidently about doing the right strategic choices. From a large set of different possible choices the top management team must select the one(s) that give competitive advantage for a company. However, many research results show that managers tend to select strategies they are familiar with, regardless of the strategic optimality. We construct and present a Strategic Choices Set model which is able to identify the available and implementable choices for top management. The model is based on well established and empirically validated theories of Upper Echelons, Industry Strategies, and Capital Structure. The ideal strategic choice should fulfill three simultaneous conditions: i) it belongs to the top management’s expertise, ii) it has recognizable and proven value in the industry, and iii) the company has financial resources to implement it. The model is tested in the ICT industry, concentrating on two companies that operate also in smart phone sector, namely Nokia and Apple. The main contributions are the presented model and the pondering of strategic options in ICT industry based on emergence of cloud computing technology.
THE DIVERSION STORY: RESOLVING THE AMBIGUITIES SURROUNDING THE CONCEPT OF DIVERSION RATIO

Carl Shapiro introduced the diversion ratio as an analytical tool in the assessment of mergers with differentiated products, but he did so with a degree of ambiguity as to its precise definition. We show that his diversion ratio between two products (A and B) can be, and has been, interpreted in two distinct ways: first, as the fraction of customers leaving Product A that switch to Product B, and second, as the increased sales of B as a fraction of the lost sales of A. To establish a proper relationship between lost and captured profits, which is the main purpose of the diversion ratio, the first interpretation does not work. This ambiguity surrounding the concept of the diversion ratio has given rise to confusion (although algebraic elaborations in the literature are usually more precise than the language used). Practitioners relying on customer surveys to estimate diversion ratios need to be aware of the potential pitfalls when tailoring the survey questions to the incorrect definition of the ratio.
JIT implementation in Egyptian manufacturing firms: some empirical evidence

Purpose – This study aims to delineate the major human modifications to be undertaken prior to just‐in‐time (JIT) implementation in Egyptian manufacturing firms; to discern the benefits obtained from JIT implementation; to identify the problems that Egyptian manufacturing companies typically encounter in implementing JIT philosophy; and to explore the relationship between human modification efforts to be undertaken prior to JIT implementation and JIT success.Design/methodology/approach – The data analyzed in this article was collected from a mail questionnaire sent to 200 manufacturing firms in Egypt. The findings of this study indicate that JIT success is significantly associated with human resources modification efforts undertaken in preparation for JIT implementation.Findings – JIT philosophy can be successfully implemented in Egyptian manufacturing companies; just like their peers in developed countries including Japan, USA and the Far East; with thoughtful attention applied to each individual company.
ER targeting and retention of the HCV NS4B protein relies on the concerted action of multiple structural features including its transmembrane domains

Abstract The Hepatitis C virus (HCV) NS4B protein, a multispanning endoplasmic reticulum (ER) membrane protein, generates intracellular rearrangements of ER-derived membranes, essential for HCV replication. In this study, we characterized NS4B elements involved in the process of targeting, association and retention in the ER membrane. We investigated the localization and membrane association of a number of C- or N-terminal NS4B deletions expressed as GFP chimeras by biochemical and fluorescence microscopy techniques. A second set of GFP-NS4B chimeras containing the plasma membrane ecto-ATPase CD39 at the C-terminus of each NS4B deletion mutant was used to further examine the role of N-terminal NS4B sequences in ER retention. Several structural elements, besides the first two transmembrane domains (TMs), within the NS4B N-terminal half (residues 1–130) were found to mediate association of the NS4B-GFP chimeras with ER membranes. Both TM1 and TM2 are required for ER anchoring and retention but are not sufficient for ER retention. Sequences upstream of TM1 are also required. These include two putative amphipathic α-helices and a Leucine Rich Repeat-like motif, a sequence highly conserved in all HCV genotypes. The N-terminal 55peptidic sequence, containing the 1st amphipathic helix, mediates association of the 55N-GFP chimera with cellular membranes including the ER, but is dispensable for ER targeting of the entire NS4B molecule. Importantly, the C-terminal 70peptidic sequence can associate with membranes positive for ER markers in the absence of any predicted TMs. In conclusion, HCV NS4B targeting and retention in the ER results from the concerted action of several NS4B structural elements.
Analysis of REITs and REIT ETFs Cointegration during the Flash Crash

In this study I revisit the “disintegration hypothesis” of financial assets around a major crisis event. I examine whether the Vanguard Real Estate Investment Trust and iShares Dow Jones US Real Estate Index Fund exchange traded funds disintegrate from the ten largest Real Estate Investment Trusts during the 14:45 Flash Crash on May 6, 2010. I find that six of the ten largest REITs are not cointegrated with the Vanguard Real Estate Investment Trust prior to the Flash Crash and that five of the ten largest REITs are not cointegrated with iShares Dow Jones US Real Estate Index Fund prior to the Flash Crash. After the Flash Crash all REITs are cointegrated with the two REIT ETFs. This clearly refutes the “disintegration hypothesis” of REITs and REIT ETFs.