Miracle-dz/UniFAR-FTUs huggingface dataset:
Symptom and chest radiographic screening for infectious tuberculosis prior to starting isoniazid preventive therapy: yield and proportion missed at screening

Objective:This analysis describes the prevalence of and risk factors for tuberculosis at screening prior to isoniazid preventive therapy (IPT); the additional yield of tuberculosis using chest radiography versus symptoms alone, and risk factors for tuberculosis missed by screening. Design:Cross-sectional analysis of a trial of community-wide IPT in South African gold mines. Methods:Participants were screened for tuberculosis prior to starting IPT using symptoms (cough >2 weeks, weight loss, night sweats) and chest radiography. Tuberculosis suspects had sputum collected for mycobacterial investigations. Those with a positive smear or culture with no speciation or culture identified as Mycobacterium tuberculosis were classified as having probable or definite tuberculosis, respectively. Among participants who were dispensed IPT, we defined a ‘missed’ case of active tuberculosis as one identified within 90 days of the enrolment screen. Results:Between July 2006 and December 2008, among 23 286 participants with complete data, the prevalence of undiagnosed tuberculosis [definite (284) and probable (31)] was high (315/23 286; 1.4%). The addition of chest radiography to symptom screening increased the number of definite tuberculosis cases detected by 2.5-fold (113 to 281 cases). Among 19 609 individuals correctly screened for tuberculosis who started IPT and had more than 90 days of follow-up, only 39 (0.2%) active tuberculosis cases were missed. Risk factors for tuberculosis missed by screening included increasing age [adjusted odds ratio (aOR) 1.66/10 year increase, 95% confidence interval (CI) 1.07–2.56], non-South African, in HIV care (aOR 4.80, 95% CI 1.63–14.1), lower weight (aOR 2.07/10 kg decrease, 95% CI 1.23–3.49) and alcohol use (aOR 2.52, 95% CI 1.31–4.86), which were similar to risk factors for tuberculosis detected by screening. Conclusion:Tuberculosis screening prior to IPT detects a substantial burden of tuberculosis and misses very few cases. Chest radiography significantly increased the yield of tuberculosis cases detected.
Rudderless in a Sea of Yellow: The European Political Economy Impasse for Renewable Transport Energy

Faced with the twin challenges of anthropogenic climate change and ‘peak oil’, the need for an urgent and radical transformation of transport energy has been widely recognised. Adopting a neo-Polanyian economic sociology approach, this article asks what conditions European governance capacity to respond to these challenges, at either national or regional levels, using biofuels as a case study. It asks if the complexity of its political institutions, and the heterogeneity of interests and economic organisations, present ‘the biggest obstacle of all’ (Cohen 2007) to reduce fossil fuel dependency. By examining the European Commission level and comparing five countries, evidence is produced for a political failure in terms of continued fossil fuel dependency. Incumbent interests in the agricultural sector and a distinctively European legacy of a transport fleet dependent on fossil diesel, have led to a marriage of convenience between rapeseed farmers and vehicle manufacturers. As a consequence, rather than escaping from the path dependency on fossil fuels (Unruh 2000), Europe has gone down a cul-de-sac of rapeseed biodiesel inherently limited in scope, and with the low levels of greenhouse gas emissions savings. Ironically this outcome is in part an unintended consequence of opposition to biofuels from environmentalist groups and politics.
Outbreak of a Cluster with Epidemic Behavior Due to Serratia marcescens after Colistin Administration in a Hospital Setting

ABSTRACT Serratia marcescens causes health care-associated infections with important morbidity and mortality. Particularly, outbreaks produced by multidrug-resistant isolates of this species, which is already naturally resistant to several antibiotics, including colistin, are usually described with high rates of fatal outcomes throughout the world. Thus, it is important to survey factors associated with increasing frequency and/or emergence of multidrug-resistant S. marcescens nosocomial infections. We report the investigation and control of an outbreak with 40% mortality due to multidrug-resistant S. marcescens infections that happened from November 2007 to April 2008 after treatment with colistin for Acinetobacter baumannii meningitis was started at hospital H1 in 2005. Since that year, the epidemiological pattern of frequently recovered species has changed, with an increase of S. marcescens and Proteus mirabilis infections in 2006 in concordance with a significant decrease of the numbers of P. aeruginosa and A. baumannii isolates. A single pulsed-field gel electrophoresis (PFGE) cluster of S. marcescens isolates was identified during the outbreak. When this cluster was compared with S. marcescens strains (n = 21) from 10 other hospitals (1997 to 2010), it was also identified in both sporadic and outbreak isolates circulating in 4 hospitals in Argentina. In132::ISCR1::bla CTX-M-2 was associated with the multidrug-resistant cluster with epidemic behavior when isolated from outbreaks. Standard infection control interventions interrupted transmission of this cluster even when treatment with colistin continued in several wards of hospital H1 until now. Optimizing use of colistin should be achieved simultaneously with improved infection control to prevent the emergence of species naturally resistant to colistin, such as S. marcescens and P. mirabilis.
The Effect of Competition on the Efficient–Responsive Choice

In determining their operations strategy, a firm chooses whether to be responsive or efficient. For firms competing in a market with uncertain demand and varying intensity of substitutability for the competitor's product, we characterize the responsive or efficient choice in equilibrium. To focus first on the competitive implications, we study a model where a firm can choose to be responsive at no additional fixed or marginal cost. We find that competing firms will choose the same configuration (responsive or efficient), and responsiveness tends to be favorable when demand uncertainty is high or when product competition is not too strong. Intense competition can drive firms to choose to be efficient rather than responsive even when there is no additional cost of being responsive. In such a case, both firms would be better off by choosing to be responsive but cannot credibly commit. We extend the basic model to study the impact of endogenized production timing, multiple productions and product holdback (or, equivalently, postponed production). For all these settings, we find structurally similar results; firms choose the same configuration, and the firms may miss Pareto‐improvements. Furthermore, through extensions to the basic model, we find that greater operational flexibility can make responsiveness look less attractive in the presence of product competition. In contrast to our basic model and other extensions, we find it is possible for one firm to be responsive while the other is efficient when there is either a fixed cost or variable cost premium associated with responsive delivery.
MorphoLibJ: integrated library and plugins for mathematical morphology with ImageJ

MOTIVATION Mathematical morphology (MM) provides many powerful operators for processing 2D and 3D images. However, most MM plugins currently implemented for the popular ImageJ/Fiji platform are limited to the processing of 2D images. RESULTS The MorphoLibJ library proposes a large collection of generic tools based on MM to process binary and grey-level 2D and 3D images, integrated into user-friendly plugins. We illustrate how MorphoLibJ can facilitate the exploitation of 3D images of plant tissues. AVAILABILITY AND IMPLEMENTATION MorphoLibJ is freely available at http://imagej.net/MorphoLibJ CONTACT: david.legland@nantes.inra. frSupplementary information: Supplementary data are available at Bioinformatics online.
Backtesting Derivative Portfolios with Filtered Historical Simulation (Fhs)

Filtered historical simulation provides the general framework to our backtests of portfolios of derivative securities held by a large sample of financial institutions. We allow for stochastic volatility and exchange rates. Correlations are preserved implicitly by our simulation procedure. Options are repriced at each node. Overall results support the adequacy of our framework, but our VaR numbers are too high for swap portfolios at long horizons and too low for options and futures portfolios at short horizons.
Market access by smallholder farmers in Malawi

In Malawi, maize is the major crop and food staple. Given limited off-farm employment opportunities, much-needed increases in household income for improving food security must come from gains in agricultural productivity through better technology and more profitable crops. In the past, agricultural policy promoted hybrid maize and, more recently, tobacco to increase smallholder income. This paper presents an analysis of what determines the adoption of these two crops and what kind of income effects follow from adoption. Apart from factor endowment and exposure to agroecological risks, differences in the household's access to financial and commodity markets significantly influence its cropping shares and farm income.
Patient demographics and health plan paid costs in chronic inflammatory demyelinating polyneuropathy

Introduction: We determined health plan paid costs and healthcare resource usage of patients with chronic inflammatory demyelinating polyneuropathy (CIDP). Methods: CIDP patients from 9 U.S. commercial health plans with claims in 2011 were identified from the Accordant Health Services claims database. We examined demographics, prevalence of comorbidities, prescribed drugs, place of service, and mean annual health plan paid costs per patient. Results: From 6.5 million covered lives, 73 (56% men; mean age 47) met study entry criteria. The most prescribed therapies were intravenous immunoglobulin (IVIg) (26% of patients), gabapentin (26%), and prednisone (16%). The annual health plan paid cost was $56,953. Pharmacy cost was the major cost driver (57% of the total), and IVIg totaled 90% of the pharmacy costs. Conclusions: Healthcare costs for CIDP patients are substantial, with a large burden in pharmacy usage. Studies are needed to determine optimal long‐term treatment strategies for CIDP, particularly related to IVIg. Muscle Nerve 50: 47–51, 2014
Beyond the fear of discretion: Flexibility, performance, and accountability in the management of regulatory bureaucracies

This study explores the implications of different approaches to performance management for inspection work and regulatory outcomes. It assesses to what extent variations in methods for controlling discretion explain why in some cases regulatory inspectors limit themselves to the narrow boundaries of their formal mandate, while in other cases they work collaboratively with inspected firms and other organizations to develop innovative strategies that solve complex regulatory and business problems. After reviewing alternative approaches to the management of discretion, I present a natural experiment that offered an opportunity for controlled comparisons of two current attempts to reconcile bureaucratic performance with accountability: New Public Management and Experimentalist Governance. Case comparisons in the area of labor inspection in Brazil – involving severance payments, fraudulent cooperatives, and safety in construction – suggest that these two approaches to the management of regulatory bureaucracies produce considerably different inspection strategies and regulatory outcomes. The different accountability mechanisms and investigation strategies inspired by each of these approaches create different sets of incentives with direct effects on inspectors' motivation and their ability to resolve compliance problems.
Artificial Grammar Learning in Tamarins (Saguinus oedipus) in Varying Stimulus Contexts

The human ability to detect regularities in sound sequences is a fundamental substrate of our language faculty. However, is this an ability exclusive to human language processing, or have we usurped a more general learning mechanism for this purpose, one shared with other species? The current study is an attempt to replicate and extend Hauser, Weiss, and Marcus’s (2002) retracted study (2010) of artificial grammar learning in tamarins to determine if tamarins can detect an underlying grammatical structure in a pattern of sounds. Human language consonant–vowel (CV) combinations from Hauser et al.’s original study, newly created tone sequences, and newly created monkey vocalizations made into sequences were used to familiarize tamarins to an AAB or ABB pattern. Tests of novel sounds in each condition were presented that either were consistent with the familiarized pattern or were different from it. Longer looking times toward the sound source (an audio speaker with a specific location in the auditory field) indicated recognition of novelty. Tamarins looked toward the speaker significantly longer with inconsistent human language CV sequences and with inconsistent tone sequences but not when an inconsistent monkey vocalization was presented. Moreover, tamarins showed differential rates of habituation to the different types of sound patterns, with more robust habituation to CV sequences and tone sequences than to monkey call sequences. The implications of these findings for the generality of learning mechanisms for linguistic and nonlinguistic input across species and the importance of testing across various stimuli are discussed.
Retinal gene expression changes related to IOP exposure and axonal loss in DBA/2J mice.

PURPOSE To determine the effects of cumulative IOP exposure and axonal damage on retinal gene expression in DBA/2 mice. METHODS DBA/2J, DBA/2J(pe) (pearl), and C57BL/6 mice from 3 to 12 months of age were used. IOP was measured with a rebound tonometer, and optic nerve (ON) damage was determined by grading of ON sections. Retinal RNA was subjected to microarray analysis. Comparisons explored the effects of cumulative IOP exposure (cIOPx) as well as ON damage (ONd) in the DBA/2J animals compared with that in the C57BL/6 and pearl mice. RT-PCR was performed to confirm some of the genes and bioinformatic analysis to identify affected gene networks. RESULTS Microarrays revealed that an increasing number of genes were up- or downregulated in 9- and 12-month DBA/2J mice with various degrees of ONd. A smaller number of genes were expressed differentially between eyes with different cIOPx at the same age, from 6 months on. Expression of 1385 and 1133 genes differed between DBA/2J animals and C57BL/6 or pearl mice, respectively, and some them were confirmed by RT-PCR. Bioinformatics analysis identified functional gene networks, including members of the complement system, that appeared to be related to cIOPx, ONd, or both. CONCLUSIONS Gene expression changes occur in retinas of DBA/2 mice with various amounts of cIOPx as well as ONd. Genes involved, code for proteins with diverse cellular functions and include among others the complement system. cIOPx and ONd affect common as well as unique gene sets.
Determinants of Pay-as-You-Go Financing of Capital Projects: Evidence from the States

Although states have long practiced pay-as-you-go in financing their capital projects as a supplement to debt, academia has paid scarce attention to pay-go financing. This study fills in the niche by providing empirical evidence on what determines the use of pay-go in financing capital projects. It develops a model that considers the preferences of both voters and politicians when they make capital financing decisions in a given institutional setting. The empirical results suggest that the use of pay-go is affected by a state's income level, its economic conditions, the presence of a divided government, as well as its budgetary institutions.
‘They all supported me but I felt like I suddenly didn't belong anymore’: an exploration of perceived disadvantages to online support seeking

In recent years, there has been a significant rise in the number of online support communities dedicated to issues surrounding infertility. The aim of this study was to focus on investigating the perceived disadvantages of online infertility support communities from the perspective of those who access and participate in them. A total of 295 participants completed an online questionnaire about their use of online support communities. Responses were analysed using inductive content analysis. Since the majority of respondents were women, the results of the study largely reflect the experiences of the female population. Over half of the sample (57.9%) reported experiencing disadvantages to online support. Content analysis revealed that the most commonly cited disadvantages were reading about negative experiences (10.9%), reading about other peoples pregnancies (8.8%), inaccurate information (7.8%) and its addictive (5.8%). These results suggest that there are many perceived disadvantages to online infertility support communities. While some of these disadvantages reflect fears commonly cited in the literature, there are also unique disadvantages associated with the experience of infertility and its treatment. The study highlights a number of important areas in which health professionals and community moderators could intervene to better support and improve the online experiences of patients experiencing infertility.
Testing Strategy with Multiple Performance Measures: Evidence from a Balanced Scorecard at Store24

ABSTRACT: This study investigates the idea that business strategies can be tested and validated based on statistical analysis of a firm's internal performance measures. The strategy literature describes business strategies using the concepts of formulation, implementation, and fit. The management accounting literature links these strategy concepts with the selection and use of performance measures. Building on these two streams we examine whether and how a multidimensional performance measurement system can be used to distinguish between strategic problems related to strategic inputs, customer-oriented strategic outputs, and financial performance. We use data from the performance measurement system of a field site that formulated, implemented, and subsequently abandoned an innovative operating strategy. Managers learned the strategy was ineffective over a two-year period. We find that the company's internal performance measures systematically reveal more timely information about problems with the strategy.
Demography, Democracy, Development and Urban Protest in Sub-Saharan Africa

Why are some countries in sub-Saharan Africa more prone to outbreaks of urban protests than others? Drawing together insights from the contentious politics and conflict studies literatures I develop an empirical model of protest incidence comprised of basic demographic, political and economic factors that theoretically influence the motives and means of potential protesters and the political opportunity structures they face. The results of a panel data analysis covering 40 African countries between 1990 and 2011 indicate that large urban populations, hybrid political institutions, election events, recent regime change and slow economic growth increase the likelihood of urban protests, as expected. However, several unexpected results emerge: urban protest incidence is negatively associated with a country’s level of urbanization and degree of press freedom and positively correlated with income. More research is required to confirm these results, clarify mechanisms and account for broader trends in contentious collective action in the region.
Multiuser MIMO Scheduling for LTE-A Downlink Cellular Networks

In this paper, we investigate multiuser MIMO scheduling in LTE downlink cellular networks. We formulate the downlink LTE-A MIMO scheduling as a weighted sum rate maximization problem by allocating the RBs to users or user pairs subject to some constraints in LTE-A. We develop a low-complexity MU-MIMO scheduling and resource allocation algorithm and propose an adaptive switching approach between SU-MIMO and MU-MIMO to improve network performance. System-level simulation results demonstrate significantly performance improvement of the proposed MU-MIMO scheduling algorithm and the adaptive switching algorithm.
Characterization of the LolA-LolB System as the General Lipoprotein Localization Mechanism of Escherichia coli *

The major outer membrane lipoprotein (Lpp) ofEscherichia coli requires LolA for its release from the cytoplasmic membrane, and LolB for its localization to the outer membrane. We examined the significance of the LolA-LolB system as to the outer membrane localization of other lipoproteins. All lipoproteins possessing an outer membrane-directed signal at the N-terminal second position were efficiently released from the inner membrane in the presence of LolA. Some lipoproteins were released in the absence of externally added LolA, albeit at a slower rate and to a lesser extent. This LolA-independent release was also strictly dependent on the outer membrane sorting signal. A lipoprotein-LolA complex was formed when the release took place in the presence of LolA, whereas lipoproteins released in the absence of LolA existed as heterogeneous complexes, suggesting that the release and the formation of a complex with LolA are distinct events. The release of LolB, an outer membrane lipoprotein functioning as the receptor for a lipoprotein-LolA complex, occurred with a trace amount of LolA, and therefore was extremely efficient. The LolA-dependent release of lipoproteins was found to be crucial for the specific incorporation of lipoproteins into the outer membrane, whereas lipoproteins released in the absence of LolA were nonspecifically and inefficiently incorporated into the membrane. The outer membrane incorporation of lipoproteins including LolB per se was dependent on LolB in the outer membrane. From these results, we conclude that lipoproteins in E. coli generally utilize the LolA-LolB system for efficient release from the inner membrane and specific localization to the outer membrane.
Nuclear translocation of Gln3 in response to nutrient signals requires Golgi-to-endosome trafficking in Saccharomyces cerevisiae

The yeast Saccharomyces cerevisiae has developed specialized mechanisms that enable growth on suboptimal nitrogen sources. Exposure of yeast cells to poor nitrogen sources or treatment with the Tor kinase inhibitor rapamycin elicits activation of Gln3 and transcription of nitrogen catabolite-repressed (NCR) genes whose products function in scavenging and metabolizing nitrogen. Here, we show that mutations in class C and D Vps components, which mediate Golgi-to-endosome vesicle transport, impair nuclear translocation of Gln3, NCR gene activation, and growth in poor nitrogen sources. In nutrient-replete conditions, a significant fraction of Gln3 is peripherally associated with light membranes and partially colocalizes with Vps10-containing foci. These results reveal a role for Golgi-to-endosome vesicular trafficking in TORC1-controlled nuclear translocation of Gln3 and support a model in which Tor-mediated signaling in response to nutrient cues occurs in these compartments. These findings have important implications for nutrient sensing and growth control via mTor pathways in metazoans.