Miracle-dz/UniFAR-FTUs huggingface dataset:
Respiration of Microbiota-Derived 1,2-propanediol Drives Salmonella Expansion during Colitis

Intestinal inflammation caused by Salmonella enterica serovar Typhimurium increases the availability of electron acceptors that fuel a respiratory growth of the pathogen in the intestinal lumen. Here we show that one of the carbon sources driving this respiratory expansion in the mouse model is 1,2-propanediol, a microbial fermentation product. 1,2-propanediol utilization required intestinal inflammation induced by virulence factors of the pathogen. S. Typhimurium used both aerobic and anaerobic respiration to consume 1,2-propanediol and expand in the murine large intestine. 1,2-propanediol-utilization did not confer a benefit in germ-free mice, but the pdu genes conferred a fitness advantage upon S. Typhimurium in mice mono-associated with Bacteroides fragilis or Bacteroides thetaiotaomicron. Collectively, our data suggest that intestinal inflammation enables S. Typhimurium to sidestep nutritional competition by respiring a microbiota-derived fermentation product.
Ireland’s Great Depression

We argue that Ireland experienced a great depression in the 1980s comparable in severity to the better known and more studied depression episodes of the interwar period. Using the business cycle accounting framework of Chari, Kehoe and McGrattan (2005), we examine the factors that led to the depression and the subsequent recovery in the 1990s. We calculate efficiency, labour, investment and government wedges and evaluate the contribution of each to the downturn and subsequent recovery. We find that the efficiency wedge on its own can account for a significant portion of the downturn, but predicts a stronger recovery in output than occurred. The labour wedge also helps account for what happened during the depression episode. We also find that the investment wedge played no role in the depression.
A chance-constraints linear programming model on the economic evaluation of flexible manufacturing systems

Abstract The implementation of flexible manufacturing systems lFMSsr normally entails a large initial investment under a long-term, uncertain environment. Many effects of installing a FMS will be due to improvement in throughput efficiency, quality, flexibility and the opportunity costs. However, most economic evaluations of FMSs assume the problem is deterministic, such that they fail to model accurately and capture the nature of FMSs. This paper uses stochastic variables to capture the.nature of a FMS under given resource limitations and leads to a multistage chance-constraints linear programming lLPr formulation. Finally, in order to incorporate the uncertainty of capital investment, the interest rate as a function of time is considered over the whole planning horizon and the decision model is extended under continuous and variable discounting.
Speech planning happens before speech execution: online reaction time methods in the study of apraxia of speech.

PURPOSE The purpose of this article is to present an argument for the use of online reaction time (RT) methods to the study of apraxia of speech (AOS) and to review the existing small literature in this area and the contributions it has made to our fundamental understanding of speech planning (deficits) in AOS. METHOD Following a brief description of limitations of offline perceptual methods, we provide a narrative review of various types of RT paradigms from the (speech) motor programming and psycholinguistic literatures and their (thus far limited) application with AOS. CONCLUSION On the basis of the review of the literature, we conclude that with careful consideration of potential challenges and caveats, RT approaches hold great promise to advance our understanding of AOS, in particular with respect to the speech planning processes that generate the speech signal before initiation. A deeper understanding of the nature and time course of speech planning and its disruptions in AOS may enhance diagnosis and treatment for AOS. RESULTS Only a handful of published studies on apraxia of speech have used reaction time methods. However, these studies have provided deeper insight into speech planning impairments in AOS based on a variety of experimental paradigms.
Uncovering and Managing the Impact of Methodological Choices for the Computational Construction of Socio-Technical Networks from Texts

Socio-technical networks are ubiquitous and impact society on many dimensions. As individuals become socialized into those networks, they alternately internalize network behavior or transform network behavior through their participation. Frequently the functioning of networks involves communication within the network or processing of communication and information originating outside the network. Such communication and information data are often available as unstructured, natural language text data. Often in prior work, text data are analyzed separately from relational data, or are reduced to the fact and frequency of the flow of information between nodes. The latter approach acknowledges that information exchange has taken place, but disregards the content of the text data. However, we know that by not considering the substance of communication and information, we are limited in our ability to understand the effects of language use in networks, including the interplay and co-evolution of information and network structure and behavior. Thus, we expect that in bringing together text data and relational data, we will be able to make substantial advances in network analysis. A complicating factor is that sometimes the structure and behavior of networks are encoded in the text data itself. In these cases, network data needs to be extracted from text data. I propose to develop, apply and evaluate a set of computational methods that facilitate the joint analysis of relational data and the content of text data. In working towards this goal, I use an interdisciplinary and computationally rigorous approach that combines theory and models from social science and socio-linguistics with methods from natural language processing and machine learning that are based on probabilistic graphical models. The datasets used for this work are the Enron email data, data about research funding, and a dataset about the Sudan. The anticipated contributions include: - Provide and evaluate methods that will be integrated into the publicly available software products AutoMap and ORA. - Clean and normalize public datasets that contain relational data and text data in order to ensure that each node represents one unique social entity and no entity is represented by more than one node. The overall goal with this thesis is to provide methods that support users in collecting rich network data that allow for meaningful and actionable analysis.
Nash-Bargained Household Decisions: Reply

Pierre-Andre Chiappori's (1988) claim that the Nash-bargaining model is of "weak empirical relevance" and "neither convenient nor really restrictive" is incorrect. Nash-bargained household behavior implies a rich set of empirical implications extending well beyond the Pareto efficiency of intrafamily distributions. By systematically accounting for the impact of opportunities outside the family on resource distribution within the family, Nash-bargained demand theory considerably expands the scope of neoclassical demand theory. Such expansion can elucidate issues ranging from the impact of alimony and child support laws in developed societies to the intrafamily distribution of nutrition in less developed countries. Copyright 1990 by Economics Department of the University of Pennsylvania and the Osaka University Institute of Social and Economic Research Association.
Effect of a ligand selective for peripheral benzodiazepine receptors on the expression of rat hepatic P-450 cytochromes: assessment of the effect in vivo and in a hepatocyte culture system.

The peripheral benzodiazepine receptor plays a role in the translocation of cholesterol into mitochondria where steroidogenesis occurs. Sterols have been suggested to be involved in the regulation of the cytochrome P-450 (CYP)2B subfamily as the endogenous suppressor of this CYP. To investigate the role of cholesterol metabolites on the expression of CYPs, the effect of PK11195, a specific ligand of the peripheral benzodiazepine receptor and a stimulator of cholesterol transportation, on CYP expression was examined in rats in vivo and in cultured hepatocytes. As judged by the change in testosterone metabolic activity catalyzed by liver microsomes, i.p. injection of PK11195 into rats increased the CYP2B subfamily significantly. A trend in the induction of the CYP2A1, 2C11, and 3A isozymes was also observed. When PK11195 was given to rats together with phenobarbital, an additive effect of these compounds on testosterone metabolic activity was observed. In cultured hepatocytes, PK11195 exhibited the same effect on CYP expression as seen in vivo, but the magnitude of the effect was much greater than that observed in vivo. The inductive effect of PK11195 toward the CYP2B and 3A subfamilies was 2.3- and 6.5-fold greater, respectively, than that with phenobarbital. The inductive effect of PK11195 was confirmed by immunoblotting with antibodies against CYP2A, 2B, 2C, and 3A proteins. These results indicate that PK11195 has an inductive effect on several subfamilies of CYPs by directly acting on liver cells and has no ability to suppress the expression of these CYPs. This observation suggests that, if certain sterols play a role in the suppressive control of the CYP2B subfamily, they are produced in organelles other than the mitochondria.
Institutional Rigidities and Their Effects on Labor Demand in Turkey

This study analyzes the effects of one of the institutional rigidities in Turkish labour market; job security regulations introduced with new labour code legislated in 2003, on the labour demand. By examining the periods before and after the year 2003 with panel data methods, the changes in the responsiveness of labour demand to the changes in labour costs are investigated. In the study in which TURKSTAT Manufacturing Industry Statistics are used, it is found that the responsiveness of labour demand to the changes in labour costs increased after 2003. It is concluded that the labour costs and job security regulations which influence these costs indirectly are effective on the hiring and firing decisions of employers. When a distinctive analysis based on gender is made, it is found that while the results related demand for male workers are similar with the total demand estimates; the demand for female workers does not have a significant response to the changes in labour costs. Estimates in which the openness variable is included show that openness effects labour demand in negative direction.
The definitive evaluation of sarcoidosis.

Thirty patients with clinical, roentgenographic, and histologic manifestations of sarcoidosis on biopsy of peripheral tissues were subjected to exhaustive diagnostic study in an attempt to establish a definitive diagnosis other than sarcoidosis. This was accomplished in 27 patients. The most rewarding diagnostic procedure was open lung biopsy, which proved to be the definitive diagnostic procedure in 16 patients. Additional diagnostic procedures included cultures of secretions and biopsied tissues, special staining techniques, chemical analysis of biopsy specimens, and immunologic studies. In the patient with suspected intrathoracic sarcoidosis, the diagnosis cannot be established without open thoracotomy unless preliminary cultures or biopsies of peripheral tissue reveal evidence of another pathologic process known to cause a granulomatous reaction. The presence of sarcoid in a patient with an abnormal chest film cannot be confirmed by scalene node biopsy, a Kveim test, or absence of bacteriologic eviden.
A simulation model to estimate cost-offsets for a disease-management program for chronic kidney disease

Aim: The aim of this paper is to develop a simulation model that analyzes cost-offsets of a hypothetical disease management program (DMP) for patients with chronic kidney disease (CKD) in Germany compared to no such program. Methods: A lifetime Markov model with simulated 65-year-old patients with CKD was developed using published data on costs and health status and simulating the progression to end-stage renal disease (ESRD), cardiovascular disease and death. A statutory health insurance perspective was adopted. Results: This modeling study shows considerable potential for cost-offsets from a DMP for patients with CKD. The potential for cost-offsets increases with relative risk reduction by the DMP and baseline glomerular filtration rate. Results are most sensitive to the cost of dialysis treatment. Conclusion: This paper presents a general ‘prototype’ simulation model for the prevention of ESRD. The model allows for further modification and adaptation in future applications.
Effects of the Brown Anole Invasion and Betelnut Palm Planting on Arthropod Diversity in Southern Taiwan

Abstract The brown anole (Anolis sagrei) occurs naturally in various localities in Central America, and an exotic invasive population was first reported in Sheishan District, Chiayi County, Taiwan, in 2000. Previous studies showed that following the invasion of A. sagrei, the diversity and abundance of local terrestrial arthropods, such as orb spiders and arboreal insects, were severely affected. In this study, we assessed the impact of A. sagrei on arthropod diversity in Taiwan by comparing spider and insect diversities among betelnut palm plantations, in which this lizard species was either present or absent, and a secondary forest. In addition, enclosures were established in which the density of A. sagrei was manipulated to investigate the effect of this predator on spiders. The results of a lizard stomach content analysis showed that spiders comprised 7% and insects 90% of the prey consumed. Among the insects consumed by A. sagrei, more than 50% were ants. The abundances of the major arthropod prey of A. sagrei, such as jumping spiders and hymenopterans, in the lizard-present sites were much lower than in the lizard-removed sites. The enclosure experiments also showed that predation by the lizards significantly reduced the abundance of jumping spiders. All these results indicated that the introduced lizard greatly affected the diversity and abundance of terrestrial arthropods in agricultural areas in southern Taiwan.
Duration: Response to critics

I n the Winter 1987 issue of this Journal, G. Bierwag, G. Kaufman, C. Latta, and G. Roberts (BKLR) disagree with the results in the paper, “Alternative Duration Specifications and Measurement of Basis Risk: Empirical Tests,” by B. Gultekin and R. Rogalski (GR) published elsewhere. ’ The central theme of the BKLR paper goes something like this: If an empirical test rejects a theory because it uses the theory’s own assumptions, which are known to be false, then it is an invalid test. We believe this is a ludicrous argument. We argue that what BKLR have to say does not negate any of our major points. To set the record straight, GR found that 1. Duration measures D1 to D7 are virtually indistinguishable empirically from one another and from maturity in explaining actual bond returns. ’ 2. Simple-minded factor models performed better empirically than duration measure D1. 3. Bond returns are not linear with respect to duration measure D1 as well as duration measures D2 to D7. 4. Bond portfolios with identical durations D1 but 83
Trace based application layer modeling in ns-3

Ns-3 is a widely used as a the network simulator of choice by researchers. It contains many well tested and high quality models of network protocols. However, the application layer models of ns-3 are very simplistic, and do not capture all aspects of real life applications. As a result, there is often a huge gap between the results of real experiments and the corresponding simulations. This problem is particularly exacerbated for wireless simulations, where many networking phenomena like wireless channel contention crucially depend on the application traffic characteristics. One way to bridge the gap between experiments and simulations is to incorporate knowledge from network traces into simulations. To this end, our work builds a trace-based application layer simulator in ns-3. Given a network trace collected from a user, our TraceReplay application layer model automatically generates traffic that is faithful to the real application in the ns-3 simulator. TraceReplay infers and replays only application layer delays like user think times, lets the simulator control the lower layer phenomena. TraceReplay extracts application layer characteristics from a single trace, and replays this information across many users in simulation, by using suitable randomization. Our model is also generic enough to replay any application layer protocol. Validation of our simulation model shows that simulation results obtained using TraceReplay are significantly different from those using other models, and are closer to experimental observations.
Modeling Government Subsidies and Project Risk for Financially Non-Viable Build-Operate-Transfer (BOT) Projects

Abstract: Governments encourage private sector participation in building infrastructure through Build-Operate-Transfer (BOT) agreements. Large projects may be financially non-viable despite their net economic benefits for the host society. Host governments might subsidize initial private investments to create financial feasibility. Small-scale subsidies might not sufficiently reduce project risks to attract private investment; however, large percentage subsidies might result in loose profit structures, discouraging the pursuit of efficiency. This article applies Monte Carlo techniques to data from the Taiwanese West Corridor High-Speed Rail Project to assess the subsidy-risk trade-off relationship. The results provide guidance for public-private negotiations.
The Efficient Frontier and the Limits on Investment for Pension Plan Administrators (AFP): A New Perspective (La frontera eficiente y los límites de inversión para las AFP: una nueva mirada)

This article provides a re-estimation of the pension plan funds administrators’ efficient frontier. The goal here is two-fold: on the one hand it measures the effect of investment limits imposed by regulators. Unlike previous studies, here the short positions are not limited; this assumption is based upon the completeness of the financial markets: when the markets are completed, any financial instrument may be replicated. On the other hand, this article measures the performance of the pension plan funds. In earlier works, the performance was measured as the difference between the profitability in the frontier and the one obtained at the level of a given risk; here the return is measured as the relationship of optimal risk profitability and the one obtained. The main conclusion drawn is that regulation supports the high level of risks taken by the administrators.
Arable Productivity in Medieval England: Some Evidence from Norfolk

Statistics on crop yields for the period 1268–1430 from 62 demesnes in the eastern half of Norfolk are used to demonstrate a new method of measuring arable productivity. The method takes into account seeding rates, the frequency of cropping, and the relative importance of the different crops grown, and it acknowledges the existence of different farming regions. Within eastern Norfolk two such regions are shown to have existed, which cut right across estate affiliations and had radically different productivities. The wider implications of these findings are then discussed.
Dynamic changes in the expression of DEP‐1 and other PDGF receptor‐antagonizing PTPs during onset and termination of neointima formation

Growth factor‐dependent tissue remodeling, such as restenosis, is believed to be predominantly regulated by changes in expression of receptor‐tyrosine‐kinases (RTKs) and their ligands. As endogenous antagonists of RTKs, protein‐tyrosine‐phosphatases (PTPs) are additional candidate regulators of these processes. Using laser‐capture‐microdissection and quantitative RT‐polymerase chain reaction (qRT‐PCR), we investigated the layer‐specific expression of the four platelet‐derived growth factor (PDGF) isoforms, the PDGF‐ and receptors, and five PTPs implied in control of PDGF‐receptor signaling 8 and 14 days after balloon injury of the rat carotid. Results were correlated with analyses of PDGF‐ receptor phosphorylation and vascular smooth muscle cell (VSMC) proliferation in vivo. The expression levels of all components, as well as receptor activation and VSMC proliferation, showed specific changes, which varied between media and neointima. Interestingly, PTP expression—particularly, DEP‐1 μlevels—appeared to be the dominating factor determining receptor‐phosphorylation and VSMC proliferation. In support of these findings, cultured DEP‐1–/–cells displayed increased PDGF‐dependent cell signaling. Hyperactivation of PDGF‐induced signaling was also observed after siRNA‐down‐regulation of DEP‐1 in VSMCs. The results indicate a previously unrecognized role of PDGF‐receptor‐targeting PTPs in controlling neointima formation. In more general terms, the observations indicate transcriptional regulation of PTPs as an important mechanism for controlling onset and termination of RTK‐dependent tissue remodeling. —FASEB J. 21, 523–534 (2007)
On Cash-in-Advance Models of Money Demand and Asset Pricing

This paper shows how a cash-in-advance model of money can be written in a way that combines a simple, yet empirically defensible, money demand function with an asset pricing equation that is similar to the standard barter-economy Euler equations. Return premia are determined as in the barter exchange model, except that a short-term, risk-free, nominal interest rate enters into the first-order conditions. In special cases, asset prices satisfy the barter-economy Euler equations exactly. In the empirical analysis, the interest rate factor adds some explanatory power, but both the barter and the monetary asset pricing model perform rather poorly. Copyright 1991 by Ohio State University Press.
Energy-balance modelling of short channel single-GB thin-film transistors

In this paper, we have investigated the effect of a single Grain Boundary (GB) on the performance of decananometre-scale Thin Film Transistors (TFTs) by using the calibrated energy balance transport model and a continuous trap state distribution at the GB. We have found that the GB potential barrier suppresses the subthreshold slope and leakage current in devices, where the DIBL effect and punchthrough currents significantly degrade device performance. We have also found that the drift-diffusion model underestimates the drain current in the single-GB TFT and the velocity overshoot effect becomes significant in the short channel regime. Inclusion of trap-to-band and band-to-band tunnelling models into our simulations have shown that the subthreshold leakage current has a significant field dependence in the negative gate bias regime.
Price volatility, hedging and variable risk premium in the crude oil market

The crude oil price exhibits a high degree of volatility which varies significantly over time. Such characteristics imply that the oil market is a promising area for testing volatility models. Testing and predicting volatility using ARCH and GARCH models have grown in the literature. A useful application of the volatility models is in the formulation of hedging strategies. In this paper we compare the optimal hedge ratio for the crude oil using the classical minimum risk approach and use ARCH to incorporate the effect of heteroskedasticity in the residuals on the hedge ratio. In addition, we test for the existence of a variable risk premium in the crude oil market. We find that, assuming rational expectations, there is a non-zero risk premium. We test for the variability of the risk premia and find evidence in its support when we employed a multivariate GARCH model. Copyright 2006 Organization of the Petroleum Exporting Countries.