Miracle-dz/UniFAR-FTUs huggingface dataset:
Phylogeny and Strain Typing of Escherichia coli, Inferred from Variation at Mononucleotide Repeat Loci

ABSTRACT Multilocus sequencing of housekeeping genes has been used previously for bacterial strain typing and for inferring evolutionary relationships among strains of Escherichia coli. In this study, we used shorter intergenic sequences that contained simple sequence repeats (SSRs) of repeating mononucleotide motifs (mononucleotide repeats [MNRs]) to infer the phylogeny of pathogenic and commensal E. coli strains. Seven noncoding loci (four MNRs and three non-SSRs) were sequenced in 27 strains, including enterohemorrhagic (six isolates of O157:H7), enteropathogenic, enterotoxigenic, B, and K-12 strains. The four MNRs were also sequenced in 20 representative strains of the E. coli reference (ECOR) collection. Sequence polymorphism was significantly higher at the MNR loci, including the flanking sequences, indicating a higher mutation rate in the sequences flanking the MNR tracts. The four MNR loci were amplifiable by PCR in the standard ECOR A, B1, and D groups, but only one (yaiN) in the B2 group was amplified, which is consistent with previous studies that suggested that B2 is the most ancient group. High sequence compatibility was found between the four MNR loci, indicating that they are in the same clonal frame. The phylogenetic trees that were constructed from the sequence data were in good agreement with those of previous studies that used multilocus enzyme electrophoresis. The results demonstrate that MNR loci are useful for inferring phylogenetic relationships and provide much higher sequence variation than housekeeping genes. Therefore, the use of MNR loci for multilocus sequence typing should prove efficient for clinical diagnostics, epidemiology, and evolutionary study of bacteria.
Cluster Transformation from a Supply Chain Perspective : Theoretical Models and the Case of the Maritime Cluster in Mid-West Norway

Through globalization cluster–based firms to a new extent are players in multiple knowledge networks, production networks and value chains on multiple geographical scales (Gereffi, Humphrey, and Sturgeon 2005; Gupta and Subramanian 2008). Some argue that in a global world economy a region or a cluster can hardly contain on its own a sufficient scale of related industries and services (Lilach and David 2003; Gertler and Wolfe 2006). Globalization links economic activity in clusters to more tightly woven and global production networks, market networks and knowledge networks (Porter 1998; Michael 2000; Bathelt, Malmberg, and Maskell 2004; Cooke 2005; Audretsch and Lehmann 2006; De Propris, Menghinello, and Sugden 2008; Hervás-Oliver and Albors-Garrigós 2008; Andersen 2006).
Measuring Fundamental Parameters of Substellar Objects. II. Masses and Radii

We present mass and radius derivations for a sample of very young, mid- to late-M, low-mass stellar and substellar objects in Upper Scorpius and Taurus. In a previous paper we determined effective temperatures and surface gravities for these targets from an analysis of their high-resolution optical spectra and comparisons to the latest synthetic spectra. We now derive extinctions, radii, masses, and luminosities by combining our previous results with observed photometry, surface fluxes from the synthetic spectra, and the known cluster distances. These are the first mass and radius estimates for young, very low mass bodies that are independent of theoretical evolutionary models (although our estimates do depend on spectral modeling). We find that for most of our sample, our derived mass-radius and mass-luminosity relationships are in very good agreement with the theoretical predictions. However, our results diverge from the evolutionary model values for the coolest, lowest mass targets: our inferred radii and luminosities are significantly larger than predicted for these objects at the likely cluster ages, causing them to appear much younger than expected. We suggest that uncertainties in the evolutionary models—e.g., in the choice of initial conditions and/or treatment of interior convection—may be responsible for this discrepancy. Finally, two of our late-M objects (USco 128 and 130) appear to have masses close to the deuterium-fusion boundary (~9MJ-14MJ within a factor of 2). This conclusion is primarily a consequence of their considerable faintness compared to other targets with similar extinction, spectral type, and temperature (difference of ~1 mag). Our result suggests that the faintest young late-M or cooler objects may be significantly lower in mass than current theoretical tracks indicate.
Generic Drug Industry Dynamics

Because of its unique institutional and regulatory features, the generic drug industry provides a useful laboratory for understanding how competition evolves. We exploit these features to estimate a system of structural relationships in this industry, including the relationship between price and the number of competitors, and between drug characteristics and the entry process. Our methodology yields a number of findings regarding industry dynamics. We find that generic drug prices fall with increasing number of competitors, but remain above long-run marginal cost until there are eight or more competitors. We also find the size and time paths of generic revenues, rents, and the number of firms are greatly affected by expected market size. Finally, we show how estimates derived from a system of structural equations can be used to simulate the effect of changes in an exogenous variable.
Gemini Mid-Infrared Imaging of Massive Young Stellar Objects in NGC 3576

We present a mid-infrared (MIR) study of NGC 3576. The high-resolution images were taken at the Gemini South Observatory through narrow- and broadband filters centered between 7.9 and 18 μm. The nearly diffraction-limited images show IRS 1 resolved into four sources for the first time in the 10 μm band. The positions of the sources are coincident with massive young stellar objects (YSOs) detected previously in the near-infrared (NIR). The properties of each object, such as spectral energy distribution, silicate absorption feature, color temperature, and luminosities were obtained and are discussed. We also report observations of two other YSO candidates and the detection of a new diffuse MIR source without an NIR counterpart. We conclude that none of these sources contributes significantly to the ionization of the H II region. A possible location for the ionization source of NGC 3576 is suggested based on both radio and infrared data.
The Intertemporal Substitution and Income Effects of a VAT Rate Increase: Evidence from Japan

One of the biggest political issues in Japan is an increase in the rate of value added tax (VAT). In this paper, we evaluate its impact on household expenditure, using Japan's April 1997 VAT rate increase from three to five percent as a case study. A rate increase induces price hikes, and provided this increase in price levels is anticipated, households should engage in intertemporal substitution of purchases. In addition, if households are not compensated for the rate increase, it has the potential to induce an income effect on household consumption. Based on monthly household expenditure data, we find that households spent 30,231 yen more in the quarter prior to the rate increase than they would have in its absence, while the income effect was negligible. Consistent with theoretical predictions, increased outlays on durable and storable non-durable goods and services were responsible for roughly three-quarters of the observed intertemporal substitution effects. Contrary to conventional wisdom, we find that the VAT rate increase had no impact on real household spending following its implementation, once we have accounted for intertemporal substitution, which caused a large transitory disturbance in household expenditures.
Optimizing Migration of Virtual Machines across Data-Centers

Managing virtual machines (VM) in large scale enterprise grid scenarios, commonly encountered in data centers, is extremely challenging. Currently, live VM migration is based on QoS non-conformance events; migration of a VM is initiated as soon as the aggregate resource (CPU and memory) requirements of the VMs on the physical machine (PM) exceed the capacity available on the PM. However, this paper establishes that, such ‘event-based’ migration can be extremely myopic. To overcome the limitations posed by the ‘event-based’ VM migration, this paper, proposes a new migration strategy based on ‘time-windows’. The paper outlines a mixed integer linear programming (MILP) model and a heuristic solution for generating near-optimal rearrangements of the VMs on the PMs. The paper evaluates the solutions on various VM scenarios which show encouraging results.
Effects of Fluvastatin on Characteristics of Stellate Ganglion Neurons in a Rabbit Model of Myocardial Ischemia

Background: Stellate ganglion (SG) plays an important role in cardiovascular diseases. The electrical activity of SG neurons is involved in the regulation of the autonomic nervous system. The aim of this research was to evaluate the effects of fluvastatin on the electrophysiological characteristics of SG neurons in a rabbit model of myocardial ischemia (MI). Methods: The MI model was induced by abdominal subcutaneous injections of isoproterenol in rabbits. Using whole-cell patch clamp technique, we studied the characteristic changes of ion channels and action potentials (APs) in isolated SG neurons in control group (n = 20), MI group (n = 20) and fluvastatin pretreated group (fluvastatin group, n = 20), respectively. The protein expression of sodium channel in SG was determined by immunohistochemical analysis. Results: MI and the intervention of fluvastatin did not have significantly influence on the characteristics of delayed rectifier potassium channel currents. The maximal peak current density of sodium channel currents in SG neurons along with the characteristics of activation curves, inactivation curves, and recovery curves after inactivation were changed in the MI group. The peak current densities of control group, MI group, and fluvastatin group (n = 10 in each group) were −71.77 ± 23.22 pA/pF, −126.75 ± 18.90 pA/pF, and −86.42 ± 28.30 pA/pF, respectively (F = 4.862, P = 0.008). Fluvastatin can decrease the current amplitude which has been increased by MI. Moreover, fluvastatin induced the inactivation curves and post-inactive recovery curves moving to the position of the control group. But the expression of sodium channel-associated protein (Nav1.7) had no significantly statistical difference among the three groups. The percentages of Nav1.7 protein in control group, MI group, and fluvastatin group (n = 5 in each group) were 21.49 ± 7.33%, 28.53 ± 8.26%, and 21.64 ± 2.78%, respectively (F = 1.495, P = 0.275). Moreover, MI reduced the electrical activity of AP and increased amplitude of AP, fluvastatin pretreatment could recover amplitude and electrical activity of AP. The probability of neurons induced continuous APs were 44.44%, 14.29%, and 28.57% in control group, MI group, and fluvastatin group, respectively. Conclusions: Fluvastatin pretreatment can recover electrophysiology characteristics of ion channel and AP in SG neurons in a rabbit model of MI. It could be considered as potential method for treating coronary heart diseases.
The Incidence and Costs of Job Loss: 1982-1991

I focus on two aspects of Job loss. First, I examine evidence on the incidence of job loss by worker and job characteristics including age, education, race, sex, industry, and tenure over the period from 1982 to 1991. Second, I examine the cost of job loss to workers in the form of 1) lower post-displacement employment probabilities, 2) lower probabilities of full-time employment for re-employed workers, and 3) lower earnings for full-time workers. Using data from Displaced Workers Surveys (DWS) from 1984 through 1992 to study job loss from 1982-91, I find that older workers and more educated workers are relatively more likely to suffer a job loss in the latter part of this period. Additionally, job loss became more common in some important service industries and relatively less common in manufacturing during the latter part of the ten-year period studied. Supplementing the DWS data with data from the outgoing rotation groups of the Current Population Survey from 1982-1991, I find that displaced workers are, relative to non-displaced workers, 1) less likely to be employed and 2) more likely to be employed part-time conditional on being employed. These effects seem to decline with time since displacement. There is no systematic secular change in these costs of displacement, either in the aggregate or for particular groups. Finally, I examine the earnings losses of full-time re-employed displaced workers by comparing their earnings change with the earnings change of full-time employed workers who were not displaced. I find, consistent with what others have found, that these earnings losses are substantial. Overall, the costs to displaced workers of job loss are substantial and come in several forms. However, the public perception that the current sluggish economy is worse than earlier downturns may reflect more who has lost jobs recently rather than either increased overall job loss or increased costs to those who are losing Jobs.
A Fast Distributed Algorithm for Large-Scale Demand Response Aggregation

A major challenge to implementing residential demand response is that of aligning the objectives of many households, each of which aims to minimize its payments and maximize its comfort level, while balancing this with the objectives of an aggregator that aims to minimize the cost of electricity purchased in a pooled wholesale market. This paper presents a fast distributed algorithm for aggregating a large number of households with a mixture of discrete and continuous energy levels. A distinctive feature of the method in this paper is that the nonconvex demand response (DR) problem is decomposed in terms of households as opposed to devices, which allows incorporating more intricate couplings between energy storage devices, appliances, and distributed energy resources. The proposed method is a fast distributed algorithm applied to the double smoothed dual function of the adopted DR model. The method is tested on systems with up to 2560 households, each with 10 devices on average. The proposed algorithm is designed to terminate in 60 iterations irrespective of system size, which can be ideal for an on-line version of this problem. Moreover, numerical results show that with minimal parameter tuning, the algorithm exhibits a very similar convergence behavior throughout the studied systems and converges to near-optimal solutions, which corroborates its scalability.
Impact of ISO 9000 registration on company performance: Evidence from Malaysia

This study investigates the determinants of corporate performance and evaluates whether ISO 9000 registration impacts corporate performance in a sample of Malaysian listed companies. A performance evaluation model was developed on the basis of four predictor variables that include return on sales (ROS), lender security, free cash flow and economic value added (EVA). The results indicate that the ROS and EVA do determine the performance of the Malaysian listed companies. We also find association between ISO 9000 registration and financial performance in the sampled companies.
The Liberalization of Tunisian Agriculture and the European Union: A Prospective Analysis

In the year 2000, Tunisia and the European Union are to begin negotiations on the liberalization of agricultural trade between them under the terms of a partnership agreement signed in 1995. The political attachment of Tunisia to Europe will provide an opportunity for it to leave behind the agricultural policy pursued hitherto, a policy aimed essentially at achieving self-sufficiency in food production. This has proved to be costly for the country since it has led to poor resource allocation. The issue is therefore one of how to reform Tunisian agriculture at the least possible cost, especially for rural households, and to determine to what extent Europe can be of help in the move to a more dynamic agricultural system. The present paper analyzes various prospective scenarios for Tunisian agriculture to the 2010 horizon, using dynamic general equilibrium modelling. The outcome is that in the absence of reciprocal concessions from the European Union, possibly in the form of a lifting of tariff quotas, Tunisia would have little incentive to reduce either its assistance to the agricultural sector or its protective barriers against outside pressure. Tunisian agriculture would in this case continue to show lacklustre performance, but the welfare of rural households would be more or less preserved. Conversely, increased access to the European market for export products for which Tunisia has a competitive edge would greatly facilitate the transition and help improve resource reallocation. Some of the gains made could then be redistributed to rural communities in order to offset marginal losses. By granting the same trade privileges to its other partners, Tunisia would however maximize its growth potential and reduce still further its losses in the agricultural sector. The European Union would lose in terms of outlets for its exports but would gain overall in terms of the economic development of Tunisia.
Systematic Monetary Policy and the Forward Premium Puzzle

Is systematic monetary policy a driver of the forward premium puzzle, i.e. the tendency of high interest-rate currencies to appreciate, thus strongly violating Uncovered Interest Parity (UIP)? We address this question by studying a battery of monetary policy rules in a small open economy that is subject to stationary but persistent domestic and foreign shocks. Each rule leads to model-implied UIP violations, which we derive analytically and then calibrate numerically. Our key finding is that only a forward-looking rule based on CPI inflation can account for frequently observed strong UIP violations.
Reflectance realism and colour constancy: What would count as scientific evidence for hilbert's ontology of colour?

Reflectance realism is an important position in the philosophy of colour. This paper is an examination of David R. Hilbert's case for there being scientific support for the theory. The specific point in question is whether colour science has shown that reflectance is recovered by the human visual system. Following a discussion of possible counter-evidence in the recent scientific literature, I make the argument that conflicting interpretations of the data on reflectance recovery are informed by different theoretical assumptions about the nature of colour, and of perception. If this is so, there cannot be neutral empirical evidence on this point, and this does seem to undermine Hilbert's claim for empirical support. In the end, I suggest alternative ways of thinking about the relationship between colour ontology and empirical work on colour.
Chemical Compounds from Femoral Gland Secretions of Male Iberian Rock Lizards, Lacerta monticola cyreni

In spite of the importance of chemoreception and chemical signals in the social organization of lizards, there are only a few studies examining the chemical composition of secretions of lizards used for scent marking. The secretion of the femoral glands of male Iberian rock lizards (Lacerta monticola cyreni) contains 44 lipophilic compounds, including several steroids (mainly cholesterol), and n-C6 to n-C22 carboxylic acids, and minor components such as esters of carboxylic acids, alcohols, squalene, and one lactone. These compounds were identified on the basis of mass spectra, obtained by GC-MS. Most lipids were detected in all individuals, although relative proportions of each chemical show a high interindividual variability. This variability might be related to the characteristics or physical and health condition of males and might be the basis of female choice based on chemical cues observed in this lizard species.
Differentiation of Human Embryonic Stem Cells into Embryoid Bodies Comprising the Three Embryonic Germ Layers

rived from totipotent cells of the embryo and therefore, can serve as a putative source of numerous types of differentiated cells. Of the various ES cell lines, murine (mES) cells have been investigated extensively and were shown to be genuinely pluripotent, being able to differentiate into all embryonic cell types (1,2). The multipotency of embryonic stem cells is evident from three main features: (A) These undifferentiated cells can be injected into the blastocyst cavity Molecular Medicine 6(2): 88–95, 2000
Optimizing Generative Dialog State Tracker via Cascading Gradient Descent

For robust spoken dialog management, various dialog state tracking methods have been proposed. Although discriminative models are gaining popularity due to their superior performance, generative models based on the Partially Observable Markov Decision Process model still remain attractive since they provide an integrated framework for dialog state tracking and dialog policy optimization. Although a straightforward way to fit a generative model is to independently train the component probability models, we present a gradient descent algorithm that simultaneously train all the component models. We show that the resulting tracker performs competitively with other top-performing trackers that participated in DSTC2.
Chemokines and chemokine receptors expression in the lesions of patients with American cutaneous leishmaniasis

American cutaneous leishmaniasis (ACL) presents distinct active clinical forms with different grades of severity, known as localised (LCL), intermediate (ICL) and diffuse (DCL) cutaneous leishmaniasis. LCL and DCL are associated with a polarised T-helper (Th)1 and Th2 immune response, respectively, whereas ICL, or chronic cutaneous leishmaniasis, is associated with an exacerbated immune response and a mixed cytokine expression profile. Chemokines and chemokine receptors are involved in cellular migration and are critical in the inflammatory response. Therefore, we evaluated the expression of the chemokines CXCL10, CCL4, CCL8, CCL11 and CXCL8 and the chemokine receptors CCR3, CXCR3, CCR5 and CCR7 in the lesions of patients with different clinical forms of ACL using immunohistochemistry. LCL patients exhibited a high density of CXCL10+, CCL4+ and CCL8+ cells, indicating an important role for these chemokines in the local Th1 immune response and the migration of CXCR3+ cells. LCL patients showed a higher density of CCR7+ cells than ICL or DCL patients, suggesting major dendritic cell (DC) migration to lymph nodes. Furthermore, DCL was associated with low expression levels of Th1-associated chemokines and CCL11+ epidermal DCs, which contribute to the recruitment of CCR3+ cells. Our findings also suggest an important role for epidermal cells in the induction of skin immune responses through the production of chemokines, such as CXCL10, by keratinocytes.
Uttar Pradesh - lagging state of India: economic development and role of banks

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