Miracle-dz/UniFAR-FTUs huggingface dataset:
Impact of HIV on host-virus interactions during early hepatitis C virus infection.

BACKGROUND Human immunodeficiency virus (HIV) may influence the outcome and natural history of hepatitis C virus (HCV) infection through an impact on acute HCV-specific T cell responses. METHODS Fifty-five HIV-positive males with acute HCV infection were identified; monoinfected individuals (n = 8) were used for peripheral blood mononuclear cell comparison. In 14 coinfected and 8 HCV-monoinfected patients, HCV-specific T cell responses against a range of HCV antigens were assessed using interferon (IFN)-gamma enzyme-linked immunospot (ELISpot) and proliferation assays. E1/E2 region genetic diversity and the selection pressure on the virus were measured in 8 coinfected patients by use of cloned sequences over time. RESULTS HCV persisted in 52 (95%) coinfected individuals. HCV/HIV coinfection significantly reduced IFN-gamma ELISpot responses versus those in HCV-monoinfected individuals, especially against nonstructural proteins (1/10 vs. 5/8; P = .008). In coinfected patients, increased HCV genetic diversity was observed between the first and subsequent time points, with no evidence for positive selection in the E1/E2 region sequenced. CONCLUSION HIV coinfection is associated with increased rates of HCV persistence and a lack of critical CD4 T cell responses, with no evidence of immune selection pressure during early HCV infection. Loss of key cellular immune responses against HCV during acute disease may contribute to the failure of early host control of HCV in HCV/HIV-coinfected patients.
Biological Crystallography Structural Biology Contributions to the Discovery of Drugs to Treat Chronic Myelogenous Leukaemia

Chronic myelogenous leukaemia (CML) results from the Bcr-Abl oncoprotein, which has a constitutively activated Abl tyrosine kinase domain. Although most chronic phase CML patients treated with imatinib as first-line therapy maintain excellent durable responses, patients who have progressed to advanced-stage CML frequently fail to respond or lose their response to therapy owing to the emergence of drug-resistant mutants of the protein. More than 40 such point mutations have been observed in imatinib-resistant patients. The crystal structures of wild-type and mutant Abl kinase in complex with imatinib and other small-molecule Abl inhibitors were determined, with the aim of understanding the molecular basis of resistance and to aid in the design and optimization of inhibitors active against the resistance mutants. These results are presented in a way which illustrates the approaches used to generate multiple structures, the type of information that can be gained and the way that this information is used to support drug discovery.
Causal models for debugging and control in cloud computing

Two challenges in the theory and practice of cloud computing are: (1) smart control (allocation) of resources under exploration constraints, on time-varying systems, and (2) understanding and debugging of the performance of complex systems that involve e.g. virtualization. In this paper, we examine how these challenges can be approached using causal models. For challenge (1) we investigate how to infer and use causal models and selection diagrams to design and integrate experiments in a principled way, as well as to cope with partially varying systems. For challenge (2) we examine how to formalize performance attribution and debugging questions by counterfactual probabilities, and how to approximately answer them based on inferred (non-deterministic) graphical causal models.
Implications of rRNA Operon Copy Number and Ribosome Content in the Marine Oligotrophic Ultramicrobacterium Sphingomonassp. Strain RB2256

ABSTRACT Sphingomonas sp. strain RB2256 is a representative of the dominant class of ultramicrobacteria that are present in marine oligotrophic waters. In this study we examined the rRNA copy number and ribosome content of RB2256 to identify factors that may be associated with the relatively low rate of growth exhibited by the organism. It was found that RB2256 contains a single copy of the rRNA operon, in contrast to Vibrio spp. , which contain more than eight copies. The maximum number of ribosomes per cell was observed during mid-log phase; however, this maximum content was low compared to those of faster-growing, heterotrophic bacteria (approximately 8% of the maximum ribosome content of Escherichia coli with a growth rate of 1.5 h−1). The low number of ribosomes per cell appears to correlate with the low rate of growth (0.16 to 0.18 h−1) and the presence of a single copy of the rRNA operon. However, on the basis of cell volume, RB2256 appears to have a higher concentration of ribosomes than E. coli (approximately double that of E. coli with a growth rate of 1.5 h−1). Ribosome numbers reached maximum levels during mid-log-phase growth but decreased rapidly to 10% of maximum during late log phase through 7 days of starvation. The cells in late log phase and at the onset of starvation displayed an immediate response to a sudden addition of excess glucose (3 mM). This result demonstrates that a ribosome content 10% of maximum is sufficient to allow cells to immediately respond to nutrient upshift and achieve maximum rates of growth. These data indicate that the bulk of the ribosome pool is not required for protein synthesis and that ribosomes are not the limiting factor contributing to a low rate of growth. Our findings show that the regulation of ribosome content, the number of ribosomes per cell, and growth rate responses in RB2256 are fundamentally different from those characteristics in fast-growing heterotrophs like E. coliand that they may be characteristics typical of oligotrophic ultramicrobacteria.
Association between sibship size and allergic diseases in the Glasgow Alumni Study

Background: Recent epidemiological studies consistently report an inverse association between sibship size and allergic disease, but evidence from individuals born before the 1980s is inconsistent. As information on relative permanence of this finding may offer clues to its biological explanation, the association between sibship size and allergic disease in individuals born between 1918 and 1952 was investigated. Methods: Cross sectional surveys conducted by the Student Health Service at the University of Glasgow (1948–68) provided data on 14 140 men and women aged 16–30 years at the time of examination. The main outcome measures studied were self-reported asthma, eczema-urticaria, and hay fever. Results: A total of 1677 individuals (11.9%) provided a positive history of at least one of the three allergic diseases: 457 (3.2%) asthma, 594 (4.2%) eczema-urticaria, and 885 (6.3%) hay fever. Compared with those without siblings (reference odds ratio = 1), the odds ratios (95% confidence intervals) for having any allergic disease among those with one, two or three siblings were 0.86 (0.75 to 0.99), 0.80 (0.69 to 0.93), and 0.70 (0.60 to 0.83), respectively (ptrend<0.001). Increasing birth order and low socioeconomic position in childhood were associated with a lower risk of allergy. Adjustment for birth order, year of birth, age, sex, socioeconomic position in childhood, and family history of allergy did not materially alter the results. Conclusions: There is a robust inverse association between sibship size and allergic disease even among people born in the first half of the 20th century. These results favour relatively time-independent explanations for this phenomenon (such as the hygiene hypothesis or parity related changes in the intrauterine environment) over new environmental exposures.
Everyday Illegal: When Policies Undermine Immigrant Families

authors examined the process whereby a state did not ever enact this type of funding for higher education. The introduction of such a state or states would be an ideal next step in drawing conclusions about the future of performance funding. Because the work is dense and aimed at scholars and policy-makers, the organization of the book around the stages of policy adoption was a smart choice. Dougherty and Natow use the eight cases as examples and data to describe the theoretical implications of policy adoption while laying out the step-by-step history of each state’s particular trajectory. Though the work provides a substantial account of performance funding for those interested in the details (and there are many details), the authors are also able to broaden their insights for the general reader. Moreover, the appendix is a must-read for scholars using case studies, as it is a clear roadmap for how to tackle this methodological style without reproach. Finally, this work stops short of describing and theorizing about the implications of performance funding. This is not a flaw in the work itself but rather a call for continued scholarship. Because of Dougherty and Natow, we know a whole lot about the origins and transformations of higher education performance funding; we know less and thus need more research to understand its effect on higher education more generally. The Politics of Performance Funding for Higher Education will not be a book that you just can’t put down. It doesn’t tell a riveting story, but it does tell an essential policy story. Higher education administrators should read this work to understand the history and context of funding decisions in their states and states around them. This is especially so since the authors believe it will affect most higher education in the next several years, even those not yet touched by this policy. Sociologists and political scientists who are often concurrently writing about diffusion and adoption of policy can benefit from the succinct and adept synthesis of the core theories from both disciplines. The scholars in these fields grappling with K– 12 educational policy, such as the spread of the Common Core, could benefit from their insights. Finally, policy-makers need to read this work. They need to see how decisions are made across states, influenced by their neighbors and non-proximate actors, and how those decisions affect the landscape of higher education.
Monetary policy and the stability of macroeconomic relationships

SUMMARY Estimates of the effect of different international monetary regimes on the parameters of the Phillips curve, the Keynesian consumption function, and other reduced-form macroeconomic relationships are given. The estimates provide a quantitative assessment of the importance of the Lucas critique for such regime shifts. The estimates are calculated by stochastically simulating an estimated multicountry economic model with rational expectations under a fixed exchange rate regime and a flexible exchange rate regime. In both regimes interest rates are the primary instrument of monetary policy. Noticeable shifts occur in most of the macroeconomic relationships, especially in the consumption function and the Phillips curve, and these shifts have simple economic interpretations based on the changes in the variance and the serial correlation of income and prices in the two regimes. However, in most cases the shifts are not large quantitatively. At least, as implemented here, this type of regime shift does not seem to generate much instability in the conventional macroeconomic relationships. Several possible reasons for this finding are discussed in the paper. In this paper I plan to follow in a tradition pioneered by A. W. Phillips almost 40 years ago. Phillips (1954) evaluated monetary and fiscal policy by examining the operating properties of simple policy rules in a fully specified economic model. He did this by applying control theory ideas from the engineering literature. By examining the performance of the model economy under different types of policy rules-for example, proportional, derivative, and integral rules-he attempted to determine which policy rule would work well and which would not work well in practice. Following in the Phillips tradition does not mean that I will use the same theoretical models, econometric methods, or computational techniques that Phillips used. To do so would, in my view, pass by fundamental developments in dynamic economic theory, econometrics, and solution procedures that have been achieved since the time that Phillips wrote. Phillip's (1954) analysis was based on Keynesian ISLM-multiplier-accelerator models that were popular in the early 1950s. The policy evaluation I describe in this lecture differs from Phillips's policy evaluation in several ways. First, it makes use of a dynamic rational expectations model with forward-looking behaviour in consumption, investment, wage-setting, and interest rates. Second, the model is international and exchange rate determination reflects the current high degree of international capital mobility which did not exist when Phillips wrote. Third, the model is empirically estimated; most of Phillips's work was based on simulation models with 'calibrated' parameters. Fourth, the simulations are done stochastically with an empirically
Quantifying the reuse of learning objects

This paper reports the findings of one case study from a larger project, which aims to quantify the claimed efficiencies of reusing learning objects to develop e-learning resources. The case study describes how an online inquiry project Diabetes: A waste of energy was developed by searching for, evaluating, modifying and then integrating as many pre-existing learning objects as possible into a learning design. Development times for the reuse approach were recorded and compared to estimates for the de novo development of an equivalent project. Outcomes suggest that considerable savings can be made using the reuse approach; we estimate a threefold increase in time to develop the Diabetes project using new objects in comparison to reuse. In this case study, gaining permission from owners to reuse objects was not a barrier to reuse. However, in some circumstances, being unable to source pre-existing objects to meet specific requirements, or having to modify objects for reuse, could be problematic.
H2O and OH Gas in the Terrestrial Planet-forming Zones of Protoplanetary Disks

We present detections of numerous 10-20 μm H2O emission lines from two protoplanetary disks around the T Tauri stars AS 205A and DR Tau, obtained using the InfraRed Spectrograph on the Spitzer Space Telescope. Follow-up 3-5 μm Keck NIRSPEC data confirm the presence of abundant water and spectrally resolve the lines. We also detect the P4.5 (2.934 μm) and P9.5 (3.179 μm) doublets of OH and 12CO/13CO v = 1 → 0 emission in both sources. Line shapes and LTE models suggest that the emission from all three molecules originates between ~0.5 and 5 AU, and so will provide a new window for understanding the chemical environment during terrestrial planet formation. LTE models also imply significant columns of H2O and OH in the inner disk atmospheres, suggesting physical transport of volatile ices either vertically or radially, while the significant radial extent of the emission stresses the importance of a more complete understanding of nonthermal excitation processes.
Best of Both Worlds

W e thank the 3 discussants for their contributions. The Women’ Health Initiative (WHI) investigators found a greater CHD risk in the estrogen plus progestin (ie, combined hormone) therapy arm than in the placebo arm of the trial (hazard ratio HR : 1.24, 95% confidence interval CI : 1.00–1.54). In contrast, the Nurses’ Health Study (NHS) investigators found a lower CHD risk in current users of combined hormone therapy than in never users (HR: 0.68, 95% CI: 0.55–0.83, in their most recent publication). We investigated possible reasons for this discrepancy by reanalyzing the NHS data; we used a novel approach that conceptualizes a follow-up observational study as a sequence of “trials. ” The discussants disagree sharply in their assessments of the value of this analytic strategy. Prentice and Hoover are positive, whereas Stampfer finds that our approach combines the limitations of both observational studies and randomized trials, gives biased adherence-adjusted HR estimates, and “adds no new insights on the relation of hormone therapy to CHD. ” He criticizes our approach for its complexity, its need for additional assumptions, and its “black box” nature, and argues for the continued use of the conventional methods routinely employed in NHS publications, owing to their transparency and validity. We now address each of these criticisms.
Fairness and Entitlement in Majoritarian Decision-Making

A method and apparatus for representing ultrasonic echo signals arriving in polar coordinates which are obtained by means of a sector scan technique and which are intermediately stored for the purpose of subsequent display conforming to television standards alternately supply the echo signals to one of at least two complete image memories having respective two-dimensional matrix memory formats. The image memories operate an alternating buffer memories and eliminate the need for conventionally employed vector memories and horizontal memories while nonetheless permitting complete representation of the ultrasonic scans in the form of television images.
Mechanical AGN feedback: controlling the thermodynamical evolution of elliptical galaxies

A fundamental gap in the current understanding of galaxies concerns the thermodynamical evolution of ordinary, baryonic matter. On the one hand, radiative emission drastically decreases the thermal energy content of the interstellar plasma (ISM), inducing a slow cooling flow towards the centre. On the other hand, the active galactic nucleus (AGN) struggles to prevent the runaway cooling catastrophe, injecting huge amount of energy into the ISM. The present study intends to investigate thoroughly the role of mechanical AGN feedback in (isolated or massive) elliptical galaxies, extending and completing the mass range of tested cosmic environments. Our previously successful feedback models in galaxy clusters and groups demonstrated that AGN outflows, self-regulated by cold gas accretion, are able to quench the cooling flow properly without destroying the cool core. Via three-dimensional hydrodynamic simulations (flash 3.3), also including stellar evolution, we show that massive mechanical AGN outflows can indeed solve the cooling-flow problem for the entire life of the galaxy, at the same time reproducing typical observational features and constraints such as buoyant underdense bubbles, elliptical shock cocoons, sonic ripples, dredge-up of metals, subsonic turbulence and extended filamentary or nuclear cold gas. In order to avoid overheating and totally emptying the isolated galaxy, the frequent mechanical AGN feedback should be less powerful and efficient (e∼ 10−4) compared with the heating required for more massive and bound ellipticals surrounded by the intragroup medium (e∼ 10−3).
Toward a Psychological Science for a Cultural Species

Humans are a cultural species, and the study of human psychology benefits from attention to cultural influences. Cultural psychology's contributions to psychological science can largely be divided according to the two different stages of scientific inquiry. Stage 1 research seeks cultural differences and establishes the boundaries of psychological phenomena. Stage 2 research seeks underlying mechanisms of those cultural differences. The literatures regarding these two distinct stages are reviewed, and various methods for conducting Stage 2 research are discussed. The implications of culture-blind and multicultural psychologies for society and intergroup relations are also discussed.
Verification of concurrent objects with asynchronous method calls

Current object-oriented approaches to distributed programs may be criticized in several respects. First, method calls are generally synchronous, which leads to much waiting in distributed and unstable networks. Second, the common model of thread concurrency makes reasoning about program behavior very challenging. A model based on concurrent objects communicating by means of asynchronous method calls has been proposed to combine object orientation and distribution in a more satisfactory way. This paper introduces a reasoning system for this model, focusing on simplicity and modularity. We believe that a simple and compositional proof system is paramount to allow verification of real programs. The proposed proof rules are derived from the Hoare rules of a standard sequential language by means of a semantic encoding preserving soundness and relative completeness.
An optimized GSDG MOSFET design for nanoscale circuit applications

In this paper, the key electrical parameters behavior of Gate Stack Double Gate (GSDG) MOSFET are studied and optimized using multi-objective genetic algorithms (MOGAs) for nanoscale CMOS-based applications. The transconductance and the OFF-current are the key electrical parameters which have been determined by the analytical explicit expressions in saturation and subthreshold regions. The optimized design is used to investigate and demonstrate the impact of the proposed technique on the nanoelectronic devices. In this context, we proposed to investigate the electrical performance of the both circuits, the ring oscillator and the inverter gate, in order to demonstrate the efficiency of the proposed method on the integrated circuit design. In this study an important improvement of the oscillation frequency and gain voltage have been recorded. The obtained results make the proposed design an alternative solution for nanoelectronics applications.
Can lean media support knowledge sharing? Investigating a hidden advantage of process improvement

Is there a positive link between the use of collaborative technologies and knowledge sharing? The body of empirical evidence compiled so far suggests a negative answer to this question. Many explanations have been proposed, the most common being that current collaborative technologies do not yet have enough sophistication, or do not yet provide enough media richness, to enable knowledge sharing. This paper presents evidence that not only suggests that this explanation is wrong, but also that simple collaborative technologies can have a positive effect on knowledge sharing in organizations. This paper shows that, when combined with appropriate social processes, collaborative technologies may foster knowledge sharing. It does so by focusing on process improvement as a group process, and showing that: 1) process improvement is a catalyst to knowledge sharing and 2) a lean communication medium, namely e-mail conferencing, has a positive impact on knowledge sharing when used to support process improvement initiatives.