Miracle-dz/UniFAR-FTUs huggingface dataset:
Structure‐based design of novel Chlamydomonas reinhardtii D1‐D2 photosynthetic proteins for herbicide monitoring

The D1‐D2 heterodimer in the reaction center core of phototrophs binds the redox plastoquinone cofactors, QA and QB, the terminal acceptors of the photosynthetic electron transfer chain in the photosystem II (PSII). This complex is the target of the herbicide atrazine, an environmental pollutant competitive inhibitor of QB binding, and consequently it represents an excellent biomediator to develop biosensors for pollutant monitoring in ecosystems. In this context, we have undertaken a study of the Chlamydomonas reinhardtii D1‐D2 proteins aimed at designing site directed mutants with increased affinity for atrazine. The three‐dimensional structure of the D1 and D2 proteins from C. reinhardtii has been homology modeled using the crystal structure of the highly homologous Thermosynechococcus elongatus proteins as templates. Mutants of D1 and D2 were then generated in silico and the atrazine binding affinity of the mutant proteins has been calculated to predict mutations able to increase PSII affinity for atrazine. The computational approach has been validated through comparison with available experimental data and production and characterization of one of the predicted mutants. The latter analyses indicated an increase of one order of magnitude of the mutant sensitivity and affinity for atrazine as compared to the control strain. Finally, D1‐D2 heterodimer mutants were designed and selected which, according to our model, increase atrazine binding affinity by up to 20 kcal/mol, representing useful starting points for the development of high affinity biosensors for atrazine.
VERTICAL EXTERNALITIES WITH LUMP-SUM TAXES: HOW MUCH DIFFERENCE DOES UNEMPLOYMENT MAKE?

This paper analyses how the existence of unemployment affects the conventional approach to vertical externalities. We discuss the optimality rule for the provision of public inputs both in a unitary and in a federal state. Our findings indicate that decentralising spending responsability on public inputs in the presence of unemployment allows output to be closer to the first best level. Moreover, we describe the inability of the federal government, behaving as a Stackelberg leader, to replicate the unitary outcome, unless there are new policy instruments at government's disposal.
Prevention of cancer through immunization: Prospects and challenges for the 21st century

Persistent infection by several microbial agents is responsible for at least 15% of cancer globally, including most cancers of the liver, stomach, and cervix. The recent development of vaccines that can prevent infection and premalignant disease caused by human papillomaviruses (HPV), which cause virtually all cases of cervical cancer as well as some other cancers, has focused renewed attention on infection control as a means of reducing the global cancer burden. For vaccines to prevent cancer‐causing infection with hepatitis C virus, Helicobacter pylori, or Epstein Barr virus, new vaccine technologies to induce more effective protective responses are required. For the two available cancer control vaccines, designed to prevent infection with HPV and hepatitis B virus, the major challenge is to promote effective vaccine deployment through education programs and increased affordability/accessibility for underserved populations, particularly in the developing world, where the cancer burden attributable to infection by these two viruses is greatest.
Myelin‐ and microbe‐specific antibodies in guillain‐barré syndrome

We surveyed the frequency of reported infections and target autoantigens in 56 Guillain Barré syndrome (GBS) patients by detecting antibodies to myelin and microbes. Sulfatide (43%), cardiolipin (48%), GD1a (15%), SGPG (11%), and GM3 (11%) antibodies were the most frequently detected heterogenous autoantibodies. A wide spectrum of antimicrobial IgG and IgM antibodies were also detected; mumps‐specific IgG (66%), adenovirus‐specific IgG (52%), varicella‐zoster virus‐specific IgG (46%), and S. pneumoniae serotype 7‐specific IgG (45%) were the most prevalent. Our results indicate that polyclonal expansion of physiologic and pathologic antibodies and/or molecular mimicry likely occurs following infection and is related to other autoimmune factors in the etiology of GBS. Although no single definitive myelin‐specific autoantibody was identified, our results suggest a unique pattern of reactivity against autoantigens.
Global status of renewable energy and market: Future prospectus and target

The World is gradually shifting focus toward its renewable energy resource. Driven by an increasing demand for electricity and widening gap between demand and supply. World has target 800 GW of Renewable power by 2035, Without including Small Hydro power plant and has been enduring a pressing need to reduce its high and increasing greenhouse gas emission. Renewable Energy in the world day by day increases its installation capacity. Renewable electric energy demand has grown by an average 30% per annum over the past 20 years against a backdrop of rapidly declining costs and prices. By early 2010, policy targets for renewable energy at the national level existed in at least 85 countries worldwide, including all 27 European Union member states . Many national targets are for shares of electricity production, typically 5-30 percent, but range from 2 percent to 90 percent. By early 2010, more than two-thirds of the 85 countries with existing national targets were aiming for 2020 or beyond in some manner. Developing countries can virtually stabilize their C02 emissions by 2025 and reduce afterwards, whilst at the same time increasing energy consumption due to economic growth. OECD countries will be able to reduce their emissions by up to 90% by 2050.
Pharmacokinetics and Safety of Tenofovir in HIV-Infected Women During Labor and Their Infants During the First Week of Life

Background:Data describing the pharmacokinetics and safety of tenofovir in neonates are lacking. Methods:The HIV Prevention Trials Network 057 protocol was a phase 1, open-label study of the pharmacokinetics and safety of tenofovir disoproxil fumarate (TDF) in HIV-infected women during labor and their infants during the first week of life with 4 dosing cohorts: maternal 600 mg doses/no infant dosing; no maternal dosing/infant 4 mg/kg doses on days 0, 3, and 5; maternal 900 mg doses/infant 6 mg/kg doses on days 0, 3, and 5; maternal 600 mg doses/infant 6 mg/kg daily for 7 doses. Pharmacokinetic sampling was performed on cohort 1 and 3 mothers and all infants. Plasma, amniotic fluid, and breast milk tenofovir concentrations were determined by liquid chromatographic–tandem mass spectrometric assay. The pharmacokinetic target was for infant tenofovir concentration throughout the first week of life to exceed 50 ng/mL, the median trough tenofovir concentration in adults receiving standard chronic TDF dosing. Results:One hundred twenty-two mother–infant pairs from Malawi and Brazil were studied. Tenofovir exposure in mothers receiving 600 and 900 mg exceeded that in nonpregnant adults receiving standard 300 mg doses. Tenofovir elimination in the infants was equivalent to that in older children and adults, and trough tenofovir plasma concentrations exceeded 50 ng/mL in 74%–97% of infants receiving daily dosing. Conclusions:A TDF dosing regimen of 600 mg during labor and daily infant doses of 6 mg/kg maintains infant tenofovir plasma concentration above 50 ng/mL throughout the first week of life and should be used in the studies of TDF efficacy for HIV prevention of mother-to-child transmission and early infant treatment.
Relapsing-remitting multiple sclerosis and human herpesvirus 6 active infection.

BACKGROUND Recent studies have focused on the relationship between human herpesvirus 6 (HHV-6) and multiple sclerosis (MS). OBJECTIVE To analyze HHV-6 messenger RNA expression in patients with relapsing-remitting (RR) MS vs healthy blood donors (HBDs). DESIGN One hundred fifty-four subjects were enrolled in the study: 105 patients with RRMS (32 in relapse) and 49 HBDs. Total DNA and messenger RNA were extracted from serum and blood samples, respectively, and analyzed by quantitative real-time reverse transcription-polymerase chain reaction for the detection of 3 HHV-6 immediate-early genes (U16/U17,U89/U90, and U94) and both HHV-6 variants (HHV-6A and HHV-6B). RESULTS Active HHV-6 infection was detected in 16% of patients with RRMS vs 0% of HBDs (P = .003). Seven patients with RRMS with exacerbation had HHV-6 active replication, and the virus remained latent in only 1 of them. We did not find any statistically significant difference between HHV-6 active or latent infection for patients in remission (P = .12). Among patients with RRMS with HHV-6 active replication, viral load was higher when they experienced an acute attack than when in remission (P = .04). In those patients with RRMS who had an active infection only, HHV-6A was found. Cell-free HHV-6 DNA detected in serum samples confirmed the results. CONCLUSIONS The results show that a subset of patients with RRMS experience HHV-6 active infection, and there likely is an association between the viral active replication and relapses; therefore, HHV-6 active infection may imply a greater risk of exacerbations in a subgroup of patients with RRMS.
Evidence for multiple OmpR-binding sites in the upstream activation sequence of the ompC promoter in Escherichia coli: a single OmpR-binding site is capable of activating the promoter

We present experimental evidence for the existence of multiple activator-binding sites in the upstream sequence of the ompC promoter, the expression of which is activated by the positive regulator OmpR in response to the osmolarity of the medium. We also found that a single OmpR-binding site can activate the ompC promoter, providing that the binding site is close and placed stereospecifically with respect to the canonical-35 and -10 regions.
EVALUATING POLICIES PROMOTING ENTREPRENEURSHIP—A CROSS-CULTURAL COMPARISON OF ENTREPRENEURSHIP CASE STUDY: SINGAPORE AND MALAYSIA

ABSTRACT Opportunities and constraints vary according to the environment. This paper examines the entrepreneur as a function of the environment to draw lessons which may be applied in future research. The study incorporates literature review with field research conducted during 1986 in the Malaysian Peninsula. The paper concludes with supporting evidence that entrepreneurs have a common driving force wherever they may be, but this may be enhanced or repressed by government intervention and environmental considerations such as culture.
Tying Everything Together: The Multiple Roles of Cysteine String Protein (CSP) in Regulated Exocytosis

In addition to the core vesicle fusion machinery, the SNARE proteins, a large number of regulatory proteins have been implicated in the process of Ca2+‐dependent exocytosis. How these exocytotic proteins are properly targeted and how their myriad interactions are temporally and spatially coordinated is poorly understood. Cysteine string protein (CSP), a secretory vesicle membrane protein and a member of the dnaJ family of co‐chaperones, may assist in performing this function. Through its interaction with the ubiquitous chaperone, Hsc70, it is thought that cysteine string protein targets chaperone complexes to the exocytotic machinery to facilitate the correct folding of polypeptides or to regulate the assembly of protein complexes. Since its discovery, there have been conflicting reports from different systems concerned with whether cysteine string protein exerts its effects on exocytosis either up‐ or down‐stream of Ca2+‐influx. In this review, we summarize recent experiments that associate cysteine string protein with the regulation of vesicle filling, vesicle docking, Ca2+‐channels and the SNARE proteins themselves, hence supporting a role for cysteine string protein as a multifunctional secretory co‐chaperone. In addition, we provide an update on the mammalian isoforms of cysteine string protein following the recent discovery of two novel cysteine string proteins.
The risk of model misspecification and its impact on solvency measurement in the insurance sector

Purpose - The purpose of this paper is to study the risk of misspecifying solvency models for insurance companies. Design/methodology/approach - Based on a basic solvency model, the authors examine the sensitivity of different risk measures with respect to model misspecification. An analysis considers the effects of introducing stochastic jumps and linear, as well as non-linear dependencies into the basic setting on the solvency capital requirements, shortfall probability and expected policyholder deficit. Additionally, the authors take a regulatory view and consider the degree to which the deviations in risk measures, due to the different model specifications, can be diminished by means of requiring interim financial reports. Findings - The simulation results suggest that the sensitivity of solvency capital as a risk measure – as it is in regulatory practice – underestimates the actual misspecification risk that policyholders are exposed to. It is also found that semi-annual mandatory interim reports can already reduce the model uncertainty faced by a regulator, significantly. This has important implications for the design of risk-based capital standards and the implementation of internal solvency models. Originality/value - The results from the Monte Carlo simulation show that changes in the specification of a solvency model have a much greater impact on shortfall probabilities and expected policyholder deficits than they have on capital requirements. The shortfall risk measures react much more sensitively to small changes in the model assumptions, than the capital requirements. This leads us to the conclusion that regulators should not solely rely on capital requirements to monitor the solvency situation of an insurer, but should additionally consider shortfall risk measures. More precisely, an analysis of model risk focusing on the sensitivity of capital requirements will typically underestimate the relevant risk of model misspecification from a policyholder's perspective. Finally, the simulation results suggest that mandatory interim reports on the solvency and financial situation of an insurance company are a powerful tool in order to reduce the model uncertainty faced by regulators.
Economics, Party, and the Vote: Causality Issues and Panel Data

Conventional wisdom argues that national economic perceptions generally have an important impact on the vote choice in democracies. Recently, a revisionist view has arisen, contending that this link, regularly observed in election surveys, is mostly spurious. According to the argument, partisanship distorts economic perception, thereby substantially exaggerating the real vote connection. These causality issues have not been much investigated empirically, despite their critical importance. Utilizing primarily American, and secondarily British and Canadian, election panel surveys, we confront directly questions of the time dynamic and independent variable exogeneity. We find, after all, economics clearly matters for the vote. Indeed, once these causality concerns are properly taken into account, the impact of economic perceptions emerges as larger than previously thought. As well, the actual impact of partisanship is clearly reduced.
The Initial Listing Decisions of Firms that Go Public

We analyze the initial listing decisions of IPOs that qualify for New York Stock Exchange listing. We find that IPOs are more likely to list on the exchange where their industry peers are listed. Further, reverse LBOs and carveouts are more likely to choose the NYSE if the firm or their parent was previously NYSE-listed. Consistent with avoidance of delisting costs, we find that smaller, riskier firms tend to list on Nasdaq. Although direct issue costs are higher on the NYSE than on Nasdaq, total issue costs do not differ across exchanges and are unlikely to affect the listing decision.
Implications of biotech traits with segregation costs and market segments: the case of Roundup Ready® Wheat

Roundup Ready-Wheat (RRW) is one of the first genetically modified (GM) traits for the wheat sector. We develop a spatial partial equilibrium model of the higher-protein hard wheat market and assess the changes in the distribution of welfare associated with release and adoption of RRW. It incorporates segments for GM aversion in each market and segregation costs for each segment. In the most likely scenario, producer and consumer welfare increases by $301 and $252 million, respectively. Producers of hard red spring wheat in the US and Canada gain. There are welfare losses to hard red winter wheat growers in the US and to EU consumers who have to import at a higher cost. Oxford University Press and Foundation for the European Review of Agricultural Economics 2008; all rights reserved. For permissions, please email journals.permissions@oxfordjournals.org, Oxford University Press.
The impact of EBV and HIV infection on the microenvironmental niche underlying Hodgkin lymphoma pathogenesis

The pathogenesis of classical Hodgkin lymphoma (cHL) is still enigmatic, largely because its tumor cells, the so‐called Hodgkin and Reed–Stenberg (HRS) cells, invariably reside in a prominent reactive microenvironment, are rare and therefore difficult to analyze. On the other hand, the broadly investigated cHL‐derived cell lines are not unequivocally considered as suitable and representative models for this puzzling disease. Based on current knowledge, it appears that the cross talk between the tumor cells and the reactive infiltrate of the microenvironment is complex and that multiple mechanisms occur, making cHL a very heterogeneous disease. In 20–40% of cHL cases, HRS cells carry a monoclonal infection by Epstein Barr virus (EBV), which is considered a tumor‐initiating factor. In these cases, EBV shows a latency type II infection pattern with the expression of latent membrane protein‐1 (LMP‐1), a viral oncoprotein that mimics CD40 activation. This scenario is particularly intriguing for the pathogenesis of cHL arising in HIV‐infected patients, which, for still obscure reasons, is invariably EBV‐associated with LMP‐1 expression in HRS cells. Recent evidences are consistent with the occurrence of different pathogenic pathways variably triggered by virus infections (EBV and HIV), genetic alterations, and interactions with critical microenvironmental components. This review focuses on the different microenvironmental niches that characterize cHL of the general population as well as cases of HIV‐infected patients. A more comprehensive understanding of the complex interplay existing between HRS and tumor microenvironment is pivotal for the development of more effective treatments, particularly for relapsed or refractory diseases.
Size and Value Premium in International Portfolios: Evidence from Fifteen European Countries

The current study evaluates the performance of the Fama and French three-factor model in a global setting with stocks selected from 15 European countries. We employed the multivariate regression approach after sorting six portfolios according to size and book-to-market. The constituent stocks were selected to represent each country of our sample. In order to homogenize the returns we used the spot exchange rates of non-euro-area countries to convert prices into euros. Since we were analyzing on a global portfolio level we used the MSCI EMU index as the proxy for the market portfolio. Daily returns were employed for a period of five years from January 2002 to December 2006. The results were not very encouraging for the three-factor model. Except for one portfolio, the three-factor model failed to explain the variations in returns, and even in the single portfolio that demonstrated size and value premiums, the market premium was insignificant. Our findings are consistent with Griffin (2002), who suggested that the three-factor model is domestic in nature and performs poorly for global portfolios.
Misspecifiation of the Panzar-Rosse Model: Assessing Competition in the Banking Industry

This paper demonstrates that the level of competition in the existing Panzar Rosse (P-R) literature is systematically overestimated and that the tests on both monopoly and perfect competition are distorted. This is due to the use of bank revenues divided by total assets as dependent variable in the P-R model instead of unscaled bank revenues. We provide both theoretical and empirical evidence to illustrate the impact of the misspecification on the estimation of competition and the statistical tests on the market structure. Inclusion of scale variables as explanatory variables, which is commonpractice in the current literature, has a similar distorting effect. Our overview of the extensive P-R literature reveals that all 28 studies considered suffer from these types of misspecification. The empirical evidence provided in this paper is based on a large sample of more than 18,000 banks in 101 countries over 16 years. We find that monopoly cannot be rejected in 28% of the countries (against 0% under misspecification) and that perfect competition cannot be rejected in 38% of the cases (against 20-30% under misspecification).
ALFA detector control system

ALFA (Absolute Luminosity For ATLAS) is one of the sub-detectors of ATLAS (A Toroidal LHC Apparatus). The ALFA system is composed by four stations installed in the LHC tunnel 240 m away from the ATLAS interaction point. Each station has a vacuum and ventilation system, movement control and all the required electronics for signal processing. The Detector Control System (DCS) provides control and monitoring of several components and ensures the safe operation of the detector contributing to good Data Quality. This paper describes the ALFA DCS system including a detector overview, operation aspects and hardware control through a SCADA system, WinCC OA.
Using a Count of Neonatal Morbidities to Predict Poor Outcome in Extremely Low Birth Weight Infants: Added Role of Neonatal Infection

OBJECTIVE. A count of 3 neonatal morbidities (bronchopulmonary dysplasia, brain injury, and severe retinopathy of prematurity) strongly predict the risk of death or neurosensory impairment in extremely low birth weight infants who survive to 36 weeks' postmenstrual age. Neonatal infection has also been linked with later impairment. We examined whether the addition of infection to the count of 3 neonatal morbidities further improves the prediction of poor outcome. METHODS. We studied 944 infants who participated in the Trial of Indomethacin Prophylaxis in Preterms and survived to 36 weeks' postmenstrual age. Culture-proven sepsis, meningitis, and stage II or III necrotizing enterocolitis were recorded prospectively. We investigated the incremental prognostic importance of neonatal infection by adding terms for the different types of infection to a logistic model that already contained terms for the count of bronchopulmonary dysplasia, brain injury, and severe retinopathy. Poor outcome at 18 months of age was death or survival with 1 or more of the following: cerebral palsy, cognitive delay, severe hearing loss, and bilateral blindness. RESULTS. There were 414 (44%) infants with at least 1 episode of infection or necrotizing enterocolitis. Meningitis and the presence of any type of infection added independent prognostic information to the morbidity-count model. The odds ratio associated with infection or necrotizing enterocolitis in this model was 50% smaller than the odds ratio associated with each count of the other 3 neonatal morbidities. Meningitis was rare and occurred in 22 (2.3%) of 944 infants. CONCLUSIONS. In this cohort of extremely low birth weight infants who survived to 36 weeks' postmenstrual age, neonatal infection increased the risk of a late death or survival with neurosensory impairment. However, infection was a weaker predictor of poor outcome than bronchopulmonary dysplasia, brain injury, and severe retinopathy.