Miracle-dz/UniFAR-FTUs huggingface dataset:
Functional characterization of the T4 DNA ligase: a new insight into the mechanism of action.

ATP-dependent DNA ligases are essential enzymes in both DNA replication and DNA repair processes. Here we report a functional characterization of the T4 DNA ligase. One N-terminal and two C-terminal deletion mutants were expressed in Escherichia coli as histidine- tagged proteins. An additional mutant bore a substitution of Lys159 in the active site that abolished ATP binding. All the proteins were tested in biochemical assays for ATP-dependent self-adenylation, DNA binding, nick joining, blunt-end ligation and AMP- dependent DNA relaxation. From this analysis we conclude that binding to DNA is mediated by sequences at both protein ends and plays a key role in the reaction. The enzyme establishes two different complexes with DNA: (i) a transient complex (T.complex) involving the adenylated enzyme; (ii) a stable complex (S.complex) requiring the deadenylated T4 DNA ligase. The formation of an S. complex seems to be relevant during both blunt-end ligation and DNA relaxation. Moreover the inactive His-K159L substitution mutant, although unable to self-adenylate, still possesses AMP-dependent DNA nicking activity.
Constraint Programming

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Why Do Public Firms Issue Private and Public Securities?

The market for public firms issuing private equity, debt, and convertible securities is large. Of the over 13,000 issues we examine, more than half are in the private market. Our results show asymmetric information plays a major role in the choice of security type within public and private markets and in the choice of market in which to issue securities. In the public market, firms’ predicted probability of issuing equity declines and issuing debt increases with measures of asymmetric information. There is a weak reversal of this sensitivity in the private market. We also find a large sensitivity of the choice of public versus private markets to asymmetric information, risk and market timing for debt, convertibles, and in particular, equity issues.
Journalistic and Commercial News Values

Why do some events fill the columns and air time of news media, while others are ignored? Why do some stories make banner headlines whereas others merit no more than a few lines? What factors decide what news professionals consider newsworthy? Such questions are often answered – by journalists and media researchers alike – with references to journalistic news values or ‘news criteria’. Some answers are normatively founded; others are pragmatic and descriptive. In the present article, I submit that editorial priorities should not be analyzed in purely journalistic terms. Instead, they should be seen as efforts to combine journalistic norms and editorial ambitions, on the one hand, with commercial norms and market objectives, on the other.
Planning for Path Dependence? The Case of a Network in the Berlin-Brandenburg Optics Cluster

abstract Much research on regional business clusters refers to path dependence as a central feature in the evolution of cluster structures. In many cases, however, little is known about the agentic processes and mechanisms that underlie path dependence. In this article, we explore changes in a specific network in the optics cluster in the German region of Berlin-Brandenburg to show that development of clusters can be driven by elements of both emergence and planning. In particular, we argue that current actors actively and purposively draw upon rules and resources that were shaped not only in the long and discontinuous history of the cluster but also in the recent process of network development that involves careful planning and well-structured planning tools. Using central concepts from structuration theory, we show how agency is implicated in the coordination of the network and how agency turns coordination into a self-reinforcing mechanism. The findings suggest that purposive planning involves a fundamental ambivalence in the processes and outcomes of path dependence, at the level of both the cluster and its constituent networks.
Radar scattering of the ocean surface and sea-roughness properties : A combined analysis from dual-polarizations airborne radar observations and models in C band

[1] An analysis of radar observations in C band combined with models is proposed to study some of the ocean surface properties and their relation with the sea surface backscatter. The electromagnetic part of the models is of different kinds: composite Bragg model with or without including effect of wave breaking zones on the normalized radar cross-section (NRCS), geometrical optics approximation and small-slope approximation model. The surface description is based on the wave spectrum proposed by Kudryavtsev et al. (2003), but tests with the spectrum of Elfouhaily et al. (1997) are also discussed to assess our conclusions. The originality is to use not only the NRCS in HH and VV polarizations, but also their difference in linear units. First, we show that the upwind-to-downwind anisotropy of the radar signal cannot be explained entirely by the modulation of Bragg waves by longer surface waves, but that an additional nonpolarized contribution must be invoked to explain it, consistently with scattering from zones of enhanced roughness associated with breaking waves. Then, combining a composite model and observations in the two polarizations, we assess the contribution of the nonpolarized backscatter on the total NRCS. Finally, the proposed full model, which takes into account the nonpolarized contribution over breaking zones, gives good agreement with the observed polarization ratio and with the NRCS in each polarization.
Monetary Union, Price Level Convergence, and Inflation: How Close is Europe to the United States?

In light of 50 years of economic policies designed to integrate Europe -- culminating in the elimination of euro zone national currencies in early 2002 -- and a vast academic literature on international economic integration, it is of interest to assess how far European integration has come in practice. Using a unique data set, I document the pattern of price dispersion across European and U.S. cities from 1990 to 2001. I find a striking decline in dispersion for traded goods prices in Europe, most of which took place between 1991 and 1994. The level of traded goods price dispersion in the euro area is now quite close to that of the United States. A decline in dispersion of non-tradeables prices in Europe has also taken place, but to a smaller extent. For U.S. cities, there is no evidence of a decline in price dispersion, even for tradeables. I examine several possible explanations for the decline in European price dispersion, including harmonization of tax rates, convergence of incomes and labor costs, liberalization of trade and factor markets, and increased coherence of monetary policy. I also investigate how much of the variation in national inflation rates in Europe can be explained by price level convergence. Finally, after showing that prices in likely next-round entrants into the euro zone are well below prices in Western Europe, I discuss the potential inflationary consequences of accession into monetary union for Eastern Europe.
SIZES AND TEMPERATURE PROFILES OF QUASAR ACCRETION DISKS FROM CHROMATIC MICROLENSING

Microlensing perturbations to the flux ratios of gravitationally lensed quasar images can vary with wavelength because of the chromatic dependence of the accretion disk's apparent size. Multiwavelength observations of microlensed quasars can thus constrain the temperature profiles of their accretion disks, a fundamental test of an important astrophysical process which is not currently possible using any other method. We present single-epoch broadband flux ratios for 12 quadruply lensed quasars in 8 bands ranging from 0.36 to 2.2 μm, as well as Chandra 0.5–8 keV flux ratios for five of them. We combine the optical/IR and X-ray ratios, together with X-ray ratios from the literature, using a Bayesian approach to constrain the half-light radii of the quasars in each filter. Comparing the overall disk sizes and wavelength slopes to those predicted by the standard thin accretion disk model, we find that on average the disks are larger than predicted by nearly an order of magnitude, with sizes that grow with wavelength with an average slope of ∼0.2 rather than the slope of 4/3 predicted by the standard thin disk theory. Though the error bars on the slope are large for individual quasars, the large sample size lends weight to the overall result. Our results present severe difficulties for a standard thin accretion disk as the main source of UV/optical radiation from quasars.
Environmental Reporting in a Post Truth World

The science publication Nature Climate Change this year published a study demonstrating Earth this century warmed substantially less than computer-generated climate models predict. Unfortunately for public knowledge, such findings don’t appear in the news. Sea levels too have not been obeying the ‘grand transnational narrative’ of catastrophic global warming. Sea levels around Australia 2011–2012 were measured with the most significant drops in sea levels since measurements began. This phenomenon was due to rainfall over Central Australia, which filled vast inland lakes. It was not predicted in the models, nor was it reported in the news. The 2015–2016 El-Niño, a natural phenomenon, drove sea levels around Indonesia to low levels such that coral reefs were bleaching. The echo chamber of news repeatedly fails to report such phenomena and yet many studies continue to contradict mainstream news discourse. Whistle-blower Dr. John Bates exposed the U.S. National Oceanic Atmospheric Administration (NOAA) when it manipulated data to meet politically predetermined conclusions for the 2015 Paris (Climate) Agreement. This was not reported. Observational scientific analyses and their data sets continue to disagree with much of climate science modelling, and are beginning to suggest that some natural phenomena, which cause variability, may never be identified.
Distribution of Phlebotomine Sand Fly Genotypes (Lutzomyia shannoni, Diptera: Psychodidae) Across a Highly Heterogeneous Landscape

Abstract Genetic variability of eight Colombian field populations and two laboratory colonies of a tropical forest sand fly, Lutzomyia shannoni Dyar, was assessed by comparing allozyme frequencies at 20 enzyme loci. Substantial genetic variability was noted in all strains, with mean heterozygosities of 13–21% and alleles per locus of 2.0–2.8. Four loci were monomorphic. Six populations in north and central Colombia showed close genetic similarity (Nei’s distances, 0.01–0.09), despite mountainous environment, discontinuous forest habitat, and elevation differences from 125 to 1,220 m. Two samples representing the Orinoco (near Villavicencio) and Amazon (near Leticia) river basins were similar (Nei’s distance, 0.08) but diverged substantially from the central six samples (Nei’s distances, 0.26–0.40). Although the range of L. shannoni extends from the southeastern United States to northern Argentina, three genetically distinct, geographically discrete, groups were discerned by the current analysis: Orinoco-Amazon river basins, north-central Colombia, and eastern United States.
Predicting Methylphenidate Response in ADHD Using Machine Learning Approaches

Background: There are no objective, biological markers that can robustly predict methylphenidate response in attention deficit hyperactivity disorder. This study aimed to examine whether applying machine learning approaches to pretreatment demographic, clinical questionnaire, environmental, neuropsychological, neuroimaging, and genetic information can predict therapeutic response following methylphenidate administration. Methods: The present study included 83 attention deficit hyperactivity disorder youth. At baseline, parents completed the ADHD Rating Scale-IV and Disruptive Behavior Disorder rating scale, and participants undertook the continuous performance test, Stroop color word test, and resting-state functional MRI scans. The dopamine transporter gene, dopamine D4 receptor gene, alpha-2A adrenergic receptor gene (ADRA2A) and norepinephrine transporter gene polymorphisms, and blood lead and urine cotinine levels were also measured. The participants were enrolled in an 8-week, open-label trial of methylphenidate. Four different machine learning algorithms were used for data analysis. Results: Support vector machine classification accuracy was 84.6% (area under receiver operating characteristic curve 0.84) for predicting methylphenidate response. The age, weight, ADRA2A MspI and DraI polymorphisms, lead level, Stroop color word test performance, and oppositional symptoms of Disruptive Behavior Disorder rating scale were identified as the most differentiating subset of features. Conclusions: Our results provide preliminary support to the translational development of support vector machine as an informative method that can assist in predicting treatment response in attention deficit hyperactivity disorder, though further work is required to provide enhanced levels of classification performance.
Ripple: A Robust and Effective Routability-Driven Placer

The significant mismatch between the objective of wirelength and routing congestion makes the routability issue even more important in placement. In this paper, we describe a routability-driven placer called Ripple. Each step, including global placement, legalization, and detailed placement, is made to trade-off between routability and wirelength. We propose a robust and effective flow by using cell inflation to relieve routing congestion. Cell inflation has traditionally been used to deal with congestion and we will discuss how this technique can be used easily and robustly in the global placement. Besides, unlike many previous works that focus on different types of swapping strategies, we analyze and propose some simple and effective approaches when considering routability in the legalization and detailed placement steps. Experimental results show that Ripple is particularly effective in improving routability. When compared to the top results in the ISPD 2011 Contest and SimPLR, Ripple can obtain the smallest overflow and half-perimeter wirelength on average, while the congestion hot spots are also distributed sparsely in Ripple.
Dementia After Stroke: The Framingham Study

Background and Purpose— Identification of risk factors for dementia after stroke is best performed in comparison with stroke-free controls, because older subjects at high risk for stroke also have a substantial risk of dementia in the absence of stroke. Previous case-control studies were hospital-based. We used a nested case-control design to prospectively evaluate these risk factors in the community-based Framingham Study cohort. Methods— We compared 212 subjects who were free of dementia in January 1982 and sustained a first stroke after this date, with 1060 age- and sex-matched, stroke- and dementia-free controls. We calculated 10-year risks of dementia (by Diagnostic and Statistical Manual of Mental Disorders, Volume IV criteria) developing in cases and controls and also estimated the hazard ratios within subgroups defined by exposure to various demographic factors (age, gender, education), stroke-related features (right or left hemisphere, stroke type, second stroke), stroke risk factors (hypertension, diabetes, atrial fibrillation, smoking) and apolipoprotein E genotype. Results— Dementia developed in 19.3% of cases and 11.0% of controls. Baseline stroke doubled the risk of dementia (hazard ratio [HR]: 2.0; 95% confidence interval [CI]: 1.5 to 3.1) and adjustment for age, sex, education, and exposure to individual stroke risk factors did not diminish the risk (HR: 2.4; 95% CI: 1.6 to 3.7). The HR was higher in younger subjects (age younger than 80 years [HR: 2.6; 95% CI: 1.5 to 4.5]), apolipoprotein E 3/3 homozygotes (HR: 3.4; 95% CI: 2.0 to 5.8), and high school graduates (HR: 2.4; 95% CI: 1.5 to 3.9). Conclusion— Stroke increases a subject's risk of dementia as compared with age- and sex-matched controls. Primary and secondary prevention of stroke should significantly decrease the risk of all dementia.
Access to medicines in Brazil based on monetary and non-monetary acquisition data obtained from the 2008/2009 Household Budget Survey

ABSTRACT OBJECTIVE To investigate the access to medicines by Brazilian families by monetary and non-monetary acquisition data. METHODS This is a cross-sectional study based on data obtained from the 2008/2009 Brazilian Household Budget Survey. The units of assessment were households that participated in the survey and the data on the acquisition of medicines over the 30 days prior to the interviews. The medicines were classified according to the Anatomical Therapeutic Chemical classification system. RESULTS Acquisition of medicines was reported by 82.9% of Brazilian households, with 2.38 medicines/household, and 0.72 medicine/individual. In the South and Southeast regions, the average acquisition was slightly greater than the national average (2.53 and 2.49, respectively). In 22.3% of Brazilian households, it was reported that a medicine was not acquired due to lack of financial resources, mainly in the North and Northeastern regions, and in rural areas. Approximately 15.0% of medicines were obtained with no costs, 90.1% of them by the Brazilian Unified Health System. The medicines most acquired were those acting on the nervous system (28.8% of Brazilian households), on the cardiovascular system (15.7%), on the digestive tract and metabolism (14.3%), and on the respiratory system (12.1%). Overall, the quantity of medicines acquired was greater in higher socioeconomic classes of the population, with the exception of antiparasitic products, most likely because of the precarious sanitary conditions faced by less privileged social classes. CONCLUSIONS The acquisition of medicines is a common practice in Brazil, being reported by over 80.0% of the Brazilian households in 2008/2009. Although the data obtained from the Brazilian Household Budget Survey have some limitations, the information obtained in this study can help health authorities to design national and regional policies to guarantee access to these products while promoting their rational use.
Stochastic dominance with respect to a capacity and risk measures

Abstract In our previous work, we have extended the classical notion of increasing convex stochastic dominance relation with respect to a probability to the more general case of a normalized monotone (but not necessarily additive) set function, also called a capacity. In the present paper, we pursue that work by studying the set of monetary risk measures (defined on the space of bounded real-valued measurable functions) satisfying the properties of comonotonic additivity and consistency with respect to the generalized stochastic dominance relation. Under suitable assumptions on the underlying capacity space, we characterize that class of risk measures in terms of Choquet integrals with respect to a distorted capacity whose distortion function is concave. Kusuoka-type characterizations are also established. A generalization to the case of a capacity of the Tail Value at Risk is provided as an example. It is also shown that some well-known results about Choquet integrals with respect to a distorted probability do not necessarily hold true in the more general case of a distorted capacity.
Beliefs, Practices, and Personalities of Software Engineers: A Survey in a Large Software Company

In this paper we present the results from a survey about the beliefs, practices, and personalities of software engineers in a large software company. The survey received 797 responses. We report statistics about beliefs of software engineers, their work practices, as well as differences in those with respect to personality traits.For example, we observed no personality differences between developers and testers; managers were conscientious and more extraverted. We observed several differences for engineers who are listening to music and for engineers who have built a tool.We also observed that engineers who agree with the statement “Agile development is awesome” were more extroverted and less neurotic.
Skew-resistant parallel in-memory spatial join

Spatial join is a crucial operation in many spatial analysis applications in scientific and geographical information systems. Due to the compute-intensive nature of spatial predicate evaluation, spatial join queries can be slow even with a moderate sized dataset. Efficient parallelization of spatial join is therefore essential to achieve acceptable performance for many spatial applications. Technological trends, including the rising core count and increasingly large main memory, hold great promise in this regard. Previous parallel spatial join approaches tried to partition the dataset so that the number of spatial objects in each partition was as equal as possible. They also focused only on the filter step. However, when the more compute-intensive refinement step is included, significant processing skew may arise due to the uneven size of the objects. This processing skew significantly limits the achievable parallel performance of the spatial join queries, as the longest-running spatial partition determines the overall query execution time. Our solution is SPINOJA, a skew-resistant parallel in-memory spatial join infrastructure. SPINOJA introduces MOD-Quadtree declustering, which partitions the spatial dataset such that the amount of computation demanded by each partition is equalized and the processing skew is minimized. We compare three work metrics used to create the partitions and three load-balancing strategies to assign the partitions to multiple cores. SPINOJA uses an in-memory column-store to store the spatial tables. Our evaluation shows that SPINOJA outperforms in-memory implementations of previous spatial join approaches by a significant margin and a recently proposed in-memory spatial join algorithm by an order of magnitude.