Miracle-dz/UniFAR-FTUs huggingface dataset:
DNA polymerase zeta generates clustered mutations during bypass of endogenous DNA lesions in Saccharomyces cerevisiae

Multiple sequence changes that are simultaneously introduced in a single DNA transaction have a higher probability of altering gene function than do single base substitutions. DNA polymerase zeta (Pol ζ) has been shown to introduce such clustered mutations under specific selective and/or DNA damage‐producing conditions. In this study, a forward mutation assay was used to determine the specificity of spontaneous mutations generated in Saccharomyces cerevisiae when either wild‐type Pol ζ or a mutator Pol ζ variant (rev3‐L979F) bypasses endogenous lesions. Mutagenesis in strains proficient for nucleotide excision repair (NER) was compared to mutagenesis in NER‐deficient strains that retain unrepaired endogenous DNA lesions in the genome. Compared to NER‐proficient strains, NER‐deficient rad14Δ strains have elevated mutation rates that depend on Pol ζ. Rates are most strongly elevated for tandem base pair substitutions and clusters of multiple, closely spaced mutations. Both types of mutations depend on Pol ζ, but not on Pol η. Rates of each are further elevated in yeast strains bearing the rev3‐979F allele. The results indicate that when Pol ζ performs mutagenic bypass of endogenous, helix‐distorting lesions, it catalyzes a short track of processive, error‐prone synthesis. We discuss the implications of this unique catalytic property of Pol ζ to its evolutionary conservation and possibly to multistage carcinogenesis.Environ. Mol. Mutagen. , 2012. © 2012 Wiley Periodicals, Inc.
COLLECTIVE DECISION MAKING IN AN INTERNATIONAL RIVER POLLUTION MODEL

In this paper, we study international river pollution problems. We introduce a model in which countries located along a river from upstream to downstream derive benefits from causing pollution, but also incur environmental costs from experiencing its own pollution and the pollution of all its upstream countries. The total welfare, being the sum of all benefits minus the sum of all costs, is maximized when all countries cooperate. Several principles from international water law are applied to find reasonable and fair distributions of the total welfare that can be obtained under full cooperation. Such a distribution of the welfare at efficient pollution levels can be implemented by monetary compensations.
Left atrial catheter ablation subsequent to Watchman® left atrial appendage device implantation: a single centre experience.

AIMS Left atrial appendage device occlusion is an increasingly accepted therapy for stroke prevention in atrial fibrillation. The feasibility and safety of left atrial catheter ablation procedures in the presence of a left atrial appendage device implant is unclear. We report on 10 cases of successful left atrial catheter ablation therapy for atrial fibrillation in patients with an implanted Watchman® device. METHODS AND RESULTS Consecutive patients with an existing Watchman® left atrial appendage implant and symptomatic antiarrhythmic-drug refractory atrial fibrillation or atrial tachycardias requiring left atrial catheter ablation therapy were included. Open irrigated tip ablation and circular mapping catheters were positioned in the left atrium via double transseptal access. Ten patients underwent successful left atrial geometry creation and complex atrial arrhythmia mapping and ablation in the presence of a chronically implanted Watchman® device. Arrhythmia targets included left atrial flutters, a focal tachycardia, left atrial CFAE zones, and pulmonary vein electrical isolation. The appearances of the Watchman® device position and device integrity were confirmed to be satisfactory in all patients at the end of the procedure based on fluoroscopy and intracardiac echocardiography imaging. There were no procedural complications. CONCLUSION Left atrial catheter ablation therapy in the presence of an implanted Watchman® left atrial appendage occlusion device was efficacious and uncomplicated in our small single centre experience.
Improving viewpoint invariance of image feature extraction methods using intensity and range images

The most common image feature extraction algorithms such as SIFT (Scale Invariant Feature Transform) and SURF (Speeded Up Robust Feature) have been proven to be invariant to changes in rotation, scale and with restrictions to illumination and viewpoint changes. These algorithms generate descriptor vectors around keypoints in 2D images. Close descriptors suggest similar image patch. In case of mobile robotics applications it is important to achieve good viewpoint invariance and stability to detect landmarks and objects with high reliability. Improving viewpoint invariance for image feature detection increases the efficiency of SLAM algorithms. In this paper we present and evaluate a method to use additional data provided by range image sensors to supplement traditional feature extraction algorithms to improve viewpoint invariance. We present the method and results of computer simulation and also real world examples comparing the SURF (OpenSURF) with and without the improvement. An active structured light based range and intensity image sensor was used to acquire real world test images.
An Instrument to Measure Adherence to Weight Loss Programs: The Compliance Praxis Survey-Diet (COMPASS-Diet)

Adherence to behavioral weight loss strategies is important for weight loss success. We aimed to examine the reliability and validity of a newly developed compliance praxis-diet (COMPASS-diet) survey with participants in a 10-week dietary intervention program. During the third of five sessions, participants of the “slim-without-diet” weight loss program (n = 253) completed the COMPASS-diet survey and provided data on demographic and clinical characteristics, and general self-efficacy. Group facilitators completed the COMPASS-diet-other scale estimating participants’ likely adherence from their perspective. We calculated internal consistency, convergent validity, and predictive value for objectively measured weight loss. Mean COMPASS-diet-self score was 82.4 (SD 14.2) and COMPASS-diet-other score 80.9 (SD 13.6) (possible range 12–108), with lowest scores in the normative behavior subscale. Cronbach alpha scores of the COMPASS-diet-self and -other scale were good (0.82 and 0.78, respectively). COMPASS-diet-self scores (r = 0.31) correlated more highly with general self-efficacy compared to COMPASS-diet-other scores (r = 0.04) providing evidence for validity. In multivariable analysis adjusted for age and gender, both the COMPASS-diet-self (F = 10.8, p < 0.001, r2 = 0.23) and other (F = 5.5, p < 0.001, r2 = 0.19) scales were significantly associated with weight loss achieved at program conclusion. COMPASS-diet surveys will allow group facilitators or trainers to identify patients who need additional support for optimal weight loss.
Gröbner bases and behaviors over finite rings

For several decades Gröbner bases have proved useful tools for different areas in system theory, particularly multidimensional system theory. These areas range from controller design to minimal realizations of linear systems over fields. In this paper we focus on the univariate case and identify the so-called “predictable leading monomial property” as a property of a minimal Gröbner basis that is crucial in many of these areas. The property is stronger than “row reducedness”. We revisit the recently developed theory of [17] in which row reducedness is extended to polynomial matrices over the finite ring ℤ<inf>p</inf><sup>r</sup> (with p a prime integer and r a positive integer), which find applications in error control coding over ℤ<inf>p</inf><sup>r</sup>. We recast the ideas of [17] in the more general setting of Gröbner bases and derive new results on how to use minimal Gröbner bases to achieve the predictable leading monomial property over ℤ<inf>p</inf><sup>r</sup>. A major advantage of the Gröbner approach is that computational packages are available to compute a minimal Gröbner basis over ℤ<inf>p</inf><sup>r</sup>, such as the SINGULAR computer algebra system. Another advantage of the Gröbner approach is its generality with respect to the choice of ordering of polynomial vectors.
A High-Resolution Digital Phase Interpolator Based CDR with a Half-Rate Hybrid Phase Detector

In this paper, we propose a low power, high-resolution digitally controlled phase interpolator based clock and data recovery (CDR) architecture for high-speed serial links. This architecture incorporates a half-rate hybrid phase detector (HyPD) consisting of a linear phase detector with a 2-tap decision feedback equalizer (DFE), a 1-bit comparator, and an 8-bit digitally controlled phase interpolator. HyPD results in better power performance over the bang-bang phase detector. DFE used in HyPD combats the effect of inter-symbol-interference (ISI) and improves the sampling margins. The phase interpolator provides an unlimited phase capture with a resolution of 1.41° per LSB for varying phase of the input clock. The differential and integral nonlinearities of the DAC based phase interpolator are within ±0.28 LSB and ±0.3 LSB respectively, which lead to low jitter in the recovered clock. We have designed a 5 Gb/s CDR in a 0.18-µm standard CMOS technology. It draws 23.4 mW of power from a 1.8-V supply.
Genetic antimicrobial susceptibility testing in Gram‐negative sepsis – impact on time to results in a routine laboratory

Diagnostic testing of positive blood cultures is among the most critical tasks performed by clinical microbiology laboratories, and the total analysis time from sampling to results should be kept as short as possible. By providing identification of pelleted bacteria directly from positive blood‐cultures, MALDI‐TOF MS opens for relatively low‐complex species‐adjusted genetic susceptibility testing from the same bacterial pellet. In our lab routine, we prospectively evaluated a rapid in‐house real‐time PCR targeting the most common aminoglycoside and cephalosporin resistance genes in Escherichia coli and Klebsiella pneumoniae and measured time to preliminary susceptibility reporting for 138 samples. The results were compared to direct phenotypic susceptibility testing with interpretation after 6 h and overnight incubation respectively. Results from the genetic susceptibility testing were available for 69.5% (96/138) of the positive blood cultures within 24 h after sample collection. No phenotypic susceptibility results were available at this time. Compared to overnight direct susceptibility testing, the average time from sample collection to preliminary susceptibility reporting was reduced with 43%, from 45 h and 5 min to 25 h and 44 min, providing an earlier adjustment of antimicrobial therapy for 12 patients. Minor logistic adjustments have the potential to save yet another 4 h.
The Ownership of Data

We study the effects of property rights over the use of data on market outcomes. For this, we consider a model in which a monopolistic firm offers a service to a set of heterogeneous users. Usage generates valuable data but data extraction entails a privacy cost to users. We show that both the firm and users prefer the users (the firm) to own the rights for low (high) values of data. We further discuss the robustness of our results by allowing more contracting possibilities to the data owner. We show that the main trade-off between the two ownership regimes is robust to these extensions.
Tanshinone IIA pretreatment protects myocardium against ischaemia/reperfusion injury through the phosphatidylinositol 3‐kinase/Akt‐dependent pathway in diabetic rats

Aim: Diabetes Mellitus (DM) is widely acknowledged to increase the risk of cardiovascular death, which warrants the use of aggressive primary prevention strategies. The aim of the present study was to investigate the pretreatment effects of tanshinone IIA (TSN), a traditional Chinese medicine, on myocardial infarct size, apoptosis, inflammation and cardiac functional recovery in diabetic rats subjected to myocardial ischaemia/reperfusion (I/R).
Estimating Potential Merger Gains with Bilevel Programming DEA

In today’s economy and society, merger has a very important role in the restructuring of many sectors. In this thesis, we introduce an innovative Bilevel Programming Data Envelopment Analysis approach to evaluate the profit efficiency of the hierarchical system both pre-merger and post-merger. This hierarchical system consists of two levels, the Leader and the Follower, and the Leader is at the dominant level. A -Strategy is proposed to stimulate the Follower to actively participate and stabilize the hierarchical structure. The potential gains from the merger are decomposed into harmony effect and scale effect. Two case studies are used to illustrate our proposed approach. The results show considerable potential gains from the promising mergers. The concept of coordinated effective merger is also discussed, and it is very important since every member in the system benefits from the merger.
'Working Families' and the 'Opportunity Society': Political Rhetoric in the 2007 Australian Federal Election Campaign

Media and political commentators argued that both Prime Minister John Howard and Opposition Leader Kevin Rudd took a 'small target' approach in the 2007 federal election rather than address longterm issues or outline a broad vision for Australia's future. This article undertakes a comparative analysis of the spoken language of these two political leaders during the formal campaign. It argues that, despite the apparent focus on short-term or 'small target' issues, Australia's political leaders invoked broader themes of national identity and belonging both implicitly and explicitly in their campaign communications. Presenting alternative images of 'working families' and the 'opportunity society', each invited voters to see themselves reflected in his party's version of 'Australianness' - and to vote accordingly.
Maternal use of acetaminophen during pregnancy and risk of autism spectrum disorders in childhood: A Danish national birth cohort study

Acetaminophen (paracetamol) is the most commonly used pain and fever medication during pregnancy. Previously, a positive ecological correlation between acetaminophen use and autism spectrum disorders (ASD) has been reported but evidence from larger studies based on prospective data is lacking. We followed 64,322 children and mothers enrolled in the Danish National Birth Cohort (DNBC; 1996–2002) for average 12.7 years to investigate whether acetaminophen use in pregnancy is associated with increased risk of ASD in the offspring. Information on acetaminophen use was collected prospectively from three computer‐assisted telephone interviews. We used records from the Danish hospital and psychiatric registries to identify diagnoses of ASD. At the end of follow up, 1,027 (1.6%) children were diagnosed with ASD, 345 (0.5%) with infantile autism. We found that 31% of ASD (26% of infantile autism) have also been diagnosed with hyperkinetic disorders. More than 50% women reported ever using acetaminophen in pregnancy. We used Cox proportional hazards model to estimate hazard ratio (HR) and 95% confident interval (CI). Prenatal use of acetaminophen was associated with an increased risk of ASD accompanied by hyperkinetic symptoms (HR = 1.51 95% CI 1.19–1.92), but not with other ASD cases (HR = 1.06 95% CI 0.92–1.24). Longer duration of use (i.e., use for >20 weeks in gestation) increased the risk of ASD or infantile autism with hyperkinetic symptoms almost twofold. Maternal use of acetaminophen in pregnancy was associated with ASD with hyperkinetic symptoms only, suggesting acetaminophen exposure early in fetal life may specifically impact this hyperactive behavioral phenotype. Autism Res 2016, 9: 951–958. © 2015 International Society for Autism Research, Wiley Periodicals, Inc.
The mechanism of iron release from transferrin. Slow-proton-transfer-induced loss of nitrilotriacetatoiron(III) complex in acidic media.

The role of protonation of amino acid ligands involved in iron release from human serum transferrin, previously saturated with nitrilotriacetatoiron(III) complex, has been elucidated in acidic media. Iron loss occurs first from the N-terminal site at pH < 6 and is followed at pH < 4 by iron release from the C-terminal iron-binding site. Nitrilotriacetatoiron(III) release from the N-terminal site is controlled by the slow protonation of the mixed protein/nitrilotriacetatoiron(III) complex; the second-order rate constant was k3a = 9.95 +/- 0.35 x 10(4) M-1.s-1. Protonation of an amino acid ligand in the C-terminal site leads to a new protein-site-C-loaded mixed complex with dissociation constant K4 = 0.300 +/- 0.025 mM. Nitrilotriacetatoiron(III) release is the result of mixed complex dissociation and the slow rate-limiting protonation of the iron-free protein with a proton dissociation constant K5a = 0.100 +/- 0.010 mM and a second-order rate constant k5a = 4.20 +/- 0.40 x 10(3) M-1.s-1. The mechanism of iron uptake and release seems to imply that slow proton transfers can induce complex formation between iron and the amino acid ligands of each of the protein iron-binding sites. These slow proton transfers may be controlled by the change of conformation of the binding sites upon iron loss.
Household Financial Access and Risk Sharing in Nigeria

We examine the role of household financial access in determining the extent of risk sharing in Nigeria using household-level panel data. We estimate changes in the response of consumption to shocks for households with formal and informal access to finance and those without, both for the country as a whole and for different regions. Our findings suggest that households with financial access who experience an unexpected negative income shock see consumption fall by 15 percentage points less than those without access. This result is mainly driven by households with informal financial access, and by household savings rather than borrowing. Regional variation in risk sharing tends to be significant, suggesting that financial inclusion efforts going forward should have a more regional focus.
Thymidylate synthase gene from Lactococcus lactis as a genetic marker: an alternative to antibiotic resistance genes

The potential of the thymidylate synthase thyA gene cloned from Lactococcus lactis subsp. lactis as a possible alternative selectable marker gene to antibiotic resistance markers has been examined. The thyA mutation is a recessive lethal one; thyA mutants cannot survive in environments containing low amounts of thymidine or thymine (such as Luria-Bertani medium) unless complemented by the thyA gene. The cloned thyA gene was strongly expressed in L. lactis subsp. lactis, Escherichia coli, Rhizobium meliloti, and a fluorescent Pseudomonas strain. In addition, when fused to a promoterless enteric lac operon, the thyA gene drove expression of the lac genes in a number of gram-negative bacteria. In transformation experiments with thyA mutants of E. coli and conjugation experiments with thyA mutants of R. meliloti, the lactococcal thyA gene permitted selection of transformants and transconjugants with the same efficiency as did genes for resistance to ampicillin, chloramphenicol, or tetracycline. Starting from the broad-host-range plasmid pGD500, a plasmid, designated pPR602, was constructed which is completely free of antibiotic resistance genes and has the lactococcal thyA gene fused to a promoterless lac operon. This plasmid will permit growth of thyA mutant strains in the absence of thymidine or thymine and has a number of unique restriction sites which can be used for cloning.
Interaction between intracortical inhibition and facilitation in human motor cortex.

1. In seven normal subjects, subthreshold transcranial magnetic conditioning stimuli (using a figure‐of‐eight coil) were applied over the motor cortex in order to evoke activity in intracortical neuronal circuits. The net effect on cortical excitability was evaluated by measuring the effect on the size of EMG responses elicited in the abductor digiti minimi (ADM) muscle by a subsequent suprathreshold test stimulus. 2. A single conditioning stimulus suppressed the size of the test response at interstimulus intervals (ISIs) of 1‐4 ms whereas the response was facilitated at ISIs of 6‐20 ms. The facilitation could be augmented if pairs of conditioning stimuli were given. 3. Inhibition and facilitation appeared to have separate mechanisms. The threshold for inhibition (0.7 active motor threshold) was slightly lower than that for facilitation (0.8 active threshold). Similarly, the inhibitory effect was independent of the direction of current flow induced in the cortex by the conditioning shock, whereas facilitation was maximal with posterior‐anterior currents and minimal with lateromedial current. 4. Direct corticospinal effects were probably not responsible for the results since facilitation of cortical test responses could be produced by conditioning stimuli which had no effect on the amplitude of H reflexes elicited in active ADM muscle. 5. Inhibition and facilitation appeared to interact in a roughly linear manner, consistent with separate inputs to a common neurone. 6. We suggest that subthreshold transcranial magnetic stimulation is capable of activating separate populations of excitatory and inhibitory interneurones in the motor cortex.
Multidecadal to centennial surface wind variability over Northeastern North America

Surface wind is relevant for society, from pollutant dispersion to structural vulnerability studies and wind power production. Over Northeastern North America the large scale combined with orography and other local features contributes to a high wind variability and the occurrence of extreme wind events all year round. Up to date no studies dealt with the surface wind variability, from intra-annual to centennial timescales, over the region as a whole, and in relation with the large scale circulation patterns. An exhaustive assessment of uncertainties has been conducted in every step of the analysis, from the construction of an observational wind dataset of acquired quality to the evaluation of the methodological uncertainty involved in the downscaling strategy.
The role of deep reefs in shallow reef recovery: an assessment of vertical connectivity in a brooding coral from west and east Australia

Approximately one quarter of zooxanthellate coral species have a depth distribution from shallow waters (<30 m) down to mesophotic depths of 30–60 m. The deeper populations of such species are less likely to be affected by certain environmental perturbations, including high temperature/high irradiance causing coral bleaching. This has led to the hypothesis that deep populations may serve as refuges and a source of recruits for shallow reef habitats. The extent of vertical connectivity of reef coral species, however, is largely unquantified. Using 10 coral host microsatellite loci and sequences of the host mtDNA putative control region, as well as ribosomal DNA (rDNA) ITS2 sequences of the coral’s algal endosymbionts (Symbiodinium), we examine population structure, connectivity and symbiont specificity in the brooding coral Seriatopora hystrix across a depth profile in both northwest (Scott Reef) and northeast Australia (Yonge Reef). Strong genetic structuring over depth was observed in both regions based on the microsatellite loci; however, Yonge Reef exhibited an additional partitioning of mtDNA lineages (associated with specific symbiont ITS2 types), whereas Scott Reef was dominated by a single mtDNA lineage (with no apparent host‐symbiont specificity). Evidence for recruitment of larvae of deep water origin into shallow habitats was found at Scott Reef, suggesting that recovery of shallow water habitats may be aided by migration from deep water refuges. Conversely, no migration from the genetically divergent deep slope populations into the shallow habitats was evident at Yonge Reef, making recovery of shallow habitats from deeper waters at this location highly unlikely.