Miracle-dz/UniFAR-FTUs huggingface dataset:
Interaction between the octamer-binding protein nuclear factor III and the adenovirus origin of DNA replication

Nuclear factor III (NFIII) is a HeLa sequence-specific DNA-binding protein that stimulates initiation of adenovirus DNA replication in vitro and may be involved in regulation of transcription of several cellular and viral genes. We have studied the interaction between NFIII and the binding site in the adenovirus type 2 (Ad2) origin in detail by methidiumpropyl-EDTA.iron(II) and hydroxyl radical footprinting and by alkylation interference experiments. Our results indicate that (i) the core of the recognition sequence is 5'-TATGATAAT-3'; (ii) both major and minor groove base contacts are detected, and all base pairs in the core are involved in binding; (iii) many backbone contacts are observed divided into a large domain coinciding with the core and a small domain; (iv) contact points are not confined to one side of the DNA helix in contrast to the nuclear factor I (NFI)-binding site; (v) the binding site overlaps the NFI-binding site for at least one nucleotide. A number of Ad2 mutants as well as related binding sites in the origins of other adenovirus serotypes were systematically compared for binding with NFIII. The results are in good agreement with the contact point studies and show that at least one AT base pair is commonly required by NFI and NFIII for optimal binding. The strongest binding site, which contains the octamer/decanucleotide motif (ATGCAAAT[NA]), was found in the Ad4 origin, which lacks an NFI-binding site. Stimulation of in vitro DNA replication of Ad2, Ad4, and Ad12 by NFIII showed that the maximal level of stimulation is dependent on the affinity of NFIII for the origin.
Disagreement in Consumer Inflation Expectations

We posit that consumers form expectations about inflation by combining two sources of information: their beliefs from shopping experience and news about inflation they learn from experts. Disagreement among consumers in our model comes from four sources: (i) consumers’ divergent prior beliefs, (ii) heterogeneity in their propensities to learn from experts, (iii) experts’ different views about future inflation, and (iv) difference in mean expectations between consumers and experts. By carefully matching the datasets from the Michigan Survey of Consumers with the Survey of Professional Forecasters, we find that inflation expectations between households and experts differ substantially and persistently from each other, and households pay close attention to salient price changes, while experts respond more to monetary policy and macro indicators. Our empirical estimates imply economically significant degrees of information rigidity and these estimates vary substantially across households. This significant heterogeneity poses a great challenge for the canonical sticky-information model that assumes a single rate of information acquisition and for noisy-information model in which all agents place the same weight on new information received.
Old Wine in a New Bottle: Implementation of Intensive Language Program in the 5th Grade in Turkey

In search of ways to better the foreign language proficiency levels of their citizens, governments frequently announce macro foreign language policies. In Turkey, the latest education reform in 2013 lowered the onset of foreign language learning to the second grade. The piloting of the latest foreign language policy is in progress to transform the fifth grade to an English Language Preparation Program (ELPP). In line with the current changes, this study collects the secondary school English language teachers’ opinions at the initial stage of the implementation. This qualitative case study questions the advantages, disadvantages, success and possible challenges of the implementation, and the necessary support mechanisms. The secondary school English language teachers reflect on their past experiences of intensive language programs and hold an overall positive approach to the new ELLP implementation. All in all, to achieve success, the findings highlight the need for teacher training on teaching English to young learners, for a sound integration of communicative language teaching with authentic materials.
Beauty, Productivity, and Discrimination: Lawyers' Looks and Lucre

We propose models with an ascriptive characteristic generating earnings differentials and causing sectoral sorting, allowing us to distinguish among sources producing such differentials. We use longitudinal data on a large sample of graduates from one law school and measure beauty by rating matriculation photographs. (1) Betterlooking attorneys who graduated in the 1970s earned more than others after 5 years of practice, an effect that grew with experience. (2) Attorneys in the private sector are better‐looking than those in the public sector, differences that rise with age. These results support theories of dynamic sorting and customer behavior.
Hepatic production of insulin-like growth factors in normal and diseased liver.

BACKGROUND/AIMS IGF-I levels are reduced in cirrhotic patients. However, it is not known whether this decreased level is the result of reduced hepatic production or modified bioavailability secondary to decreased binding proteins. We determined the hepatic production of IGF-I and IGF-II and their receptors in normal and diseased liver. METHODOLOGY Twenty-five patients included, 11 controls with normal liver and 14 with either chronic hepatitis or cirrhosis. mRNA for IGF-1, IGF-II and their receptors were measured. Immunohistochemical staining was performed to localize the IGF-producing cells. RESULTS In 11 normal livers, the IGF-I mRNA levels were 4.95 +/- 1.8; in the 14 diseased livers, the levels were 1.22 +/- 0.69 (p < 0.001). IGF-II mRNA levels were 3.78 +/- 1.45 for the control and 5.11 +/- 2.15 in the diseased livers (NS). IGF-I receptor levels were 1.15 +/- 0.83 in the normal and 0.31 +/- 0.22 in the liver disease group (p < 0.05). There was no statistical difference between the two groups for IGF-II receptor. CONCLUSIONS Patients with chronic liver disease have a significant reduction in their hepatic production of IGF-I, whereas IGF-II tends to be elevated. Treatment with recombinant IGF-I in patients with metabolic or endocrine complications of cirrhosis might prove useful.
Fluid-Filled Solid-Core Photonic Bandgap Fibers

We review the field of fluid-filled solid-core photonic bandgap fibers (SC-PBGF): we present the mechanisms and models of light guidance in these fibers, and how the guidance properties are sensitive to the refractive index of the infiltrated fluid. We discuss how this sensitivity can be used for creating tunable devices such as filters, delay lines and tunable non-linear pulse propagation experiments. We review refractive index sensors based on SC-PBGFs, including band edge sensing, SC-PBGF based long period grating sensing and new results on selectively filled SC-PBGFs which are the most sensitive microstructured fiber based sensors to date. We also discuss practical aspects of fluid filling.
The Diversity of Prokaryotic DDE Transposases of the Mutator Superfamily, Insertion Specificity, and Association with Conjugation Machineries

Transposable elements (TEs) are major components of both prokaryotic and eukaryotic genomes and play a significant role in their evolution. In this study, we have identified new prokaryotic DDE transposase families related to the eukaryotic Mutator-like transposases. These genes were retrieved by cascade PSI-Blast using as initial query the transposase of the streptococcal integrative and conjugative element (ICE) TnGBS2. By combining secondary structure predictions and protein sequence alignments, we predicted the DDE catalytic triad and the DNA-binding domain recognizing the terminal inverted repeats. Furthermore, we systematically characterized the organization and the insertion specificity of the TEs relying on these prokaryotic Mutator-like transposases (p-MULT) for their mobility. Strikingly, two distant TE families target their integration upstream σA dependent promoters. This allowed us to identify a transposase sequence signature associated with this unique insertion specificity and to show that the dissymmetry between the two inverted repeats is responsible for the orientation of the insertion. Surprisingly, while DDE transposases are generally associated with small and simple transposons such as insertion sequences (ISs), p-MULT encoding TEs show an unprecedented diversity with several families of IS, transposons, and ICEs ranging in size from 1.1 to 52 kb.
Does ethanol production affect corn basis volatility

Purpose - South Dakota is ranked sixth nationally for corn and ethanol production (EP). The purpose of this paper is to investigate the relationship between corn-EP and corn basis volatility using South Dakota data. Design/methodology/approach - A mixed regression modeling approach was adopted to analyze state EP data, and quarterly corn production and price data for five crop reporting regions in South Dakota (1990-2014). Findings - From 2004-Q4 to 2013-Q4, ethanol and corn production in South Dakota increased by 735.50 million gallons and 228.30 million bushel per year, respectively. Empirical estimates indicate that increased EP narrowed the corn basis by 6.16 cents per bushel, and increased corn basis absolute volatility by 2.25 cents. However, increased corn production widened the corn basis by 27.56 cents per bushel and decreased absolute basis volatility by 4.32 cents. On average, for this period, increased EP offset the effect of rapid corn production on average basis and basis volatility in the State of South Dakota. Empirical evidence presented clarifies how the relationship between EP and corn production variability effects the cash basis and basis volatility in local markets. Research limitations/implications - Research limitations include the use of statewide EP due to the lack of regional data, and the use of aggregate price data rather than local cash market data. Practical implications - During normal crop production years, corn production is a predominant driver for impacting corn basis and basis volatility. In this case, EP plays a secondary role and dampens the corn production effect by narrowing the cash basis and increasing volatility. However, when a negative corn production shock occurs, then EP amplifies the effect of reduced corn production. In this case, EP strengthens market forces that are narrowing the cash basis and amplifies the market forces that are increasing the volatility of the cash basis. Social implications - Negative corn production shocks occurring in regions where corn production and corn-based EP are dominant agricultural activities will increase basis volatility, reducing hedging effectiveness. Expansion of the ethanol blending wall in the future may exacerbate the market forces that have evolved in local cash corn markets as EP renews its expansion in major corn production regions. As a result, producers and grain elevator managers need to be aware that traditional hedging strategies may become less effective as one consequence of a renewed expansion of EP in the USA. Originality/value - The literature on the effect of corn-EP on corn basis volatility is limited. This is the first study to apply a mixed modeling approach to the issue of how EP affected corn basis and basis volatility.
Approaches to Prolong the Use of Uncuffed Hemodialysis Catheters: Results of a Randomized Trial

Background: Use of uncuffed catheters (UCs) in hemodialysis patients is common practice. An antibiotic lock has been recommended to prevent catheter-related bacteremia (CRB), although insufficient data are available about the appropriate antimicrobial agent and dose with prolonged use of UCs. Methods: This open-label randomized study was conducted to compare gentamicin/heparin (group A) and taurolidine/citrate (group B), as catheter-lock solutions, in 119 chronic hemodialysis patients in whom a total of 150 UCs were placed. A well-matched historical control group (heparin) included 67 UCs in 58 patients (group C). Results: CRB episodes developed in 6 and 8 patients in groups A and B, respectively, significantly fewer than in group C (20 patients). Cumulative CRB-free catheter survival at 90 days was 82% for A and 78% for B, which is significantly higher than the 26% for C. Similar Gram-positive infection rates were found in all groups. The Gram-negative infection rate was significantly lower in B compared to C. No significant differences in thrombosis rates were observed between the groups. Conclusions: Gentamicin/heparin and taurolidine/citrate, used for locking UC, were similarly effective at preventing CRB and catheter thrombosis for up to 3 months, until a functional permanent vascular access became available. Both antimicrobial lock solutions were superior to heparin in CRB prevention with similar thrombosis rates.
Cooperating with Universities and R&D Organizations: Mainstream Practice or Peculiarity?

This paper develops an integrated framework to examine the determinants of industry-science cooperation in the general process of developing innovation. Based on the literature review and using firm-level data on innovation strategies of 805 manufacturing enterprises in Russia we investigate what are the incentives to firms (1) to cooperate with universities and R&D organizations and (2) to choose a particular mode of interaction that ranges from purchasing S&T services to a full scale original R&D aimed at creating new-to-market innovation. We suggest that a broad range of intramural and external determinants, including competition regime, absorptive capacity, technological opportunities, appropriability conditions, public support, as well as barriers to the practical application of R&D results influence the firm’s decision on cooperation with knowledge producers. The findings indicate that the scale of industry-science linkages in Russian manufacturing is limited and generally hampered by low propensity of business to the R&D-based innovation strategies
Experimental and Theoretical Study of Strata Formation in Sedimentary Basins

Abstract : A major goal of our stratigraphy project is to obtain experimental evidence and to develop quantitative models of the formation of strata on continental margins. Experiments and analytical models can greatly contribute to bridge the gap between variation in forcing functions such as sediment supply, sea-level changes and subsidence, and the resulting stratigraphy in depositional basins, and therefore allow for (1) inferring the history of external forcing from preserved strata (inversion problem) or (2) predicting the nature of preserved strata in areas where the forcing history is known. By applying techniques from geophysics and engineering to stratigraphic problems, we are also helping to convert stratigraphy from a purely descriptive to a more quantitative, analytical science.
Does urban form matter for innovation productivity? A national multi-level study of the association between neighbourhood innovation capacity and urban sprawl

Geography of innovation, creative clustering, urban buzz and innovation districts are place-based concepts that have emerged as a result of the US economy’s transformation to knowledge-intensive economies. The notable built environment characteristics of these concepts are spatial clustering, walkability and proximity to urban amenities, diversity, regional connectivity and agglomeration. While several of these characteristics have been associated with urban sprawl in previous studies, there is a lack of direct evidence on how urban sprawl affects innovation productivity. This national study seeks to examine the relationship between urban sprawl, place-based characteristics and innovation productivity. We used Multilevel Modelling to account for built environment characteristics at both neighbourhood and regional levels. We found that innovative firms tend to locate more in census tracts that are less compact but offer spatial proximity to firms in related business sectors. This is likely due to the higher land and property value in compact areas, which could make it unaffordable for small businesses. We also found that the regional compactness positively and significantly affects the number of innovative firms. This is likely due to the role of compact regions in supporting public transit investments, enhancing social capital and reducing poverty and racial segregation.
Economic Structure, Growth, and Evolution of Inequality and Poverty in Africa: An Overview

Is Africa experiencing a growth ‘miracle’? Rodrik (2018) seems sceptical, and provides evidence based on modern growth theory to support the scepticism: the recent relatively impressive growth does not seem sustainable. Related to the issue of sustainability is economic structure. Diao et al. (2018) find that accompanying the recent growth record has been improving agricultural labour productivity, a reduction of the agricultural labour share and increasing manufacturing employment, evidence that is consistent with that observed for industrialised economies. Thorbecke and Ouyang (2018) also find that while the efficacy of translating growth into poverty reduction remains lower for Africa than elsewhere, there is evidence of poverty convergence recently in Africa, contrary to that for developing countries generally. Fosu (2018) observes the dominant importance, on average, of growth for poverty reduction in Africa, but also underscores the critical role of inequality, especially for certain countries. Exploring why inequality is particularly high in Africa, Shimeles and Nabassaga (2018) uncover ethnic fractionalisation, limited tertiary education, and poor governance as major culprits, and inequality of opportunity as the dominant component. Bigsten (2018) identifies the dual-economy nature of colonial arrangements as the genesis for Africa’s high inequality, and proposes an enhanced pro-poor Lewis-type modern-sector enlargement as a potential solution.
Risk, mobility or population size? Drivers of technological richness among contact-period western North American hunter–gatherers

Identifying factors that influence technological evolution in small-scale societies is important for understanding human evolution. There have been a number of attempts to identify factors that influence the evolution of food-getting technology, but little work has examined the factors that affect the evolution of other technologies. Here, we focus on variation in technological richness (total number of material items and techniques) among recent hunter–gatherers from western North America and test three hypotheses: (i) technological richness is affected by environmental risk, (ii) population size is the primary determinant of technological richness, and (iii) technological richness is constrained by residential mobility. We found technological richness to be correlated with a proxy for environmental risk—mean rainfall for the driest month—in the manner predicted by the risk hypothesis. Support for the hypothesis persisted when we controlled for shared history and intergroup contact. We found no evidence that technological richness is affected by population size or residential mobility. These results have important implications for unravelling the complexities of technological evolution.
Cerebrospinal fluid flow measured by phase-contrast cine MR.

PURPOSE This prospective study was designed to establish the temporal and quantitative relationship between blood flow and cerebrospinal fluid (CSF) flow using a phase-contrast cine MR pulse sequence. METHODS A cine phase-contrast MR pulse sequence using peripheral gating was used to measure CSF flow direction and velocity. Data were acquired continuously and interpolated into 16 images throughout the cardiac cycle. RESULTS The timing of systolic CSF flow in the cervical subarachnoid space (SAS) correlated very closely to the brain arteriovenous blood flow difference during the cardiac cycle. This arteriovenous difference was a measure of brain expansion. Aqueduct CSF flow during the cardiac cycle differed from SAS flow in that systolic flow was delayed in comparison with systolic cervical SAS flow. The normal aqueductal oscillatory flow volume was 1.7 +/- . 4 mL/min or 0.03 +/- 0.01 mL per cardiac cycle. This represented 14.5% +/- 3.1% of the total CSF flow and tissue displacement through the incisura which was 14.5 +/- 2.2 mL/min or 0.22 +/- 0.03 mL per cycle. CSF oscillatory flow volume in the cervical SAS was 39.0 +/- 4.0 mL/min or 0.65 +/- 0.08 mL per cycle. CONCLUSION CSF flow can be measured. Results in healthy subjects show relatively low oscillatory flow through the aqueduct which is slightly out of phase (delayed) compared with SAS CSF flow.
Regulation of Synaptic Efficacy in Hypocretin/Orexin-Containing Neurons by Melanin Concentrating Hormone in the Lateral Hypothalamus

The lateral hypothalamus (LH) is a central hub that integrates inputs from, and sends outputs to, many other brain areas. Two groups of neurons in the LH, expressing hypocretin/orexin or melanin concentrating hormone (MCH), have been shown to participate in sleep regulation, energy homeostasis, drug addiction, motor regulation, stress response, and social behaviors. The elucidation of crosstalk between these two systems is essential to understand these behaviors and functions because there is evidence that there are reciprocal innervations between hypocretin/orexin and MCH neurons. In this study, we used MCH receptor-1 knock-out (MCHR1 KO) and wild-type (WT) mice expressing green fluorescent protein in hypocretin/orexin-containing neurons to examine the hypothesis that MCH modulates hypocretin/orexin-mediated effects on behavioral state and synaptic transmission in the LH. In MCHR1 KO mice, the efficacy of glutamatergic synapses on hypocretin/orexin neurons is potentiated and hypocretin-1-induced action potential firing is facilitated, potentially explaining an increased effect of modafinil observed in MCHR1 KO mice. In wild-type mice with intact MCHR1 signaling, MCH significantly attenuated the hypocretin-1-induced enhancement of spike frequency in hypocretin/orexin neurons. The MCH effect was dose dependent, pertussis toxin sensitive, and was abolished in MCHR1 KO mice. Consistent with this effect, MCH attenuated hypocretin-1-induced enhancement of the frequency of miniature EPSCs in hypocretin/orexin neurons. These data from MCHR1 KO and WT mice demonstrate a novel interaction between these two systems, implying that MCH may exert a unique inhibitory influence on hypocretin/orexin signaling as a way to fine-tune the output of the LH.
The relation between family socioeconomic trajectories from childhood to adolescence and dental caries and associated oral behaviours

Objectives: To investigate the influence of family socioeconomic trajectories from childhood to adolescence on dental caries and associated behaviours. Design: Population-based birth cohort. Setting: Representative sample of the population of subjects born in 1982 in Pelotas, Brazil. Participants: Adolescents (n = 888) aged 15 years old were dentally examined and interviewed. Main outcome measures: Dental caries index (DMFT), care index (F/DMFT), tooth brushing, flossing and pattern of dental services use. Main results: Adolescents who were always poor showed, in general, a worse pattern of dental caries, whereas adolescents who never were poor had a better pattern of dental caries. Adolescents who had moved from poverty in childhood to non-poverty in adolescence and those who had moved from non-poverty in childhood to poverty in adolescence had similar dental pattern to those who were always poor except for the pattern of dental services use, which was higher in the first group. In all groups girls had fewer carious teeth, better oral hygiene habits and higher dental services use than boys. Conclusion: Poverty in at least one stage of the lifespan has a harmful effect on dental caries, oral behaviours and dental services use. Belonging to upwardly mobile families between childhood and adolescence only contributed to improved dental care.