Miracle-dz/UniFAR-FTUs huggingface dataset:
Identification of linear DNA sequences that specifically bind the adeno-associated virus Rep protein

We have used baculovirus-expressed Rep68 that has been purified to homogeneity to reexamine the binding properties of the Rep protein. We find that Rep68 is capable of binding to a linear DNA sequence that is contained within a 25-bp sequence of the A stem of the adeno-associated virus (AAV) terminal repeat proximal to the B and C palindromes. This has been shown conclusively by demonstrating that Rep68 could specifically bind to a synthetic oligonucleotide containing the 25-bp region in the absence of the other sequences within the terminal repeat. Rep78 was also capable of binding the A stem recognition element, as demonstrated by the fact that a DNA affinity column containing the 25-bp sequence can be used to purify Rep78. The ability to recognize the linear DNA sequence within the A stem provides a mechanism by which the Rep protein can be oriented on the terminal repeat so that only the correct strand is cut at the terminal resolution site (trs site) during terminal resolution. In addition, computer analysis suggests that sequences similar to the A stem element are present within the three AAV promoter regions. Electrophoretic mobility shift experiments clearly demonstrate that the p5 promoter contains a Rep binding sequence. DNase protection experiments indicate that the Rep binding sequence within the p5 promoter is located between the YY1 initiator sequence and the TATA binding site. This position immediately suggests a mechanism by which the Rep protein could act as a repressor or a transactivator of p5 transcription by interacting with either YY1 or TBP. In addition, gel shift experiments suggest that the p19 promoter also contains a Rep binding site. The presence of Rep binding sites upstream of both promoters suggests that these sites may be involved in coordinate regulation of AAV transcription. In addition, we have identified a heterologous Rep binding sequence within pBR322 DNA. A comparison of the sequences within the A stem, p5, and pBR322 binding sites suggests that a repeating GAGC motif is at least part of the Rep recognition sequence. In the accompanying report (D. M. McCarty, J. H. Ryan, S. Zolutukhin, X. Zhou, and N. Muzyczka, J. Virol. 68:4998-5006, 1994), we examine the relative affinity of Rep to the A stem site and the complete terminal repeat. Finally, we also have reexamined the ability of Rep68 and Rep78 to cut at the trs site in substrates that do not contain the B and C palindromes or any apparent secondary structure. (ABSTRACT TRUNCATED AT 400 WORDS)
ARMS: an automatic knowledge engineering tool for learning action models for AI planning

Abstract We present an action model learning system known as ARMS (Action-Relation Modelling System) for automatically discovering action models from a set of successfully observed plans. Current artificial intelligence (AI) planners show impressive performance in many real world and artificial domains, but they all require the definition of an action model. ARMS is aimed at automatically learning action models from observed example plans, where each example plan is a sequence of action traces. These action models can then be used by the human editors to refine. The expectation is that this system will lessen the burden of the human editors in designing action models from scratch. In this paper, we describe the ARMS in detail. To learn action models, ARMS gathers knowledge on the statistical distribution of frequent sets of actions in the example plans. It then builds a weighted propositional satisfiability (weighted SAT) problem and solves it using a weighted MAXSAT solver. Furthermore, we show empirical evidence that ARMS can indeed learn a good approximation of the finally action models effectively.
Oil price shocks and stock market behavior: empirical evidence for the U.S. and European Countries

This dissertation analyze the relationship between oil price shocks and stock market for the US and 13 European countries with monthly data from 1986.1 – 2005.12. Three countries (Denmark, Norway and the UK) among 13 European countries are oil exporting countries. Unrestricted multivariate Vector Autoregression (VAR) with 4 variables (interest rates, real oil price changes, industrial production and real stock returns) is estimated as well as impulse response function and variance decomposition. With regard to impact of oil price shocks on the stock market, in most oil importing countries oil price shocks have significantly negative effect on the stock market in the same month or in one month, while among oil exporting countries only Norway shows a significantly positive response of real stock returns to oil price shocks. Comparing the impacts of oil price shocks and interest rate (monetary) shocks on the stock market, in most oil importing countries oil price shocks have a greater impact than interest rate shocks, except for a few countries where monetary policy responds systemically to oil price shocks by raising interest rates, which leads to a decline in real stock returns. Therefore, taking into account the response of monetary policy to oil price shocks, oil prices play a crucial role in the stock market of oil importing countries. On the contrary, in oil exporting countries oil price shocks have a smaller impact on the stock market than interest rate shocks, and monetary policy does not respond to the oil price shocks. According to the literature, oil price shocks have an asymmetric effect on economic activity and the stock market in that oil price increases have a greater impact than oil price decreases. However, in this dissertation, the asymmetric pattern is a little different. In the sub-sample period (1996.5-2005.12) when oil price increases more frequently than oil price decreases and the average magnitude of oil price increases is smaller than that of oil price decreases, stock markets in most countries are more influenced by oil price decreases than oil price increases in the variance decomposition analysis. In particular, statistically significant evidence at the 5% level is found that oil price decreases have a greater impact on real stock returns than oil price increases after the mid 1990’s in the US.
Increased Athletic Performance in Lighter Basketball Shoes: Shoe or Psychology Effect?

PURPOSE To determine the effect of shoe mass on performance in basketball-specific movements and how this affects changes if an athlete is aware or not of the shoe's mass relative to other shoes. METHODS In an experimental design, 22 male participants were assigned to 2 groups. In the "aware" group, differences in the mass of the shoes were disclosed, while participants in the other group were blinded to the mass of shoes. For both groups lateral shuffle-cut and vertical-jump performances were quantified in 3 different basketball-shoe conditions (light, 352 ± 18.4 g; medium, 510 ± 17 g; heavy, 637 ± 17.7 g). A mixed ANOVA compared mean shuffle-cut and vertical-jump performances across shoes and groups. For blinded participants, perceived shoe-weight ratings were collected and compared across shoe conditions using a Friedman 2-way ANOVA. RESULTS In the aware group, performance in the light shoes was significantly increased by 2% (vertical jump 2%, P < .001; shuffle cut 2.1%, P < .001) compared with the heavy shoes. In the blind group, participants were unable to perceive the shoe-weight variation between conditions, and there were no significant differences in vertical-jump and shuffle-cut performance across shoes. CONCLUSIONS Differences in performance of the aware participants were most likely due to psychological effects such as positive and negative expectancies toward the light and heavy shoes, respectively. These results underline the importance for coaches and shoe manufacturers to communicate the performance-enhancing benefits of products or other interventions to athletes to optimize their performance outcome.
Fibroblast Growth Factors Lead to Increased Msx2 Expression and Fusion in Calvarial Sutures

Craniosynostosis, the premature fusion of the skull bones at the sutures, represents a disruption to the coordinated growth and development of the expanding brain and calvarial vault and is the second most common birth defect that affects the craniofacial complex. Mutations in the human homeobox‐containing gene, Msx2, have been shown to cause Boston type craniosynostosis, and we have shown that overexpression of Msx2 leads to craniosynostosis in mice. Activating mutations in fibroblast growth factor (FGF) receptors are thought to cause craniosynostosis in Crouzon, Apert, Jackson‐Weiss, Beare‐Stevenson, and Muenke syndromes. To mimic activated signaling by mutated FGF receptors, we used heparin acrylic beads to deliver FGF ligands to mouse calvaria and demonstrated increased Msx2, Runx2, Bsp, and Osteocalcin gene expression, decreased cell proliferation, and suture obliteration and fusion. FGF2 elicited the greatest increase in Msx2 expression, and FGF1 was most likely to cause suture obliteration and fusion. Of the three sutures studied, the coronal suture exhibited the greatest increase in Msx2 expression and was the most likely to undergo obliteration and fusion. These results are intriguing because the coronal suture is the most commonly affected suture in syndromic craniosynostosis. These results suggest that Msx2 is a downstream target of FGF receptor signaling and that increased FGF signaling leads to osteogenic differentiation by sutural mesenchyme in mouse calvaria. These results are consistent with the hypotheses that increased Msx2 expression and activated signaling by mutated FGF receptors lead to craniosynostosis.
Draft Genome Sequences of the Avirulent Coxiella burnetii Dugway 7D77-80 and Dugway 7E65-68 Strains Isolated from Rodents in Dugway, Utah

ABSTRACT Here, we present the draft genome sequences of the Coxiella burnetii Dugway 7D77-80 and Dugway 7E65-68 strains, which were isolated from rodents in Dugway, UT, in the 1950s. The strains reside in a distinct genomic group of C. burnetii and are considered avirulent despite having the largest genomes of the Coxiella genus.
Safer sex practices among newly diagnosed HIV-positive men who have sex with men in China: results from an ethnographic study

ABSTRACT The study reported here sought to understand the rationales of safer sex practices adopted by newly diagnosed HIV-positive men who have sex with men (MSM). Guided by a socio-ecological framework, an ethnography was conducted among newly diagnosed HIV-positive MSM. In-depth interviews and participant observation were employed to produce an account of the social and cultural settings that was faithful to the perspectives of participants. A total of 31 participants with diverse backgrounds were recruited in a southern city of China. Participant observation was conducted in local healthcare settings, MSM venues, and NGO offices. Most participants (24/31) reported stopping unprotected anal intercourse (UAI) immediately after being diagnosed as HIV-positive. Factors associated with safer sex practices were identified at both individual and environmental levels, including self-protection, establishment of self-esteem, dignity, altruism and reciprocity, disease experience as a source of personal growth, and organizational culture and values. Newly diagnosed HIV-positive MSM navigate their sexual practices within the context of multiple competing factors. Implications for sustained behaviour change enabling safer sex practices include stimulating survival instinct, facilitating safer sex decision making, motivating and facilitating personal growth, and encouraging volunteerism to promote intentional activities for safer sex practices.
On Security in Publish/Subscribe Services: A Survey

Publish/subscribe services have encountered considerable success in the building of modern large-scale mission-critical systems. Such systems are characterized by several non-functional requirements, among which security plays a pivotal role due to the emergence of numerous cyber attacks targeting most mission-critical systems. This requires that the adopted publish/subscribe services have to be equipped with the proper means to protect the exchanged data, to preserve their correct behavior and to face possible attack scenarios. Although significant efforts have been made in this field, many issues are still open. This paper includes an introduction to the principles of securing event notification, and an analysis of the relevant state-of-the-art by both surveying the academic literature over the period 1998-2014 on secure publish/subscribe services and overviewing the current standards for the marketed products. Next, it presents the main challenges that are still unresolved and are worthy of further attention in future research efforts.
Metabolic channeling of 5-fluoro-2'-deoxycytidine utilizing inhibitors of its deamination in cell culture.

The metabolism of 5-fluoro-2'-deoxycytidine (FdC) with and without tetrahydrouridine (H4U) or 2'-deoxytetrahydrouridine (dH4U) was examined in log phase HEp-2 cells using HPLC and TLC methods which quantified: the incorporation of FdC-related antimetabolites into RNA and DNA and pool size levels of FdC-related antimetabolites. [3H]-FdC administered to log phase HEp-2 cells at a concentration of 0.01 microM for 24 hr resulted in the incorporation of 5.22 X 10(-8) mol of FdC/mol of DNA phosphate, a 0.021% substitution of FdC for dC. Coadministration of 1.0 mM H4U or dH4U resulted in 2- and 25-fold increases in the incorporation of FdC, respectively. No detectable incorporation of 5-fluoro-2'-deoxyuridine (FdU) into HEp-2 DNA resulted (detection limit, approximately 5 fmol). In contrast, treatment of HEp-2 cells with 0.1 microM FdU resulted in the incorporation of 1.83 X 10(-9) mol of FdU (74.7 fmol detected)/mol of DNA phosphate. A linear incorporation of FdC into the DNA of HEp-2 cells was found with increasing concentrations of FdC and 1.0 mM dH4U . 0.1 microM FdC resulted in the incorporation of 2.39 X 10(-6) mol of FUMP/mol of cytoplasmic RNA phosphate and 2.23 X 10(-5) mol of FUMP/mol of nuclear RNA phosphate. Similarly, HEp-2 cells treated with 0.1 microM FdU resulted in the incorporation of 1.10 X 10(-5) mol of FUMP/mol of nuclear RNA phosphate and 9.44 X 10(-7) mol of FUMP/mol of cytoplasmic RNA phosphate. In contrast, no detectable FUMP incorporation into either nuclear or cytoplasmic RNAs of HEp-2 cells resulted when H4U or dH4U was coadministered with 0.1 microM FdC. Pool size analyses of log phase HEp-2 cells following a 30-min exposure to FdU or FdC with and without H4U or dH4U were also performed; 0.1 microM FdC treatment resulted in the formation of 169 fmol of FUMP/1.0 X 10(6) viable HEp-2 cells. Treatment with 0.1 microM FdU produced 253 fmol of FUMP/1.0 X 10(6) viable HEp-2 cells. In contrast, no detectable FUMP pools were formed when H4U or dH4U was coadministered with 0.1 microM FdC (detection limit, approximately 5 fmol). Pool levels of FdUMP, the inhibitor of thymidylate synthetase, were also assayed; 36.9 fmol of FdUMP/1.0 X 10(6) viable HEp-2 cells were detected upon administration of 0.1 microM FdC. (ABSTRACT TRUNCATED AT 400 WORDS)
Protein Kinase C Phosphorylation Regulates Membrane Insertion of GABAA Receptor Subtypes That Mediate Tonic Inhibition*

Tonic inhibition in the brain is mediated largely by specialized populations of extrasynaptic receptors, γ-aminobutyric acid receptors (GABAARs). In the dentate gyrus region of the hippocampus, tonic inhibition is mediated primarily by GABAAR subtypes assembled from α4β2/3 with or without the δ subunit. Although the gating of these receptors is subject to dynamic modulation by agents such as anesthetics, barbiturates, and neurosteroids, the cellular mechanisms neurons use to regulate their accumulation on the neuronal plasma membrane remain to be determined. Using immunoprecipitation coupled with metabolic labeling, we demonstrate that the α4 subunit is phosphorylated at Ser443 by protein kinase C (PKC) in expression systems and hippocampal slices. In addition, the β3 subunit is phosphorylated on serine residues 408/409 by PKC activity, whereas the δ subunit did not appear to be a PKC substrate. We further demonstrate that the PKC-dependent increase of the cell surface expression of α4 subunit-containing GABAARs is dependent on Ser443. Mechanistically, phosphorylation of Ser443 acts to increase the stability of the α4 subunit within the endoplasmic reticulum, thereby increasing the rate of receptor insertion into the plasma membrane. Finally, we show that phosphorylation of Ser443 increases the activity of α4 subunit-containing GABAARs by preventing current run-down. These results suggest that PKC-dependent phosphorylation of the α4 subunit plays a significant role in enhancing the cell surface stability and activity of GABAAR subtypes that mediate tonic inhibition.
UK REITs don’t like Mondays

Purpose The purpose of this paper is to examine whether Real Estate Investment Trusts (REITs) returns on the different days of the week differ from each other. Design/methodology/approach It uses European Public Real Estate Association (EPRA)/National Association of Real Estate Investment Trusts (NAREIT) UK index daily closing values (GBP) and its two sub-indices FTSE EPRA/NAREIT UK REITs and non-REITs as dependent variables. It employs Kruskal-Wallis tests and dummy-variable regression to test the hypothesis. Findings The overall findings provide evidence that return anomalies exist in the UK REITs. Practical implications Thought significant, the absolute returns differences are modest for investors to gain superior returns in UK REITs. However, by recognising the day-of-the-week effect, investors can buy/sell UK REITs more effectively. Originality/value This research brings updated evidence of the contested calendar anomalies issues in REITs.
Association of Antidepressant Medication Use During Pregnancy With Intellectual Disability in Offspring

Importance Maternal antidepressant medication use during pregnancy has previously been associated with adverse outcomes in offspring, but to our knowledge, the association with intellectual disability (ID) has not been investigated. Objectives To examine the association of maternal antidepressant medication use during pregnancy with ID in offspring and investigate the importance of parental mental illness for such an association. Design, Setting, and Participants A population-based cohort study of 179 007 children born from January 1, 2006, through December 31, 2007, with complete parental information from national registers who were followed up from birth throughout 2014. Main Outcomes and Measures We estimated relative risks (RRs) and 95% CIs of ID in children exposed during pregnancy to any antidepressant medication or specifically to selective serotonin reuptake inhibitor (SSRI) antidepressants, all other non-SSRI antidepressants, or other nonantidepressant psychotropic medications. Analyses were adjusted for potential confounders. In addition to full population analyses, we used a subsample to compare mothers who used antidepressants during pregnancy with mothers who had at least one diagnosis of depression or anxiety before childbirth but did not use antidepressants during pregnancy. Results Of the 179 007 children included in the study (mean [SD] age at end of follow-up, 7.9 [0.6] years; 92 133 [51.5%] male and 86 874 [48.5%] female), ID was diagnosed in 37 children (0.9%) exposed to antidepressants and in 819 children (0.5%) unexposed to antidepressants. With adjustment for potential confounders, the RR of ID after antidepressant exposure was estimated at 1.33 (95% CI, 0.90-1.98) in the full population sample and 1.64 (95% CI, 0.95-2.83) in the subsample of women with depression. Results from analyses of SSRI antidepressants, non-SSRI antidepressants, and nonantidepressant psychotropic medications and analyses in the clinically relevant subsample did not deviate from the full-sample results. Conclusions and Relevance The unadjusted RR of ID was increased in offspring born to mothers treated with antidepressants during pregnancy. After adjustment for confounding factors, however, the current study did not find evidence of an association between ID and maternal antidepressant medication use during pregnancy. Instead, the association may be attributable to a mechanism integral to other factors, such as parental age and mother’s psychiatric disorder.
Alanine Scanning of the Hepatitis C Virus Core Protein Reveals Numerous Residues Essential for Production of Infectious Virus

ABSTRACT Hepatitis C virus (HCV) is an important human pathogen affecting an estimated 3% of the world's population. Recent advances have enabled in vitro propagation of the virus and allow assembly and egress to be investigated for the first time. As a component of the virion, the HCV core protein likely functions primarily in infectious virus production, although little is known about the determinants of this activity. To investigate the roles of core in the viral life cycle, we performed a comprehensive deletion and alanine scanning mutagenesis study of this protein in the context of a genotype 2a reporter virus. We have confirmed that core protein is essential for infectious virion production and have identified numerous residues required for this role. The infectivity of several assembly-defective core mutants could be rescued by compensatory mutations identified in p7 and NS2, suggesting genetic interactions with core and highlighting the importance of these nonstructural proteins in infectious virion morphogenesis.
Investigation on dynamics of the flow control unit in ventilator systems and its fundamental performance limitations

In the design of a flow servo for critical care ventilator systems, control engineers are often troubled by unwanted oscillations or instability problems since these devices are typically operated under a wide variation conditions. Without knowing the dynamic behavior and its fundamental limitations of the flow control unit in ventilators, even ad-hoc extensions to standard PI control, as usually done in practice, is not able to solve all the problems and satisfy the overall performance required. In this paper, through analytical modeling and experimental identification, the root of the control problem is investigated by analyzing the dynamics of the flow control unit. Here the so called flow control unit includes a type of solenoid operated flow control valve and its exit manifold. A controller is designed by using model linearization methods, and the fundamental control limitation of the flow control unit is examined.