Miracle-dz/UniFAR-FTUs huggingface dataset:
Suppression of ctc promoter mutations in Bacillus subtilis

Transcription from the Bacillus subtilis ctc promoter is induced as cells enter stationary phase under conditions in which the enzymes of the tricarboxylic acid cycle are repressed. This transcription requires the presence of a secondary form of RNA polymerase, E sigma B, that is found in exponentially growing cells and in early-stationary-phase cells. Starting with a defective ctc promoter that had either a base substitution at position -15 or a base substitution at position -36, we were able to identify four independent second-site mutations within these mutated promoters that suppressed the effect of the original mutations and thereby restored function to the ctc promoter. Three of these mutated promoters had an additional base substitution(s) at positions -5, -9, or both -5 and -9 that enhanced their utilization in vivo by E sigma B, whereas one of the promoters had a single-base-pair deletion in the -15 region that placed it under a completely different form of regulation than that of the wild-type ctc promoter. In addition to mutations in the ctc promoter region, we also isolated three classes of mutants that exhibited increased ctc expression. The effects of the mutations in these strains were not allele specific, since they increased expression from both mutant and wild-type ctc promoters. One class of mutants which affected expression from the ctc promoter carried mutations that blocked the activity of the tricarboxylic acid cycle. A second class of mutations mapped near cysA and was unable to sporulate. Three-factor transformation crosses and complementation analysis indicated that one of these mutations was an allele of spo0H. The third class of mutations is closely linked to dal and may define a regulatory gene for sigB, the sigma B structural gene.
Shared intelligence platform for collaborative simulations using sequences of algorithms: An electricity market participation case study

SEAS Shared Intelligence (SEAS SI) is a platform for algorithms sharing and execution developed under the scope of Smart Energy Aware Systems (SEAS) project to promote the intelligent management of smart grids and microgrids, by means of the shared usage of algorithms and tools, while ensuring code and intellectual protection. In this paper the platform goals and architecture are described, focusing on the recent achievement regarding the connection of distinct algorithms, which enables the execution of dynamic simulations using sequences of algorithms from distinct sources. A case study based on several SEAS SI available algorithms is presented with the objective of showing the advantages of the SEAS SI capability of supporting simulations based on sequences of algorithms. Namely, electricity market bid values are calculated by a metalearner, which is fed by market price forecasts using different methods, and by their respective forecasting errors. A case study presents some results to validate the presented work, through the simulation of the MIBEL electricity market using MASCEM (Multi-Agent Simulator of Competitive Electricity Markets).
Microsatellite markers for standardized genetic management of captive colonies of rhesus macaques (Macaca mulatta)

To preserve genetic variability and minimize genetic subdivision among captive Macaca mulatta at each of the U.S. National Institutes of Health (NIH)‐sponsored regional research colonies, the genetic structure of each colony must be characterized. To compare population genetic and demographic parameters across colonies and generations, one standard panel of highly informative genetic markers is required. We assembled a core marker set of four multiplex polymerase chain reaction (PCR) panels comprising 15 autosomal short tandem repeat (STR) loci with high information content selected from existing panels of well‐characterized markers that are currently used for parentage assessment and genetic management of rhesus macaques. We then assessed the effectiveness of these loci for providing high probabilities of individual identification and parentage resolution, and for estimating population genetic parameters that are useful for genetic management. Am. J. Primatol. 68:73–95, 2006. © 2006 Wiley‐Liss, Inc.
Short-term effects of intravenous benzodiazepines on autonomic neurocardiac regulation in humans: A comparison between midazolam, diazepam, and lorazepam

ObjectivesTo evaluate the effects of intravenously applied diazepam, lorazepam, and midazolam on autonomic neurocardiac regulation assessed by standardized measurements of heart rate variability. DesignProspective, randomized clinical study. SettingUniversity teaching hospital. PatientsForty-five patients, who underwent a gastroscopy, were randomly assigned to intravenous premedication with midazolam (5 mg), diazepam (10 mg), or lorazepam (4 mg). Six subjects refused an injection and served as nonpremedicated controls. InterventionsSerial recordings of the 5-min resting heart rate variability were obtained before and 15 and 30 mins after premedication. Seven benzodiazepine-treated patients received intravenous flumazenil (0.5 mg). Measurements and Main ResultsThe average doses applied were 0.07 mg/kg for midazolam, 0.13 mg/kg for diazepam, and 0.06 mg/kg for lorazepam. Fifteen minutes after intravenous benzodiazepines were administered, we found an increase in resting heart rate and a reduction of vagal tone compared with baseline in all three benzodiazepine-treated subgroups. Multivariate analysis (covariate age) of the changes in heart rate variability indices over the experimental course revealed a significant reduction in absolute high-frequency power with midazolam or diazepam compared with nonpremedicated subjects. Moreover, midazolam-treated subjects showed a significantly larger reduction in relative high-frequency power not only compared with nontreated subjects, but also compared with lorazepam- or diazepam-treated subjects. Vagal tone remained reduced compared with baseline even 30 mins after benzodiazepine application, however, the resting heart rate decreased toward baseline levels. After flumazenil administration, there was a linear correlation between an increase in high-frequency power and a corresponding decrease in resting heart rate. ConclusionsBenzodiazepines can influence autonomic neurocardiac regulation in man, probably through their interaction with the &ggr;-aminobutyric acidA-receptor chloride ion channel complex. The pattern of findings suggests that intravenous midazolam, diazepam, and lorazepam influence human autonomic neurocardiac regulation in a biphasic way. First, they cause a reduction of central vagal tone, and second, they may decrease the cardiac pacemaker directly. Flumazenil completely abolished the autonomic neurocardiac regulation effects of benzodiazepines.
Put on that colour, it fits your emotion: Colour appropriateness as a function of expressed emotion

People associate affective meaning with colour, and this may influence decisions about colours. Hue is traditionally considered the most salient descriptor of colour and colour–affect associations, although colour brightness and saturation seem to have particularly strong affective connotations. To test whether colour choices can be driven by emotion, we investigated whether and how colour hue, brightness, and saturation are systematically associated with bodily expressions of positive (joy) and negative (fear) emotions. Twenty-five non-colour-blind participants viewed videos of these expressions and selected for each video the most appropriate colour using colour sliders providing values for hue, brightness, and saturation. The overall colour choices were congruent with the expressed emotion—that is, participants selected brighter and more saturated colours for joy expressions than for fear expressions. Also, colours along the red–yellow spectrum were deemed more appropriate for joy expressions and cyan–bluish hues for fear expressions. The current study adds further support to the role of emotion in colour choices by (a) showing that emotional information is spontaneously used in an unconstrained choice setting, (b) extending to ecologically valid stimuli occurring in everyday encounters (dressed bodies), and (c) suggesting that all colour parameters are likely to be important when processing affective nonverbal person information, though not independently from each other.
The decline in volatility in the US economy. A historical perspective

In this paper, we analyse the volatility of US GDP growth using quarterly series starting in 1875. We find structural breaks in volatility at the end of World War II and at the beginning of the Great Moderation period. We show that the Great Moderation volatility reduction is only linked to changes in expansions, whereas that after World War II is due to changes in both expansions and recessions. We also propose several methodologies to date the US business cycle in this long period. We find that taking volatility into account improves the characterization of the business cycle.
Poly[[bis(μ2-6-methylpyrazin-2-carboxylato-κ3 N 1,O:N 4)copper(II)] dihydrate]

In the title compound, {[Cu(C6H5N2O2)2]·2H2O}n, the CuII ion (site symmetry ) is coordinated by two N,O-bidentate ligands and two N-monodentate ligands in a distorted CuO2N4 octahedral geometry. Each anion acts as a bridge between two cations, thus forming a two-dimensional polymeric network parallel to the ab plane. The packing is consolidated by O—H⋯O hydrogen bonds. One of the O atoms of the ligand and both water molecules are disordered.
Analysis of the Roles of ICAM-1 in Neutrophil Transmigration Using a Reconstituted Mammalian Cell Expression Model: Implication of ICAM-1 Cytoplasmic Domain and Rho-Dependent Signaling Pathway1

Interaction between ICAM-1 (CD54) and fibrinogen (fg) has been shown to enhance leukocyte adhesion, but its specific role in the process of migration across endothelial cell junctions remains unclear. To overcome the problem of multiple adhesion receptors found on endothelial cells, we have engineered stable Chinese hamster ovary cell lines expressing ICAM-1 (Chinese hamster ovary ICAM-1). The transfection of ICAM-1 alone in these cells is sufficient to recapitulate the entire process of neutrophil adhesion and transmigration. This phenomenon was mediated by fg-ICAM-1 interactions, as depletion of fg, as well as the use of an Ab that specifically inhibits ICAM-1-fg interaction (2D5), completely abolished the effect of ICAM-1 expression on PMN transmigration. In addition, this ICAM-1-mediated transmigration is clearly dependent on the occurrence of fg-ICAM-1 interactions on the monolayer, and not on neutrophils, as the preincubation of the PMN with the mAb was ineffective. Furthermore, PMN transmigration, but not adhesion, is totally abolished when the ICAM-1 cytoplasmic domain is deleted, indicating that signaling inside the cell is required to mediate the fg-ICAM-1 effect on transmigration. Using a specific inhibitor of the small GTP-binding protein Rho, we have obtained evidence that this signaling cascade is involved. Thus, our results clearly show that ICAM-1 plays a key role in the migration of leukocytes across cell junctions, and indicate that this phenomenon is not a direct consequence of the enhanced adhesion mediated by the expression of ICAM-1.
Optimization and Application of Integrated Land Use and Transportation Model in Small- and Medium-Sized Cities in China

Integrated land use and transportation models are helpful when policy, planning, or environment impacts are being evaluated, but the strengths and limitations in these models must be optimized. To optimize the ITLUP (Integrated Transportation and Land-Use Planning) model and apply it in small- and medium-sized cities in China, this study considered the constraints of land use intensity and introduced two critical indicators (the maximum number of households and maximum employment) to characterize the land capacity and improve the practicality of the model. Then, Monte Carlo simulation analysis was used to analyze the uncertainty factors using the coefficient of variation (C.V) and standardized regression coefficient (SRC). The results suggest that the maximum future employment and households may exceed the land limit and must be adjusted to a new zone, and the model operation simulation was closer to the actual situation of small- and medium-sized cities. The C.V value of the model output showed the increasing trend of the uncertainty of the model output variable over time, especially affected by DRAM model parameters, traffic demand forecasting model parameters and the peak hourly flow ratio. Such findings are meaningful for policymakers, planners, and others when the ITLUP model is used to anticipate the zonal employment and household allocation and to further explore the interaction between land use and transportation.
Cognitive Declines After Unilateral Deep Brain Stimulation Surgery in Parkinson's Disease: A Controlled Study Using Reliable Change, Part II

Deep brain stimulation (DBS) surgery, an effective treatment for medication-refractory Parkinson's disease (PD), may also lead to selective cognitive declines. In this continuation of a report by Zahodne et al. (2009), we compare cognitive performance of 24 PD patients who underwent unilateral implantation of the globus pallidus internal segment (GPi) or subthalamic nucleus (STN) to that of 19 PD controls. We used group statistical comparisons as well as Reliable Change Indexes (RCIs) to examine performance on measures of memory, processing speed, executive function, and visuospatial perception at baseline and 16 months after surgery. Significant between-group differences were noted on a psychomotor processing speed task. However, a significantly higher proportion of DBS patients than controls demonstrated reliable individual decline on a word list recall task (HVLT-R) and on several processing speed tests. Reliable improvements were noted on tests of visuospatial functioning. There was variability in individual outcome on executive functioning tests, with a small proportion of DBS patients demonstrating reliable decline and some demonstrating reliable improvement. Use of Reliable Change highlights the occurrence of individual variability, revealing declines and improvements in a small proportion of unilateral DBS patients that were not evident upon group comparison. These findings must be interpreted in light of group-level differences between the PD control and DBS patients on demographic and disease-related factors.
Cysteine S-Glutathionylation Promotes Stability and Activation of the Hippo Downstream Effector Transcriptional Co-activator with PDZ-binding Motif (TAZ)*

Transcriptional co-activator with PDZ-binding motif (TAZ) and Yes-associated protein (YAP) are critical transcriptional co-activators downstream of the Hippo pathway involved in the regulation of organ size, tissue regeneration, proliferation, and apoptosis. Recent studies suggested common and distinct functions of TAZ and YAP and their diverse impact under several pathological conditions. Here we report differential regulation of TAZ and YAP in response to oxidative stress. H2O2 exposure leads to increased stability and activation of TAZ but not of YAP. H2O2 induces reversible S-glutathionylation at conserved cysteine residues within TAZ. We further demonstrate that TAZ S-glutathionylation is critical for reactive oxygen species (ROS)-mediated, TAZ-dependent TEA domain transcription factor (TEAD) trans-activation. Lysophosphatidic acid, a physiological activator of YAP and TAZ, induces ROS elevation and, subsequently, TAZ S-glutathionylation, which promotes TAZ-mediated target gene expression. TAZ expression is essential for renal homeostasis in mice, and we identify basal TAZ S-glutathionylation in murine kidney lysates, which is elevated during ischemia/reperfusion injury in vivo. This induced nuclear localization of TAZ and increased expression of connective tissue growth factor. These results describe a novel mechanism by which ROS sustains total cellular levels of TAZ. This preferential regulation suggests TAZ to be a redox sensor of the Hippo pathway.
Bone response to loaded implants with non-matching implant-abutment diameters in the canine mandible.

BACKGROUND One way to evaluate various implant restorations is to measure the amount of bone change that occurs at the crestal bone. The objective of this study was to histologically evaluate the alveolar bone change around a bone-level, non-matching implant-abutment diameter configuration that incorporated a horizontal offset and a Morse taper internal connection. METHODS The study design included extraction of all mandibular premolars and first molars in five canines. After 3 months, 12 dental implants were placed at three levels in each dog: even with the alveolar crest, 1 mm above the alveolar crest, and 1 mm below the alveolar crest. The implants were submerged on one side of the mandible. On the other side, healing abutments were exposed to the oral cavity (non-submerged). Gold crowns were attached 2 months after implant placement. The dogs were sacrificed 6 months postloading, and specimens were processed for histologic and histometric analyses. RESULTS Evaluation of the specimens indicated that the marginal bone remained near the top of the implants under submerged and non-submerged conditions. The amount of bone change for submerged implants placed even with, 1 mm below, and 1 mm above the alveolar crest was -0.34, -1.29, and 0.04 mm, respectively (negative values indicate bone loss). For non-submerged implants, the respective values were -0.38, -1.13, and 0.19 mm. For submerged and non-submerged implants, there were significant differences in the amount of bone change among the three groups (P <0.05). The percentage of bone-to-implant contact for submerged implants was 73.3%, 71.8%, and 71.5%. For non-submerged implants, the respective numbers were 73.2%, 74.5%, and 76%. No significant differences occurred with regard to the percentage of bone contact. CONCLUSIONS Minimal histologic bone loss occurred when dental implants with non-matching implant-abutment diameters were placed at the bone crest and were loaded for 6 months in the canine. The bone loss was significantly less (five- to six-fold) than that reported for bone-level implants with matching implant-abutment diameters (butt-joint connections).
Social Determinants and Inequalities in Urban Health

Social and environmental factors are health determinants, in association with behavior, biological factors, and health services. Whereas socioeconomic characteristics (age, gender, ethnicity, social status) describe individuals, social determinants work through broader policies that are influenced by governments. The relation between health and four social areas is discussed. Social capital, measured as social networks and social support, appears to be protective in developing some heart disease and mental illnesses; job control at work is also found to protect against heart disease; early life experiences affect both biological and social development; and the degree of income inequality within societies correlates with health status. The Independent Report on Inequalities in Health, published in the United Kingdom in 1998, is also reviewed. The report (a) briefly describes inequalities in health by social class, sex, and ethnicity; (b) reviews the literature on policy areas that affect health; (c) includes a section indicating relatively little inequality of access or provision in the National Health Service; and (d) makes 132 recommendations. Social determinants is a new area of research having the potential to link epidemiology and environmental sciences at small area level.
Mixture models for quantitative HIV RNA data

Clinical investigators are increasing their use of quantitative determinations of HIV viral load in their study populations. The distributions of these measures may be highly skewed, left-censored, and with an extra spike below the detection limit of the assay. We recommend use of a mixture model in this situation, with two sets of explanatory covariates. We extend this model to incorporate multiple measures across time, and to employ shared parameters as a way of increasing model efficiency and parsimony. Data from a cohort of HIV-infected men are used to illustrate these features, and simulations are performed to assess the utility of shared parameters.
Seq2SQL: Generating Structured Queries from Natural Language using Reinforcement Learning

Relational databases store a significant amount of the worlds data. However, accessing this data currently requires users to understand a query language such as SQL. We propose Seq2SQL, a deep neural network for translating natural language questions to corresponding SQL queries. Our model uses rewards from in the loop query execution over the database to learn a policy to generate the query, which contains unordered parts that are less suitable for optimization via cross entropy loss. Moreover, Seq2SQL leverages the structure of SQL to prune the space of generated queries and significantly simplify the generation problem. In addition to the model, we release WikiSQL, a dataset of 80654 hand-annotated examples of questions and SQL queries distributed across 24241 tables fromWikipedia that is an order of magnitude larger than comparable datasets. By applying policy based reinforcement learning with a query execution environment to WikiSQL, Seq2SQL outperforms a state-of-the-art semantic parser, improving execution accuracy from 35.9% to 59.4% and logical form accuracy from 23.4% to 48.3%.
Corticospinal Tracts by Diffusion Tensor Tractography in Patients With Arteriovenous Malformations

Objective: To visualize the corticospinal tract (CST) in patients with arteriovenous malformations (AVMs) by using diffusion tensor tractography (DTT) and to confirm the clinical reliability of DTT in patients with AVMs. Methods: We performed DTT in 24 patients who had their AVMs near the CST. Tracts and AVMs were shown simultaneously, providing information on their spatial relationships. We also counted numbers of voxels in the DTT-CST at the level of the AVM. Results: DTT was visualized in 23 patients. In all 9 patients with hemiparesis, their DTT-CSTs were involved in the AVM or its surrounding lesion. Their volume of DTT-CST at the affected side was significantly decreased when compared with the contralateral side (P = 0.0469). All 14 patients whose DTT-CSTs were free from lesion had no hemiparesis. Conclusions DTT was safe and clinically applicable in patients with AVMs. DTT is recommended when an AVM is located near the corticospinal tract.