Miracle-dz/UniFAR-FTUs huggingface dataset:
Genomic Analysis of Melioribacter roseus, Facultatively Anaerobic Organotrophic Bacterium Representing a Novel Deep Lineage within Bacteriodetes/Chlorobi Group

Melioribacter roseus is a moderately thermophilic facultatively anaerobic organotrophic bacterium representing a novel deep branch within Bacteriodetes/Chlorobi group. To better understand the metabolic capabilities and possible ecological functions of M. roseus and get insights into the evolutionary history of this bacterial lineage, we sequenced the genome of the type strain P3M-2T. A total of 2838 open reading frames was predicted from its 3.30 Mb genome. The whole proteome analysis supported phylum-level classification of M. roseus since most of the predicted proteins had closest matches in Bacteriodetes, Proteobacteria, Chlorobi, Firmicutes and deeply-branching bacterium Caldithrix abyssi, rather than in one particular phylum. Consistent with the ability of the bacterium to grow on complex carbohydrates, the genome analysis revealed more than one hundred glycoside hydrolases, glycoside transferases, polysaccharide lyases and carbohydrate esterases. The reconstructed central metabolism revealed pathways enabling the fermentation of complex organic substrates, as well as their complete oxidation through aerobic and anaerobic respiration. Genes encoding the photosynthetic and nitrogen-fixation machinery of green sulfur bacteria, as well as key enzymes of autotrophic carbon fixation pathways, were not identified. The M. roseus genome supports its affiliation to a novel phylum Ignavibateriae, representing the first step on the evolutionary pathway from heterotrophic ancestors of Bacteriodetes/Chlorobi group towards anaerobic photoautotrophic Chlorobi.
Educational Adequacy: Alternative Perspectives and Their Implications for Educational Finance.

adequacy is an issue in the United States largely because the schools apparently are not performing up to a standard that exists in the minds of the client public.1 Traditionally, the responsibility for doing well in school was placed on the student and family. Even today, with much more emphasis given to institutional responsibility, disadvantage or lack of pupil motivation is considered a principal cause of school failure. In practice, therefore, the educational adequacy question cannot be separated from the social background of those in school. There are many ways to discuss educational adequacy, and each way can lead to a different strategy. Almost everyone assumes that knowledge taught in school is significant either in and of itself or as a function of its social value; therefore, raising the learning level in school is an important social objective, not just an objective for individuals receiving knowledge through the schools. This is not a particularly obvious characteristic of schooling; yet, it is so widely accepted that to depart from it would constitute a major political acta shift in ideology so profound that it probably would involve major social conflict. Put another way, the case for public schoolingor at least compulsory schooling financed by public fundsrests on the assumption that an educated citizenry has social value that is greater than the sum of individual valuations of education. The state, therefore, cannot leave the choice of how much schooling to individuals and their families. The other side of this coin is that once the belief in publicly financed education becomes ideology, adequate schooling is rapidly transformed into a right, something that children should have in order to be equal members of society. Thus, social membership and adequate schooling become intimately identified once it is assumed that schooling has an im-
Ambiguity Made Precise : A Comparative Foundation ( Extended Abstract )

1 We thank Kim Border, Peter Klibanoff, Tony Kwasnica, Antonio Rangel, and especially Simon Grant and Peter Wakker for helpful comments and discussions. Our greatest debt of grati tude is however to Larry Epstein, who sparked our interest on this subject with his paper (Epstein 1997), and stimulated it with many helpful discussions. The second author is grateful to the Social Sciences and Humanities Research Council of Canada for financial support. A longer version of this paper, titled "Ambiguity Made Precise: A Comparative Foundation and Some Implications," was circulated as Caltech Social Science Working Paper # 1026. 2 Division of the Humanities and Social Sciences, California Insti tute of Technology, Pasadena, CA 91125, U.S.A. E-maih pao lo~hss , c a l t e c h , edu. 3 Department of Economics, University of Toronto, Toronto, Ontario M5S 3G7, Canada. E-maih massimo0chass, u t o r o n t o , ca.
A Numerical Differentiation Method for Scattered Data and It's Application a Numerical Differentiation Method for Scattered Data and It's Application

In this paper, we discuss a classical ill-posed problem– numerical differentiation by the Tikhonov regularization. Based on the conditional stability estimate for this ill-posed problem, a new simple method for choosing regularization parameters is proposed. We show that it has an almost optimal convergence rate when the exact solution is in H2. The advantages of our method are: 1. We can get a similar computational results with much less computation, in comparison with other methods; 2. We can find out the discontinuous points numerically.
SETX sumoylation

Senataxin (SETX) is a putative RNA:DNA helicase that is mutated in two distinct juvenile neurological disorders, AOA2 and ALS4. SETX is involved in the response to oxidative stress and is suggested to resolve R loops formed at transcription termination sites or at sites of collisions between the transcription and replication machineries. R loops are hybrids between RNA and DNA that are believed to lead to DNA damage and genomic instability. We discovered that Rrp45, a core component of the exosome, is a SETX-interacting protein and that the interaction depends on modification of SETX by sumoylation. Importantly, we showed that AOA2 but not ALS4 mutations prevented both SETX sumoylation and the Rrp45 interaction. We also found that upon replication stress induction, SETX and Rrp45 co-localize in nuclear foci that constitute sites of R-loop formation generated by transcription and replication machinery collisions. We suggest that SETX links transcription, DNA damage and RNA surveillance, and discuss here how this link can be relevant to AOA2 disease.
Part and Whole Practice

A four-component aiming movement was used to examine the relative effectiveness of part and whole practice. Following a pretest, participants were assigned to one of three practice groups. Participants in a “Whole” group practiced the four components together as a unit. A “No Overlap” group practiced the first two and last two components of the task, alternating every fifth trial. An “Overlap” group practiced the transition between the second and third components on every trial by alternating practice of the first three and last three components every five trials. Participants in all groups improved significantly from pretest to immediate posttest and maintained their performance over a 24-hr delay. Contrary to the “chunking hypothesis,” participants in the No Overlap group improved as much as those in the other two groups. Kinematic data indicated that participants in all three groups learned to use response-produced feedback earlier in the individual movement trajectories. Moreover, participants appeared to acquire a general ability to make transitions between movement components rather than specific transitions. The results suggest that segmented or segmented “overlap” practice regimes may benefit learning movement sequences of short duration.
Mother-child verbal communication and self-regulation in four-year-olds

OLDS by DIAN YU (Under the Direction of Hui-Chin Hsu) ABSTRACT This study aims to explore the association between the pragmatic function of maternal verbal communication (i.e., message) and their 4-year-olds’ self-regulation and the moderation effect of child sex on this association. Eighty-three children (45 boys) and their mothers participated in this study. Mother-child verbal communication was observed during a game. Maternal verbal communication was transcribed and classified as collaborative (e.g., support) and non-collaborative (e.g., control) acts. In a series of laboratory procedures, children’s emotion regulation (affective expression and behavioral regulatory strategies) and inhibitory control (IC) were assessed to index self-regulation. Overall, results showed that maternal collaborative acts were unexpectedly associated with more negative and less neutral affective expressions (i.e., poorer emotion regulation skills). As expected, more maternal noncollaborative acts were related to poorer IC. Additionally, the association between maternal noncollaborative acts and IC were stronger for girls than boys. Limitations of this study and suggestions for future studies were discussed.
Selective attention to sound location or pitch studied with event‐related brain potentials and magnetic fields

Event‐related brain potentials (ERPs) and magnetic fields (ERFs) were used to compare brain activity associated with selective attention to sound location or pitch in humans. Sixteen healthy adults participated in the ERP experiment, and 11 adults in the ERF experiment. In different conditions, the participants focused their attention on a designated sound location or pitch, or pictures presented on a screen, in order to detect target sounds or pictures among the attended stimuli. In the Attend Location condition, the location of sounds varied randomly (left or right), while their pitch (high or low) was kept constant. In the Attend Pitch condition, sounds of varying pitch (high or low) were presented at a constant location (left or right). Consistent with previous ERP results, selective attention to either sound feature produced a negative difference (Nd) between ERPs to attended and unattended sounds. In addition, ERPs showed a more posterior scalp distribution for the location‐related Nd than for the pitch‐related Nd, suggesting partially different generators for these Nds. The ERF source analyses found no source distribution differences between the pitch‐related Ndm (the magnetic counterpart of the Nd) and location‐related Ndm in the superior temporal cortex (STC), where the main sources of the Ndm effects are thought to be located. Thus, the ERP scalp distribution differences between the location‐related and pitch‐related Nd effects may have been caused by activity of areas outside the STC, perhaps in the inferior parietal regions.
Learning an Optimization Algorithm through Human Design Iterations

Solving optimal design problems through crowdsourcing faces a dilemma: On one hand, human beings have been shown to be more effective than algorithms at searching for good solutions of certain real-world problems with high-dimensional or discrete solution spaces; on the other hand, the cost of setting up crowdsourcing environments, the uncertainty in the crowd's domain-specific competence, and the lack of commitment of the crowd, all contribute to the lack of real-world application of design crowdsourcing. We are thus motivated to investigate a solution-searching mechanism where an optimization algorithm is tuned based on human demonstrations on solution searching, so that the search can be continued after human participants abandon the problem. To do so, we model the iterative search process as a Bayesian Optimization (BO) algorithm, and propose an inverse BO (IBO) algorithm to find the maximum likelihood estimators of the BO parameters based on human solutions. We show through a vehicle design and control problem that the search performance of BO can be improved by recovering its parameters based on an effective human search. Thus, IBO has the potential to improve the success rate of design crowdsourcing activities, by requiring only good search strategies instead of good solutions from the crowd.
Pulmonary responses to selective phosphodiesterase-5 and phosphodiesterase-3 inhibitors.

OBJECTIVE To compare the direct pulmonary vasodilating activity and specificity of phosphodiesterase-5 (zaprinast) and phosphodiesterase-3 (milrinone) inhibitors on the pulmonary vascular (PV) bed of the spontaneously breathing cat with an intact chest. DESIGN Prospective, randomized animal study. SETTING Laboratory of university hospital. SUBJECTS Experiments were performed in vivo in intact-chest, spontaneously breathing cats with controlled pulmonary blood flow and constant left atrial pressure. INTERVENTIONS The responses to intralobar injections of zaprinast and milrinone were investigated at low PV tone. PV tone was then increased by intralobar arterial infusion of a thromboxane A(2) mimic, U46619. Animals received intralobar bolus injections of zaprinast or milrinone, followed by continuous IV infusion of the drug, which was administered in incremental doses titrated to produce a 20% reduction in mean systemic arterial pressure. MEASUREMENTS AND MAIN RESULTS At low PV tone, zaprinast, but not milrinone, decreased lobar arterial pressure (LoAP). At elevated PV tone, both drugs caused dose-dependent decreases in LoAP; however, milrinone caused significantly less pulmonary vasodilation. Dose-related decreases in mean systemic arterial pressure were observed with milrinone, but not with zaprinast. When the continuous IV infusion was titrated to produce a 20% reduction in mean systemic arterial pressure, the decreases in lobar arterial pressure with zaprinast infusion were significantly greater than those produced by milrinone. CONCLUSIONS These data show that zaprinast and milrinone exert a direct in vivo vasodilator effect on the PV bed at low (zaprinast) and elevated (zaprinast and milrinone) PV tone; however, at elevated PV tone, the pulmonary vasodilator effect was greater with zaprinast then with milrinone. This suggests that phosphodiesterase-5 inhibitors may potentially offer a therapeutic alternative in the management of acute pulmonary hypertension.
Urban Agglomeration and CEO Compensation

We examine the relation between the agglomeration of firms around big cities and chief executive officer (CEO) compensation. We find a positive relation among the metropolitan size of a firm’s headquarters, the total and equity portion of its CEO’s pay, and the quality of CEO educational attainment. We also find that CEOs gradually increase their human capital in major metropolitan areas and are rewarded for this upon relocation to smaller cities. Taken together, the results suggest that urban agglomeration reflects local network spillovers and faster learning of skilled individuals, for which firms are willing to pay a premium and which are therefore important factors in CEO compensation.
Teacher assessment of student reading skills as a function of student reading achievement and grade

This paper investigates teacher ratings in relation to the student test score in PIRLS 2001. Teacher assessment relates to concerns of equity and equality, and of making correct judgments of the students’ skills. It is thus crucial for a teacher to think about these issues. But do teachers assess the same skills equally? Previous research suggests that teacher assessments lack in equality. As an extension of the PIRLS 2001 study, Swedish teachers rated each and every student on 18 different statements about students’ literacy skills on a scale ranging from 1-10. It is therefore possible to investigate the relationship between teacher ratings and student achievement in reading literacy. The analysis was conducted in three steps. First a two-level model was fitted to the data and the variance of the teacher ratings were studied by creating a latent model of the teacher ratings. Second students’ achievement was used to explain variance between both students and teachers. In a later step effects of students’ grade and teacher background were examined. Results show that the variance among the teacher ratings was high and that a substantial part of the variance was due to between class differences. The variance at the within class level was to a large degree accounted for by student achievement. No substantial effect arose when introducing explanatory indicators, such as teachers education or experience to account for the between class differences in teachers ratings. However, grade had a significant effect on the level of ratings between classes. Grade 3 teachers tended to rate their students higher than did the grade 4 teachers at the same performance level.
On-Line Incremental Learning for Unknown Conditions during Assembly Operations with Robots

To be effective in real operations where the environment is continuously changing, robots have to perceive the environment and to adapt accordingly. Unfortunately, there are uncertainties due to ageing of mechanisms, isturbances, backlash, etc. that limit the usage of current control algorithms. In this paper we propose an on-line incremental learning technique using Fuzzy ARTMAP and a pattern selection criterion. The technique starts by training the ANN with a primitive knowledge base. In the presence of new patterns, the criterion-based on the success of the current action-decides autonomously if the pattern should be learned, if the ANN has to recall, or if a recovery action must be performed. The incremental learning approach is based on the online update of the neural network weights and the defined criterion decides should the new pattern be learned. The peg in hole operation (PIH) is selected as the study case in order to evaluate the performance of the technique, which is described in detail as well as the basics of the peg in hole operation. Promising results obtained with real operations with an industrial robot without over training/forgetting is presented that validate the approach.
High-Resolution Recording of the Circadian Oscillator in Primary Mouse α- and β-Cell Culture

Circadian clocks have been developed in evolution as an anticipatory mechanism allowing for adaptation to the constantly changing light environment due to rotation of the Earth. This mechanism is functional in all light-sensitive organisms. There is a considerable body of evidence on the tight connection between the circadian clock and most aspects of physiology and metabolism. Clocks, operative in the pancreatic islets, have caught particular attention in the last years due to recent reports on their critical roles in regulation of insulin secretion and etiology of type 2 diabetes. While β-cell clocks have been extensively studied during the last years, α-cell clocks and their role in islet function and orchestration of glucose metabolism stayed unexplored, largely due to the difficulty to isolate α-cells, which represents a considerable technical challenge. Here, we provide a detailed description of an experimental approach for the isolation of separate mouse α- and β-cell population, culture of isolated primary α- and β-cells, and their subsequent long-term high-resolution circadian bioluminescence recording. For this purpose, a triple reporter ProGlucagon-Venus/RIP-Cherry/Per2:Luciferase mouse line was established, carrying specific fluorescent reporters for α- and β-cells, and luciferase reporter for monitoring the molecular clockwork. Flow cytometry fluorescence-activated cell sorting allowed separating pure α- and β-cell populations from isolated islets. Experimental conditions, developed by us for the culture of functional primary mouse α- and β-cells for at least 10 days, will be highlighted. Importantly, temporal analysis of freshly isolated α- and β-cells around-the-clock revealed preserved rhythmicity of core clock genes expression. Finally, we describe the setting to assess circadian rhythm in cultured α- and β-cells synchronized in vitro. The here-described methodology allows to analyze the functional properties of primary α- and β-cells under physiological or pathophysiological conditions and to assess the islet cellular clock properties.
Improving personality and interest measurement for purposes of selection and assessment

A matter of context: A comparison of two types of contextualized personality measures The present study compared the effect of two types of Frame-of-Reference modifications to each other and to a baseline generic measure. Generic personality scales, tagged scales with ‘at school’, and completely modified scales were compared in their prediction of academic performance, counterproductive academic behavior, and participant reactions. To this end the HEXACO-PI-R (n = 215) and the MPT-BS (n = 316) were filled out by students in a within-subject design. Results showed a significant increase in criterion validity from generic, to tagged, to completely contextualized personality scales. Face validity and perceived predictive validity improved with increasing contextualization. The current study indicates that completely contextualizing personality items increases criterion validity more than just adding a tag to items. ______________________ This chapter has been published as Holtrop, D. , Born, M. Ph. , De Vries, R. E. , & De Vries, A. (2014). A matter of context: A comparison of two types of contextualized personality measures. Personality and Individual Differences, 68, 234-240. DOI:10.1016/j.paid. 2014.04. 029 Grateful acknowledgement is provided to Corine Sonke, and Remko van der Berg. Support was provided by Rotterdam University of Applied Sciences. A matter of context: A comparison of two types of contextualized personality measures
Alarming Proportions of Methicillin-Resistant Staphylococcus aureus (MRSA) in Wound Samples from Companion Animals, Germany 2010–2012

Staphylococcus (S.) aureus is an important cause of wound infections in companion animals, and infections with methicillin-resistant S. aureus (MRSA) are of particular concern due to limited treatment options and their zoonotic potential. However, comparable epidemiological data on MRSA infections in dogs, cats and horses is scarce, also limiting the knowledge about possible links to MRSA isolates from human populations. To gain more knowledge about the occurrence and genotypic variation of MRSA among wound swabs of companion animal origin in Germany we performed a survey (2010–2012) including 5,229 samples from 1,170 veterinary practices. S. aureus was identified in 201 (5.8%) canine, 140 (12.2%) feline and 138 (22.8%) equine swabs from a total of 3,479 canine, 1,146 feline and 604 equine wounds, respectively. High MRSA rates were identified with 62.7%, 46.4% and 41.3% in S. aureus of canine, feline and equine origin, respectively. Further genotyping including spa typing and multilocus sequence typing (MLST) revealed a comparable distribution of spa types among canine and feline MRSA with CC22 (47.6%; 49.2%) and CC5 (30.2%; 29.2%) as predominant lineages followed by CC398 (13.5%; 7.7%) and CC8 (4.0%; 9.2%). In contrast, the majority of equine MRSA belonged to CC398 (87.7%). Our data highlight the importance of S. aureus and MRSA as a cause of wound infections, particularly in cats and horses in Germany. While “human-associated” MRSA lineages were most common in dogs and cats, a remarkable number of CC398-MRSA was detected in horses, indicating a replacement of CC8-MRSA as the predominant lineage within horses in Germany. These data enforce further longitudinal epidemiological approaches to examine the diversity and temporal relatedness of MRSA populations in humans and animals to assess probable sources of MRSA infections. This would enable a sound risk assessment and establishment of intervention strategies to limit the additional spread of MRSA.