Miracle-dz/UniFAR-FTUs huggingface dataset:
Evolutionarily Stable Attenuation by Genome Rearrangement in a Virus

Live, attenuated viruses provide many of the most effective vaccines. For the better part of a century, the standard method of attenuation has been viral growth in novel environments, whereby the virus adapts to the new environment but incurs a reduced ability to grow in the original host. The downsides of this approach were that it produced haphazard results, and even when it achieved sufficient attenuation for vaccine production, the attenuated virus was prone to evolve back to high virulence. Using bacteriophage T7, we apply a synthetic biology approach for creating attenuated genomes and specifically study their evolutionary stability. Three different genome rearrangements are used, and although some initial fitness recovery occurs, all exhibit greatly impaired abilities to recover wild-type fitness over a hundred or more generations. Different degrees of stable attenuation appear to be attainable by different rearrangements. Efforts to predict fitness recovery using the extensive background of T7 genetics and biochemistry were only sometimes successful. The use of genome rearrangement thus offers a practical mechanism of evolutionary stable viral attenuation, with some progress toward prediction.
Homolog of tocopherol C methyltransferases catalyzes N methylation in anticancer alkaloid biosynthesis

Madagascar periwinkle (Catharanthus roseus) is the sole source of the anticancer drugs vinblastine and vincristine, bisindole alkaloids derived from the dimerization of the terpenoid indole alkaloids vindoline and catharanthine. Full elucidation of the biosynthetic pathways of these compounds is a prerequisite for metabolic engineering efforts that will improve production of these costly molecules. However, despite the medical and commercial importance of these natural products, the biosynthetic pathways remain poorly understood. Here we report the identification and characterization of a C. roseus cDNA encoding an S-adenosyl-L-methionine-dependent N methyltransferase that catalyzes a nitrogen methylation involved in vindoline biosynthesis. Recombinant enzyme produced in Escherichia coli is highly substrate specific, displaying a strict requirement for a 2,3-dihydro bond in the aspidosperma skeleton. The corresponding gene transcript is induced in methyl jasmonate-elicited seedlings, along with the other known vindoline biosynthetic transcripts. Intriguingly, this unique N methyltransferase is most similar at the amino acid level to the plastidic γ-tocopherol C methyltransferases of vitamin E biosynthesis, suggesting an evolutionary link between these two functionally disparate methyltransferases.
Allelic loss on chromosomes 4q and 16q in hepatocellular carcinoma: association with elevated alpha-fetoprotein production.

BACKGROUND & AIMS In human hepatocellular carcinoma, restriction fragment length polymorphism analysis has shown frequent allelic loss on chromosomes 4q and 16q. To better define the commonly affected region for further positional cloning of the putative tumor-suppressor genes contained in these two chromosome arms, microsatellite polymorphism analysis was conducted to analyze extensively the allelic loss on both chromosome loci. METHODS DNA from 42 pairs of large hepatocellular carcinoma (> 5 cm) and corresponding nonneoplastic liver tissues were prepared. Allelic loss on chromosome 4q and 16q was investigated by 13 or 12 sets of microsatellite polymorphic markers. RESULTS The frequency of allelic loss on chromosome 16q was 70%, and the common region was mapped to 16q22-23. An even higher frequency (77%) was found on chromosome 4q with the common region mapped to 4q12-23. The allelic loss of chromosome 4q was significantly associated with hepatocellular carcinoma of elevated serum alpha-fetoprotein but not with those of normal level (91% vs. 30%; Fisher's Exact Test, two-tailed P = 1.12 x 10(-4)). CONCLUSIONS The results form the basis for further positional cloning of putative tumor-suppressor genes on chromosome 4q and 16q. Moreover, the one on chromosome 4q might shed light on the mechanism of alpha-fetoprotein expression in hepatocellular carcinoma.
Full-fledged temporal processing: bridging the gap between deep linguistic processing and temporal extraction

The full-fledged processing of temporal information presents specific challenges. These difficulties largely stem from the fact that the temporal meaning conveyed by grammatical means interacts with many extra-linguistic factors (world knowledge, causality, calendar systems, reasoning). This article proposes a novel approach to this problem, based on a hybrid strategy that explores the complementarity of the symbolic and probabilistic methods. A specialized temporal extraction system is combined with a deep linguistic processing grammar. The temporal extraction system extracts eventualities, times and dates mentioned in text, and also temporal relations between them, in line with the tasks of the recent TempEval challenges; and uses machine learning techniques to draw from different sources of information (grammatical and extra-grammatical) even if it is not explicitly known how these combine to produce the final temporal meaning being expressed. In turn, the deep computational grammar delivers richer truth-conditional meaning representations of input sentences, which include a principled representation of temporal information, on which higher level tasks, including reasoning, can be based. These deep semantic representations are extended and improved according to the output of the aforementioned temporal extraction module. The prototype implemented shows performance results that increase the quality of the temporal meaning representations and are better than the performance of each of the two components in isolation.
Recognition in a visuospatial memory task: The effect of presentation

The influence of the mode of presentation (simultaneous vs. sequential) on accuracy and latency of visuospatial recognition was explored in three experiments. In Experiment 1, two groups were administered a visuospatial task in which a number of positions were shown either simultaneously or sequentially (in a random order); memory was tested using a recognition procedure of visuospatial patterns, either identical or different (a single cell displaced). The results showed that (1) performance was higher in the simultaneous than in the sequential presentation, and (2) decision time increased with complexity in the sequential presentation but not in the simultaneous presentation. In Experiment 2, the same task was used in three conditions of presentation, simultaneous, random sequential, and ordered sequential; at test, a single location, rather than a pattern, was presented for recognition. The results showed that (1) performance was higher in the simultaneous and in the ordered sequential presentations than in the random sequential one, and (2) decision time increased with complexity. In Experiment 3, the same task was used in the same three conditions of presentation, simultaneous, random sequential, and ordered sequential; at test either an identical or a “displaced” pattern was presented for recognition. The results showed that (1) performance was equivalent in the three types of presentation, and (2) decision time increased with complexity for “hit” items; different patterns of linear relations were observed for “correct rejections” items. The results are interpreted in terms of the organisation of visuospatial working memory, and three types of encoding—extrafigural spatial encoding, visual pattern encoding, and spatial path encoding—were proposed.
A Resonant DC-DC transformer with Zero Current Ripple

The paper presents a resonant converter topology capable of providing zero ripple conditions (ZRC) at either its input or output current. The basic properties of the proposed topology are discussed in detail. The remarkable symmetry and the proportional voltages of the circuit allow it to maintain ripple-less current independent of the load or switching frequency. Theoretical predictions are well supported by simulation and experimental results
Improvements to the Strong Planning Algorithm

This paper points out some drawbacks and gives some modifications to the strong planning algorithm. In particular, a set of states is found by using of adjacency matrix that corresponds to a non-deterministic state-transition system. The set of states is composed of four parts, the first part is a part of initial states which can not reach goal states, if the first part is not empty, there is not strong planning; if a state which is not a initial state can not reach goal states,we put the state into the second part; the third part are the states that are unreachable from the initial states; so the station-action pairs which relate to the second part or third part are absolutely useless; the fourth part are the states which the initial states can not reach without passing any goal state before, the state-action pairs which relate to the fourth part are useless as well, because they move the execution away from the goal. So a great many of state-action pairs can be eliminated directly from the universal policy. Finally, the efficiency of the modified algorithm is illustrated by an example and some experiments.
The effect of temperature on the growth of Bacterium coli at pH 7-0 with a constant food supply.

SUMMARY: The effect of temperature on the growth of Bact. coli under accurately controlled conditions has been examined in an apparatus which permits food to be supplied at any desired rate by means of an automatic syringe mechanism. Six temperatures were used, from 15° to 40° at 5° intervals, with a single rate of food supply. Total and viable cell counts were frequently made and growth curves constructed. In some cases the changes in numbers were followed after stopping the food supply. At all stages the total counts greatly exceeded the viable. There was always first an ‘initial’ phase in which the daily increments in total cells varied with time. Very early in this phase cell division lagged behind cell growth. At 15° this condition probably persisted throughout the whole experiment. The initial phase was longest when the temperature was lowest, but the time taken to reach 300×106 total cells/ml. did not vary greatly, except at 15° when the time was markedly increased. The yield of total cells at the end of the initial phase was highest when the temperature was lowest and depended on the amount of food added, i.e. on the duration of the phase, but relatively more cells were formed in a long than in a short phase. The viable cell count at the end of the initial phase was also enhanced by low temperature, except at 15° where the viable cells were fewer than expected in comparison with the other experiments. The ratio of the total to the viable count at the end of the initial phase was often close to 2·0. The initial phase was followed by a ‘steady’ phase in which there were, on the whole, constant daily increments in both total and viable counts, although there were indications of stepwise increments. In the steady phase the calculated rates of increase in both total and viable cells were highest when the temperature was low, and bore a linear relation to the temperature. The rate of increase in viable cells was almost zero at 35°, which was apparently a critical temperature for viability. At 40° there was only a slow decline in viable cells, but nevertheless at both 35° and 40° growth of the cultures occurred since the total counts continually increased, but approximately half the cells formed were non-viable. To express the difference between the total and viable counts a non-viability index was calculated. This was constant throughout the steady phase and was smallest when the temperature was lowest. The amount of food previously shown to be required for the formation of a new cell at 35° was found to be not inconsistent with the experimental data at any of the other temperatures, but if this amount were constant the food used per cell for maintenance and wastage must have declined with decreasing temperature. After cessation of the food supply the total count declined at both 15° and 30°, being slightly faster at the lower temperature. The viable count also declined during starvation at 15°; the rate of decrease of the viable count was greater at 30°.
Performance of neural network feature subset selection in injected fuel flow forecasting

This paper compares the performance of some feature subset selection in injected fuel flow forecasting. Injected fuel flow leads to an accurate measurement of car's fuel consumption. The fuel consumption of a car depends on many factors like road, weather, and driver behaviour that are rigid for a car manufacturer to influence. Speed, stepper speed_step, stepper speed_angle, revolution, stepper rev_step, stepper rev_angle, fuel volume, stepper fuel_step, stepper fuel_angle, fuel transducer input, current fuel consumption, gear, distance to empty in volume, distance to empty in kilometre, current distance, and battery voltage are measured from the experimented car. The multilayered perceptron network trained by Levenberg-Marquardt algorithm was selected as a black box model for forecasting purposes. The input variables were taped from car sensors. The criterions for comparison are based on the coefficient of determination (R2). Three difference feature subset selection (A, B and C) consists of 1267 data samples have been collected. The first 700 data were used for training and the rest were used in validation and forecasting process. The three subset of the feature (A, B and C) are selected based on trial and error. The results show that feature subset selection B outperformed feature subset selection A and C significantly.
A Rare Novel Deletion of the Tyrosine Hydroxylase Gene in Parkinson Disease

Tyrosine hydroxylase (TH) enzyme is a rate limiting enzyme in dopamine biosynthesis. Missense mutation in both alleles of the TH gene is known to cause dopamine‐related phenotypes, including dystonia and infantile Parkinsonism. However, it is not clear if single allele mutation in TH modifies the susceptibility to the adult form of Parkinson disease (PD). We reported a novel deletion of entire TH gene in an adult with PD. The deletion was first identified by copy number variation (CNV) analysis in a genome‐wide association study using Illumina Infinium BeadChips. After screening 635 cases and 642 controls, the deletion was found in one PD case but not in any control. The deletion was confirmed by multiple quantitative PCR (qPCR) assays. There is no additional exonic single nucleotide variant in the one copy of TH gene of the patient. The patient has an age‐at‐onset of 54 years, no evidence for dystonia, and was responsive to L‐DOPA. This case supports the importance of the TH gene in PD pathogenesis and raises more attention to rare variants in candidate genes being a risk factor for Parkinson disease. © 2010 Wiley‐Liss, Inc.
Monocular SLAM for Real-Time Applications on Mobile Platforms

The current state-of-the-art in monocular visual SLAM comprises of 2 systems: Large-Scale Direct Monocular SLAM (LSD-SLAM), and Oriented FAST and Rotated BRIEF SLAM (ORB-SLAM). This paper experiments with an adapted version of ORB-SLAM, and is also inspired by other groundbreaking SLAM implementations including LSD-SLAM. It outlines a lean pipeline for development of a monocular SLAM system on a mobile device, and highlights the key insights and results of developing such a system.
Correction: Bayesian Genome Assembly and Assessment by Markov Chain Monte Carlo Sampling

due to Figure 4 and Figure 5 being ordered incorrectly. Please download the PDF again to view the corrected article. The originally published, uncorrected article and the republished, corrected article are provided here for reference. Copyright: ß 2014 The PLOS ONE Staff. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
Editorial: personality, learning, and education

In this Special Issue personality sets foot on momentous ground. The field of learning and education forms a great challenge to personality psychology because central issues with personality are fought out right there. Though the mere question of whether personality matters in the field of learning and education is answered (see Sternberg’s commentary), many aspects regarding the exact role personality should play and the required proper ties to stage personality remain unclear. The recent ‘recuperation’ of human behavioural genetics, for example, unarguably poses restraints on the malleability orientation of the field of learning and education (cf. Loehlin, 1992). Many educational programmes may have to be rewritten, if taking into account basic facts about the genetic basis of personality. All of the Big Five factors of personality are found to be related to educational outcomes, but the extent to which this is the case and especially the way they determine educational outcomes have yet to be established. Two basic trait factors deserve special attention. Conscientiousness, because its typical task-colouring makes it particularly apt theoretically, but, more so, because it is hard to find empirical studies that do not give prominence to this basic trait in education and learning (see, for example, Wlickle and De Fruyt and Mervielde, this Issue); Agreeableness, because of its more elusive place amidst the myriad indicators of educational performance. This basic trait possibly captures to a large extent the substance of interpersonal relations and communication constituting the system of transfer of ideas, knowledge, skills, and values. Not only do these two basic traits mark the different sorts of complexity that are met when basic research joins an applied field, but also their roles teach us about the scope of the use of a small set of abstract constructs for predictive purposes in applied settings. This conclusion is reinforced by the more telling and field-tailored behavioural constructs such as styles and strategies (cf. Blickle, Boekaerts and Messick, this Issue). Alternative clues may be provided at the facet level of the Big-Five model (cf. Costa and McCrae, 1992; De Raad and Schouwenburg, this Issue). Though the choice of an optimal level of constructs (cf. Briggs, 1989) is an issue deserving permanent attention. , we feel a reserved attitude is in order here from both personality researchers and applied researchers. When, for example, personality researchers give way to demands of applied researchers to invest in proximate rather than basic measures, predictive validities may be increased indeed, even drastically,
Extending Pictorial Structures for Object Recognition

The goal of this paper is to recognize various deformable objects from images. To this end we extend the class of generative probabilistic models known as pictorial structures. This class of models is particularly suited to represent articulated structures, and has previously been used by Felzenszwalb and Huttenlocher for pose estimation of humans. We extend pictorial structures in three ways: (i) likelihoods are included for both the boundary and the enclosed texture of the animal; (ii) a complete graph is modelled (rather than a tree structure); (iii) it is demonstrated that the model can be tted in polynomial time using belief propagation. We show examples for two types of quadrupeds, cows and horses. We achieve excellent recognition performance for cows with an equal error rate of 3% for 500 positive and 5000 negative images.
Education investment effects of affirmative action policy. Contest game argument

In this paper we investigate the problem of effort effects of the affirmative action policy. We develop a version of a rent-seeking game in the style of Tullock (1980) with two heterogeneous players and two stages, considering that ahead of the formal competition players can invest to lower their effort cost. Using this model we show that there are instances in which the normative objective of affirmative action policy to make a level-playing field may be missed. Namely, we demonstrate that if in relative terms the cost of acquiring skills for the ex-ante weaker player (a member of a discriminated group) is low enough as compared to the ex-ante stronger player (non-discriminated), then in the actual competition the ex-ante weaker player may become stronger than the ex-ante stronger player. This result shows that AA programmes cannot be effective if they are designed in isolation based on the minority-group membership only and without taking into account the actual costs of acquiring skills (that is education or learning) by individuals.
Direction and Sequence in Copying

To explore the nature of directional experience and directional behavior in countries with different scripts, children and adults in the United States and in Israel were asked to copy a number of geometric shapes. The paths or sequences of strokes displayed some common developmental trends together with some specific differences stemming from the patterns taught for forming letters. Generalization from letter patterns, however, followed a nonlinear course: strongest at the time when writing is first being mastered and then declining. A similar course, it is suggested, may occur in generalizations among other cognitive or perceptual behaviors.
Uniprocessor Scheduling Strategies for Self-Suspending Task Systems

We study uniprocessor scheduling for hard real-time self-suspending task systems where each task may contain a single self-suspension interval. We focus on improving state-of-the-art fixed-relative-deadline (FRD) scheduling approaches, where an FRD scheduler assigns a separate relative deadline to each computation segment of a task. Then, FRD schedules different computation segments by using the earliest-deadline first (EDF) scheduling policy, based on the assigned deadlines for the computation segments. Our proposed algorithm, Shortest Execution Interval First Deadline Assignment (SEIFDA), greedily assigns the relative deadlines of the computation segments, starting with the task with the smallest execution interval length, i.e., the period minus the self-suspension time. We show that any reasonable deadline assignment under this strategy has a speedup factor of 3. Moreover, we present how to approximate the schedulability test and a generalized mixed integer linear programming (MILP) that can be formulated based on the tolerable loss in the schedulability test defined by the users. We show by both analysis and experiments that through designing smarter relative deadline assignment policies, the resulting FRD scheduling algorithms yield significantly better performance than existing schedulers for such task systems.