Miracle-dz/UniFAR-FTUs huggingface dataset:
The role of cell-free circulating microRNA in diagnostics in patients with rheumatoid arthritis

Within the past years, more and more attention has been devoted to epigenetic anomalies which regulate gene expression without altering the DNA sequence. Therefore, epigenetic modifications are emerging as key pathogenic features of immune diseases, including rheumatoid arthritis (RA), and provide an additional window for understanding the possible mechanisms involved in the pathogenesis of disease [1, 2]. DNA methylation, histone modification, nucleosome positioning and microRNAs (miRNAs) are major mechanisms of epigenetic gene regulation. These epigenetic modifications modulate chromatin architecture, thereby participating in the regulation of gene transcription and final interpretation of the encoded genetic information.
Protein annotators' assistant: A novel application of information retrieval techniques

The Protein Annotators' Assistant (or PAA) (http://www.ebi.ac.uk/paa/) is a software system which assists protein annotators in the task of assigning functions to newly sequenced proteins. Working backward from SwissProt, a database which describes known proteins, and a prior sequence similarity search that returns a list of known proteins similar to a query, PAA suggests keywords and phrases which may describe functions performed by the query. In a preprocessing step, a database is built from the protein names that appear in the SwissProt database, and against each protein are listed key words and phrases that are extracted from the corresponding text records. Common words either in general English usage or from the biological domain are removed as the phrases are assembled. This process is assisted by the use of a simple stemming algorithm, which extends the list of stop‐words (i.e., reject words), together with a list of accept‐words. At runtime, the search algorithm, invoked by a user via a Web interface, takes a list of protein names and clusters the named proteins around keywords/phrases shared by members of the list. The assumption is that if these proteins have a particular keyword/phrase in common, and they are related to a query protein, then the keyword/phrase may also describe the query. Overall, PAA employs a number of IR techniques in a novel setting and is thus related to text categorization, where multiple categories may be suggested, except that in this case none of the categories are specified in advance.
Analyzing Measure Annotations for Western Classical Music Recordings

This paper approaches the problem of annotating measure positions in Western classical music recordings. Such annotations can be useful for navigation, segmentation, and cross-version analysis of music in different types of representations. In a case study based on Wagner’s opera “Die Walk¨ure”, we analyze two types of annotations. First, we report on an experiment where several human listeners generated annotations in a manual fashion. Second, we examine computer-generated annotations which were obtained by using score-to-audio alignment techniques. As one main contribution of this paper, we discuss the inconsistencies of the different annotations and study possible musical reasons for deviations. As another contribution, we propose a kernel-based method for automatically estimating conﬁdences of the computed annotations which may serve as a ﬁrst step towards improving the quality of this automatic method.
Effects of Emotional Experience in Lexical Decision

Previous research has examined the effects of emotional experience (i.e., the ease with which words evoke emotion information) in semantic categorization (SCT), word naming, and Stroop tasks (Newcombe et al., 2012; Siakaluk et al., 2014; Moffat et al., 2015). However, to date there are no published reports on whether emotional experience influences performance in the lexical decision task (LDT). In the present study, we examined the influence of emotional experience in LDT using three different stimulus sets. In Experiment 1 we used a stimulus set used by both Kousta et al. (2009; Experiment 1) and Yap and Seow (2014) that is comprised of 40 negative, 40 positive, and 40 neutral words; in Experiment 2 we used a stimulus set comprised of 150 abstract nouns; and in Experiment 3 we used a stimulus set comprised of 373 verbs. We observed facilitatory effects of emotional experience in each of the three experiments, such that words with higher emotional experience ratings were associated with faster response latencies. These results are important because the influence of emotional experience: (a) is observed in stimulus sets comprised of different types of words, demonstrating the generalizability of the effect in LDT; (b) accounts for LDT response latency variability above and beyond the influences of valence and arousal, and is thus a robust dimension of conceptual knowledge; (c) suggests that a richer representation of emotional experience provides more reliable evidence that a stimulus is a word, which facilitates responding in LDT; and (d) is consistent with grounded cognition frameworks that propose that emotion information may be grounded in bodily experience with the world (Barsalou, 2003, 2009; Vigliocco et al., 2009).
Anterior Chamber Measurements by Pentacam and AS-OCT in Eyes With Normal Open Angles

Purpose To assess the reproducibility and agreement of anterior chamber measurements between the Pentacam (PTC) and the Anterior segment optical coherence tomography (AOCT) in normal healthy eyes with open angle. Methods Prospective cross-sectional comparative case series. A total of 162 eyes of 81 healthy volunteers with normal open angle were included in this study. Anterior chamber angle (ACA) and anterior chamber depth (ACD) were measured with PTC and AOCT. Intra-observer variability and inter-methods agreement of both instruments for ACA and ACD were evaluated. Results Values of temporal and nasal ACA measured by two instruments were similar, and the results of ACD were also not significantly different between modalities (p>0.01). ACA and ACD measurements by PTC and AOCT showed good intra-observer and inter-method agreements (all >0.9). Conclusions PTC and AOCT are presumed to be very useful for the anterior chamber angle examination. They may provide good images and quantitative data about the angle structures including ACA and ACD.
Steel surface defects recognition based on multi-label classifier with hyper-sphere support vector machine

Aiming at steel surface defects recognition, this paper proposed a multi-label classifier with hyper-sphere support vector machine (HSVM-MC). Firstly, in order to describe steel surface defects well, a new set of edge distance statistical features are proposed. Then, based on twin-hypersphere support vector machine (THSVM), HSVM-MC is built by introducing binary relevance(BR) idea. This novel classifier has merits of THSVM and BR. Moreover, it can make up the shortcomings of BR method. Experimental resuslts show that the novel multi-label classificatin method has superior accuracy and efficiency for steel surface defects recognition.
An Affordable open-source multifunctional upper-limb prosthesis with intrinsic actuation

The strict development processes of commercial upper-limb prosthesis and complexity of research projects makes them expensive for end users, both in terms of acquisition and maintenance. The advent of 3D printers and the internet, allows for distributed open-source research projects that follow new design principles; these take into account simplicity without neglecting performance in terms of grasping capabilities, power consumption and controllability. We propose a simple yet functional design based on 3D printing with the aim to reduce cost and save time in the manufacturing process. Its modular, parametric and self-contained design is intended to be fitted in a wide range of people with different transradial amputation levels. Moreover, the system brings an original user-friendly user-prosthesis interface (UPI), in order to trigger and increase the amount of customized hand postures that can be performed by the users. Surface electromyography (sEMG) control allows the user to consciously activate the prosthetic actuation mechanism, a graphical interface enables the possibility to select between different sets of predefined gestures. A five-fingered prosthetic hand integrating intuitive myoelectric control and a graphical UPI was tested, obtaining great mechanical performance, in addition to high accuracy and responsiveness of the sEMG controller.
Neotropical Mammals and the Myth of Amazonian Biodiversity

Data were compiled on the distribution of mammal taxa (883 species, 242 genera, 45 families, and 10 orders) among South America's six major macrohabitats: lowland Amazon forest, western montane forests, Atlantic rain forest, upland semideciduous forest, southern mesophytic forest, and drylands. The drylands are the richest area in numbers of species supported and are more diverse than the other habitats, including the lowland Amazon rain forest, when endemics are considered. An analysis of number of endemic and nonendemic taxa versus size of area found a simple positive linear relationship: the drylands, almost twice as extensive as the Amazon lowlands, support more endemic taxa. Conservation plans that emphasize the wet tropics and fail to consider the drylands as special repositories of mammal diversity will be unable to preserve a significant number of novel taxa.
Adaptivity and approximation for stochastic packing problems

We study stochastic variants of Packing Integer Programs (PIP) --- the problems of finding a maximum-value 0/1 vector <i>x</i> satisfying <i>Ax</i> ≤ <i>b</i>, with <i>A</i> and <i>b</i> nonnegative. Many combinatorial problems belong to this broad class, including the knapsack problem, maximum clique, stable set, matching, hypergraph matching (a.k.a. set packing), <i>b</i>-matching, and others. <b>PIP</b> can also be seen as a "multidimensional" knapsack problem where we wish to pack a maximum-value collection of items with vector-valued sizes. In our stochastic setting, the vector-valued sizes of each item is known to us apriori only as a probability distribution, and the size of an item is instantiated once we commit to including the item in our solution.Following the framework of [3], we consider both adaptive and non-adaptive policies for solving such problems, adaptive policies having the flexibility of being able to make decisions based on the instantiated sizes of items already included in the solution. We investigate the <i>adaptivity gap</i> for these problems: the maximum ratio between the expected values achieved by optimal adaptive and non-adaptive policies. We show tight bounds on the adaptivity gap for set packing and <i>b</i>-matching, and we also show how to find efficiently non-adaptive policies approximating the adaptive optimum. For instance, we can approximate the adaptive optimum for stochastic set packing to within <i>O</i>(<i>d</i><sup>1/2</sup>), which is not only optimal with respect to the adaptivity gap, but it is also the best known approximation factor in the deterministic case. It is known that there is no polynomial-time <i>d</i><sup>1/2-ε</sup> approximation for set packing, unless <i>NP</i> = <i>ZPP</i>. Similarly, for <i>b</i>-matching, we obtain algorithmically a tight bound on the adaptivity gap of <i>O</i>(λ) where λ satisfies Σ λ<sup><i>b</i><inf><i>j</i></inf>+1</sup> = 1.For general Stochastic Packing, we prove that a simple greedy algorithm provides an <i>O</i>(<i>d</i>)-approximation to the adaptive optimum. For <i>A</i> ∈ [0, 1]<sup><i>d</i>x<i>n</i></sup>, we provide an <i>O</i>(λ) approximation where Σ 1/λ<sup><i>b</i></sup><inf><i>j</i></inf> = 1. (For <i>b</i> = (<i>B</i>, <i>B</i>,., <i>B</i>), we get λ = <i>d</i><sup>1/<i>B</i></sup>. ) We also improve the hardness results for deterministic PIP: in the general case, we prove that a polynomial-time <i>d</i><sup>1-ε</sup>-approximation algorithm would imply <i>NP</i> = <i>ZPP</i>. In the special case when <i>A</i> ∈ [0,1]<sup><i>d</i>x<i>n</i></sup> and <i>b</i> = (<i>B</i>,<i>B</i>,.,<i>B</i>), we show that a <i>d</i><sup>1/B-∈</sup>-approximation would imply <i>NP</i> = <i>ZPP</i>. Finally, we prove that it is PSPACE-hard to find the optimal adaptive policy for Stochastic Packing in any fixed dimension <i>d</i> ≥ 2.
A Study on Information Sharing between Members in a Virtual Team Based on the KMRW Model

The rapid development of information and communication technology has been greatly promoting the practice of virtual teams. However, the issues of information sharing between members have always existed, which cause some problems or even conflicts in virtual teams. Those affect the performance of virtual teams fundamentally. To improve the cooperation of virtual teams, information sharing between members in a virtual team deserves more attention in the academic field. In this paper, the KMRW model of the game theory is adopted to analyze the existing issues of information sharing between members and the causes of these issues. Based on the detailed discussions, the study finds out the conditions of team members stepping out of "Prisoner's Dilemma", that is, the game occurs under incomplete information and their personality need to satisfy some specific conditions. At the moment, cooperative equilibrium can come forth as the Perfect Bayesian Equilibrium, thus team members are willing to share information. At the end of this paper, some suggestions are provided to improve the status of information sharing between members in a virtual team and enhance the performance of the virtual team.
Cooperation and Deception Recruit Different Subsets of the Theory-of-Mind Network

The term “theory of mind” (ToM) describes an evolved psychological mechanism that is necessary to represent intentions and expectations in social interaction. It is thus involved in determining the proclivity of others to cooperate or defect. While in cooperative settings between two parties the intentions and expectations of the protagonists match, they diverge in deceptive scenarios, in which one protagonist is intentionally manipulated to hold a false belief about the intention of the other. In a functional magnetic resonance imaging paradigm using cartoons showing social interactions (including the outcome of the interaction) between two or three story characters, respectively, we sought to determine those brain areas of the ToM network involved in reasoning about cooperative versus deceptive interactions. Healthy volunteers were asked to reflect upon the protagonists' intentions and expectations in cartoons depicting cooperation, deception or a combination of both, where two characters cooperated to deceive a third. Reasoning about the mental states of the story characters yielded substantial differences in activation patterns: both deception and cooperation activated bilateral temporoparietal junction, parietal and cingulate regions, while deception alone additionally recruited orbitofrontal and medial prefrontal regions. These results indicate an important role for prefrontal cortex in processing a mismatch between a character's intention and another's expectations as required in complex social interactions.
Effects of Diazepam on a Belief-Updating Task

This study examined the effects of a minor tranquilizer, diazepam, on a cognitive task that involved the updating of beliefs. On this task, subjects are first asked to express their strength of belief in a hypothesis and then to update this on the basis of new evidence. Past research has shown that revision of beliefs can be affected by many variables including the strength with which the initial belief is held, whether new information is perceived as positive or negative vis-à-vis the hypothesis, and the order in which evidence is processed. The purpose of this study was to assess whether a tranquilizer, diazepam, would affect the updating of beliefs, and specifically whether it would dampen the extent to which people revise their opinions. 12 healthy subjects participated in four experimental sessions, in which they received diazepam (0.14 mg/kg) or placebo and completed an updating task in which they received information in either of two orders, positive-negative or negative-positive. In each session, subjects saw a different experimental stimulus determined by a Latin-square design, and also completed pre- and postdrug mood questionnaires. Analysis showed order of presentation induced a recency effect similar to that obtained in previous studies, and the diazepam produced significant tranquilizer-like effects on self-report questionnaires. However, the diazepam had no effect on the updating task. These findings indicate that previously reported order effects in the belief updating task are robust and unaffected by a drug that has known sedative and memory-impairing properties.
The validity of verbal reports in children's subtraction

To assess the validity of verbal reports in children's subtraction, students in Grades 1, 3, and 5 were asked to solve a set of simple subtraction problems and were placed in the no-report, retrospective-report, or concurrent-report conditions. Two aspects of verbal report validity were assessed: reactivity, or whether providing a verbal report alters subsequent task performance, and veridicality, or whether the verbal reports are accurate reflections of solution strategies. Students in all grades and in both the retrospective-report and concurrent-report conditions were able to provide veridical strategy reports, and the instruction to verbally report had few effects on task performance. Informal findings indicate that students had less difficulty reporting retrospectively than concurrently.
Sexual practices, attitudes toward premarital sex and condom use among a sample of South African university students

We sought to ascertain sexual practices and attitudes toward premarital sex and condom use among a sample of South African university students. The participants were 117 female and 36 male undergraduates whose average age was 19.7 years. Results showed that half of the participants reported having sex in the past 12 months, with 8% indicating that they had been coerced into having sex. Although two-thirds reported that between 18 and 21 years was a good age to have sex, only 43% approved of sex before marriage. Over 80% of the participants reported that they would refuse to have sex if their partner was unwilling to use a condom. These results suggest that South African university students may be aware of the dangers of risky sexual practices.
Mycobacteriophages: Windows into Tuberculosis

Mycobacteriophages are viruses that infect mycobacterial hosts, such as Mycobacterium tuberculosis and Mycobacterium smegmatis [1]. Because the discovery and genomic characterization of mycobacteriophages has been the focus of integrated research and education programs, including the Phage Hunters Integrating Research and Education (PHIRE) and the Howard Hughes Medical Institute Science Education Alliance Phage Hunters Advancing Genomics and Evolutionary Science (HHMI SEAPHAGES), thousands of phages have been isolated using a single host strain, M. smegmatis mc155, over 500 of which have been completely sequenced [2–5]. These are mostly from environmental samples, but mycobacteriophages have also been isolated from stool samples of tuberculosis patients [6], although these have yet to be genomically analyzed. Clearly, these mycobacteriophages represent only a tiny piece of the overall phage population, which is predicted to include 10 particles, making them the majority of all life-forms in the biosphere [7]. Mycobacteriophages display a remarkable genetic diversity (Figure 1). About 30 distinct types (called clusters, or singletons if they have no relatives) that share little or no nucleotide sequence similarity have been identified. Many of the clusters span sufficient diversity that the genomes warrant division into subclusters (Figure 1). However, the genomes are characteristically mosaic in their architecture [8], which is readily evident from the shared genes revealed by amino acid sequence comparisons [9]. There is also considerable range in overall guanine plus cytosine content (GC%), from 50.3% to 70%, with an average of 64% (M. smegmatis is 67.3%). Thus, phage GC% does not necessarily match that of its host, and the consequent mismatch of codon usage profiles does not appear to be detrimental. Because new mycobacteriophages lacking extensive DNA similarity with the extant collection are still being discovered, and as there are at least seven singletons for which no relatives have been isolated, we clearly have yet to saturate the diversity of this particular population. The pace of discovery is rapid, so the profile of diversity is constantly changing. The collection of . 50,000 genes can be sorted into . 3,900 groups (phamilies) according to their shared amino acid sequences. Most of these phamilies (,75%) do not have homologues outside of the mycobacteriophages and are of unknown function. Extrapolation to the broader population suggests that phages have the largest repertoire of unexplored sequences in nature. Genetic studies with mycobacteriophage Giles show that 45% of the genes are nonessential for lytic growth, raising questions as to how and why they were acquired [10].
ESRI vs BREWER: An Evaluation of Map Use with Alternative Colour Schemes amongst the General Public

This small study evaluates the effectiveness of selected sets of colour schemes used in ESRI‟s ArcMap and ColorBrewer in communicating information on choropleth maps. Subjects conducted map reading tasks using online questionnaires and their performance was captured. The results did not show significant differences in performance associated with colour scheme - subjects were highly successful in direct acquisition tasks irrespective of the set(s) of scheme used. However, performances were consistently poor for „distribution‟ tasks. The results suggest limited spatial capabilities in the sample and highlight the need to test for general spatial ability in such experiments.
Puppet Master: designing reactive character behavior by demonstration

Puppet Master is a system that enables designers to rapidly create interactive and autonomous animated character behaviors that react to a main character controlled by an end-user. The behavior is designed by demonstration, allowing non-technical artists to intuitively design the style, personality, and emotion of the character, traits which are very difficult to design using conventional programming. During training, designers demonstrate paired behavior between the main and reacting characters. During run time, the end user controls the main character and the system synthesizes the motion of the reacting character using the given training data. The algorithm is an extension of Image Analogies [HJO*01], modified to synthesize dynamic character behavior instead of an image. We introduce non-trivial extensions to the algorithm such as our selection of features, dynamic balancing between similarity metrics, and separate treatment of path trajectory and high-frequency motion texture. We implemented a prototype system using physical pucks tracked by a motion-capture system and conducted a user study demonstrating that novice users can easily and successfully design character personality and emotion using our system and that the resulting behaviors are meaningful and engaging.
Research news and Comment: Jim Coleman: A Personal Story

This paper was written under funding of the Office of Educational Research and Improvement, U.S. Department of Education (Grant No. OERI-R-117-D40005). However, any opinions expressed are those of the author and do not necessarily represent the positions or policies of the U.S. Department of Education. I would like to thank John Anderson, Liz Berry, Kalman Hettleman, Nancy Madden, and Tom Glennan for their comments on an earlier draft of this paper.