Miracle-dz/UniFAR-FTUs huggingface dataset:
Flavodiiron Protein from Trichomonas vaginalis Hydrogenosomes: the Terminal Oxygen Reductase

ABSTRACT Trichomonas vaginalis is one of a few eukaryotes that have been found to encode several homologues of flavodiiron proteins (FDPs). Widespread among anaerobic prokaryotes, these proteins are believed to function as oxygen and/or nitric oxide reductases to provide protection against oxidative/nitrosative stresses and host immune responses. One of the T. vaginalis FDP homologues is equipped with a hydrogenosomal targeting sequence and is expressed in the hydrogenosomes, oxygen-sensitive organelles that participate in carbohydrate metabolism and assemble iron-sulfur clusters. The bacterial homologues characterized thus far have been dimers or tetramers; the trichomonad protein is a dimer of identical 45-kDa subunits, each noncovalently binding one flavin mononucleotide. The protein reduces dioxygen to water but is unable to utilize nitric oxide as a substrate, similarly to its closest homologue from another human parasite Giardia intestinalis and related archaebacterial proteins. T. vaginalis FDP is able to accept electrons derived from pyruvate or NADH via ferredoxin and is proposed to play a role in the protection of hydrogenosomes against oxygen.
Knowledge to action? Evidence-based health care in context

Health care organisations often fail to implement good research findings in practice and are therefore, not able to increase efficiency and quality. The implementation gap that exists between ‘knowledge’ and ‘action’ in an evidence-based health care context is well known as such, but has in my opinion rarely been researched in depth. Dopson’s and Fitzgerald’s ‘Knowledge to action? Evidence-based health care in context’ is an interesting book that thoroughly describes this subject. For those concerned about why it takes so long before research has been totally adopted in work practices, the book provides enough insight to understand the matter. The book is very complete and still comprehensive enough to be valuable in practice.
A self-organizing feature-map-based fuzzy system

This paper presents a neuro-fuzzy system by using the Kohonen's self-organizing feature map algorithm, not only for its vector quantization feature, but also for its topological property. This property prevents the proposed neuro-fuzzy system from suffering from a drawback like any of the conventional clustering-algorithm-based fuzzy systems, i.e. the optimal number of clusters or some kind of similarity threshold must be predetermined. Associated with the self-organizing feature-map-based fuzzy system is a hybrid learning algorithm, which is for initial parameters setting and fine-tuning the parameters of the system.
State-of-the-Art Database of Terahertz Spectroscopy Based on Modern Web Technology

We present a review of a pioneering database on terahertz spectroscopy established by the National Institute of Information and Communication Technology and RIKEN. The database is universally available on the World Wide Web via the Internet since 2008 and was recently restructured on the basis of contemporary HTML5 technology. Flexibility and convenience to browse spectroscopic data are much improved. In the database, no less than 1500 spectroscopic data have been consolidated and provided for various materials under different conditions. Furthermore, a data upload system from general users has been prepared to enrich the database further.
Multicategory composite least squares classifiers

Classification is a very useful statistical tool for information extraction. In particular, multicategory classification is commonly seen in various applications. Although binary classification problems are heavily studied, extensions to the multicategory case are much less so. In view of the increased complexity and volume of modern statistical problems, it is desirable to have multicategory classifiers that are able to handle problems with high dimensions and with a large number of classes. Moreover, it is necessary to have sound theoretical properties for the multicategory classifiers. In the literature, there exist several different versions of simultaneous multicategory support vector machines (SVMs). However, the computation of the SVM can be difficult for large scale problems, especially for problems with large number of classes. Furthermore, the SVM cannot produce class probability estimation directly. In this article, we propose a novel efficient multicategory composite least squares classifier (CLS classifier), which utilizes a new composite squared loss function. The proposed CLS classifier has several important merits: efficient computation for problems with large number of classes, asymptotic consistency, ability to handle high‐dimensional data, and simple conditional class probability estimation. Our simulated and real examples demonstrate competitive performance of the proposed approach. Copyright © 2010 Wiley Periodicals, Inc. Statistical Analysis and Data Mining 3: 272‐286, 2010
Initial Reliability and Validity of Childhood Truama Questinnaire(CTQ-SF) Apllied in Chinese College Students

Objective: To explore the relaibility and validity of childhood trauma quanstionnaire(CTQ-SF) applied in Chinese college students . Methods: CTQ-SF was administrated to a sample of 593 cases of Chinese college students. Results: Among 593 cases, the test-retest correlations of subscales(except physical neglect scale) were 0.43-0.82 and the total-scale was 0.71; the split-reliability of subscales were 0.45～0.70 and the total-scale was 0.55; the Cronbach's α coefficients of subscales were 0.51～0.71,total-scale was 0.60. The scores of male student was higher than female's except emotional abuse ; scores of all suscales of CTQ-SF were significantly lower than those of control sample(personality disorders). The result of validated factorial analyses demostrated that the CTQ-SF was in accord with its theory constrtuction. Conclusion: CTQ-SF applied to Chinese college students can get pretty good validity and reliability, so it is applicable; but the physical neglect scale needs to be modified.
A Genome-Wide Analysis of the Effects of Sucrose on Gene Expression in Arabidopsis Seedlings under Anoxia[w]

Exogenous sucrose (Suc) greatly enhances anoxia tolerance of Arabidopsis (Arabidopsis thaliana) seedlings. We used the Affymetrix ATH1 GeneChip containing more than 22,500 probe sets to explore the anaerobic transcriptome of Arabidopsis seedlings kept under anoxia for 6 h in presence or absence of exogenous Suc. Functional clustering was performed using the MapMan software. Besides the expected induction of genes encoding enzymes involved in Suc metabolism and alcoholic fermentation, a large number of genes not related to these pathways were affected by anoxia. Addition of exogenous Suc mitigated the effects of anoxia on auxin responsive genes that are repressed under oxygen deprivation. Anoxia-induced Suc synthases showed a lower induction in presence of exogenous Suc, suggesting that induction of these genes might be related to an anoxia-dependent sugar starvation. Anoxic induction of genes coding for heat shock proteins was much stronger in presence of exogenous Suc. Interestingly, a short heat treatment enhanced anoxia tolerance, suggesting that heat shock proteins may play a role in survival to low oxygen. These results provide insight into the effects of Suc on the anoxic transcriptome and provide a list of candidate genes that enhance anoxia tolerance of Suc-treated seedlings.
Randomized Trial on Fluorides and Sealants for Fissure Caries Prevention

To investigate the effectiveness of topical fluorides in preventing fissure caries, we conducted a randomized controlled trial with parallel groups. In total, 501 children (1,539 molars, 3,078 sites), mean age 9.1 years, who had at least one sound permanent first molar with deep fissures or fissures with signs of early caries were recruited. They were randomly allocated among four groups: (1) resin sealant, single placement; (2) 5% NaF varnish, semi-annual application; (3) 38% silver diamine fluoride (SDF) solution, annual application; and (4) placebo control. Follow-up examinations were conducted every 6 months by a masked examiner. After 24 months, 485 children (97%) were examined. Proportions of pit/fissure sites with dentin caries in the sealant, NaF, SDF, and control groups were 1.6%, 2.4%, 2.2%, and 4.6%, respectively. A multi-level logistic regression analysis accounting for the effects of data clustering and confounding factors showed that fissures in any of the three treatment groups had significantly lower risks of carious cavity development into dentin than did controls (p < 0.05). We concluded that placement of resin sealant, semi-annual application of NaF varnish, and annual application of SDF solution are all effective in preventing pit and fissure caries in permanent molars (ClinicalTrials.gov number CT01446107).
RLS Adaptive Filter With Inequality Constraints

In practical implementations of estimation algorithms, designers usually have information about the range in which the unknown variables must lie either due to physical constraints (such as power always being non-negative) or due to hardware constraints (such as in implementations using fixed-point arithmetic). In this letter, we propose a fast (i.e., whose complexity grows linearly with the filter length) version of the dichotomous coordinate descent recursive least-squares (RLS) adaptive filter which can incorporate constraints on the variables. The constraints can be in the form of lower and upper bounds on each entry of the filter, or norm bounds. We compare the proposed algorithm with the recently proposed normalized non-negative least-mean-squares (N-NLMS) and projected-gradient normalized LMS (PG-NLMS) filters, which also include inequality constraints in the variables.
Breast‐conserving surgery and radiation after augmentation mammoplasty

Background. Although breast‐conserving therapy (tumor excision, axillary node dissection, and postoperative radiation) for women with breast cancer yields survival and local recurrence rates comparable with those of modified radical mastectomy, studies suggest that postoperative radiation leads to capsular contractures and poor cosmesis in patients with breast implants.
Focal-sweep for large aperture time-of-flight cameras

Time-of-flight (ToF) imaging is an active method that utilizes a temporally modulated light source and a correlation-based (or lock-in) imager that computes the round-trip travel time from source to scene and back. Much like conventional imaging ToF cameras suffer from the trade-off between depth of field (DOF) and light throughput-larger apertures allow for more light collection but results in lower DoF. This trade-off is especially crucial in ToF systems since they require active illumination and have limited power, which limits performance in long-range imaging or imaging in strong ambient illumination (such as outdoors). Motivated by recent work in extended depth of field imaging for photography, we propose a focal sweep-based image acquisition methodology to increase depth-of-field and eliminate defocus blur. Our approach allows for a simple inversion algorithm to recover all-in-focus images. We validate our technique through simulation and experimental results. We demonstrate a proof-of-concept focal sweep time-of-flight acquisition system and show results for a real scene.
Contour extraction for breast tumor in ultrasound image

Shape features are usually considered for discriminating benign and malignant breast tumors in ultrasound image. A contour extraction method is presented for the purpose of discrimination. A half contouring is devised for reducing the influence of shadow effect resulting from the ultrasonic energy decay. Based on the cue of contour variation, degree standard variation and texture information are developed as useful features for the discrimination. Above 70% accuracy could be obtained by using the adopted half contour information. Experiments confirm the feasibility of the proposed method.
Sensorless Control of PM Synchronous Motors in the Whole Speed Range Including Standstill Using a Combined INFORM/EMF Model

The paper presents the combination of a lowspeed model ("INFORM method") and a specially adapted high speed model ("Voltage model or EMF model") for covering the full speed range of sensorless permanent magnet (PM-) synchronous motor drives. Both models generate "measuring information" for a linear observer, modelling the mechanical structure of the motor. A special feedback loop is introcuded, coupling back the observer information to the integrating voltage model. Thus, a stable operation with high robustness against parameter uncertainties and low frequency disturbances is achieved.
Exercising musicianship anew through soundpainting: Speaking music through sound gestures

In this thesis I focus on soundpainting-mediated musical experiences. Proposed in the mid seventies by the American musician Walter Thompson (b. 1952), soundpainting is a conventionalized artistic practice designed to create artistic works in real time. Thompson’s definition of soundpainting as a sign language is central to the present artistic inquiry, based on different moments of artistic practice and on interviews with students and professional artists, and informed by an existentialist hermeneutic and yet pragmatic perspective. What does it mean to have an experience in soundpainting? Considering soundpainting as an artistic language, what does it mean to know and speak it? How is meaning mediated in soundpainting? What does a knowledge of soundpainting bring to classically trained musicians? Classically trained orchestral flutist as I am, my starting point has been the similarities and differences between the production and interpretation of signs as they occur in soundpainting-mediated practices and in personal experience of playing from scores and relating to conductors’ gestures.The artistic, hermeneutic circle turns on transpositions across horizons of understanding, since in soundpainting one’s own practices are extended, and one frequently acts as instrumentalist, composer, and conductor. This is formulated as an example of artistic transaction, in the sense of acting across borders that usually separate roles. In addition to critical reflections on the indeterminacy of soundpainting as a practice and on the two performative perspectives possible in soundpainting (performance leader and performer), I explore soundpainting as an individual instrumental practice too. Although a particularization of soundpainting, this transposition from moments of qualitative transaction between two or more artists to an individual practice retains the significant aspects of standard practice in a soundpainting-mediated musical experience. In the process, significant opportunities were found to exercise different forms of embodying musical knowledge, wherein aspects of ownership and responsibility could be re-contextualized as different intentionalities (in the phenomenological sense) came to play. Through the exploration of such strategies for a systematic development of an improvisational mindset, it was also possible to nurture an empathic understanding of the activities of one’s fellow musicians (performers, conductors, composer, improvisers). All these findings speak to the all-important sense of presence in the moment of performance and can be extended to other forms of music-making, disclosing potential directions for further research on both artistic and educational grounds. (Less)
Stigma and Divorce: A Relevant Lens for Emerging and Young Adult Women?

ABSTRACT Historically, divorced women have been vulnerable to devaluation. This study examined the experiences of divorce-related stigma in emerging and young adult women, who at the time of divorce were between the ages of 23 and 32. Using consensual qualitative research methodology, (Hill et al., 2005), the authors identified 5 categories pertaining to stigma and divorce: (a) self-stigma versus public stigma; (b) failure, embarrassment, and perceptions of blame; (c) religion and stigma; (d) nondisclosure and impression management; and (e) contextual considerations: “it would have been different if. ” Analyses suggest that stigma informs the behavior of emerging and young adult women in nuanced and contradictory ways. Although a significant number of the participants acted in ways that were consistent with the belief that stigmatization is relevant to their lives, when they spoke of stigma, they assessed that stigma is no longer relevant. Implications for clinicians and related professionals are discussed.
Compact low profile antenna based on MSRR-AMC reflector

This paper is dedicated to the study of volumetric MSRR-based AMC structure. The characteristics of a single MSRR unit cell are investigated; and a volumetric miniaturized AMC block is then designed. In order to validate the approach used to simulate an infinite periodic structure, a block of nine aligned layers is then simulated. The next step is to add a printed dipole antenna as an application to validate the performance of the AMC block. The results are very excellent and promising if compared with the simple dipole antenna as an enhancement of 5 dB is achieved considering the directivity. The front to back ratio is found to be about 20 dB.
D-OAMP: A denoising-based signal recovery algorithm for compressed sensing

Approximate message passing (AMP) is an efficient iterative signal recovery algorithm for compressed sensing (CS). For sensing matrices with independent and identically distributed (i.i.d.) Gaussian entries, the behavior of AMP can be asymptotically described by a scaler recursion called state evolution. Orthogonal AMP (OAMP) is a variant of AMP that imposes a divergence-free constraint on the denoiser. In this paper, we extend OAMP to incorporate generic denoisers, hence the name D-OAMP. Our numerical results show that state evolution predicts the performance of D-OAMP well for generic denoisers when i.i. d. Gaussian or partial orthogonal sensing matrices are involved. We compare the performances of denosing-AMP (D-AMP) and D-OAMP for recovering natural images from CS measurements. Simulation results show that D-OAMP outperforms D-AMP in both convergence speed and recovery accuracy for partial orthogonal sensing matrices.
Collective Solitude and Social Networks in World of Warcraft

This chapter investigates the nature and structure of social networks formed between the players of massively multiplayer online games (MMOGs), an incredibly popular form of Internet-based entertainment attracting millions of subscribers. To do so, we use data collected about the behavior of more than 300,000 characters in World of Warcraft (the most popular MMOG in America). We show that these social networks are often sparse and that most players spend time in the game experiencing a form of “collective solitude”: they play surrounded by, but not necessarily with, other players. We also show that the most successful player groups are analogous to the organic, team-based forms of organization that are prevalent in today’s workplace. Based on these findings, we discuss the relationship between online social networks and “real-world” behavior in organizations in more depth.
Anchored LTL separation

Gabbay's separation theorem is a fundamental result for linear temporal logic (LTL). We show that separating a restricted class of LTL formulas, called anchored LTL, is elementary if and only if the translation from LTL to the linear temporal logic with only future temporal connectives is elementary. To prove this result, we define a canonical separation for LTL, and establish a correspondence between a canonical separation of anchored LTL formulas and the ω-automata that recognize these formulas. The canonical separation of anchored LTL formulas has two further applications. First, we constructively prove that the safety closure of any LTL property is an LTL property, thus proving the decomposition theorem for LTL: every LTL formula is equivalent to the conjunction of a safety LTL formula and a liveness LTL formula. Second, we characterize safety, liveness, absolute liveness, stable, and fairness properties in LTL. Our characterization is effective: We reduce the problem of deciding whether an LTL formula defines any of these properties to the validity problem for LTL.
Genetic diversity of Korean Bacillus anthracis isolates from soil evaluated with a single nucleotide repeat analysis

Bacillus (B.) anthracis, the etiological agent of anthrax, is one of the most genetically monomorphic bacteria species in the world. Due to the very limited genetic diversity of this species, classification of isolates of this bacterium requires methods with high discriminatory power. Single nucleotide repeat (SNR) analysis is a type of variable-number tandem repeat assay that evaluates regions with very high mutation rates. To subtype a collection of 21 isolates that were obtained during a B. anthracis outbreak in Korea, we analyzed four SNR marker loci using nucleotide sequencing analysis. These isolates were obtained from soil samples and the Korean Center for Disease Control and Prevention. The SNR analysis was able to detect 13 subgenotypes, which allowed a detailed evaluation of the Korean isolates. Our study demonstrated that the SNR analysis was able to discriminate between strains with the same multiple-locus variable-number tandem repeat analysis genotypes. In summary, we obtained SNR results for four SNR marker loci of newly acquired strains from Korea. Our findings will be helpful for creating marker systems and help identify markers that could be used for future forensic studies.
From Video Matching to Video Grounding

This paper addresses the background estimation problem for videos captured by moving cameras, referred to as video grounding. It essentially aims at reconstructing a video, as if it would be without foreground objects, e.g. cars or people. What differentiates video grounding from known background estimation methods is that the camera follows unconstrained motion so that background undergoes ongoing changes. We build on video matching aspects since more videos contribute to the reconstruction. Without loss of generality, we investigate a challenging case where videos are recorded by in-vehicle cameras that follow the same road. Other than video synchronization and spatiotemporal alignment, we focus on the background reconstruction by exploiting inter- and intra-sequence similarities. In this context, we propose a Markov random field formulation that integrates the temporal coherence of videos while it exploits the decisions of a support vector machine classifier about the background ness of regions in video frames. Experiments with real sequences recorded by moving vehicles verify the potential of the video grounding algorithm against state-of-art baselines.
Feature, Configuration, History - A Bio-inspired Framework for Information Representation in Neural Networks

Artificial Neural Networks are very efficient adaptive models but one of their recognized weaknesses is about information representation, often carried out in an input vector without a structure. Beyond the classical elaboration of a hierarchical representation in a series of layers, we report here inspiration from neuroscience and argue for the design of heterogenous neural networks, processing information at feature, configuration and history levels of granularity, and interacting very efficiently for high-level and complex decision making. This framework is built from known characteristics of the sensory cortex, the hippocampus and the prefrontal cortex and is exemplified here in the case of pavlovian conditioning, but we propose that it can be advantageously applied in a wider extent, to design flexible and versatile information processing with neuronal computation.