Miracle-dz/UniFAR-FTUs huggingface dataset:
Mining Spatial Motifs from Protein Structure Graphs

Finding recurring structural features among proteins three-dimensional (3D) structures is an important problem in bioinformatics. In this paper we apply a novel subgraph mining algorithm to three related graph representations of the sequence and proximity characteristics of a protein’s amino acid residues. The subgraph mining algorithm is used to discover spatial motifs that can be used to discriminate among proteins in different families found in the SCOP database. The results indicate that an Delaunay Tessellation (and its recent developed extension almost-Delaunay ) subset of the contact graph is robust, sparse, and adequate to produce asymptotically simplified graphs (with increasing interaction radius) for mining spatial motifs, yielding motifs with discrimination qualities similar to, or better than, those obtained from the full contact graph.
Nurturing Collaborative Relations

Many organizations aspire to gain collaborative advantage by working in partnerships across organizational, sectoral, and even national boundaries. Such collaborations, however, are difficult to manage, and the likelihood of disappointing outputs is high. To create advantage, practitioners need to engage in a continuous process of nurturing the collaborative processes. One issue that appears significant in the nurturing process is trust. This article incorporates a synthesis of research on trust with research on other aspects of collaboration. It develops a trust-building loop and examines its validity to inform practice. It argues that trust building is problematic and that management of trust implies both the ability to cope in situations where trust is lacking and the ability to build trust in situations where this is possible. It summarizes pragmatic implications in a tool for thinking about and addressing trust management in different collaborative situations.
Noncoding RNAs in the Brain

Cells transcribe thousands of RNAs that do not appear to encode proteins. The neuronal functions of these noncoding RNAs (ncRNAs) are for the most part not known, but specific ncRNAs have been shown to regulate dendritic spine development, neuronal fate specification and differentiation, and synaptic protein synthesis. ncRNAs have been implicated in a number of neuronal diseases including Tourette's syndrome and Fragile X syndrome. Future studies will likely identify additional neuronal functions for ncRNAs as well as roles for these molecules in other neuropsychiatric and neurodevelopmental disorders.
Inclusive accountancy programmes in South African higher education: a revised teaching approach

ABSTRACT The primary objective of the study was to propose a teaching approach for first-year Financial Accounting modules, that may improve the success rates of marginalised students enrolled for inclusive diploma type accountancy programmes. The study followed a multi-phased approach with a research methodology for each phase. These include an extensive literature study, qualitative focus group discussions and a survey questionnaire. A teaching approach was developed from the results and findings, which was pilot tested. The study is underpinned by the theory of reasoned action – focussing on the notion of changing student attitude through classroom management and student engagement. Results from the statistical analyses of student academic performance on completion of the academic semester following the pilot test, revealed that the teaching approach significantly improved students’ success. The revised teaching approach can be successfully implemented at all universities teaching accounting.
Supplementary materials for Statistical Estimation and Testing via the Sorted ` 1 Norm

In this note we give a proof showing that even though the number of false discoveries and the total number of discoveries are not continuous functions of the parameters, the formulas we obtain for the false discovery proportion (FDP) and the power, namely, (B.3) and (B.4) in the paper Statistical Estimation and Testing via the Sorted `1 Norm are mathematically valid. We recall that these formulas are derived from [1, Theorem 1.5]. Consider the linear model y = Xβ + z, where X ∈ Rn×p is the design matrix, β ∈ R is the unknown parameter of interest and z ∈ R is a vector of i.i. d. standard Gaussian independent of X and β. The lasso estimate β̂ with penalty λ > 0 is the solution to min b∈Rp 1 2 ‖y −Xb‖2`2 + λ‖b‖`1 . (1) As in the main paper, we let φV (x, y) = 1(x 6= 0)1(y = 0) and φR(x, y) = 1(x 6= 0) so that the number V of false discoveries is equal to V = ∑ i φV (β̂i, βi), and the number R of discoveries is equal to R = ∑ i φR(β̂i, βi). We can now state the main result in this note, which generalizes [1, Theorem 1.5]. Theorem 1. Suppose thatX is an n×p Gaussian design matrix with i.i. d.N (0, 1 n ) entries, βi’s are non-degenerate i.i. d. random variables with bounded second moment independent of X . Below, Θ is a variable with the same distribution as βi. As p→∞ and n/p→ δ > 0, the lasso solution β̂ obeys FDP ≡ ∑p i=1 φV (β̂i, βi) max{ ∑p i=1 φR(β̂i, βi), 1} P −−→ 2P(Θ = 0)Φ(−α) P(|Θ + τZ| > ατ) , where τ > 0 and α > αmin are the unique solutions to τ = 1 + 1 δ E ( ηατ (Θ + τZ)−Θ )2 , λ = ( 1− 1 δ P(|Θ + τZ| > ατ) ) ατ. Here η is the soft-thresholding operator defined as ηt(x) = sign(x)(|x| − t)+ and Z is a standard Gaussian independent of Θ. *Departments of Mathematics and Computer Science, Wrocław University of Technology and Jan Długosz University, Poland †IBM T.J. Watson Research Center, Yorktown Heights, NY 10598, U.S.A. ‡Department of Statistics, Stanford University, Stanford, CA 94305 §Departments of Statistics and of Mathematics, Stanford University, Stanford, CA 94305
Imperfect Markets: a Case Study in Senegal

Farmers in developing countries are confronted with imperfect markets. This has an impact on their production activities. When implementing developing projects these market imperfections should be taken into account. This paper is an attempt to discuss the impact of imperfect markets in the context of an irrigation project in village Pata, Senegal. The first section models the production decision of the agricultural household. The second section presents the irrigation project in Pata. The third section tests for the presence of imperfections in the credit and labour markets of Pata. I conclude by discussing the implications for the project.
Identification and control of the Phantom 500 body motion

Addresses the identification and the control of the vertical motion of the ROV Phantom. The problems are split in two decoupled problems. : the propeller motion and the diving motion. A maximum likelihood based identification method is used for each dynamic model. The design of the inner and outer controllers is based on the classical root locus method. Numerical experiments demonstrate that the designed controllers yield satisfactory results in terms of stability, tracking performance and robustness.
The longitudinal development of clusters in French*

ABSTRACT Studies of English and German find that children tend to acquire word-final consonant clusters before word-initial consonant clusters. This order of acquisition is generally attributed to articulatory, frequency and/or morphological factors. This contrasts with recent experimental findings from French, where two-year-olds were better at producing word-initial than word-final clusters (Demuth & Kehoe, 2006). The purpose of the present study was to examine French-speaking children's longitudinal acquisition of clusters to determine if these results replicate developmentally. Analysis of spontaneous speech productions from two French-speaking children between one and three years confirmed the earlier acquisition of initial clusters, even when sonority factors were controlled. The findings suggest that French-speaking children acquire complexity at the beginnings of words before complexity appears word-finally. The role of frequency, morphological, structural and input factors is discussed.
EBC: Application-level migration on multi-site cloud

Cloud computing providers offer their services that help IT organizations to increase hardware utilization dramatically, and to scale up computational infrastructure instantly. The cloud resource management system could suspend/migrate some running jobs/virtual machines in order to reserve resources for other ones to improve resource utilization. In this case, the cost of moving the whole virtual machines is too high due to the big size of virtual machines. Moreover, supporting communication between the two migrated virtual machines is still a hard problem. We are interested in using checkpointing and recovery technique (C&R) to stop and restart running programs on virtual machines. The paper introduces the event-based checkpointing tool (EBC), in which users can easily checkpoint and restart running programs in cloud systems. EBC is based on event-driven architecture and so it is integrated into cloud infrastructures like OpenNebula easily. EBC supports not only sequential programs but also MPI programs. Moreover, any C&R included in MPI libraries is reused in EBC and so it is independent from MPI library versions. EBC is a useful tool supporting migration as well as scheduling in cloud systems.
Characteristics of Saccharomyces cerevisiae yeasts exhibiting rough colonies and pseudohyphal morphology with respect to alcoholic fermentation

Among the native yeasts found in alcoholic fermentation, rough colonies associated with pseudohyphal morphology belonging to the species Saccharomyces cerevisiae are very common and undesirable during the process. The aim of this work was to perform morphological and physiological characterisations of S. cerevisiae strains that exhibited rough and smooth colonies in an attempt to identify alternatives that could contribute to the management of rough colony yeasts in alcoholic fermentation. Characterisation tests for invasiveness in Agar medium, killer activity, flocculation and fermentative capacity were performed on 22 strains (11 rough and 11 smooth colonies). The effects of acid treatment at different pH values on the growth of two strains (“52” - rough and “PE-02” - smooth) as well as batch fermentation tests with cell recycling and acid treatment of the cells were also evaluated. Invasiveness in YPD Agar medium occurred at low frequency; ten of eleven rough yeasts exhibited flocculation; none of the strains showed killer activity; and the rough strains presented lower and slower fermentative capacities compared to the smooth strains in a 48-h cycle in a batch system with sugar cane juice. The growth of the rough strain was severely affected by the acid treatment at pH values of 1.0 and 1.5; however, the growth of the smooth strain was not affected. The fermentative efficiency in mixed fermentation (smooth and rough strains in the same cell mass proportion) did not differ from the efficiency obtained with the smooth strain alone, most likely because the acid treatment was conducted at pH 1.5 in a batch cell-recycle test. A fermentative efficiency as low as 60% was observed with the rough colony alone.
It’s More the Exception Rather Than the Rule: African American Families’ Neighborhoods and Youth’s Academic Performance During Middle School

Neighborhoods are an important part of the social milieu of adolescence and academic performance. Using experiential neighborhood profiles, this study examined risks and assets to determine how neighborhood structural and relational dynamics were associated with academic achievement during early adolescence. The sample included 723 African American socioeconomically diverse families (Myouth age = 12.27 years, SD = 0.55). Results showed that neighborhood structural disadvantage was unrelated to academic achievement, whereas neighborhood profiles were associated with academic performance in eighth grade, after adjusting for seventh grade GPA. Neighborhood profiles characterized by positive social relationships were associated with higher achievement. Authors discuss the importance of examining neighborhood risks and supports for African American youth’s academic adjustment.
The Phenotype-Fitness Map in Experimental Evolution of Phages

Evolutionary biologists commonly interpret adaptations of organisms by reference to a phenotype-fitness map, a model of how different states of a phenotype affect fitness. Notwithstanding the popularity of this approach, it remains difficult to directly test these mappings, both because the map often describes only a small subset of phenotypes contributing to total fitness and because direct measures of fitness are difficult to obtain and compare to the map. Both limitations can be overcome for bacterial viruses (phages) grown in the experimental condition of unlimited hosts. A complete accounting of fitness requires 3 easily measured phenotypes, and total fitness is also directly measurable for arbitrary genotypes. Yet despite the presumed transparency of this system, directly estimated fitnesses often differ from fitnesses calculated from the phenotype-fitness map. This study attempts to resolve these discrepancies, both by developing a more exact analytical phenotype-fitness map and by exploring the empirical foundations of direct fitness estimates. We derive an equation (the phenotype-fitness map) for exponential phage growth that allows an arbitrary distribution of lysis times and burst sizes. We also show that direct estimates of fitness are, in many cases, plausibly in error because the population has not attained stable age distribution and thus violates the model underlying the phenotype-fitness map. In conjunction with data provided here, the new understanding appears to resolve a discrepancy between the reported fitness of phage T7 and the substantially lower value calculated from its phenotype-fitness map.
Effects of Epidural Needle Rotation on Evolution of Unilateral Epidural Block and Patients’ Hemodynamics beside Recovery Profile in Patients Undergoing Arthroscopic Knee Surgeries; A Randomized Clinical Trial

Objective: To evaluate the evolution pattern of epidural block after rotating the needle tip 45° to the operative side and evaluate its effects on patients’ hemodynamics and recovery profile in those undergoing arthroscopic knee surgery. Methods: Forty participants were randomly subdivided into control and rotation group (n=20). An 18-gauge, 3.5 inch, Tuohy needle was placed at the level of L4-5 and pushed forward into the epidural space through parasagittal approach, in control group, the needle was pushed forward to the epidural space in cephaldad 90 degrees. For the rotation group, the needle was pushed forward to the epidural space and the tip was rotated 45 degrees to the surgical side.15 mL of bupivacaine 0.5% was injected and evolution of sensory and motor blocks until 2-segment regression of the sensory level below to T10 as well as total duration of motor block and surgery were recorded. Hemodynamic parameters (HR, MAP, and SPO2), hypotension, fluid intake, vasopressors, first ambulation and spontaneous urination were recorded. Statistical analysis was performed using SPSS and P≤0.5 considered significant. Results: Sensory block up to T10 level, Complete motor block and time for 2-segment regression of sensory level were earlier in the 45°-rotation than in the control group (p<0.001). Total duration of motor block in control group was lower than rotation group (p<0.001). Hypotension, N&V, vasopressors and fluid intake showed no statistically difference between the two groups (p=0.219). First spontaneous urination and ambulation were significantly lower in rotation group (p<0.001). Conclusion: 45 degrees’ needle rotation to the surgical side provides a faster block evolution and hastened recovery profile with no significant difference in hemodynamic fluctuations. Clinical trial registry: IRCT20130518013364N7
Risk Factors for Metachronous Recurrence after Endoscopic Submucosal Dissection of Early Gastric Cancer

Although endoscopic submucosal dissection (ESD) is widely accepted as a curative treatment method for early gastric cancer (EGC) worldwide, metachronous recurrence often occurs after ESD for EGC. However, there are insufficient data about the role of Helicobacter pylori (H. pylori) infection and other risk factors for recurrence. We aimed to compare the metachronous lesion in the H. pylori persistent group and the eradicated group, and to identify risk factors for metachronous lesion. We retrospectively analyzed 782 patients who underwent ESD between January 2008 and December 2013. We excluded patients with dysplasia or patients who were not tested for H. pylori infection. One hundred eighty-five patients were enrolled. We studied risk factors for recurrence, and used survival analysis to test. There were 24 patients with metachronous recurrence after ESD for EGC among the group. The incidence of metachronous gastric lesions after ESD for EGC developed more in the over 70-year-old group (P = 0.025) and more in the H. pylori persistent group (P = 0.008). In conclusion, H. pylori infection and old age are independent risk factors for metachronous gastric lesions after ESD in EGC.
Interest estimation based on dynamic bayesian networks for visual attentive presentation agents

In this paper, we describe an interface consisting of a virtual showroom where a team of two highly realistic 3D agents presents product items in an entertaining and attractive way. The presentation flow adapts to users' attentiveness, or lack thereof, and may thus provide a more personalized and user-attractive experience of the presentation. In order to infer users' attention and visual interest regarding interface objects, our system analyzes eye movements in real-time. Interest detection algorithms used in previous research determine an object of interest based on the time that eye gaze dwells on that object. However, this kind of algorithm is not well suited for dynamic presentations where the goal is to assess the user's focus of attention regarding a dynamically changing presentation. Here, the current context of the object of attention has to be considered, i.e., whether the visual object is part of (or contributes to) the current presentation content or not. Therefore, we propose a new approach that estimates the interest (or non-interest) of a user by means of dynamic Bayesian networks. Each of a predefined set of visual objects has a dynamic Bayesian network assigned to it, which calculates the current interest of the user in this object. The estimation takes into account (1) each new gaze point, (2) the current context of the object, and (3) preceding estimations of the object itself. Based on these estimations the presentation agents can provide timely and appropriate response.
Convex relaxations of structured matrix factorizations

We consider the factorization of a rectangular matrix $X $ into a positive linear combination of rank-one factors of the form $u v^\top$, where $u$ and $v$ belongs to certain sets $\mathcal{U}$ and $\mathcal{V}$, that may encode specific structures regarding the factors, such as positivity or sparsity. In this paper, we show that computing the optimal decomposition is equivalent to computing a certain gauge function of $X$ and we provide a detailed analysis of these gauge functions and their polars. Since these gauge functions are typically hard to compute, we present semi-definite relaxations and several algorithms that may recover approximate decompositions with approximation guarantees. We illustrate our results with simulations on finding decompositions with elements in $\{0,1\}$. As side contributions, we present a detailed analysis of variational quadratic representations of norms as well as a new iterative basis pursuit algorithm that can deal with inexact first-order oracles.
Influence of winding design on thermal dynamics of permanent magnet traction motor

This paper presents summarized electromagnetic and thermal design of interior permanent magnet motor for a low-floor tram TMK 2200. Motor geometry is optimized for maximum torque density using differential evolution algorithm. The influences of winding configuration on power losses and thermal transients in the motor during one driving cycle of the tram have been analyzed. The results indicate that an optimal number of turns per slot and parallel paths can be found to yield minimum temperatures in various parts of the motor considering the intermittent character of the load.
Influenza Pneumonia Surveillance among Hospitalized Adults May Underestimate the Burden of Severe Influenza Disease

Background Studies seeking to estimate the burden of influenza among hospitalized adults often use case definitions that require presence of pneumonia. The goal of this study was to assess the extent to which restricting influenza testing to adults hospitalized with pneumonia could underestimate the total burden of hospitalized influenza disease. Methods We conducted a modelling study using the complete State Inpatient Databases from Arizona, California, and Washington and regional influenza surveillance data acquired from CDC from January 2003 through March 2009. The exposures of interest were positive laboratory tests for influenza A (H1N1), influenza A (H3N2), and influenza B from two contiguous US Federal Regions encompassing the study area. We identified the two outcomes of interest by ICD-9-CM code: respiratory and circulatory hospitalizations, as well as critical illness hospitalizations (acute respiratory failure, severe sepsis, and in-hospital death). We linked the hospitalization datasets with the virus surveillance datasets by geographic region and month of hospitalization. We used negative binomial regression models to estimate the number of influenza-associated events for the outcomes of interest. We sub-categorized these events to include all outcomes with or without pneumonia diagnosis codes. Results We estimated that there were 80,834 (95% CI 29,214–174,033) influenza-associated respiratory and circulatory hospitalizations and 26,760 (95% CI 14,541–47,464) influenza-associated critical illness hospitalizations. When a pneumonia diagnosis was excluded, the estimated number of influenza-associated respiratory and circulatory hospitalizations was 24,816 (95% CI 6,342–92,624). The estimated number of influenza-associated critical illness hospitalizations was 8,213 (95% CI 3,764–20,799). Around 30% of both influenza-associated respiratory and circulatory hospitalizations, as well as influenza-associated critical illness hospitalizations did not have pneumonia diagnosis codes. Conclusions Surveillance studies which only consider hospitalizations that include a diagnosis of pneumonia may underestimate the total burden of influenza hospitalizations.
Sentiment Analysis of a Student Q&A Board for Computer Science

A process for producing chlorofluorobenzenes, which comprises reacting fluorine-containing nitrobenzenes of the following formula (1) with chlorine gas to obtain chlorofluorobenzenes of the following formula (2): (1) (2) wherein n and m are integers satisfying 1</=n</=3, 0</=m</=2 and 1</=n+m</=3.
On Implementing Temporal Query Answering in DL-Lite

Ontology-based data access augments classical query answering over fact bases by adopting the open-world assumption and by including domain knowledge provided by an ontology. We implemented temporal query answering w.r. t. ontologies formulated in the Description Logic DL-Lite. Focusing on temporal conjunctive queries (TCQs), which combine conjunctive queries via the operators of propositional linear temporal logic, we regard three approaches for answering them: an iterative algorithm that considers all data available; a window-based algorithm; and a rewriting approach, which translates the TCQs to be answered into SQL queries. Since the relevant ontological knowledge is already encoded into the latter queries, they can be answered by a standard database system. Our evaluation especially shows that implementations of both the iterative and the window-based algorithm answer TCQs within a few milliseconds, and that the former achieves a constant performance, even if data is growing over time.