Miracle-dz/UniFAR-FTUs huggingface dataset:
e-LEA3D: a computational-aided drug design web server

e-LEA3D web server integrates three complementary tools to perform computer-aided drug design based on molecular fragments. In drug discovery projects, there is a considerable interest in identifying novel and diverse molecular scaffolds to enhance chances of success. The de novo drug design tool is used to invent new ligands to optimize a user-specified scoring function. The composite scoring function includes both structure- and ligand-based evaluations. The de novo approach is an alternative to a blind virtual screening of large compound collections. A heuristic based on a genetic algorithm rapidly finds which fragments or combination of fragments fit a QSAR model or the binding site of a protein. While the approach is ideally suited for scaffold-hopping, this module also allows a scan for possible substituents to a user-specified scaffold. The second tool offers a traditional virtual screening and filtering of an uploaded library of compounds. The third module addresses the combinatorial library design that is based on a user-drawn scaffold and reactants coming, for example, from a chemical supplier. The e-LEA3D server is available at: http://bioinfo.ipmc. cnrs.fr/lea.html.
No Inter-observer Variability in 18F-FDG PET Maximal Standardized Uptake Value Measurements in Lymphoma

Background: 18F-FDG PET standardized uptake values (SUV) is important for the diagnosis and follow-up for lymphoma patients. However, numerous patient-and technique-related factors could affect the measurement of SUV. This study was performed to determine the inter-observer variability of 18F-FDG PET SUV in lymphoma patients. To our knowledge, there is no study to date about this issue. Methods: We retrospectively reviewed 54 18F-FDG PET/CT scans in 48 consecutive patients with lymphoma. The SUV(subscript max) and SUV mean were measured independently by three readers. The regions of interest were drawn manually around the tumors on all of the consecutive transaxial slices that contained the tumors. The inter-observer variability was determined by the use of the coefficient of variation (COV). The Pearson correlation coefficient for the SUV(subscript max) and SUV mean was also performed. Results: The SUV(subscript max) by the three readers were identical. The mean ± the SD of the SUV(subscript max) in the 54 scans measured by the three readers was 10.31 ± 6.32. The mean ± the SD of the SUV(subscript mean) in the 54 scans measured by the three readers were 5.51 ± 3.0, 4.91 ± 2.47 and 5.25 ± 2.76, respectively. The overall interobserver variability as described by the root-meansquare of the COVs of the SUV(subscript max) and SUV(subscript mean) was 0% and 9.42%, respectively. There was good correlation between the average of SUV(subscript max) and the average of SUV mean from the three readers (r=0.949; P＜0.01). Conclusion: The SUV max in a tumor volume can be calculated without any inter-observer variation and is highly correlated with the SUV mean. These findings indicate the SUV max is a reliable parameter in the 18F-FDG-PET imaging of lymphoma.
Optical BVI Imaging and HI Synthesis Observations of the Dwarf Irregular Galaxy ESO 364-G 029

As part of an effort to enlarge the number of well-studied Magellanic-type galaxies, we obtained broadband optical imaging and neutral hydrogen radio synthesis observations of the dwarf irregular galaxy ESO 364-G 029. The optical morphology characteristically shows a bar-like main body with a one-sided spiral arm, an approximately exponential light distribution, and offset photometric and kinematic centers. The HI distribution is mildly asymmetric and, although slightly offset from the photometric center, roughly follows the optical brightness distribution, extending to over 1.2 Holmberg radii (where mu_B = 26.5 mag/arcsec^2). In particular, the highest HI column densities closely follow the bar, one-arm spiral, and a third optical extension. The rotation is solid-body in the inner parts but flattens outside of the optical extent. The total HI flux F_HI = 23.1 pm 1.2 Jy km/s, yielding a total HI mass M_HI= (6.4 pm 1.7) x 10^8 Msun (for a distance D = 10.8 pm 1.4 Mpc) and a total HI mass-to-blue-luminosity ratio M_HI/L_B = (0.96 pm 0.14) Msun / Lsun,B (distance independent). The HI data suggest a very complex small-scale HI structure, with evidence of large shells and/or holes, but deeper observations are required for a detailed study. Follow-up observations are also desirable for a proper comparison with the Large Magellanic Cloud, where despite an optical morphology very similar to ESO 364-G 029 the HI bears little resemblance to the optical.
Imitation-based Learning of Bipedal Walking Using Locally Weighted Learning

Walking is an extremely challenging problem due to its dynamically unstable nature. It is further complicated by the high dimensional continuous state and action spaces. We use locally weighted projection regression (LWPR) as a locally structurally adaptive nonlinear function approximator as the basis for learned control policies. Empirical evidence suggests that control policies for high dimensional problems exist on low dimensional manifolds. The LWPR algorithm models this manifold in a computationally efficient manner as it only models those states which are visited using a local dimensionality reduction technique based on partial least squares regression. We show that local models are capable of learning control policies for physicsbased simulations of planar bipedal walking. Locally structured control policies are learned from observation of a variety of different inputs including observation of human control and existing parametrized control policies. We extend the pose control graph to the concept of policy control graph and show that this representation allows for the learning of transition points between different control policies.
Cognitive reactivity, rumination, stressful life events in childhood, and their relationship as vulnerability factors to depression: A cross-sectional retrospective study

4 Table of contents . 5 Introduction . 6 Aims of the study . 8 Method . 9 Participants . 9 Measures . 10 Mood induction. 12 Procedure . 12 Statisitcal Analysis . 13 Results . 14 Sample characteristics . 14 Cognitive vulnerability factors . 14 Number and duration of depressive episodes . 16 Stressful life events in childhood and mediation analysis . 19 Discussion . 21 Limitations . 24 Conclutions . 24 Future directions . 24 References . 25
DOES IDIOSYNCRATIC BUSINESS RISK MATTER FOR GROWTH

Several imperfections can prevent entrepreneurs from diversifying away the idiosyncratic risk of their business. As a result idiosyncratic risk discourages entrepreneurial activity and hinders growth, with the effects being stronger in economies with lower risk diversification opportunities. In accordance with this prediction, we find that OECD countries with low levels of risk diversification opportunities (as measured by the relevance of family firms or of widely held companies) perform relatively worse (in terms of productivity, investment, and business creation) in sectors characterized by high idiosyncratic risk. Differently from previous literature, we allow risk to be country specific. Since risk is endogenous to risk diversification opportunities, we instrument its value using sectoral risk in the United States, a country where idiosyncratic business risk can be more easily diversified away. Tackling the endogeneity of risk and recognizing that it varies by country magnifies the estimated effects of risk on growth.
Multimodal Biometrics Information Fusion for Efficient Recognition using Weighted Method

Biometrics do not provide unique identification. The matching process is probabilistic and is liable to measureable lapse error. A mistaken verfication or identification where the wrong person is matched against an enrolled user is termed a False Acceptance and the rate at which these occur is the False Acceptance Rate (FAR). Conversely, an error that occurs where a legitimate user fails to be recognised is termed a False Rejection and the corresponding rate is the False Rejection Rate (FRR). These errors are dependent not only on the technology but also on the application and the environment of use.
Geodesic patterns

Geodesic curves in surfaces are not only minimizers of distance, but they are also the curves of zero geodesic (sideways) curvature. It turns out that this property makes patterns of geodesics the basic geometric entity when dealing with the cladding of a freeform surface with wooden panels which do not bend sideways. Likewise a geodesic is the favored shape of timber support elements in freeform architecture, for reasons of manufacturing and statics. Both problem areas are fundamental in freeform architecture, but so far only experimental solutions have been available. This paper provides a systematic treatment and shows how to design geodesic patterns in different ways: The evolution of geodesic curves is good for local studies and simple patterns; the level set formulation can deal with the global layout of multiple patterns of geodesics; finally geodesic vector fields allow us to interactively model geodesic patterns and perform surface segmentation into panelizable parts.
Improving speech privacy in personal sound zones

This paper proposes two methods for providing speech privacy between spatial zones in anechoic and reverberant environments. The methods are based on masking the content leaked between regions. The masking is optimised to maximise the speech intelligibility contrast (SIC) between the zones. The first method uses a uniform masker signal that is combined with desired multizone loudspeaker signals and requires acoustic contrast between zones. The second method computes a space-time domain masker signal in parallel with the loudspeaker signals so that the combination of the two emphasises the spectral masking in the targeted quiet zone. Simulations show that it is possible to achieve a significant SIC in anechoic environments whilst maintaining speech quality in the bright zone.
On Mitigating the Risk of Cross-VM Covert Channels in a Public Cloud

Virtualization is one of the key enablers in cloud computing. At the same time, though, it is also widely considered as a double-edged sword that may cause information leakage between virtual machines (VM) co-residing on the same physical server via various cross-VM covert channels. In this paper, we first explore the impact of different bystander workloads on cross-VM covert channels. Then, we use a Continuous Time Markov Process to model the impact of bystanders on the cross-VM covert channel in terms of both the work scheduling of the virtualization platform and the intensity of the bystander workloads. Based on empirical study, we quantify the relationship between the influential factors and the transmission quality of the covert channel. A tailored and lightweight VM provisioning strategy, which aims to ensure that bystander workloads on each server can cause sufficiently high error rates to covert channels, is proposed to mitigate the threat of cross-VM covert channels while maintaining the resource efficiency of virtualization. The efficiency and efficacy of the proposed VM provisioning strategy is evaluated through trace-driven simulations.
Grishin homologous to herpesvirus protease Double-stranded DNA bacteriophage prohead protease is

Double-stranded DNA bacteriophages and herpesviruses assemble their heads in a similar fashion; a preformed precursor called a prohead or procapsid undergoes a conformational transition to give rise to a mature head or capsid. A virus-encoded prohead or procapsid protease is often required in this maturation process. Through computational analysis, we infer homology between bacteriophage prohead proteases (MEROPS families U9 and U35) and herpesvirus protease (MEROPS family S21), and unify them into a procapsid protease superfamily. We also extend this superfamily to include an uncharacterized cluster of orthologs (COG3566) and many other phage or bacteria-encoded hypothetical proteins. On the basis of this homology and the herpesvirus protease structure and catalytic mechanism, we predict that bacteriophage prohead proteases adopt the herpesvirus protease fold and exploit a conserved Ser and His residue pair in catalysis. Our study provides further support for the proposed evolutionary link between dsDNA bacteriophages and herpesviruses.
Noise Reduction in Medical DECT Data

Dual energy computed tomography (DECT) recently gained popularity for medical diagnostic imaging. It has been demonstrated how DECT can improve density measurement and material differentiation, and practical applications for DECT imaging in medicine. Noise reduction is standard operation in the process of image enhancement which is necessary operation prior to image evaluation done by radiologist. In this work, we describe two approaches for noise reduction using DECT data. First, we show in the work that the cross or joint bilateral filter can be effectively used on DECT images to reduce noise while preserving edges. Second, noise in two DECT images is anti-correlated and can be effectively removed by the KCNR algorithm. Even better results can be achieved by using algorithms that exploit an additional characteristic information of DECT data, such as the spectral information. It was shown that the KCNR can increase its performance regarding quality when the spectral information is corrected before applying the KCNR [1]. AngioVis framework provides ability to present and manipulate CT data. All discussed image enhancement algorithms are implemented in AngioVis as a plugin.
Robust acquisition and recognition of spoken location names by domestic robots

This paper presents a method that enables a conversational domestic robot to learn location names through speech interaction. Each acquired name is associated with a point on the map coordinate system of the robot. Both for acquisition and recognition of location names, a bag- of-words-based categorization technique is used. Namely, the robot acquires a location name as a frequency pattern of words, and recognizes a spoken location name by computing similarity between the patterns. This makes the robot robust not only against speech recognition errors but also against out- of-vocabulary names. We designed a dialogue and behavior management subsystem that learns location names by using our proposed method and navigates to indicated locations, and implemented the subsystem on an omnidirectional cart robot. The result of a preliminary evaluation of the implemented robot with human subjects suggested this approach is promising.
LIPN-IIMAS at SemEval-2016 Task 1: Random Forest Regression Experiments on Align-and-Differentiate and Word Embeddings penalizing strategies

This paper describes the SOPA-N system used by the LIPN-IIMAS team in Semeval 2016 Semantic Textual Similarity (Task 1). We based our work on the SOPA 2015 system. The SOPA-2015 system used 16 similarity features (including Wordnet, Information Retrieval and Syntactic Dependencies) within a Random Forest learning model. We expanded this system with an Align and Differentiate based strategy, word embeddings and penalization, which showed 6 . 8% of improvement on the development set. However, we found that on the evaluation data for the 2016 STS shared task, the 2015 system outperformed our newer systems.
A corpus of preposition supersenses in English web reviews

We present the first corpus annotated with preposition supersenses, unlexicalized categories for semantic functions that can be marked by English prepositions (Schneider et al., 2015). That scheme improves upon its predecessors to better facilitate comprehensive manual annotation. Moreover, unlike the previous schemes, the preposition supersenses are organized hierarchically. Our data will be publicly released on the web upon publication.
Supporting Stakeholder Collaboration In Infrastructure Projects Using Ontology Merger

Semantic (ontology-based) collaborative web tools are promising means for supporting stakeholder collaboration for integrated infrastructure development. However, the development of a single ontology to serve the variety of collaborating stakeholders is not feasible given the multidisciplinary nature of the domain and the uniqueness of each project. As such, to efficiently develop and deploy such collaborative tools, ontology merging techniques are required for facilitating interoperability among ontologies of collaborating stakeholders. However, since none of the existing ontology merging tools allow for the merging of ontology axioms, there is still a need for developing tools for axiom merging to provide full interoperability between stakeholder ontologies. This paper discusses the relation between knowledge base integration and ontology axiom merging. It then presents an existing methodology for knowledge base integration. Further, a discussion of this methodology is provided in the context of ontology axiom merging. Finally, the paper proposes a semi-automatic approach for ontology axiom merging.
Characterization of Supersonic Radical Source

Experimental setup for spectroscopic measurements of molecular radicals at low temperatures is presented. Radicals are created in a DC discharge and cooled by supersonic expansion. Absorption spectroscopy in the near IR region is used to probe the neutral transient species formed in the discharge, using tuneable extended cavity diode lasers. Initial characteristics of the radical source are presented; discharge current-voltage characterization, molecular OH radical concentrations and temperature were measured.
"Fun place within a serious space": stimulating community interaction and engagement through situated snapshots in a university setting

Networked public displays can stimulate interaction between members of place-based communities, e.g., through situated snapshots - photos taken through a display attached camera. Previous work pointed the need for deploying networked public display applications in various settings in order to make the findings transferable and generalizable and recommends that findings should be connected with research from community psychology. In this paper we report a 15-week "in the wild" deployment of the Moment Machine 2.0 that allowed taking situated snapshots at a university. The application's evaluation involved in-depth interviews (n=20), survey (n=119), and log file analysis. We synthesize our findings with prior work and show how certain effects transfer across settings. We show how the application affected community interaction and sense of community as defined by McMillan and Chavis. We provide implications for design of similar experiences. Overall, our work contributes to the general knowledge of common effects produced by public displays.
Explaining Missing Answers to Top-k SQL Queries

Due to the fact that existing database systems are increasingly more difficult to use, improving the quality and the usability of database systems has gained tremendous momentum over the last few years. In particular, the feature of explaining why some expected tuples are missing in the result of a query has received more attention. In this paper, we study the problem of explaining missing answers to top-k queries in the context of SQL (i.e., with selection, projection, join, and aggregation). To approach this problem, we use the query-refinement method. That is, given as inputs the original top-k SQL query and a set of missing tuples, our algorithms return to the user a refined query that includes both the missing tuples and the original query results. Case studies and experimental results show that our algorithms are able to return high quality explanations efficiently.
Soil carbon and plant diversity distribution at the farm level in the savannah region of Northern Togo (West Africa)

In western Africa, soil organic matter is a source of fertility for food provision and a tool for climate mitigation. In the Savannah region, strong soil degradation linked to an increase in population threatens organic matter conservation and agricultural yield. Soil degradation is also expected to impact biodiversity and, with it, increase the vulnerability of ecosystem goods and services, including the storage of soil organic carbon. Studies of land use, plant species composition and soil fertility were conducted for a conservation project at a demonstration farm in Northern Togo (West Africa), host to various management regimes. Results showed a low organic matter content of the surface soil horizons, often around 0.5%. The highest values were found in a sacred forest within the farm (2.2%). Among crops, rice had the highest soil organic matter, around 1%. In a survey of grasslands, pastures showed the highest organic matter content, with vegetation composition differing from grazed fallows and abandoned grasslands. Plant species richness showed a positive relationship with soil organic matter (R2adj=41.2%), but only by the end of the wet season, when species richness was also highest. Sampling date had a strong effect on vegetation composition. Results showed a strong influence of human activity on soil formation and distribution, and also on plant diversity. The soil characteristics found under the permanent forest suggest a high potential of the soils of the region for improvement of both agricultural yields and as a potential carbon sink relevant to global change policies.
Development of Incompletely Fused Carpels in Maize Ovary Revealed by miRNA, Target Gene and Phytohormone Analysis

Although the molecular basis of carpel fusion in maize ovary development remains largely unknown, increasing evidence suggests a critical role of microRNAs (miRNAs). In this study, a combination of miRNA sequencing, degradome and physiological analyses was used to characterize carpel fusion development in maize ovaries showing incompletely (IFC) and completely fused carpels (CFC). A total of 162 known miRNAs distributed across 33 families were identified, of which 20 were differentially expressed. In addition, 53 miRNA candidates were identified, of which 10 were differentially expressed in the IFC and CFC ovaries. In degradome analysis, a total of 113 and 11 target genes were predicted for the known and novel miRNAs, respectively. Moreover, 24 (60%) target genes of the differentially expressed known miRNAs were found to code transcription factors, including auxin response factor (ARF), TB1-CYC-PCFs (TCP), APETALA2 (AP2), growth regulating factor (GRF), MYB, NAC, and NF-YA, all of which have been shown to play a role in carpel fusion development. Correlation analysis of these differentially expressed known miRNAs and their targets with phytohormone signals revealed significant correlations with at least one phytohormone signal, the main regulator of carpel fusion development. These results suggest that incomplete carpel fusion is partly the result of differential expression of certain miRNAs and their targets. Overall, these findings improve our knowledge of the effect of miRNA regulation on target expression, providing a useful resource for further analysis of the interactions between miRNAs, target genes and phytohormones during carpel fusion development in maize.