Miracle-dz/UniFAR-FTUs huggingface dataset:
ESyPred3D: Prediction of proteins 3D structures

MOTIVATION Homology or comparative modeling is currently the most accurate method to predict the three-dimensional structure of proteins. It generally consists in four steps: (1) databanks searching to identify the structural homolog, (2) target-template alignment, (3) model building and optimization, and (4) model evaluation. The target-template alignment step is generally accepted as the most critical step in homology modeling. RESULTS We present here ESyPred3D, a new automated homology modeling program. The method gets benefit of the increased alignment performances of a new alignment strategy. Alignments are obtained by combining, weighting and screening the results of several multiple alignment programs. The final three-dimensional structure is build using the modeling package MODELLER. ESyPred3D was tested on 13 targets in the CASP4 experiment (Critical Assessment of Techniques for Proteins Structural Prediction). Our alignment strategy obtains better results compared to PSI-BLAST alignments and ESyPred3D alignments are among the most accurate compared to those of participants having used the same template. AVAILABILITY ESyPred3D is available through its web site at http://www.fundp.ac.be/urbm/bioinfo/esypred/ CONTACT christophe.lambert@fundp.ac.be; http://www.fundp.ac.be/~lambertc
Using non-linear dynamical systems for web searching and ranking

In the recent years there has been a surge of research activity in the area of information retrieval on the World Wide Web, using link analysis of the underlying hypertext graph topology. Most of the algorithms in the literature can be described as dynamical systems, that is, the repetitive application of a function on a set of weights. Algorithms that rely on eigenvector computations, such as HITS and PAGERANK, correspond to linear dynamical systems. In this work we consider two families of link analysis ranking algorithms that no longer enjoy the linearity property of the previous approaches. We study in depth an interesting special case of these two families. We prove that the corresponding non-linear dynamical system converges for any initialization, and we provide a rigorous characterization of the combinatorial properties of the stationary weights. The study of the weights provides a clear and insightful view of the mechanics of the algorithm. We also present extensive experimental results that demonstrate that our algorithm performs well in practice.
A MODULAR EVENT-BASED ARCHITECTURE FOR WORKFLOW SYSTEMS

Real life work processes are dynamic and much richer in variation to be expressed by typical static workflow models. Two conflicting goals to be addressed include: flexibility to handle changing situations, and simplicity to design workflows that can be understood and implemented efficiently. This paper addresses these two issues by introducing a novel architecture for workflow systems. In this architecture, a workflow is defined in terms of modules and templates. Modularity provides simplicity and reusability for a workflow system. In our approach, problem independent modules are adopted for a special workflow system by placing them in problem dependent templates. Also different users in the system can interact with the workflow to make appropriate changes via events. Modules and templates have their own event handlers that allow them to be modified based on changes in user requests or situations. We illustrate these features in our architecture using two case studies, one in healthcare domain and another in a banking system.
Putting Raven into context: a response to Roberts & Stevenson

In this response to Roberts & Stevenson I question their claims about the nature of the information in the commentaries to socio-cognitive items; question the distinction between ‘strong’ and ‘weak’ guidance in those commentaries; argue that their results actually support my earlier findings; and challenge their arguments about the existence of domain-free reasoning processes.
Heat-processed Panax ginseng and diabetic renal damage: active components and action mechanism

Diabetic nephropathy is one of the serious complications in patients with either type 1 or 2 diabetes mellitus but current treatments remain unsatisfactory. Results of clinical research studies demonstrate that Panax ginseng can help adjust blood pressure and reduce blood sugar and may be advantageous in the treatment of tuberculosis and kidney damage in people with diabetes. The heat-processing method to strengthen the efficacy of P. ginseng has been well-defined based on a long history of ethnopharmacological evidence. The protective effects of P. ginseng on pathological conditions and renal damage associated with diabetic nephropathy in the animal models were markedly improved by heat-processing. The concentrations of less-polar ginsenosides (20(S)-Rg3, 20(R)-Rg3, Rg5, and Rk1) and maltol in P. ginseng were significantly increased in a heat-processing temperature-dependent manner. Based on researches in animal models of diabetes, ginsenoside 20(S)-Rg3 and maltol were evaluated to have therapeutic potential against diabetic renal damage. These effects were achieved through the inhibition of inflammatory pathway activated by oxidative stress and advanced glycation endproducts. These findings indicate that ginsenoside 20(S)-Rg3 and maltol are important bioactive constituents of heat-processed ginseng in the control of pathological conditions associated with diabetic nephropathy.
The method is the message

Whether, and how, gender affects the news product is one of the most challenging areas in the field of gender and the media. This article analyzes the impact of specific research methodologies on findings regarding gender news influence - based on survey questionnaires and in-depth interviews of female and male editors working in Israeli public radio, as well as on content analysis of their editorial product. Based on different results obtained from these qualitative and quantitative methodologies, we conclude that gender/news research cannot rely on either method exclusively, as heretofore has been overwhelmingly the case. Editorial interviewees’ responses can be as unreliable as autobiographies due to socio-organizational exigencies, while content analyses of news product must also be viewed critically as they do not necessarily reflect underlying gender ‘otherness’. This study discusses the research implications of the findings as well as the extent of ‘real’ gender influence on news product/ion.
An advanced network visualization system for financial crime detection

We present a new system, VISFAN, for the visual analysis of financial activity networks. It supports the analyst with effective tools to discover financial crimes, like money laundering and frauds. If compared with other existing systems and methodologies for the analysis of criminal networks, VISFAN presents the following main novelties: (i) It combines bottom-up and top-down interaction paradigms for the visual exploration of complex networks; (ii) It makes it possible to mix automatic and manual clustering; (iii) It allows the analyst to interactively customize the dimensions of each cluster region and to apply different geometric constraints on the layout. VISFAN also implements several tools for social network analysis other than clustering. For example, it computes several indices to measure the centrality of each actor in the network.
DWDP: A Double Warning Thresholds with Double Preemptive Scheduling Scheme for Wireless Rechargeable Sensor Networks

Wireless power transfer technique provides new alternatives for solving the limited power capacity problem for so many popular mobile wireless devices, and makes wireless rechargeable sensor networks (WRSNs) promising. However, mainly due to the underestimate of the unbalanced influences of spatial and temporal constraints posed by charging requests, traditional scheduling strategies for on-demand WRSNs architecture achieve rather low charging request throughput or successful rate, posing as a major bottleneck for further improvement. In this paper, we propose a Double Warning Thresholds with Double Preemption (DWDP) charging scheme, in which double warning thresholds are used when residual energy levels of sensor nodes fall below certain thresholds. By introducing specific comparison rules, warning thresholds can be used to adjust charging priorities of different sensors, warn the upcoming recharge deadlines, as well as support preemptive scheduling. We perform extensive simulations to manifest the advantages of DWDP. Simulation results reveal that DWDP can achieve better scheduling performance, in guaranteeing the scheduling success of the high-priority task and improving stability of the system.
On Multiclass Active Learning with Support Vector Machines

In supervised machine learning, a training set of examples which are assigned to the correct target labels is a necessary prerequisite. However, in many applications, the task of assigning target labels cannot be conducted in an automatic manner, but involves human decisions and is therefore time-consuming and expensive. In the case of classification learning, the active learning framework has been considered to address this problem. While most research on active learning in the field of kernel machines has focused on binary problems, less attention has been given to the problem of learning classifiers in the case of multiple classes. We consider three common decomposition methods to express multiclass problems in terms of sets of binary classification problems and propose novel active learning heuristics in order to reduce the labeling effort. Various experiments conducted on real-world datasets demonstrate the merits of our approach in comparison to previous research.
Rate analysis of spatial multiplexing in MIMO heterogeneous networks with wireless backhaul

In this paper, we develop a general framework to analyze the rate performance of a two-tier MIMO heterogeneous network (HetNet) with wireless backhaul under spatial multiplexing. We consider linear precoding and receive filtering in the presence of interference from uplink and downlink transmissions. We find that the sum rate per area of the HetNet is sensitive to the network load, i.e., the number of users served by each base station. We show that a two-tier HetNet with wireless backhaul can achieve higher sum rate per area than a one-tier cellular network. However, this requires the bandwidth division between radio access links and wireless backhaul to be optimally designed according to the load conditions.
The Impact of Delayed Chemotherapy on Its Completion and Survival Outcomes in Stage II Colon Cancer Patients

Background Delayed chemotherapy is associated with inferior survival in stage III colon and stage II/III rectal cancer patients, but similar studies have not been performed in stage II colon cancer patients. We investigate the association between delayed and incomplete chemotherapy, and the association of delayed chemotherapy with survival in stage II colon cancer patients. Patients and Methods Patients (age ≥66) diagnosed as stage II colon cancer and received chemotherapy from 1992 to 2005 were identified from the linked SEER–Medicare database. The association between delayed and incomplete chemotherapy was assessed using unconditional and conditional logistic regressions. Survival outcomes were assessed using stratified Cox regression based on propensity score matched samples. Results 4,209 stage II colon cancer patients were included, of whom 73.0% had chemotherapy initiated timely (≤2 months after surgery), 14.7% had chemotherapy initiated with moderate delay (2–3 months), and 12.3% had delayed chemotherapy (≥3 months). Delayed chemotherapy was associated with not completing chemotherapy (adjusted odds ratio (OR): 1.33 (95% confidence interval: 1.11, 1.59) for moderately delayed group, adjusted OR: 2.60 (2.09, 3.24) for delayed group). Delayed chemotherapy was associated with worse survival outcomes (hazard ratio (HR): 1.75 (1.29, 2.37) for overall survival; HR: 4.23 (2.19, 8.20) for cancer-specific survival). Conclusion Although the benefit of chemotherapy is unclear in stage II colon cancer patients, delay in initiation of chemotherapy is associated with an incomplete chemotherapy course and poorer survival, especially cancer-specific survival. Causal inference in the association between delayed initiation of chemotherapy and inferior survival requires further investigation.
Screening for oxygen intolerance in U.S. Navy divers.

All U.S. Navy diving candidates are screened for their tolerance to hyperbaric oxygen by taking an oxygen tolerance test (OTT). During a recent experimental oxygen dive series at the U.S. Navy Experimental Diving Unit, three divers were noted to be reproducibly oxygen sensitive. These three divers were then given additional OTTs to see if any evidence of central nervous system oxygen toxicity would be detected by these multiple tests. The additional OTTs did not produce any signs or symptoms of oxygen toxicity in these already proven susceptible divers. A subsequent review of the records of the Naval Safety Center yielded a total of 1347 OTTs from 1 January 1972 to 31 December 1981. A review of diving accidents reported during this period revealed that 26 episodes of oxygen toxicity were noted during OTTs for a derived failure rate of 1.9%. Analysis of oxygen toxicity episodes encountered during operational Navy diving for this period found that 9 episodes of nonconvulsive oxygen toxicity were seen in mixed gas diving and 3 episodes of nonconvulsive oxygen toxicity were noted in closed circuit oxygen diving. Conclusions from this paper are: Screening for oxygen intolerance is complicated by intraindividual variation in oxygen tolerance; U.S. Navy diving using 100% oxygen during the period studied has had an acceptable safety record according to the data on record at the Naval Safety Center; the OTT as currently administered by the U.S. Navy does not identify all individuals who are relatively susceptible to oxygen toxicity; those individuals who do fail the OTT are unusually susceptible to oxygen toxicity; and because of the need to continue to identify these unusually susceptible individuals, the OTT should continue to be administered to U.S. Navy diver candidates.
Web graph similarity for anomaly detection (poster)

Web graphs are approximate snapshots of the web, created by search engines. Their creation is an error-prone procedure that relies on the availability of Internet nodes and the faultless operation of multiple software and hardware units. Checking the validity of a web graph requires a notion of graph similarity. Web graph similarity helps measure the amount and significance of changes in consecutive web graphs. These measurements validate how well search engines acquire content from the web. In this paper we study five similarity schemes: three of them adapted from existing graph similarity measures and two adapted from well-known document and vector similarity methods. We compare and evaluate all five schemes using a sequence of web graphs for Yahoo! and study if the schemes can identify anomalies that may occur due to hardware or other problems.
Automated Quality Defect Detection in Software Development Documents

Quality of software products typically has to be assured throughout the entire software development life-cycle. However, software development documents (e.g. requirements specifications, design documents, test plans) are often not as rigorously reviewed as source code, although their quality has a major impact on the quality of the evolving software product. Due to the narrative nature of these documents, more formal approaches beyond software inspections are difficult to establish. This paper presents a tool-based approach that supports the software inspection process in order to determine defects of generally accepted documentation best practices in software development documents. By means of an empirical study we show, how this tool-based approach helps accelerating inspection tasks and facilitates gathering information on the quality of the inspected documents. Keywords-quality defect detection; software development document; tool-based approach; software inspection
Working in the Field as the Female Friend

This article describes a researcher's subjective experience of fieldwork conducted among her own group: returning women graduate students. It builds upon the work of feminist ethnographers who have sought to connect their feelings about the research process to their research accounts. It focuses on interactions between the researcher and her informants and discusses how these interactions affected the course of the research, the study's findings, and the researcher. The article also explores the emotional stresses and ethical dilemmas encountered by a feminist researcher working within her own culture. FEMINIST ETHNOGRAPHY, RESEARCHER ROLE, WOMEN IN HIGHER EDUCATION In this article I reflect on the fieldwork for my dissertation research on returning women graduate students and how my personal response to that experience affected the course of the research. I believe these reflections are an appropriate contribution to this volume because it has been women anthropologists who have most often sought to connect their subjective experience of the research process to their ethnographic accounts. Further, because feminist social science assumes the oppression of women and, as Rosaldo and Lamphere (1974) explain, seeks to transform, as well as understand, women's experience, feminist ethnographers must grapple with issues of power and exploitation not only in the larger society but also in their research endeavors. And so this article also discusses how such issues arose in my fieldwork and how my response to them affected me, my interactions with informants, and my findings. When my curiosity about my experience as a returning woman graduate student encouraged me to explore a dissertation on the topic, I was surprised how little resemblance the literature on returning women bore to the issues I had tentatively identified as relevant and provocative. That literature reflected higher education's desire to effectively recruit this rapidly growing student population and to accommodate its perceived special needs. Researchers had not looked at the process of returning to school and therefore had little empirical evidence about these women's experience that could inform programmatic development. It seemed ironic that more was known about program interventions than about the process (reentry) the interventions were designed to facilitate.
The DEK1 Calpain Linker Functions in Three-Dimensional Body Patterning in Physcomitrella patens1[OPEN]

Full and partial deletion of the DEK1 Linker implicate DEK1 in the three major developmental phases of the moss Physcomitrella patens. The DEFECTIVE KERNEL1 (DEK1) calpain is a conserved 240-kD key regulator of three-dimensional body patterning in land plants acting via mitotic cell plane positioning. The activity of the cytosolic C-terminal calpain protease is regulated by the membrane-anchored DEK1 MEM, which is connected to the calpain via the 600-amino acid residue Linker. Similar to the calpain and MEM domains, the Linker is highly conserved in the land plant lineage, the similarity dropping sharply compared with orthologous charophyte sequences. Using site-directed mutagenesis, we studied the effect on Physcomitrella patens development by deleting the Linker and two conserved Linker motifs. The results show that removal of the Linker has nearly the same effect as removal of the entire DEK1 gene. In contrast, deletion of the conserved Laminin_G3 (LG3) domain had a milder effect, perturbing leafy gametophore patterning and archegonia development. The LG3 domain from Marchantia polymorpha is fully functional in P. patens, whereas angiosperm sequences are not functional. Deletion of a C-terminal Linker subsegment containing a potential calpain autolytic site severely disturbs gametophore development. Finally, changing one of the three calpain active-site amino acid residues results in the same phenotype as deleting the entire DEK1 gene. Based on the conserved nature of animal and DEK1 calpains, we propose that the DEK1 MEM-Linker complex inactivates the calpain by forcing apart the two calpain subunits carrying the three amino acids of the active site.
A model of face space

Faces vary in their distinctiveness, and it has been suggested that—more distinctive faces are located further from the mean face in internal or perceptual face space (Valentine, 1991), than typical faces. This paper proposes a pixel-based computational model of face distinctiveness. I show that the notion of psychological distinctiveness is correlated with the metrical Euclidean distance, from the mean face. Distances are measured in pixel-based face space, which serves as the basis of the computational model. A prediction of the model is that pairwise perceptual distances between distinctive faces are, on average, greater than between typical faces. This is affirmed by psychophysical experiment. This finding confirms a key axiom of the norm-based coding model, which states that face space is centrally distributed with typical faces packed densely near the centre of the space and distinctive faces spread sparsely in the periphery. This assumption has previously been confirmed by Davidenko (2007) using face silhouettes, and here I show that this axiom also generalizes to full frontal face images.
Case Based Reasoning for Knowledge Management in KDD Projects

In this paper we introduce our departments organizational and technical infrastructure for knowledge-intensive and weak-structured processes: A framework for Knowledge Management in the case of projects in Knowledge Discovery in Databases (KDD). It is based on the experience factory approach and the method of case based reasoning. We introduce both approaches in the context of knowledge management, derive application-areas and introduce our realization for projects in knowledge discovery in databases.
An Adaptive Psychoacoustic Model for Automatic Speech Recognition

Compared with automatic speech recognition (ASR), the human auditory system is more adept at handling noise-adverse situations, including environmental noise and channel distortion. To mimic this adeptness, auditory models have been widely incorporated in ASR systems to improve their robustness. This paper proposes a novel auditory model which incorporates psychoacoustics and otoacoustic emissions (OAEs) into ASR. In particular, we successfully implement the frequency-dependent property of psychoacoustic models and effectively improve resulting system performance. We also present a novel double-transform spectrum-analysis technique, which can qualitatively predict ASR performance for different noise types. Detailed theoretical analysis is provided to show the effectiveness of the proposed algorithm. Experiments are carried out on the AURORA2 database and show that the word recognition rate using our proposed feature extraction method is significantly increased over the baseline. Given models trained with clean speech, our proposed method achieves up to 85.39% word recognition accuracy on noisy data.
N,N,N′,N′,N′′-Pentamethyl-N′′-[3-(1,3,3-trimethylureido)propyl]guanidinium tetraphenylborate

In the crystal structure of the title molecular salt, C13H30N5O+·C24H20B−, discrete guanidinium cations and tetraphenylborate anions are present. The C—N bond lengths in the CN3 unit are 1.3427 (12), 1.3445 (12) and 1.3453 (13) Å, indicating double-bond character. The central C atom is surrounded in a nearly ideal trigonal-planar geometry by three N atoms and the positive charge is delocalized on the CN3 plane. The bonds between the N atoms and the terminal C-methyl groups all have values close to a typical single bond [1.4595 (15)–1.4688 (12) Å]. In the crystal, cations are connected by C—H⋯O contacts generating a chain along the c axis.