Miracle-dz/UniFAR-FTUs huggingface dataset:
Search engine visibility: a pilot study towards the design of a model for e-commerce websites.

Herewith to testify that the papers accepted for the 7th Annual Conference on World Wide Web Applications, 29-31 August 2005, Cape Town have been peer-reviewed by independent and external peer-reviewers. Abstract In this research project, the authors attempt to compile a model that consists of guidelines towards achieving an electronically visible and well optimised website. This model will provide a strategy for achieving website visibility which could be used by e-Commerce companies to achieve higher page ranking within most search services. This model is expected to also improve the website usability, benefiting the client and searcher. There are many methods for finding a website on the Internet, one being the use of a search service which usually is a directory or a search engine. Each one of these services has their own search strategy for categorising websites, which in the end will determine where a site would be listed. Due to the importance of these search strategies, one should emphasize the importance of improving visibility techniques in the development of a website, to satisfy both directory and search engine strategies. For the purpose of explaining the effective use of optimisation techniques, an e-commerce based website was selected to be used as an example. Elements gathered through academic literature were then applied on the website without modifying the layout of the site. Areas affected were: meta tags, frames, graphics descriptions, JavaScript and a site map. It should be noted that the testing of the applied changes would only occur at a later stage due to the nature of the research project. The model that is based on principles identified in academic literature, if applied, is expected to increase the visibility of most websites and in the process satisfy some of the requirements of the directories and search engines to index webpages.
Parsing fashion image into mid-level semantic parts based on chain-conditional random fields

In this study, the authors address the problem of parsing fashion images into mid-level semantic parts including upper-clothing, lower-clothing, skin, hair and background. These mid-level parts provide the regional information of fashion items and have potential value in high-level parsing process. The key idea of the method is to parse the mid-level parts by region expanding. Owing to the co-occurrence of pose skeleton and the proposed parts, the region expanding process starts from the super-pixels crossed by specific segments of pose skeleton. The super-pixels are then merged with their neighbours by conditional inference based on their position and perceptual similarity. To avoid the difficulties of training on arbitrary graph structures, conditional random fields (CRFs) are constructed on super-pixel chains, which are extracted from the generated expanding trees. This is followed by a voting stage to mix up the probabilities estimated by the chain-CRFs to obtain the final result. Experiments on two datasets show that the new method outperforms related approaches in regional accuracy and has good generalisation capability. Furthermore, the method can be easily employed to improve the performance of high-level parsing. Its effectiveness has been verified by another group of experiments on two state-of-the-art high-level parsing approaches.
Predicting Success in Goal-Driven Human-Human Dialogues

In goal-driven dialogue systems, success is often defined based on a structured definition of the goal. This requires that the dialogue system be constrained to handle a specific class of goals and that there be a mechanism to measure success with respect to that goal. However, in many human-human dialogues the diversity of goals makes it infeasible to define success in such a way. To address this scenario, we consider the task of automatically predicting success in goal-driven human-human dialogues using only the information communicated between participants in the form of text. We build a dataset from stackoverflow.com which consists of exchanges between two users in the technical domain where ground-truth success labels are available. We then propose a turn-based hierarchical neural network model that can be used to predict success without requiring a structured goal definition. We show this model outperforms rule-based heuristics and other baselines as it is able to detect patterns over the course of a dialogue and capture notions such as gratitude.
Evolution of poor reporting and inadequate methods over time in 20 920 randomised controlled trials included in Cochrane reviews: research on research study

Objective To examine how poor reporting and inadequate methods for key methodological features in randomised controlled trials (RCTs) have changed over the past three decades. Design Mapping of trials included in Cochrane reviews. Data sources Data from RCTs included in all Cochrane reviews published between March 2011 and September 2014 reporting an evaluation of the Cochrane risk of bias items: sequence generation, allocation concealment, blinding, and incomplete outcome data. Data extraction For each RCT, we extracted consensus on risk of bias made by the review authors and identified the primary reference to extract publication year and journal. We matched journal names with Journal Citation Reports to get 2014 impact factors. Main outcomes measures We considered the proportions of trials rated by review authors at unclear and high risk of bias as surrogates for poor reporting and inadequate methods, respectively. Results We analysed 20 920 RCTs (from 2001 reviews) published in 3136 journals. The proportion of trials with unclear risk of bias was 48.7% for sequence generation and 57.5% for allocation concealment; the proportion of those with high risk of bias was 4.0% and 7.2%, respectively. For blinding and incomplete outcome data, 30.6% and 24.7% of trials were at unclear risk and 33.1% and 17.1% were at high risk, respectively. Higher journal impact factor was associated with a lower proportion of trials at unclear or high risk of bias. The proportion of trials at unclear risk of bias decreased over time, especially for sequence generation, which fell from 69.1% in 1986-1990 to 31.2% in 2011-14 and for allocation concealment (70.1% to 44.6%). After excluding trials at unclear risk of bias, use of inadequate methods also decreased over time: from 14.8% to 4.6% for sequence generation and from 32.7% to 11.6% for allocation concealment. Conclusions Poor reporting and inadequate methods have decreased over time, especially for sequence generation and allocation concealment. But more could be done, especially in lower impact factor journals.
Multi-haem cytochromes in Shewanella oneidensis MR-1: structures, functions and opportunities

Multi-haem cytochromes are employed by a range of microorganisms to transport electrons over distances of up to tens of nanometres. Perhaps the most spectacular utilization of these proteins is in the reduction of extracellular solid substrates, including electrodes and insoluble mineral oxides of Fe(III) and Mn(III/IV), by species of Shewanella and Geobacter. However, multi-haem cytochromes are found in numerous and phylogenetically diverse prokaryotes where they participate in electron transfer and redox catalysis that contributes to biogeochemical cycling of N, S and Fe on the global scale. These properties of multi-haem cytochromes have attracted much interest and contributed to advances in bioenergy applications and bioremediation of contaminated soils. Looking forward, there are opportunities to engage multi-haem cytochromes for biological photovoltaic cells, microbial electrosynthesis and developing bespoke molecular devices. As a consequence, it is timely to review our present understanding of these proteins and we do this here with a focus on the multitude of functionally diverse multi-haem cytochromes in Shewanella oneidensis MR-1. We draw on findings from experimental and computational approaches which ideally complement each other in the study of these systems: computational methods can interpret experimentally determined properties in terms of molecular structure to cast light on the relation between structure and function. We show how this synergy has contributed to our understanding of multi-haem cytochromes and can be expected to continue to do so for greater insight into natural processes and their informed exploitation in biotechnologies.
A Relative Entropy Approach to Constructing Hierarchical Summaries

Hierarchies provide a means of organizing, summarizing and accessing information. This paper describes a method for automatically generating hierarchies from smal l col ections of text. A formal framework is presented which uses relative entropy to identify words that are both t pical and predictive of the vocabulary used to discuss the topics in the collection. These two features lead to the c reation of hierarchies that can be used to summarize the collection and provide a means of navigating to particul ar parts of a collection in which a user has interest. The hierarchy overcomes some of the limitations of the traditio nal ranked list as a means of describing the results of a search by providing multiple paths to a particular document , which are described by the topics and subtopics discussed in the document.
From N to N+1: Multiclass Transfer Incremental Learning

Since the seminal work of Thrun [16], the learning to learn paradigm has been defined as the ability of an agent to improve its performance at each task with experience, with the number of tasks. Within the object categorization domain, the visual learning community has actively declined this paradigm in the transfer learning setting. Almost all proposed methods focus on category detection problems, addressing how to learn a new target class from few samples by leveraging over the known source. But if one thinks of learning over multiple tasks, there is a need for multiclass transfer learning algorithms able to exploit previous source knowledge when learning a new class, while at the same time optimizing their overall performance. This is an open challenge for existing transfer learning algorithms. The contribution of this paper is a discriminative method that addresses this issue, based on a Least-Squares Support Vector Machine formulation. Our approach is designed to balance between transferring to the new class and preserving what has already been learned on the source models. Extensive experiments on subsets of publicly available datasets prove the effectiveness of our approach.
Rician noise attenuation in the wavelet packet transformed domain for brain MRI

Preprocessing stage for denoising is a crucial task in image analysis in general, and in computer-aided diagnosis using medical images in particular. Standard acquisition of Magnetic Resonance Images MRI presents statistical Rician noise which degrades the performance of the image analysis. This paper presents a new technique to reduce Rician noise of brain MRI. The new method for noise filtering is achieved in the discrete Wavelet Packets Transform WPT domain. Four methodologies for thresholding the detail coefficients in the same 2D WPT domain have been experimented considering two scenarios with and without a previous adaptive Wiener filtering in the spatial domain. Best quantitative and qualitative results have been obtained by the new method presented in this work specifically tailored for brain MRI, which is adaptive to each subband and dependent on the data. It has been compared with other traditional methods considering the Signal to Noise Ratio SNR, Normalized Cross Correlation NCC and execution time ∼ 0.1 s/slice. A complete dataset of structural T1-w brain MRI of the BrainWeb database has been used for experiments. An important aspect is that these experiments with synthetic images proved that the common prior adaptive Wiener filtering often used by many authors is a dispensable procedure.
Structural studies on the short-chain lipopolysaccharide of Vibrio cholerae O139 Bengal.

A Vibrio cholerae O139 strain, MO10-T4, lacking capsular polysaccharide, produces a short-chain lipopolysaccharide (LPS), similar to enterobacterial SR strains. It was studied by acidic and alkaline degradation, dephosphorylation, sugar and methylation analysis, high-performance anion-exchange chromatography, one- and two-dimensional 1H-, 13C-, and 31P-NMR spectroscopy, and electrospray ionization mass spectrometry. The following structure was proposed for the core region of the LPS: [structure: see text] where PEtn stands for 2-aminoethyl phosphate, Fru for fructose, Hep for L-glycero-D-manno-heptose, and Kdo for 3-deoxy-D-manno-octulosonic acid; unless otherwise stated, the monosaccharide residues are D and present in the pyranose form. An O-acetyl group is present on a secondary position, tentatively O4 of the alpha-linked glucosyl group. Some LPS species contain an additional putative fructose residue whose location remains unknown. An O139-negative mutant strain, Bengal-2R, derived from V. cholerae O139, has also been investigated and shown to produce an O-antigen-lacking LPS similar to those from enterobacterial R strains, some of the LPS species containing the same core region as the strain MO10-T4 LPS and the other lacking the lateral heptose residue. The carbohydrate backbone core structure is the same for the V. cholerae O139 and V. cholerae O1 LPS, thus confirming the close relation between these bacteria; however, the 2-aminoethyl phosphate, the O-acetyl group, and the second fructose residue have not been reported for the O1 LPS. In the V. cholerae O139 strain MO10-T4 LPS, a short O-side chain is attached at position 3 of the 7-substituted heptose residue and has the same structure as one repeating unit of the V. cholerae O139 capsular polysaccharide. Some details of the structure proposed are at variance with those recently published for another V. cholerae O139 strain [Cox, A. D. , Brisson, J.-R. , Varma, V. & Perry, M. B. (1996) Carbohydr. Res. 290, 43-58; Cox, A. D. & Perry, M. B. (1996) Carbohydr. Res. 290, 59-65. ]
Revenue Allocation Formula and Its Impact On Economic Growth Process In Nigeria

This study attempts to analyze the impact of allocation formula on the Nigeria growth process. The analysis reveals the extent to which revenue allocation formula adopted in the past has affected the path of economic growth and development in Nigeria. The data is purely secondary data and was sourced from the world bank publication, CBN, Journal and other published and unpublished materials. There is need, therefore to address the problem by formulating a move efficient revenue allocation wastage and mismanagement of founds. Also effort should be geared towards articulation of policies that will enhance capital formulation, employment of the abundant and measures may include attachment of more weight to the share of local government from the federal collected revenue, placing more emphasis on the internal revenue generation, redefinition of the concept of definition and sustaining the present effort of government as regards budget monitoring and implementation.
Voting Behavior, Coalitions and Government Strength through a Complex Network Analysis

We analyze the network of relations between parliament members according to their voting behavior. In particular, we examine the emergent community structure with respect to political coalitions and government alliances. We rely on tools developed in the Complex Network literature to explore the core of these communities and use their topological features to develop new metrics for party polarization, internal coalition cohesiveness and government strength. As a case study, we focus on the Chamber of Deputies of the Italian Parliament, for which we are able to characterize the heterogeneity of the ruling coalition as well as parties specific contributions to the stability of the government over time. We find sharp contrast in the political debate which surprisingly does not imply a relevant structure based on established parties. We take a closer look to changes in the community structure after parties split up and their effect on the position of single deputies within communities. Finally, we introduce a way to track the stability of the government coalition over time that is able to discern the contribution of each member along with the impact of its possible defection. While our case study relies on the Italian parliament, whose relevance has come into the international spotlight in the present economic downturn, the methods developed here are entirely general and can therefore be applied to a multitude of other scenarios.
Defensin deficiency, intestinal microbes, and the clinical phenotypes of Crohn’s disease

Crohn’s disease is a chronic, inflammatory disease of the intestinal mucosa. Although intestinal bacteria are implicated in disease pathogenesis, the etiology is still unclear. The main location of disease is the small intestine (ileum) and the colon. Ileal disease has been linked to a mutation in the NOD2 gene. Defensins are antimicrobial peptides and in the ileum, are mainly expressed in Paneth cells, epithelial cells that also express NOD2. In the colon, defensins are expressed by enterocytes or metaplastic Paneth cells. Crohn’s disease patients with ileal involvement, compared with controls or Crohn’s patients without ileal involvement, have diminished expression of ileal Paneth cell defensins. This decrease is even more pronounced in Crohn’s patients displaying a NOD2 mutation. In contrast, Crohn’s disease of the colon is characterized by an impaired induction of β‐defensins in enterocytes. The colonic expression of the constitutive β‐defensin 1 is also decreased in the inflamed colonic mucosa, but this decrease is less specific to Crohn’s disease, as it can also be found in ulcerative colitis patients. In conclusion, the regional localizations of Crohn’s disease, ileal or colonic disease, can be linked to different defensin profiles. Crohn’s disease of the ileum is associated with diminished defensin expression in Paneth cells. Crohn’s disease of the colon is associated with diminished β‐defensin expression in enterocytes. Thus, it can be speculated that decreased defensin levels lead to a weakened intestinal barrier function to intestinal microbes and might be crucial in the pathophysiology of Crohn’s disease.
A New Normalizing Algorithm for BAC CGH Arrays with Quality Control Metrics

The main focus in pin-tip (or print-tip) microarray analysis is determining which probes, genes, or oligonucleotides are differentially expressed. Specifically in array comparative genomic hybridization (aCGH) experiments, researchers search for chromosomal imbalances in the genome. To model this data, scientists apply statistical methods to the structure of the experiment and assume that the data consist of the signal plus random noise. In this paper we propose “SmoothArray”, a new method to preprocess comparative genomic hybridization (CGH) bacterial artificial chromosome (BAC) arrays and we show the effects on a cancer dataset. As part of our R software package “aCGHplus,” this freely available algorithm removes the variation due to the intensity effects, pin/print-tip, the spatial location on the microarray chip, and the relative location from the well plate. removal of this variation improves the downstream analysis and subsequent inferences made on the data. Further, we present measures to evaluate the quality of the dataset according to the arrayer pins, 384-well plates, plate rows, and plate columns. We compare our method against competing methods using several metrics to measure the biological signal. With this novel normalization algorithm and quality control measures, the user can improve their inferences on datasets and pinpoint problems that may arise in their BAC aCGH technology.
Capture of a Dimeric Intermediate during Transthyretin Amyloid Formation*

Point mutations in the human plasma protein transthyretin are associated with the neurological disorder familial amyloidosis with polyneuropathy type 1. The disease is characterized by amyloid fibril deposits causing damage at the site of deposition. Substitution of two amino acids in the hydrophobic core of transthyretin lead to a mutant that was very prone to form amyloid. In addition, this mutant has also been shown to induce a toxic response on a neuroblastoma cell line. Renaturation of the transthyretin mutant at low temperature facilitated the isolation of an amyloid-forming intermediate state having the apparent size of a dimer. Increasing the temperature effectively enhanced the rate of interconversion from a partly denatured protein to mature amyloid. Using circular dichroism the β-sheet content of the formed mature fibrils was significantly lower than that of the native fold of transthyretin. Morphology studies using electron microscopy also indicated a temperature-dependent transformation from amorphous aggregates toward mature amyloid fibrils. In addition, 1-anilino-8-naphtalenesulfonate fluorescence studies suggested the loss of the thyroxin-binding channel within both the isolated intermediate and the mature fibrils.
Performance driven global routing through gradual refinement

We propose a method for VLSI interconnect global routing that can optimize routing congestion, delay and number of bends, which are often competing objectives. Routing flexibilities under timing constraints are obtained and exploited to reduce congestion subject to timing constraints. The wire routes are determined through gradual refinement according to probabilistic estimation on congestions so that the congestion is minimized while the number of bends on wires are limited. The experiments on both random generated circuits and benchmark circuits confirm the effectiveness of this method.
Modulation of nutrient composition of black soldier fly (Hermetia illucens) larvae by feeding seaweed-enriched media

Black soldier fly (Hermetia illucens) larvae are a promising source of protein and lipid for animal feeds. The nutritional composition of the BSF larvae depend partly on the composition of the feeding medium. The BSF lipid profile in part mimics the feeding media lipid profile, and micronutrients, like minerals and vitamins, can readily accumulate in black soldier fly larvae. However, investigative studies on bioconversion and accumulation of nutrients from media to black soldier fly larvae are scarce. Here we show that inclusion of the brown algae Ascophyllum nodosum in the substrate for black soldier fly larvae can introduce valuable nutrients, commonly associated with the marine environment, into the larvae. The omega-3 fatty acid eicosapentaenoic acid (20:5n-3), iodine and vitamin E concentrations increased in the larvae when more seaweed was included in the diet. When the feeding media consisted of more than 50% seaweed, the larvae experienced poorer growth, lower nutrient retention and lower lipid levels, compared to a pure plant based feeding medium. Our results confirm the plasticity of the nutritional make-up of black soldier fly larvae, allowing it to accumulate both lipid- and water-soluble compounds. A broader understanding of the effect of the composition of the feeding media on the larvae composition can help to tailor black soldier fly larvae into a nutrient profile more suited for specific feed or food purposes.