Miracle-dz/UniFAR-FTUs huggingface dataset:
Severe 5‐fluorouracil toxicity secondary to dihydropyrimidine dehydrogenase deficiency. A potentially more common pharmacogenetic syndrome

This study describes the inheritance of a defect in pyrimidine catabolism and its association with drug‐induced toxicity in a patient receiving 5‐fluorouracil (FUra) as adjuvant chemotherapy for breast carcinoma. The study population included the affected patient (proband), nine of her blood relatives, and seven healthy volunteers. The activity of dihydropyrimidine dehydrogenase (DPD), the initial enzyme of pyrimidine (and FUra) catabolism, in peripheral blood mononuclear cells was measured in each subject by a specific radiometric assay using FUra as the substrate. The proband had no detectable DPD activity. When enzyme levels in the proband and relatives were compared with that in controls, an autosomal recessive pattern of inheritance was demonstrated. This is the third patient with severe FUra toxicity secondary to an alteration in pyrimidine catabolism and the second from our clinic population suggesting that the frequency of this genetic defect may be greater than previously thought. Monitoring DPD activity may be important in the management of patients experiencing severe toxicity secondary to FUra chemotherapy.
The Possible Role of the Microbiota-Gut-Brain-Axis in Autism Spectrum Disorder

New research points to a possible link between autism spectrum disorder (ASD) and the gut microbiota as many autistic children have co-occurring gastrointestinal problems. This review focuses on specific alterations of gut microbiota mostly observed in autistic patients. Particularly, the mechanisms through which such alterations may trigger the production of the bacterial metabolites, or leaky gut in autistic people are described. Various altered metabolite levels were observed in the blood and urine of autistic children, many of which were of bacterial origin such as short chain fatty acids (SCFAs), indoles and lipopolysaccharides (LPS). A less integrative gut-blood-barrier is abundant in autistic individuals. This explains the leakage of bacterial metabolites into the patients, triggering new body responses or an altered metabolism. Some other co-occurring symptoms such as mitochondrial dysfunction, oxidative stress in cells, altered tight junctions in the blood-brain barrier and structural changes in the cortex, hippocampus, amygdala and cerebellum were also detected. Moreover, this paper suggests that ASD is associated with an unbalanced gut microbiota (dysbiosis). Although the cause-effect relationship between ASD and gut microbiota is not yet well established, the consumption of specific probiotics may represent a side-effect free tool to re-establish gut homeostasis and promote gut health. The diagnostic and therapeutic value of bacterial-derived compounds as new possible biomarkers, associated with perturbation in the phenylalanine metabolism, as well as potential therapeutic strategies will be discussed.
Estimating Available Bandwidth Using Packet Pair Probing

Abstract : The packet pair mechanism has been shown to be a reliable method to measure the bottle-neck link bandwidth of a network path. However, the use of packet pairs to measure available bandwidth has had more mixed results. In this paper, we study how packet pairs and packet trains can be used to estimate the available bandwidth on a network path. As a starting point for our study, we construct the gap model, a simple model that captures the relationship between the competing traffic and the input and output packet pair gap for a single hop network. We validate the model using measurements on a testbed. The gap model shows that the initial probing gap is a critical parameter when using packet pairs to estimate available bandwidth. Based on this insight, we propose a new technique to measure the available bandwidth -- the Initial Gap Increasing (IGI) algorithm, which experimentally determines the best initial gap for measuring available bandwidth. Our experiments show that measurements that take 4-6 round trip times allow us to estimate the available bandwidth to within about 10%.
Hacking HTML5 canvas to create a stereo 3D renderer

In this article, we present a drawing toolkit developed to create stereoscopic side-by-side 3D stimuli. The toolkit is based in the HTML5 canvas element and drawing is achieved using intermediate stereo scripting methods that correspond to the `2d' context of the canvas. We include performance marks of the toolkit running on desktop and mobile browsers. Also, a discussion of how the tool is used for implementing a stereo 3D UI is specified.
Partitioned Sparse A-1 Methods

This paper solves the classic Ax=b problem by constructing factored components of the inverses of L and U, the triangular factors of A. The number of additional fill-ins in the partitioned inverses of L and U can be made zero. The number of partitions is related to the path length of sparse vector methods. Allowing some fill-in in the partitioned inverses of L and U results in fewer partitions. Ordering algorithms most suitable for sparsity preservation in the inverses of L and U require additional fill-in in L and U themselves. Tests on practical power system matrices from 118 to 1993 nodes indicate that the proposed approach is competitive in serial environments, and appears more suitable for parallel environments. Because sparse vectors are not required, the approach works not only for shortcircuit calculations but also for power flow and stability computations. Kevwords: Power Flow, Stability, Parallel computing, Sparse Matrices, Linear equations, Partitioning.
Inference of microbial interactions from time series data using vector autoregression model

Microbial interaction, such as species competition and symbiotic relationships, plays important role to enable microorganisms to survive by establishing a homeostasis between microbial neighbors and local environments. Thanks to the recent accumulation of large-scale high-throughput sequencing data of complex microbial communities, there are increasing interests in identifying microbial interactions. Computational methods for microbial interactions inference are currently focused on the similarity among microbial individuals (i.e. cooccurrence and correlation patterns), however, less methods considered the dynamics of a single complex community over time. In this paper, we propose to use a multivariate statistical method - Multivariate Vector Autoregression (MVAR) to infer dynamic microbial interactions from the time series of human gut microbiomes. Specifically, we apply MVAR model on a time series data of human gut microbiomes which were treated with repeated antibiotics. The referred microbial interactions identify novel interactions which may provide a novel complementary to similarity or correlation-based methods.
Inference of molecular phylogeny of Sarcocystis felis (Sarcocystidae) from cats based on nuclear-encoded ribosomal gene sequences.

The phylogenetic position of four clinical isolates of Sarcocystis felis was assessed using ssurRNA and ITS1 gene sequences in the context of a wide array of other Sarcocystis sp. Phylogenetic reconstructions using neighbour-joining and maximum parsimony methods generated identical tree topologies with strong support values at each node. High ssurRNA sequence similarity (> or =99%) and the resulting phylogeny demonstrated that S. felis and S. neurona are significantly closely related to each other. The two Sarcocystis formed a monophyletic group distinct from the other Sarcocystis sp. , irrespective of the alignment algorithms or tree-building method used. The absolute (100%) identity of ssurRNA sequences of sarcocysts and sporocysts obtained from one cat raised the question regarding the cat's role as a potential intermediate host besides its known role as a definitive host of S. felis. On the other hand, S. felis sarcocyst DNA sequence was found to be quite dissimilar over the ITS1 region when compared to S. neurona. These findings indicated that using sequences from two different genetic loci provided a stronger comparative basis than would have been possible using either one.
Patterns in Authoring of Adaptive Educational Hypermedia: A Taxonomy of Learning Styles

This paper describes the use of adaptation patterns in the task of formulating standards for adaptive educational hypermedia (AEH) systems that is currently under investigation by the EU ADAPT project. Within this project, design dimensions for high granularity patterns have been established. In this paper we focus on detailing lower granularity adaptive patterns based upon learning styles. Several patterns from existing AEH system case studies are identified and classified according to an extended learning style "onion" model. This model forms the basis of a learning style taxonomy, introduced here, whose components determine adaptation patterns for AEH. These patterns are of importance both for authoring, as well as for interfacing between adaptive hypermedia systems. From an authoring point of view, these patterns may be used to establish a fine-grain approach to instructional strategies that can be implemented in AEH systems, as a response to a particular learning style. The implementation of this adaptation pattern taxonomy is discussed, both generally and in detail.
New Coleoptera records from New Brunswick, Canada: Tenebrionidae and Zopheridae

Abstract Thirteen species of Tenebrionidae are newly reported for New Brunswick, Canada. Paratenetus punctatus Spinola, Pseudocistela brevis (Say), Mycetochara foveata (LeConte), and Xylopinus aenescens LeConte are recorded for the first time from the Maritime provinces. Platydema excavatum (Say) is removed from the faunal list of New Brunswick, and the presence of Platydema americanum Laporte and Brullé for the province is confirmed. This brings the total number of species of Tenebrionidae known from New Brunswick to 42. Two species of Zopheridae, Bitoma crenata Fabricius and Synchita fuliginosa Melsheimer, are newly recorded for New Brunswick, bringing the number of species known from the province to four. Bitoma crenata is new to the Maritime provinces. Collection and habitat data are presented for these species.
Railway Fastener Inspection by Real-Time Machine Vision

In this paper, a real-time railway fastener detection system using a high-speed laser range finder camera is presented. First, an extensive analysis of various methods based on pixel-wise and histogram similarities are conducted on a specific railway route. Then, a fusing stage is introduced which combines least correlated approaches also considering the performance upgrade after fusing. Then, the resulting method is tested on a larger database collected from a different railway route. After observing repeated successes, the method is implemented on NI LabVIEW and run real-time with a high-speed 3-D camera placed under a railway carriage designed for railway quality inspection.
De la conception d'une plateforme de télétravail virtualisée et unifiée : Analyses socio-techniques du travail "à distance" équipé

Cette these de doctorat, en Sciences de Gestion, a pour terrain de reflexions et d’actions de recherche, le projet WITE 2.0 consacre a l’analyse technico-organisationnelle d’un dispositif TIC en developpement : une plateforme integree de teletravail. Cette plateforme permet de travailler «a distance» en mode connecte ou non, a partir de n’importe quel terminal (PC, telephone, tablette), sur un mode «client leger» et dans un environnement de type cloud computing. De la conception de cette plateforme ont emerge des questionnements relatifs a la place des technologies d’information et de communication (TIC) dans les activites de travail realisees «a distance» de son collectif de travail. Notre strategie de recherche est constituee de deux grandes phases d’actions de recherche : la premiere consistait a connaitre la diversite des configurations de «teletravail» et la seconde a comprendre les modes d’appropriation et les limites des technologies de communication unifiee entrant en jeu dans la conception de la plateforme. Ces deux phases ont ete conduites dans une perspective de l’«action situee» et suivant une methodologie qualitative fondee sur des etudes par entretiens et par observations. Les resultats rendent compte des realites des pratiques de travail a distance en situation de mobilite equipee, des limites des equipements et des tactiques construites par les acteurs pendant la «mise en pratique» de la technologie. Ces resultats revelent aussi les normes, souvent tacites, et valeurs d’usages de ces nouvelles technologies et permettent d’apprehender leur conception au travers des recommandations manageriales englobant leurs aspects technique, d’usage et de service.
Role of Candida albicans polymorphism in interactions with oral epithelial cells.

BACKGROUND Candida albicans is a polymorphic organism which undergoes morphologic transition between yeast, pseudohyphal and hyphal forms. The ability of C. albicans to change from yeast to filamentous types is a major virulence determinant of this organism. However, the exact role of hyphal transformation in establishing oral mucosal infection is still poorly understood. METHODS In this study we used mutants with defects in filamentation, as well as oral strains, which differ in their capacity to form true hyphae, to examine the role of hyphal transformation in the interactions of C. albicans with oral epithelial cells in vitro. These interactions included the ability of these strains to adhere to and injure epithelial cells, as well as their ability to trigger a proinflammatory cytokine response. RESULTS We found that strains SC5314 and ATCC28366 formed true hyphae on epithelial cells, whereas strain ATCC32077 and the tup1/tup1 mutant formed only pseudohyphae. Double mutant efg1/efg1cph1/cph1 grew exclusively as blastospores. We also found that yeast and pseudohyphal strains showed reduced adherence capacity to oral keratinocytes and caused minimal cell damage. Moreover, we showed that both yeast and pseudohyphal forms have a strongly attenuated proinflammatory phenotype, since they failed to induce significant interleukin (IL)-1alpha and IL-8 responses by oral epithelial cells. CONCLUSIONS Germination of C. albicans into true hyphae is particularly important in the interactions with oral epithelial cells in vitro.
Susceptibility of Escherichia coli isolates with TEM-1 beta-lactamase to combinations of BRL42715, tazobactam or clavulanate with piperacillin or amoxycillin .

Production of TEM-1 beta-lactamase is the commonest cause of acquired resistance to amoxycillin and piperacillin in Escherichia coli, now occurring in c. 50% of isolates. Consecutive E. coli isolates producing TEM-1 beta-lactamase were collected at The London Hospital in 1982 (n = 50) and 1989 (n = 46). Enzyme quantities varied 150-fold amongst the isolates. Randomly-selected isolates from both years (n = 36; nine per quartile of the beta-lactamase activity distribution) were tested for susceptibility to combinations of amoxycillin or piperacillin with clavulanate or tazobactam or with BRL42715, a novel penem. The inhibitor concentrations needed to potentiate the penicillins related to the amount of beta-lactamase produced. BRL42715, at 1 mg/l, rendered all the isolates, including TEM-1 hyperproducers, susceptible to the recommended BSAC breakpoints of 8 mg amoxycillin/1 and 16 mg piperacillin/l. At 2 mg/l, BRL42715 almost always reduced amoxycillin and piperacillin MICs to the levels (1-2 mg/l) expected for E. coli isolates that lack TEM-1 enzyme. Tazobactam, at 1-2 mg/l, reduced piperacillin MICs to 1-2 mg/l for strains in the lower half of the beta-lactamase distribution, but greater than 8 mg tazobactam/l was required to reduce piperacillin MICs to 16 mg/l for one-third of the top quartile isolates. Clavulanate was a stronger potentiator of piperacillin than was tazobactam. On the other hand, amoxycillin was a more difficult substrate to potentiate than piperacillin, and isolates with enzyme levels in the top half of the distribution generally required greater than or equal to 8 mg clavulanate/l to reduce amoxycillin MICs to less than or equal to 8 mg/l.
Perfis de empresas varejistas quanto à adoção de práticas de responsabilidade social

Nos ultimos anos, o interesse dos administradores pelo tema responsabilidade social das empresas tem crescido substancialmente. Estudos estao sendo realizados com o objetivo de identificar o comportamento das empresas quanto a adocao de praticas de responsabilidade social. Neste trabalho, apresenta-se um delineamento de perfis de empresas varejistas de Belo Horizonte quanto a adocao de praticas de responsabilidade social, e a distribuicao dessas empresas segundo os seus estagios de atuacao social. A pesquisa foi baseada em estudos desenvolvidos por Maignan e Ferrell (2001), utilizando-se do modelo de Archie Carroll para o desempenho social corporativo. Os dados foram analisados com a utilizacao do metodo de Grade of Membership (GoM) e os resultados indicaram a caracterizacao de tres perfis de empresas medio, alto e baixo. A maioria das empresas (65,87%) apresentou caracteristicas mais proximas aos perfis de medio e baixo estagios de adocao de praticas de responsabilidade social.
Bioinformatic methods for the analysis and comparison of metagenomes and metatranscriptomes

Microbial communities play an important role in the whole life of planet earth. The fields metagenomics and metatranscriptomics have developed to reveal the taxo- nomic composition and functional diversity of heterogeneous microbial communities. With the development of new sequencing methods studies in those fields are accelerated. At the same time the new sequencing methods provide a challenge for bioinformatics to process and store a high amount of data. In the scope of this thesis, methods for the analysis of metagenome and metatranscriptome data were developed. At first, the taxonomic classifier metaBEETL was developed and implemented. metaBEETL is based on the Burrows-Wheeler transformation and analyses metagenome sequences to gain a taxonomic profile of microbial communities. Using several bias controls, it provides accurate taxonomic profiles while being memory efficient. In this thesis the accuracy of the classifier is shown by the analysis of an artificial metagenome dataset. Secondly, the rich client software platform Metrans was developed for the analysis and comparison of metatranscriptome datasets. Metrans consists of a pipeline designed for the analysis of metatranscriptomes. It also includes storage and visualization of the analysis results. The software is currently used in a number of projects. The analysis of a metatranscriptome gained from the infected ear of a man and a time series from tidal flat are presented as analysis examples in this thesis.
Dynamic Memory-Aware Task-Tree Scheduling

Factorizing sparse matrices using direct multifrontal methods generates directed tree-shaped task graphs, where edges represent data dependency between tasks. This paper revisits the execution of tree-shaped task graphs using multiple processors that share a bounded memory. A task can only be executed if all its input and output data can fit into the memory. The key difficulty is to manage the order of the task executions so that we can achieve high parallelism while staying below the memory bound. In particular, because input data of unprocessed tasks must be kept in memory, a bad scheduling strategy might compromise the termination of the algorithm. In the single processor case, solutions that are guaranteed to be below a memory bound are known. The multi-processor case (when one tries to minimize the total completion time) has been shown to be NP-complete. We present in this paper a novel heuristic solution that has a low complexity and is guaranteed to complete the tree within a given memory bound.We compare our algorithm to state of the art strategies, and observe that on both actual execution trees and synthetic trees, we always perform better than these solutions, with average speedups between 1.25 and 1.45 on actual assembly trees. Moreover, we show that the overhead of our algorithm is negligible even on deep trees (10 5), and would allow its runtime execution.
Influenza A Virus Monitoring in Urban and Free-Ranging Pigeon Populations in Germany, 2006–2008

SUMMARY. Tracheal and cloacal swabs as well as blood samples from 408 feral urban (Columba livia forma domestica) and 170 free-ranging wood pigeons (Columba palumbus) in Germany were tested for infection with avian influenza viruses (AIVs). Neither influenza A virus was isolated in the swab samples nor influenza A virus RNA detected using real-time reverse transcriptase–PCR (RT-qPCR). In three urban feral pigeons, avian paramyxovirus (APMV) serotype 1 was isolated. Two of 123 serum samples from hunted free-ranging wood pigeons contained specific antibodies against influenza A virus but not against the subtypes H5 and H7. In conclusion, our study indicates that even after the occurrence of zoonotic highly pathogenic avian influenza virus (HPAIV) subtype H5N1 in the area of investigation in Germany, pigeons do not play a major part in the transmission of influenza viruses. The risk of AIV infection for humans from urban and free-ranging wood pigeons is, if at all, of minimal importance.
Malwise System for Packed and Polymorphic Malware

Signature based malware detection systems have been a much used response to the pervasive problem of malware. Identification of malware variants is essential to a detection system and is made possible by identifying invariant characteristics in related samples. To classify the packed and polymorphic malware, this paper proposes a novel system, named malwise, for malware classification using a fast application level emulator to reverse the code packing transformation, and two flowgraph matching algorithms to perform classification. An exact flowgraph matching algorithm is employed that uses string based signatures, and is able to detect malware with near real-time performance. Additionally, a more effective approximate flow graph matching algorithm is proposed that uses the decompilation technique of structuring to generate string based signatures amenable to the string edit distance. We use real and synthetic malware to demonstrate the effectiveness and efficiency of Malwise. Using more than 15,000 real malware, collected from honeypots, the effectiveness is validated by showing that there is an 88% probability that new malware is detected as a variant of existing malware. The efficiency is demonstrated from a smaller sample set of malware where 86% of the samples can be classified in under 1.3 seconds. Index Terms— Computer security, malware, control flow, structural classification, structured control flow, unpacking.