Miracle-dz/UniFAR-FTUs huggingface dataset:
Streptococcus mutans, Caries and Simulation Models

Dental caries and dental plaque are among the most common diseases worldwide, and are caused by a mixture of microorganisms and food debris. Specific types of acid-producing bacteria, especially Streptococcus mutans, colonize the dental surface and cause damage to the hard tooth structure in the presence of fermentable carbohydrates e.g., sucrose and fructose. This paper reviews the link between S. mutans and caries, as well as different simulation models that are available for studying caries. These models offer a valuable approach to study cariogenicity of different substrates as well as colonization of S. mutans.
A Connectionist Cognitive Model for Temporal Synchronisation and Learning

The importance of the efforts towards integrating the symbolic and connectionist paradigms of artificial intelligence has been widely recognised. Integration may lead to more effective and richer cognitive computational models, and to a better understanding of the processes of artificial intelligence across the field. This paper presents a new model for the representation, computation, and learning of temporal logic in connectionist systems. The model allows for the encoding of past and future temporal logic operators in neural networks, through a neural-symbolic translation algorithms introduced in the paper. The networks are relatively simple and can be used for reasoning about time and for learning by examples with the use of standard neural learning algorithms. We validate the model in a well-known application dealing WIth temporal synchronisation in distributed knowledge systems. This opens several interesting research paths in cognitive modelling, with potential applications in agent technology, learning and reasoning.
Are Suggestions of Coupled File Changes Interesting?

Software repositories include information which can be made available for bug fixing or maintenance using repository mining. The identification of coupled changes have been proposed several times. Yet, existing studies focus on the found couplings and ignore feedback from developers. We investigate three development projects and their repositories to find files that frequently change together to support the software developers. We complement the coupled files information with details from the issue tracking system and the project documentation. We contrast our findings with feedback from the developers about how interesting our findings are for them. We found that the small size of the repositories made an insightful analysis difficult. The response to coupled changes both from experienced and inexperienced developers was mostly neutral. They accepted most of the additional attributes we presented. Furthermore, developers also suggested other additional issues to be relevant, e.g. the context of the coupled changes and the way they are presented, which we did not cover in this study. Therefore, coupled change analysis research will need to take the presentation and context information into account.
Study and Realisation of Controlling a Twin Rotor

In this paper, a twin rotor system as a model for a helicopter is studied. This system consists of two rotors acting as propellers, connected to a massive body. Not only the mathematical derivation is shown, but also some important simplifications are explained and described. Finally, the twin rotor system is also realised and measurements show that the controlling of this system works fine.
ORIENTAÇÃO MOTIVACIONAL DE METAS NA MODALIDADE DO BASQUETEBOL

O presente estudo tem por objetivo verificar a orientacao motivacional com o uso da escala TEOSQ (TEOSQ – TASK AND EGO ORIENTATION IN SPORT QUESTIONAIRE), Questionario do Esporte de orientacao para Tarefa ou Ego desenvolvido por Duda (1992), traduzido, adaptado e validado por Hirota e De Marco (2006), apresentando como proposta metodologica uma pesquisa experimental (MARCONI e LAKATOS, 2006), contando com 37 praticantes do basquetebol de idade entre 11 e 17 (media de idade de 14,02 +1,42 anos) da Cidade de Sao Caetano do Sul – Sao Paulo, Brasil. Como metodo estatistico utilizamos o software SPSS, versao 15.0, a fim de obter o Alfa de Cronbach e as medias, desvio padrao e mediana de cada orientacao – meta de Tarefa e meta Ego. Observamos com os resultados que a escala apresenta bons valores referente a estatistica de Alfa para Tarefa de 0.69 e Alfa para Ego de 0.67. As medias de idade entre 11 e 13 anos referente a orientacao para tarefa foi de 4,60 (+0,62) e orientacao para ego de 3,11 (+0,84); para idade entre 14 e 15 anos a media de tarefa foi de 4,23 (+0,78) e referente ao ego 2,74 (+1,02), e nas idade de 16 e 17 anos a media de orientacao para tarefa foi de 4,78 (+0,1) e ego de 2,66 (+0,47). O resultado total do grupo referente a tarefa foi de 4,36 (+0,75) e ego de 2,83 (+0,97). Concluimos que o processo de validacao esta de acordo com as expectativas, mostrando valores consistentes de Alfa, demonstrando assim que os alunos durante a aprendizagem do basquetebol sao mais seguros de seus atos, mas otimistas, persistentes em seus objetivos e adotam uma postura de responsabilidade com o restante do time.
The conserved 5′ apical hairpin stem loops of bamboo mosaic virus and its satellite RNA contribute to replication competence

Satellite RNAs associated with Bamboo mosaic virus (satBaMVs) depend on BaMV for replication and encapsidation. Certain satBaMVs isolated from natural fields significantly interfere with BaMV replication. The 5′ apical hairpin stem loop (AHSL) of satBaMV is the major determinant in interference with BaMV replication. In this study, by in vivo competition assay, we revealed that the sequence and structure of AHSL, along with specific nucleotides (C60 and C83) required for interference with BaMV replication, are also involved in replication competition among satBaMV variants. Moreover, all of the 5′ ends of natural BaMV isolates contain the similar AHSLs having conserved nucleotides (C64 and C86) with those of interfering satBaMVs, suggesting their co-evolution. Mutational analyses revealed that C86 was essential for BaMV replication, and that replacement of C64 with U reduced replication efficiency. The non-interfering satBaMV interfered with BaMV replication with the BaMV-C64U mutant as helper. These findings suggest that two cytosines at the equivalent positions in the AHSLs of BaMV and satBaMV play a crucial role in replication competence. The downregulation level, which is dependent upon the molar ratio of interfering satBaMV to BaMV, implies that there is competition for limited replication machinery.
Extended-Release Epidural Morphine (DepoDur) Following Epidural Bupivacaine in Patients Undergoing Lower Abdominal Surgery: A Randomized Controlled Pharmacokinetic Study

Background and Objectives: The primary objective was to compare the serum pharmacokinetic profile of a single dose of extended-release epidural morphine (EREM) administered alone versus 15 to 60 mins after an analgesic epidural dose of bupivacaine. Methods: This multicenter study enrolled 144 patients, 18 years or older, with scheduled lower abdominal surgery under general anesthesia. Patients were randomly assigned to a single 15-mg dose of EREM; the same dose administered 15, 30, or 60 mins after epidural bupivacaine (20 mL 0.25%); or epidural placebo (normal saline) administered 15, 30, or 60 mins after bupivacaine. Postoperatively, fentanyl patient-controlled analgesia was offered for breakthrough pain. Multiple serum samples were analyzed for morphine and morphine metabolites. Safety and efficacy were assessed. Results: The mean maximum serum concentration and area under the concentration-time curve for morphine and metabolites were not significantly different when EREM was administered alone versus 15, 30, or 60 mins after bupivacaine. Median time to maximum serum concentration and median apparent terminal elimination half-life were also comparable. Total fentanyl patient-controlled analgesia consumption was comparable among all EREM groups (with/without prior bupivacaine) but significantly (P < 0.05) lower compared with the bupivacaine + placebo group. Nausea, vomiting, and dizziness were consistently more frequent in groups receiving EREM after bupivacaine versus EREM alone. Conclusions: The pharmacokinetic and efficacy profiles of a single 15-mg dose of EREM were not significantly altered when administered 15, 30, or 60 mins after an analgesic epidural dose of bupivacaine.
An improved method for the molecular identification of single dinoflagellate cysts

Background Dinoflagellate cysts (i.e., dinocysts) are biologically and ecologically important as they can help dinoflagellate species survive harsh environments, facilitate their dispersal and serve as seeds for harmful algal blooms. In addition, dinocysts derived from some species can produce more toxins than vegetative forms, largely affecting species through their food webs and even human health. Consequently, accurate identification of dinocysts represents the first crucial step in many ecological studies. As dinocysts have limited or even no available taxonomic keys, molecular methods have become the first priority for dinocyst identification. However, molecular identification of dinocysts, particularly when using single cells, poses technical challenges. The most serious is the low success rate of PCR, especially for heterotrophic species. Methods In this study, we aim to improve the success rate of single dinocyst identification for the chosen dinocyst species (Gonyaulax spinifera, Polykrikos kofoidii, Lingulodinium polyedrum, Pyrophacus steinii, Protoperidinium leonis and Protoperidinium oblongum) distributed in the South China Sea. We worked on two major technical issues: cleaning possible PCR inhibitors attached on the cyst surface and designing new dinoflagellate-specific PCR primers to improve the success of PCR amplification. Results For the cleaning of single dinocysts separated from marine sediments, we used ultrasonic wave-based cleaning and optimized cleaning parameters. Our results showed that the optimized ultrasonic wave-based cleaning method largely improved the identification success rate and accuracy of both molecular and morphological identifications. For the molecular identification with the newly designed dinoflagellate-specific primers (18S634F-18S634R), the success ratio was as high as 86.7% for single dinocysts across multiple taxa when using the optimized ultrasonic wave-based cleaning method, and much higher than that (16.7%) based on traditional micropipette-based cleaning. Discussion The technically simple but robust method improved on in this study is expected to serve as a powerful tool in deep understanding of population dynamics of dinocysts and the causes and consequences of potential negative effects caused by dinocysts.
Using Multivariate Geostatistics to Assess Patterns of Spatial Dependence of Apparent Soil Electrical Conductivity and Selected Soil Properties

The apparent soil electrical conductivity (ECa) was continuously recorded in three successive dates using electromagnetic induction in horizontal (ECa-H) and vertical (ECa-V) dipole modes at a 6 ha plot located in Northwestern Spain. One of the ECa data sets was used to devise an optimized sampling scheme consisting of 40 points. Soil was sampled at the 0.0–0.3 m depth, in these 40 points, and analyzed for sand, silt, and clay content; gravimetric water content; and electrical conductivity of saturated soil paste. Coefficients of correlation between ECa and gravimetric soil water content (0.685 for ECa-V and 0.649 for ECa-H) were higher than those between ECa and clay content (ranging from 0.197 to 0.495, when different ECa recording dates were taken into account). Ordinary and universal kriging have been used to assess the patterns of spatial variability of the ECa data sets recorded at successive dates and the analyzed soil properties. Ordinary and universal cokriging methods have improved the estimation of gravimetric soil water content using the data of ECa as secondary variable with respect to the use of ordinary kriging.
Is question answering an acquired skill?

We present a question answering (QA) system which learns how to detect and rank answer passages by analyzing questions and their answers (QA pairs) provided as training data. We built our system in only a few person-months using off-the-shelf components: a part-of-speech tagger, a shallow parser, a lexical network, and a few well-known supervised learning algorithms. In contrast, many of the top TREC QA systems are large group efforts, using customized ontologies, question classifiers, and highly tuned ranking functions. Our ease of deployment arises from using generic, trainable algorithms that exploit simple feature extractors on QA pairs. With TREC QA data, our system achieves mean reciprocal rank (MRR) that compares favorably with the best scores in recent years, and generalizes from one corpus to another. Our key technique is to recover, from the question, fragments of what might have been posed as a structured query, had a suitable schema been available. comprises selectors: tokens that are likely to appear (almost) unchanged in an answer passage. The other fragment contains question tokens which give clues about the answer type, and are expected to be replaced in the answer passage by tokens which specialize or instantiate the desired answer type. Selectors are like constants in where-clauses in relational queries, and answer types are like column names. We present new algorithms for locating selectors and answer type clues and using them in scoring passages with respect to a question.
“It was fight or flight...and flight was not an option”: An Existential Phenomenological Investigation of Military Service Members’ Experience of Hand-to-Hand Combat

Hand-to-hand combat is one of the more psychologically challenging performance environments for those in the military (Grossman, 1995). Even with the technological advances of modern warfare military leaders still believe hand-to-hand combat is an important and relevant challenge for service members (Blanton, 2007; Clark, 2009; Collins, 2007; Wojdakowski, 2007; Wood & Micaelson, 2000). Despite its importance, the hand-to-hand combat experience has, to date, attracted very little research attention. Therefore, the purpose of this study was to explore military service members’ experiences of hand-to-hand combat. To accomplish this objective, phenomenological interviews were conducted with 17 male military service members. Each participant was asked to respond to the following open-ended statement: “Please describe your experience of hand-to-hand combat with an enemy combatant during combat operations. ” Follow-up questions were asked only to obtain additional details and further clarification of the participant’s comments. All interviews were audio recorded and transcribed verbatim. The transcripts were analyzed qualitatively, revealing a total of 584 meaning units. The data were then grouped into sub-themes and major themes that depicted the participants’ experiences. A final thematic structure revealed four major, figural dimensions that illustrated these service members’ experiences of hand-to-hand combat: enemy threat, fall to your training, fast, and close. These major figural themes emerged against the contextual background of the major theme: everyday combat operations. The results were somewhat consistent with previous literature, mainly information presented in hand-to-hand combat training manuals, but several findings represented extensions of
Feedback-based architecture for reading courtesy amounts on checks

The processing of bank checks is one application that continues to rely heavily on the movement of paper. Checks are currently read by human eyes and physically transported to the bank of the payer, involving significant time and cost. Since paper checks constitute a popular mechanism for noncash payments, and the vol- ume of checks continues to be high, there is a significant interest in the banking industry for new approaches that can read paper checks automatically. We propose a new approach to read the nu- merical amount field on the check; this field is also called the cour- tesy amount field. In the case of check processing, the segmenta- tion of unconstrained strings into individual digits is a challenging task because one must accommodate special cases involving con- nected or overlapping digits, broken digits, and digits physically con- nected to a piece of stroke that belongs to a neighboring digit. The described system involves three stages: the segmentation of the string into a series of individual characters, the normalization of each isolated character, and the recognition of each character based on a neural network classifier. © 2003 SPIE and IS&T.
Anxiolytic effect of indole-3-pyruvic acid (IPA) in mice.

In an elevated plus-maze indole-3-pyruvic acid (IPA, 100-200 mg/kg), an endogenous metabolite of tryptophan, possesses in mice an activity typical of anxiolytics. IPA increased the ratio of the number of entries into open arms over the total number of entries into open and closed arms and the time spent in open arms. Similar effect was observed for diazepam, a standard anxiolytic. Pretreatment with IPA attenuated the anxiogenic effect of caffeine (50 mg/kg) and 3-hydroxykynurenine (1.2 micrograms, i.c.v.) but not that of pentylenetetrazole (10 mg/kg), or phenylethylamine (5 and 10 mg/kg). Pretreatment with IPA (50-200 mg/kg) did not attenuate pentylenetetrazole- or phenylethylamine-induced seizures in contrast to diazepam which prevents both types of seizures. The data suggest that IPA is an endogenous anxiolytic with novel profile.
Off-Loading of Cyclic Hydrostatic Pressure Promotes Production of Extracellular Matrix by Chondrocytes

The addition of cyclic hydrostatic pressure (cHP) to cell culture medium has been used to promote extracellular matrix (ECM) production by articular chondrocytes. Though a combination of cHP followed by atmospheric pressure (AP) has been examined previously, the rationale of such a combination was unclear. We compared the effects of loading once versus twice (combinations of cHP followed by AP) regarding both gene expression and biochemical and histological phenotypes of chondrocytes. Isolated bovine articular chondrocytes were embedded in a collagen gel and incubated for 14 days under conditions combining cHP and AP. The gene expression of aggrecan core protein and collagen type II were upregulated in response to cHP, and those levels were maintained for at least 4 days after cHP treatment. Accumulation of cartilage-specific sulfated glycosaminoglycans following cHP for 7 days and subsequent AP for 7 days was significantly greater than that of the AP control (p < 0.05). Therefore, incubation at AP after loading with cHP was found to beneficially affect ECM accumulation. Manipulating algorithms of cHP combined with AP will be useful in producing autologous chondrocyte-based cell constructs for implantation.
Compositions of Graphs and Polyhedra I: Balanced Induced Subgraphs and Acyclic Subgraphs

Let $P(G)$ be the balanced subgraph polytope of $G$. If $G$ has a two-node cutset, the $G$ decomposes into $G_1$ and $G_2$. It is shown that $P(G)$ can be obtained as a projection of a polytope defined by a system of inequalities that decomposes into two pieces associated with $G_1$ and $G_2$. The problem max $cx, x \in P(G)$ is decomposed in the same way. This is applied to series-parallel graphs to show that, in this case, $P(G)$ is a projection of a polytope defined by a system with $O(n)$ inequalities and $O(n)$ variables, where $n$ is the number of nodes in $G$. Also for this case of graphs, an algorithm is given that finds a maximum weighted balanced subgraph in $O(n \log n)$ time. This approach is also used to obtain composition of facets of $P(G)$. Analogous results are presented for acyclic induced subgraphs.
Method and apparatus for detecting defects in freeform fabrication

A method for detecting defects in three-dimensional articles. Provided is a model of said article. Providing a first powder layer on a substrate, directing an energy beam over said substrate causing said first powder layer to fuse in selected locations forming a first cross section of said three-dimensional article, providing a second powder layer on said substrate, directing the energy beam over said substrate causing said second powder layer to fuse in selected locations to form a second cross section of said three-dimensional article. A first and second image of a first and second fusion zone of said first powder layer respectively is captured. Comparing said first and second images with corresponding layers in said model. Detecting a defect in the three-dimensional article if a deviation in said first image with respect to said model is at least partially overlapping a deviation in said second image with respect to said model.
Negative Glucocorticoid Response-Like Element from the First Intron of the Chicken Growth Hormone Gene Represses Gene Expression in the Rat Pituitary Tumor Cell Line

The effects of introns, especially the first intron, on the regulation of gene expression remains unclear. Therefore, the objective of the present study was to investigate the transcriptional regulatory function of intron 1 on the chicken growth hormone (cGH) gene in the rat pituitary tumor cell line (GH4-C1). Transient transfection using first-intron-inserted cGH complete coding sequences (CDSs) and non-intron-inserted cGH CDS plasmids, quantitative RT-PCR (qRT-PCR) and western blot assays were used to detect the expression of cGH. The reporter gene assay was also used to investigate the effect of a series of fragments in the first intron of cGH on gene expression in GH4-C1. All of the results revealed that a 200-bp fragment located in the +485/+684 region of intron 1 was essential for repressing the expression of cGH. Further informatics analysis showed that there was a cluster of 13 transcriptional factor binding sites (TFBSs) in the +485/+684 region of the cGH intron 1. Disruption of a glucocorticoid response-like element (the 19-nucleotide sequence 5′-AGGCTTGACAGTGACCTCC-3′) containing a T-box motif (TGACCT) located within this DNA fragment increased the expression of the reporter gene in GH4-C1. In addition, an electrophoretic mobility shift assay (EMSA) revealed a glucocorticoid receptor (GR) protein of rat binding to the glucocorticoid response-like element. Together, these results indicate that there is a negative glucocorticoid response-like element (nGRE) located in the +591/+609 region within the first intron of cGH, which is essential for the down-regulation of cGH expression.
On quantification of anchor placement

This paper attempts to answer a question: for a given traversal area, how to quantify the geometric impact of anchor placement on localization performance. We present a theoretical framework for quantifying the anchor placement impact. An experimental study, as well as the field test using a UWB ranging technology, is presented. These experimental results validate the theoretical analysis. As a byproduct, we propose a two-phase localization method (TPLM) and show that TPLM outperforms the least-square method in localization accuracy by a huge margin. TPLM performs much faster than the gradient descent method and slightly better than the gradient descent method in localization accuracy. Our field test suggests that TPLM is more robust against noise than the least-square and gradient descent methods.