Miracle-dz/UniFAR-FTUs huggingface dataset:
Comparison of commercial RNA extraction kits and qPCR master mixes for studying gene expression in small biopsy tissue samples from the equine gastric epithelium

ABSTRACT Gastric tissue biopsy and gene expression analysis are important tools for disease diagnosis and study of the physiology of the equine stomach. However, RNA extraction from gastric biopsy samples is a complex procedure because the samples contain low quantities of RNA and are contaminated with mucous protein and bacterial flora. The objectives of these studies were to compare the performance of RNA extraction methods and to investigate the sensitivity of commercial qPCR master mixes for gene expression analysis of gastric biopsy samples. Three commercial RNA extraction methods (TRIzol™, GENEzol™ and MiniPrep™) and four qPCR master mixes with SYBR® green (qPCRBIO, KAPA, QuantiNova, and PerfeCTa) were compared. RNA qualification and quantitation were compared. Real-time PCR was used to compare qPCR master mixes. The results revealed that TRIzol and GENEzol obtained significantly higher yield of RNA (P<0.01) but that TRIzol had the highest contamination of protein and DNA (P<0.05). Conversely, MiniPrep resulting in a significantly higher purification of RNA (P<0.05) but provided the lowest yield of RNA (P<0.01). For PCR master mixes, KAPA was significantly (P<0.05) more sensitive than other qPCR kits for all amounts of DNA template, particularly at the lowest amount of cDNA. In conclusion, GENEzol is the best method to obtain a high RNA yield and purification and it is more cost-effective than the others as well. Regarding the qPCR master mixes, KAPA SYBR qPCR Master Mix (2x) Universal is superior to the other tested master mixes for studying gene expression in equine gastric biopsies.
Nutrition and Disease ( n-3 ) Long-Chain Polyunsaturated Fatty Acids Prolong Survival following Myocardial Infarction in Rats 1 , 2

Many clinical studies report that (n-3) PUFAs decrease the incidence of sudden death in patients with coronary artery disease after myocardial infarction (MI). However, the mechanisms for the beneficial effects of (n-3) PUFAs are unknown. The objectives of the present study were to confirm the findings from clinical trials using an animal model of MI in which dietary intake could be closely controlled and to utilize the model to investigate molecular mechanisms for the beneficial effects of (n-3) PUFAs. Male rats were subjected to coronary ligation to induce MI and were randomly assigned to diets high in (n-6) (58% of lipid) or (n-3) (28% of lipid) PUFAs for 6 mo. A diet high in (n-3) PUFAs was associated with an improvement in 6-mo survival (89.2% vs. 64.9%, P 1⁄4 0.013) compared with rats consuming a diet high in (n-6) PUFAs (n 1⁄4 37/group). In a separate study (n 1⁄4 5 rats/diet group), the (n-3) PUFA diet decreased the (n-6):(n-3) PUFA ratio in plasma (0.66 0.1 vs. 7.96 1.8,P, 0.05) and cardiac tissue (0.96 0.1 vs. 11.86 1.6, P, 0.05) of rats fed for 4 wk. The increased survival in the (n-3) diet group was associated with decreased cardiac activities of protein kinase A and calcium calmodulin–dependent kinase II by 33–38% (P, 0.05) and a 28% decrease (P , 0.05) in phosphorylation (activation) of the ryanodine receptor calcium release channel. Based upon our results, we speculate that decreased activities of protein kinases induced by diets high in (n-3) PUFAs are associated with a decrease in sudden death after MI in rats. J. Nutr. 136: 1874–1878, 2006.
Value Gains in Alliances: The Role of Related Experience and Information Technology

This paper investigates the role of related alliance experience and information technology in value creation through strategic alliances. Past research has shown that alliance experience is an important antecedent of the value of an alliance. Built on the existing literature on alliance experience, this study highlights the importance of relatedness in alliance experience and examines how various kinds of related experience affect value creation differently. This study also looks at IT-enabled knowledge management capability and proposes a moderating effect on value creation in alliances. Using abnormal returns as the measure for value gains in alliances, this paper finds evidence of the different effects on value creation of related experience as well as the interaction effect of alliance experience and IT-enabled knowledge management capability.
Shapelets correlated with surface normals produce surfaces

This paper addresses the problem of deducing the surface shape of an object given just the surface normals. Many shape measurement algorithms such as shape from shading and shape from texture only return the surface normals of an object, often with an ambiguity of pi in the surface tilt. The surface shape has to be inferred from these normals, typically via some integration process. However; reconstruction through the integration of surface gradients is sensitive to noise and the choice of integration paths across the surface. In addition, existing techniques cannot accommodate ambiguities in tilt. This paper presents a new approach to the reconstruction of surfaces from surface normals using basis functions, referred to here as shapelets. The surface gradients of the shapelets are correlated with the gradients of the surface and the correlations summed to form the reconstruction. This results in a simple reconstruction process that is very robust to noise. Where there is an ambiguity of it in the surface tilt, reconstructions of reduced quality are still possible up to a positive/negative shape ambiguity. Intriguingly, some form of reconstruction is also possible using just slant information
Child and adolescent psychological disorders : a comprehensive textbook

1. A Brief History of the DSM-IV and ICD-10 2. Mental Retardation: A Symptom and a Syndrome 3. Learning and Motor Skills Disorders 4. Psychological Assessment and Treatment of Communication Disorders: Childhood Language Subtypes 5. Pervasive Developmental Disorders 6. Attention-Deficit/Hyperactivity Disorder 7. Disruptive Behavior: Oppositional Defiant Disorder and Conduct Disorder 8. Feeding Disorders of Infancy and Early Childhood 9. Tic Disorders and Stereotype Movement Disorders 10. Elimination Disorders 11. Organic Symptoms 12. Substance-Related Disorders 13. Depression and Bipolar Disorder in Children and Adolescents 14. Anxiety Disorders 15. Factitious Disorders and Factitious Disorders by Proxy 16. Somatoform Disorders 17. Dissociative Disorders in Childhood and Adolescence 18. Gender Identity Disorders and Transvestic Fetishes 19. Eating Disorders 20. Sleep Disorders in Childhood and Adolescence 21. Impulse Control Disorders Not Classified Elsewhere 22. Adjustment Disorders in Children and Adolescents 23. Personality Disorders 24. Relational Problems: The Social Context of Child and Adolescent Disorders 25. Problems Related to Child Abuse and Neglect 26. Psychological Factors Affecting Medical Condition 27. Noncompliance
Time and Motion Studies: The Dynamics of Cognition, Computation and Humanoid Walking

Abstract. Why is walking easy for us and difficult for robots? The conceptual framework of traditional Artificial Intelligence, and constraints from the background of industrial robot designers, means that commercial humanoid design has often ignored the role of natural dynamics of a mechanical system, as illustrated in a Passive Dynamic Walker. We show, using a Dynamical Systems approach and Evolutionary Robotics, how power and control can be added to such systems, demonstrating bipeds in simulation with many degrees of freedom that can walk, balance on a moving platform, and run.
A Web-service oriented framework for building SCORM compatible learning management systems

Managing the large amount of learning content involved in the development of an expandable learning management system (LMS) is a critical task for most educational organizations. In designing such a system, consideration must be given not only to the requirement of instructors and students, but also to the adaptive qualities of the system itself, because of the rapidly changing software environment. Unlike most enterprises, educational organization can't afford high system maintenance. Development of a flexible, expandable and reliable learning management system is, therefore, imperative. This paper proposes a Web service oriented framework in building a sharable content object reference model (SCORM) compatible LMS. We integrated the SCORM concept with distributed computing technologies to build the components of the LMS and demonstrate how these services can be configured to create a complete system. This framework increases reusability and reduces the maintenance requirements of the LMS. It provides a way for small educational organizations, with limited resources, to build a complete SCORM compatible LMS. In such an ideal situation, the content provider not only provides the content, but also the service for the consumers of that content.
The possession game? A comparative analysis of ball retention and team success in European and international football, 2007–2010

Abstract Possession is thought of as central to success in modern football, but questions remain about its impact on positive team outcomes (Bate, 1988; Hughes & Franks, 2005; Pollard & Reep, 1997; Stanhope, 2001). Recent studies (e.g. Bloomfield, Polman, & O'Donoghue, 2005; Carling, Williams, & Reilly, 2005; James, Mellallieu, & Holley, 2002; Jones, James, & Mellalieu, 2004; Lago, 2009; Lago & Martin, 2007; Lago-Peñas & Dellal, 2010; Lago-Peñas, Lago-Ballesteros, Dellal, & Gómez, 2010; Taylor, Mellalieu, & James, 2005; Tucker, Mellalieu, James, & Taylor, 2005) that have examined these questions have often been constrained by an exclusive focus on English or Spanish domestic play. Using data from five European leagues, UEFA and FIFA tournaments, the study found that while possession time and passing predicted aggregated team success in domestic league play, both variables were poor predictors at the individual match level once team quality and home advantage were accounted for. In league play, the effect of greater possession was consistently negative; in the Champions League, it had virtually no impact. In national team tournaments, possession failed to reach significance when offensive factors were accounted for. Much of the success behind the ‘possession game’ was thus a function of elite teams confined in geographic and competitive space. That ball hegemony was not consistently tied to success suggests that a nuanced approach to possession is needed to account for variant strategic environments (e.g. James et al., 2002) and compels match analysts to re-examine the metric's overall value.
Prevention of caries with probiotic bacteria during early childhood. Promising but inconsistent findings.

PURPOSE This review summarized the available literature on the prevention of childhood caries through biofilm engineering with probiotic bacteria in early childhood. METHODS Three databases (PubMed, Cochrane Library and Trip) were searched through January, 2016 for randomized controlled trials published in English. Out of 144 abstracts, seven studies fulfilled the predetermined inclusion criteria and were quality assessed with respect to risk of bias independently by two examiners. Due to the paucity and heterogeneity, a narrative synthesis was performed. The effect size was estimated from the caries prevalence and expressed as prevented fraction and number needed to treat. RESULTS Probiotic supplements were better than placebo in preventing early childhood caries in all seven studies although the difference was statistically significant in only four of them. The prevented fraction ranged from 11% to 61% with a median of 48%. However, the quality of the evidence was low or very low and further translational research is needed to investigate this preventive approach in the clinic.
Do 9-Month-Olds Perceive Causation-at-a-Distance?

Humans understand mechanical events to involve physical bodies interacting by contact, but intentional events involve agents that can also interact at a distance. We investigated infant sensitivity to causality in a simple event in which one agent appears to react to another without contact. Infants 9 months old were habituated to one of two events involving a computer-animated red square moving nonrigidly—like a caterpillar—towards a green square. In the ‘reaction event’, the green object moved in turn before the red one stopped, while in the ‘pause event’ the green object moved after the red one stopped. After habituation, each infant saw the habituation movie played in reverse. This test involved identical spatiotemporal changes for reaction and pause event, but the reversed reaction additionally involved a change in the causal roles. Infants dis-habituated to reversal of the reaction but not the pause event, a result which suggests sensitivity to causation-at-a-distance. This ability could support development of social cognition and theory of mind.
Interaction Signatures Stabilizing the NAD(P)-Binding Rossmann Fold: A Structure Network Approach

The fidelity of the folding pathways being encoded in the amino acid sequence is met with challenge in instances where proteins with no sequence homology, performing different functions and no apparent evolutionary linkage, adopt a similar fold. The problem stated otherwise is that a limited fold space is available to a repertoire of diverse sequences. The key question is what factors lead to the formation of a fold from diverse sequences. Here, with the NAD(P)-binding Rossmann fold domains as a case study and using the concepts of network theory, we have unveiled the consensus structural features that drive the formation of this fold. We have proposed a graph theoretic formalism to capture the structural details in terms of the conserved atomic interactions in global milieu, and hence extract the essential topological features from diverse sequences. A unified mathematical representation of the different structures together with a judicious concoction of several network parameters enabled us to probe into the structural features driving the adoption of the NAD(P)-binding Rossmann fold. The atomic interactions at key positions seem to be better conserved in proteins, as compared to the residues participating in these interactions. We propose a “spatial motif” and several “fold specific hot spots” that form the signature structural blueprints of the NAD(P)-binding Rossmann fold domain. Excellent agreement of our data with previous experimental and theoretical studies validates the robustness and validity of the approach. Additionally, comparison of our results with statistical coupling analysis (SCA) provides further support. The methodology proposed here is general and can be applied to similar problems of interest.
Economic costs of protistan and metazoan parasites to global mariculture

SUMMARY Parasites have a major impact on global finfish and shellfish aquaculture, having significant effects on farm production, sustainability and economic viability. Parasite infections and impacts can, according to pathogen and context, be considered to be either unpredictable/sporadic or predictable/regular. Although both types of infection may result in the loss of stock and incur costs associated with the control and management of infection, predictable infections can also lead to costs associated with prophylaxis and related activities. The estimation of the economic cost of a parasite event is frequently complicated by the complex interplay of numerous factors associated with a specific incident, which may range from direct production losses to downstream socio-economic impacts on livelihoods and satellite industries associated with the primary producer. In this study, we examine the world's major marine and brackish water aquaculture production industries and provide estimates of the potential economic costs attributable to a range of key parasite pathogens using 498 specific events for the purposes of illustration and estimation of costs. This study provides a baseline resource for risk assessment and the development of more robust biosecurity practices, which can in turn help mitigate against and/or minimise the potential impacts of parasite-mediated disease in aquaculture.
Inversion of seismic refraction data using genetic algorithms

The use of genetic algorithms in geophysical inverse problems is a relatively recent development and offers many advantages in dealing with the nonlinearity inherent in such applications. However, in their application to specific problems, as with all algorithms, problems of implementation arise. After extensive numerical tests, we implemented a genetic algorithm to efficiently invert several sets of synthetic seismic refraction data. In particular, we aimed at overcoming one of the main problems in the application of genetic algorithms to geophysical problems: i.e., high dimensionality. The addition of a pseudo-subspace method to the genetic algorithm, whereby the complexity and dimensionality of a problem is progressively increased during the inversion, improves the convergence of the process. The method allows the region of the solution space containing the global minimum to be quickly found. The use of local optimization methods at the last stage of the search further improves the quality of the inversion. The genetic algorithm has been tested on a field data set to determine the structure and base of the weathered layer (regolith) overlaying a basement of granite and greenstones in an Archaean terrain of Western Australia.
UNITED NATIONS FOOD AND AGRICULTURE ORGANIZATION UNITED NATIONS

Termites are the most important soil fauna in the Sahelian zone of Africa, intensely interacting with the soil. Both the biotic and abiotic state of the soil affect the termite population and activity. The construction by termites of nests, gallery systems or sheetings from soil or from a mixture of soil and other material within the soil horizons or on the soil surface affect the physical and chemical status of both the material used for the construction and the surrounding soil from which the materials were taken. In fact, structure, structure stability, porosity, chemical status of the soil and the decomposition of organic residues are to a large extent altered by termite activity. This presentation focuses on the contribution of termite activity triggered by the use of various types of mulch to the rehabilitation of crusted soils in the SaheloSoudanian zone. It appeared that mulch, when placed on a crusted and bare soil, can trigger termite activity within a few months. Termite activity results in a change in soil structure. Many burrows are opened through the sealed surface of the soil due to the burrowing activity of the termites. Throughout the soil profile, macropores with irregular shapes and with different diameter sizes are created. The aggregation of the soil by termites through their building systems is also observed. As a result of changes in soil structure, other soil physical properties are also improved. Soil resistance to cone penetration is reduced from a critical to a suitable level for vegetation growth. Bulk density is decreased and soil hydraulic conductivity is greatly increased. Water infiltration and drainage are also greatly improved. The combination of the increase of porosity and infiltration and the cover effect of mulch results in an increase of soil water availability in the soil profile during the growing season. Termite activity enhanced the decomposition of the mulch and hence nutrient release in the soil. The crown was the spectacular response of both the natural vegetation and a cowpea crop which both showed an increase from virtually nothing to a lush vegetation. This was indicated in the natural vegetation by a highly significantly increased percentage of cover, aboveground biomass, number of native plant species and rainfall use efficiency. It was concluded that termite activity can create conditions necessary for natural vegetation and crop growth and therefore, termite in the Sahel could change from being an enemy to a friend.
Moving Beyond Fun: Evaluating Serious Experience in Digital Games

Games are normally considered to be "fun", though recently there is growing interest in how gameplay can promote empathy and encourage reflection through "serious experience". However, when looking beyond enjoyment, it is not clear how to actually evaluate serious experience. We present an evaluation of four games that were submitted to a student game design competition; the competition challenged teams to design a game that inspired curiosity around human error and blame culture within the context of healthcare. The entries were judged by a panel of six experts and subjected to a round of play testing by twelve participants. Methods included gameplay observation, questionnaires, post-play interviews and follow-up email questions. We discuss the utility of these methods, with particular emphasis on how they enabled a consideration of the immediate and longer term impact of serious experience on players.
Leveraging Node Attributes for Incomplete Relational Data

Relational data are usually highly incomplete in practice, which inspires us to leverage side information to improve the performance of community detection and link prediction. This paper presents a Bayesian probabilistic approach that incorporates various kinds of node attributes encoded in binary form in relational models with Poisson likelihood. Our method works flexibly with both directed and undirected relational networks. The inference can be done by efficient Gibbs sampling which leverages sparsity of both networks and node attributes. Extensive experiments show that our models achieve the state-of-the-art link prediction results, especially with highly incomplete relational data.
Dissociation between Epitope Hierarchy and Immunoprevalence in CD8 Responses to Vaccinia Virus Western Reserve1

Understanding immunity to vaccinia virus (VACV) is important for the development of safer vaccines for smallpox- and poxvirus-vectored recombinant vaccines. VACV is also emerging as an outstanding model for studying CD8+ T cell immunodominance because of the large number of CD8+ T cell epitopes known for this virus in both mice and humans. In this study, we characterize the CD8+ T cell response in vaccinated BALB/c mice by a genome-wide mapping approach. Responses to each of 54 newly identified H-2d-restricted T cell epitopes could be detected after i.p. and dermal vaccination routes. Analysis of these new epitopes in the context of those already known for VACV in mice and humans revealed two important findings. First, CD8+ T cell epitopes are not randomly distributed across the VACV proteome, with some proteins being poorly or nonimmunogenic, while others are immunoprevalent, being frequently recognized across diverse MHC haplotypes. Second, some proteins constituted the major targets of the immune response by a specific haplotype as they recruited the majority of the specific CD8+ T cells but these proteins did not correspond to the immunoprevalent Ags. Thus, we found a dissociation between immunoprevalence and immunodominance, implying that different sets of rules govern these two phenomena. Together, these findings have clear implications for the design of CD8+ T cell subunit vaccines and in particular raise the exciting prospect of being able to choose subunits without reference to MHC restriction.
Algorithm Xxx: Gqrat | Gauss Quadrature for Rational Functions

The concern here is with Gauss-type quadrature rules that are exact for a mixture of polynomials and rational functions, the latter being selected so as to simulate poles that may be present in the integrand. The underlying theory is presented as well as methods for constructing such rational Gauss formulae. Relevant computer routines are provided and applied to a number of examples, including Fermi-Dirac and Bose-Einstein integrals of interest in solid state physics.