Miracle-dz/UniFAR-FTUs huggingface dataset:
Estimating Allele Frequency from Next-Generation Sequencing of Pooled Mitochondrial DNA Samples

Background: Both common and rare mitochondrial DNA (mtDNA) variants may contribute to genetic susceptibility to some complex human diseases. Understanding of the role of mtDNA variants will provide valuable insights into the etiology of these diseases. However, to date, there have not been any large-scale, genome-wide association studies of complete mtDNA variants and disease risk. One reason for this might be the substantial cost of sequencing the large number of samples required for genetic epidemiology studies. Next-generation sequencing of pooled mtDNA samples will dramatically reduce the cost of such studies and may represent an appealing approach for large-scale genetic epidemiology studies. However, the performance of the different designs of sequencing pooled mtDNA has not been evaluated. Methods: We examined the approach of sequencing pooled mtDNA of multiple individuals for estimating allele frequency using the Illumina genome analyzer (GA) II sequencing system. In this study the pool included mtDNA samples of 20 subjects that had been sequenced previously using Sanger sequencing. Each pool was replicated once to assess variation of the sequencing error between pools. To reduce such variation, barcoding was used for sequencing different pools in the same lane of the flow cell. To evaluate the effect of different pooling strategies pooling was done at both the pre- and post-PCR amplification step. Results: The sequencing error rate was close to that expected based on the Phred score. When only reads with Phred ≥ 20 were considered, the average error rate was about 0.3%. However, there was significant variation of the base-calling errors for different types of bases or at different loci. Using the results of the Sanger sequencing as the standard, the sensitivity of single nucleotide polymorphism detection with post-PCR pooling (about 99%) was higher than that of the pre-PCR pooling (about 82%), while the two approaches had similar specificity (about 99%). Among a total of 298 variants in the sample, the allele frequencies of 293 variants (98%) were correctly estimated with post-PCR pooling, the correlation between the estimated and the true allele frequencies being >0.99, while only 206 allele frequencies (69%) were correctly estimated in the pre-PCR pooling, the correlation being 0.89. Conclusion: Sequencing of mtDNA pooled after PCR amplification is a viable tool for screening mitochondrial variants potentially related to human diseases.
The phenotypic expression of mitochondrial tRNA-mutations can be modulated by either mitochondrial leucyl-tRNA synthetase or the C-terminal domain thereof

Mutations in mitochondrial (mt) DNA determine important human diseases. The majority of the known pathogenic mutations are located in transfer RNA (tRNA) genes and are responsible for a wide range of currently untreatable disorders. Experimental evidence both in yeast and in human cells has shown that the detrimental effects of mt-tRNA point mutations can be attenuated by increasing the expression of the cognate mt-aminoacyl-tRNA synthetases (aaRSs). In addition, constitutive high levels of isoleucyl-tRNA syntethase have been shown to reduce the penetrance of a homoplasmic mutation in mt-tRNAIle in a small kindred. More recently, we showed that the isolated carboxy-terminal domain of human mt-leucyl tRNA synthetase (LeuRS-Cterm) localizes to mitochondria and ameliorates the energetic defect in transmitochondrial cybrids carrying mutations either in the cognate mt-tRNALeu(UUR) or in the non-cognate mt-tRNAIle gene. Since the mt-LeuRS-Cterm does not possess catalytic activity, its rescuing ability is most likely mediated by a chaperon-like effect, consisting in the stabilization of the tRNA structure altered by the mutation. All together, these observations open potential therapeutic options for mt-tRNA mutations-associated diseases.
Structures and activities of archaeal members of the LigD 3′-phosphoesterase DNA repair enzyme superfamily

LigD 3′-phosphoesterase (PE) is a component of the bacterial NHEJ apparatus that performs 3′-end-healing reactions at DNA breaks. The tertiary structure, active site and substrate specificity of bacterial PE are unique vis–à-vis other end-healing enzymes. PE homologs are present in archaea, but their properties are uncharted. Here, we demonstrate the end-healing activities of two archaeal PEs—Candidatus Korarchaeum cryptofilum PE (CkoPE; 117 amino acids) and Methanosarcina barkeri PE (MbaPE; 151 amino acids)—and we report their atomic structures at 1.1 and 2.1 Å, respectively. Archaeal PEs are minimized versions of bacterial PE, consisting of an eight-stranded β barrel and a 310 helix. Their active sites are located in a crescent-shaped groove on the barrel’s outer surface, wherein two histidines and an aspartate coordinate manganese in an octahedral complex that includes two waters and a phosphate anion. The phosphate is in turn coordinated by arginine and histidine side chains. The conservation of active site architecture in bacterial and archaeal PEs, and the concordant effects of active site mutations, underscore a common catalytic mechanism, entailing transition state stabilization by manganese and the phosphate-binding arginine and histidine. Our results fortify the proposal that PEs comprise a DNA repair superfamily distributed widely among taxa.
CaliforniaOperation planning in cranio-maxillofacial surgery

Surgery in the cranio-maxillo-facial area is complex. However, planning a surgical operation can help the surgeon in enhancing the quality of the operation. On the other hand, progress in planning seems not to be completely justiied if the planning strategy cannot be replicated during its execution. Problems occur during planning as well as during execution. A system that optimally supports the surgeon should support planning and simulation as well as execution by the surgeon, execution guided by a navigation system and autonomous execution by a robot. In this paper we present our approach for an integrated system for planning and execution of cranio-maxillo-facial surgery operations. This approach is based on a hierarchical architecture and the decomposition of planning levels being either independent or dependent of the execution system via implicit and explicit elementary operations. The architecture of our system can be applied to operations in general. Operation speciic parts of our system have been applied to two speciic operations in the mandible/maxilla region, the LeFort I osteotomy and sagittal dissection of the mandible. Results of simulated and robotized execution of some elementary operations are presented.
The role of multicultural art education in a cultural diversified society

The Public Life of the Arts in AmericaCreative FrictionsCreative Arts MarketingThe Art of MulticulturalismMulticultural PartnershipsRethinking Contemporary Art and Multicultural EducationMulticultural StoryboardsArts IntegrationArts Education and Cultural DiversityResources in EducationCelebrating PluralismContemporary Art and Multicultural EducationArt Education 11-18Multicultural Educ AroraMusic, Education, and DiversityAmerican Multicultural StudiesBeyond Multicultural Art EducationVoices of Black Girls in TorontoCumulative List of Organizations Described in Section 170 (c) of the Internal Revenue Code of 1986Rethinking Contemporary Art and Multicultural EducationArts and Cultural Education in a World of DiversityCultural Diversity and the Structure and Practice of Art EducationHandbook of Research and Policy in Art EducationMulticulturalism's Double-BindContemporary Art and Multicultural EducationArt, Culture, and PedagogyMulticulturalism in Art Museums TodayCultural Policy and Cultural DiversityMulticultural Art ActivitiesMixed BlessingsArt in the Early YearsArtists in SchoolsCultural Centers of ColorAesthetics in a Multicultural AgeRethinking Multicultural EducationJournal of Multi-cultural and Cross-cultural Research in Art EducationThe Kids Multicultural Art BookHearings on the National Endowment for the ArtsArt, Activism, and OppositionalityRoutledge International Companion to Education
Is food insecurity more severe in South Asia or Sub-Saharan Africa?: A comparative analysis using household expenditure survey data

"This paper uses data from national household expenditure surveys to explore whether food insecurity is more severe in South Asia or Sub-Saharan Africa. It employs two indicators of the diet quantity dimension of food insecurity, or the inability to access sufficient food: the prevalence of food energy deficiency and the prevalence of severe food energy deficiency. It also employs two indicators of the diet quality dimension, indicating lack of access to nutritious food: the prevalence of low diet diversity and the percent of energy from staple foods. It finds the regions' food energy deficiency prevalences to be quite close (51 percent in South Asia, 57 percent in Sub-Saharan Africa). However, the prevalence of severe food energy deficiency, which is more life threatening, is higher in Sub-Saharan Africa (51 percent versus 35 percent in South Asia). From a diet quality standpoint, the regions appear to suffer from a comparable and high reliance on staple foods in the diet to the neglect of foods rich in protein and micronutrients, but that Sub-Saharan Africa may be doing worse, as reflected in less diverse diets. The results confirm that both regions suffer from deep food insecurity problems but point to Sub-Saharan Africa as the region with the more severe problem, particularly when it comes to the diet quantity dimension of food insecurity. In deciding which region should be given greater emphasis in the international allocation of scarce development resources, the fact that the numbers of people affected by food insecurity are higher in South Asia should be taken into consideration. " from Authors' Abstract
PARTICLE SPECTRUM OF NON-ABELIAN TENSOR GAUGE FIELDS

We review the non-Abelian tensor gauge field theory and analyze its free field equations for lower rank gauge fields when the interaction coupling constant tends to zero. The free field equations are written in terms of the first-order derivatives of extended field strength tensors similar to the electrodynamics and non-Abelian gauge theories. We determine the particle content of the free field equations and count the propagating modes which they describe. In four-dimensional spacetime the rank-2 gauge field describes propagating modes of helicity two and zero. We show that the rank-3 gauge field describes propagating modes of helicity-three and a doublet of helicity-one gauge bosons. Only four-dimensional spacetime is physically acceptable, because in five- and higher-dimensional spacetime the equation has solutions with negative norm states. We discuss the structure of the particle spectrum for higher rank gauge fields.
A fuzzy logic approach for reasoning under uncertainty and vagueness - a matchmaking case study

Matchmaking problems have been studied extensively in literature. Today's World Wide Web provides us with the ability to have access to a vast amount of data. The manual matchmaking cannot be considered a feasible solution and automatic methods by machines have been evolved. The matchmaking task is always based on a set of criteria, but these criteria may not have a well-defined meaning. In this paper, a matchmaking method of web data based on fuzzy criteria is outlined.
Anatomical and Functional Description of the Radius of White Footed Tamarin (Saguinus leucopus)

Saguinus leucopus es un primate neotropical, endemico y monotipico de Colombia, con escasos estudios sobre su anatomia, y por ende de la morfologia radial, elemento fundamental para la locomocion cuadrupeda de este animal arboreo que permanece desconocida. El objetivo fue describir la anatomia macroscopica y funcional de los relieves oseos del radio del titi gris (Saguinus leucopus). Se tomaron como base del estudio ocho especimenes fijados con formalina al 10% y de ellos se extrajeron sus radios, describiendo completamente su anatomia macroscopica. Los principales relieves oseos con sus funciones de fijacion muscular y ligamentosa, y canalizaciones neurovasculares. El radio del Saguinus leucopus presenta algunas prominencias oseas fijaciones musculares y ligamentosas, ademas presenta regiones de cartilago sinovial para articular con otras partes del miembro anterior. Los variados relieves anatomicos del radio del Saguinus leucopus presentan caracteristicas tipicas particulares, adaptadas a funciones motoras para su ambiente propio de una posicion arborea cuadrupeda.
Digital technology and outdoor experiential learning

ABSTRACT Any use or non-use of digital technology in outdoor experiential learning requires critical examination. Digital technology can undermine the aim of being outdoors, but it can also create opportunities to enhance outdoor learning experiences. This paper presents a conceptual framework, based on a systematic review of the literature, that facilitators can use to think critically about their use (or non-use), of digital technology in outdoor experiential learning. The three key parts of the framework are pedagogical considerations, affordances of digital technology and consequences of decisions. The framework is designed to help facilitators of outdoor experiential learning make informed decisions or retrospectively review the decisions they made about the use (or non-use) of digital technology. The strength of the framework is that it encourages facilitators to engage in the critical evaluation of the intended and unintended consequences of digital technology use (or non-use) in outdoor experiential learning.
Interactive semantic analysis of Clause-Level Relationships

Natural Language Processing (NLP) systems usually require large amounts of pre-coded domain knowledge to perform semantic analysis automatically. Until repositories of such background knowledge are widely available, these systems may not scale up to non-trivial applications of NLP. This paper describes the design and implementation of a system that uses surface-syntactic information to interpret interactively semantic relationships between clauses. English technical texts are analyzed by a domain-independent parser that produces detailed parse trees of the input. The system then examines clausal connectives and syntactic verb phrase features to determine what kinds of semantic relationships exist between clauses. The results of this activity are used in a large Knowledge Acquisition system that, by design, requires little a priori semantic knowledge. We present a set of semantic labels appropriate to syntactically connected clauses (Clause-Level Relationships) and a description of the theory behind assigning these labels to particular inputs (Clause-Level Relationship Analysis). We also discuss elements of the implementation of the ClauseLevel Relationship Analyzer and look at its performance.
Cortical N400-potentials generated by adults in response to semantic incongruities

Eight adult participants were investigated in a pre-experiment for the future assessment of semantic N400 effects in children. The materials were words resented in semantically incongruent vs. congruent picture contexts. For example, he word duck was played while a picture of a tree was shown in the incongruent est condition vs. the word duck was played while a picture of a duck was shown in the congruent test condition. A larger N400 effect was expected in response to the incongruent audio-visual pairings. The results showed in time extended peak-to peak differences between congruent and incongruent audio-visual pairings at the centroparietal, parietal and parieto-occipital recording sites. This study was performed to validate the current materials to be used to answer questions on appearance of the N400 component in children.
Inferring protein-protein interactions from sequence using sequence order information

Identification of protein-protein interaction is crucial for nearly all biological process. In this paper, we introduce a new transformation of protein sequence based on sequence order information. We use 5594 interacting pairs of yeast organism from DIP core database as training data set, seven types organism as independent data set. The model with a new protein coding scheme obtains 88.927% accuracy, 88.243% sensitivity, 89.468% specificity, 77.864% MCC. The average performance on independent data set is 79.4999%.
A discrete Kernel Approach to Support Vector Machine Learning in Language Independent Named Entity Recognition

In this paper we discuss a discrete kernel approach to Support Vector Machine (SVM) learning to do Language Independent Named Entity Recognition (LINER). The kernel we use is called the polynomial overlap kernel (POK). It is derived from a distance function that has been succesfully used in memory-based learning for various natural language problems. The POK is a discrete function and it works on discrete examples represented by multi-valued string attributes. We will compare our approach to the bag-of-words approach making use of a continuous kernel function and we will argue that the POK and other related kernels can serve as a valid alternative to the bag-ofwords approach to do SVM learning in natural language settings.
Unsupervised change detection by kernel clustering

This paper presents a novel unsupervised clustering scheme to find changes in two or more coregistered remote sensing images acquired at different times. This method is able to find nonlinear boundaries to the change detection problem by exploiting a kernel-based clustering algorithm. The kernel k-means algorithm is used in order to cluster the two groups of pixels belonging to the 'change' and 'no change' classes (binary mapping). In this paper, we provide an effective way to solve the two main challenges of such approaches: i) the initialization of the clustering scheme and ii) a way to estimate the kernel function hyperparameter(s) without an explicit training set. The former is solved by initializing the algorithm on the basis of the Spectral Change Vector (SCV) magnitude and the latter is optimized by minimizing a cost function inspired by the geometrical properties of the clustering algorithm. Experiments on VHR optimal imagery prove the consistency of the proposed approach.
Approaches for a Fair Comparison and Benchmarking of Electromagnetic Vibration Energy Harvesters

The performance of more than 60 different electromagnetic energy harvesters described in more than 100 publications is benchmarked. The benchmarking is based on earlier published parameters from literature as well as on two novel parameters introduced in this paper. The former allow to compare different harvester conversion principles as well as harvesters of different electrodynamic design principles. The latter consider the impact of ambient and boundary conditions for the most important sub-group, namely the resonant electrodynamic harvesters. The special consideration of how the mechanical damping and the energy conversion effectiveness depend on these conditions enables a fairer benchmarking of this common harvester type. High performing prototypes are identified, and the key parameters are provided for explanation. Finally, beneficial design approaches and the main challenges to maximize the output power are pointed out.
Cytochrome b Mutations That Modify the Ubiquinol-binding Pocket of the Cytochrome bc1 Complex and Confer Anti-malarial Drug Resistance in Saccharomyces cerevisiae*

Atovaquone is a new anti-malarial agent that specifically targets the cytochrome bc1 complex and inhibits parasite respiration. A growing number of failures of this drug in the treatment of malaria have been genetically linked to point mutations in the mitochondrial cytochrome b gene. To better understand the molecular basis of atovaquone resistance in malaria, we introduced five of these mutations, including the most prevalent variant found in Plasmodium falciparum (Y268S), into the cytochrome b gene of the budding yeast Saccharomyces cerevisiae and thus obtained cytochrome bc1 complexes resistant to inhibition by atovaquone. By modeling the variations in cytochrome b structure and atovaquone binding with the mutated bc1 complexes, we obtained the first quantitative explanation for the molecular basis of atovaquone resistance in malaria parasites.
Evaluation of the Inaugural Australian Inside Out Prison Exchange Program (IOPEP)

In 2008 Dr Martinovic developed an interest in the idea of bringing together students from RMIT University to learn with men and women incarcerated in Victorian prisons. This interest was instigated by Dr Martinovic's employment as a Community Corrections Officer when she realised the difficult plight people face when they are sentenced in the Criminal Justice System (CJS) and the complexities involved in trying to break their cycle of offending. Dr Martinovic also recognised the importance of criminal justice practitioners advocating for social justice initiatives and having an empathetic understanding toward those in the CJS. Upon hearing about the Inside Out Prison Exchange Program (IOPEP) she realised that this would provide a unique opportunity to teach graduates understanding of and compassion for this oftenmaligned group. To facilitate this teaching interest, Dr Martinovic undertook the IOPEP training at Temple University in Philadelphia, Pennsylvania in 2008. She was the first Australian academic to complete this training. IOPEP was developed at Temple University by Lori Pompa in 1997. Since that time the program has expanded USA-wide and internationally. IOPEP provides an opportunity for university students to "go behind the prison walls" to reconsider what they have come to know about crime and justice policies and practices. At the same time, it is also an opportunity for those inside prisons to place their life experiences in a larger framework and share these with people from the outside. Through classes and community exchanges, students are able to engage in a collaborative, dialogic examination of issues of social significance.
Effect of Ligusticum wallichii Aqueous Extract on Oxidative Injury and Immunity Activity in Myocardial Ischemic Reperfusion Rats

We investigated the efficacy of Ligusticum wallichi aqueous extract (LWE) for myocardial protection against ischemia-reperfusion injury. Rats were fed for five weeks with either a control diet (sham and ischemia reperfusion (IR) model control groups) or a diet mixed with 0.2%, 0.4% or 0.6% Ligusticum wallichi extract. At the end of the five week period, hearts were excised and subjected to global ischemia for 30 min followed by reperfusion for 2 h. The hearts were compared for indices of oxidative stress and immunity activities. Administration of Ligusticum wallichi extract significantly decreased serum TNF-α, IL-6, IL-8, NO, MIP-1α, CRP and myocardium MDA levels, and serum CK, LDH and AST activities, and increased myocardium Na+-K+-ATPase, Ca2+-Mg2+-ATPase, NOS, SOD, CAT, GSH-Px and TAOC activities. The results indicate that Ligusticum wallichii extract treatment can enhance myocardial antioxidant status and improve the immunity profile in ischemic-reperfusion rats.