Miracle-dz/UniFAR-FTUs huggingface dataset:
Machine learning approach to identify resting-state functional connectivity pattern serving as an endophenotype of autism spectrum disorder

Endophenotype refers to a measurable and heritable component between genetics and diagnosis and exists in both individuals with a diagnosis and their unaffected siblings. We aimed to identify a pattern of endophenotype consisted of multiple connections. We enrolled adult male individuals with autism spectrum disorder (ASD) endophenotype (i.e., individuals with ASD and their unaffected siblings) and individuals without ASD endophenotype (i.e., pairs of typical development (TD) siblings) and utilized a machine learning approach to classify people with and without endophenotypes, based on resting-state functional connections (FCs). A sparse logistic regression successfully classified people as to the endophenotype (area under the curve=0.78, classification accuracy=75%), suggesting the existence of endophenotype pattern. A binomial test identified that nine FCs were consistently selected as inputs for the classifier. The least absolute shrinkage and selection operator with these nine FCs predicted severity of communication impairment among individuals with ASD (r=0.68, p=0.021). In addition, two of the nine FCs were statistically significantly correlated with the severity of communication impairment (r=0.81, p=0.0026 and r=-0.60, p=0.049). The current findings suggest that an ASD endophenotype pattern exists in FCs with a multivariate manner and is associated with clinical ASD phenotype.
A Multi-Step Approach to Knowledge Integration Using Graph-Based Relational Learning Method: A Case of Developing A New Technology

Fuzzy cognitive maps (FCMs) are a flexible and powerful soft computing technique for modeling and simulating systems. FCMs can successfully depict knowledge and human experience, introducing concepts to represent the essential elements and the cause and effect relationships among the concepts to model the behavior of any system. In this paper, the process of gathering and integrating knowledge from experts in form of fuzzy cognitive maps is enhanced with a graph-based learning method in order to the improve effectiveness of the final digraph.
Robotics and mechatronics in aerospace

The paper briefly addresses DLR's (German Aerospace Center) expertise in space robotics by hand of corresponding milestone projects including systems on the International Space Station (ISS). It then discusses the key technologies needed for the development of an artificial "robonaut" generation with mechatronic ultralight weight arms and multifingered hands. The third arm generation is nearly finished now, approaching the limits of what is technologically achievable today with respect to light-weight and power losses. In a similar way DLR's second generation of artificial 4-fingered hands was a big step towards higher reliability, manipulability and overall performance.
One of the ultimate switches could be an atomic switch, where two terminals in a metal-oxide-metal structure are connected or disconnected by a metal atomic bridge or wire-like filament.

An atomic switch is a nanoionic device that controls the diffusion of metal ions and their reduction/ oxidation processes in the switching operation to form/ annihilate a metal atomic bridge, which is a conductive path between two electrodes in an ON-state. Since metal atoms can provide a highly conductive channel even if their size is in the nanometer scale, atomic switches may enable downscaling to smaller than the 11-nm technology node. Two-terminal atomic switches have the potential for use in memories and program- mable switches. Three-terminal atomic switches, where the formation/annihilation of a metal atomic bridge between a source electrode and a drain electrode are controlled by a third (gate) electrode, work as nonvolatile transistors. Recent development of two-terminal atomic switches that use a metal oxide as the ionic conductive material, in which a metal atomic bridge is formed, has enabled the integration of atomic switches with complementary metal—oxide—semiconductor (CMOS) devices. Also introduced are the novel characteristics of atomic switches, such as their small size, low power consumption, low ON-resistance, nonvolatility, and learning abilities.
Dimensionality Reduction of very large document collections by Semantic Mapping

This paper describes improving in Semantic Mapping (1), a feature extraction method useful to dimensionality reduction of vectors representing documents of large text collections. This method may be viewed as a specialization of the Random Mapping, method used in WEBSOM project (2). Semantic Mapping, Random Mapping and Principal Component Analysis (PCA) are applied to categorization of document collections using Self-Organizing Maps (SOM) (3). Semantic Mapping generated document representation as good as PCA and much better than Random Mapping.
The impact of body posture on intrinsic brain activity: The role of beta power at rest

Tying the hands behind the back has detrimental effect of sensorimotor perceptual tasks. Here we provide evidence that beta band oscillatory activity in a resting state condition might have a crucial role in such detrimental effects. EEG activity in a resting state condition was measured from thirty participants in two different body posture conditions. In one condition participants were required to keep their hands freely resting on the table. In the other condition, participants were required to keep the hands tied behind their back. Increased beta power was observed in the left inferior frontal gyrus (l-IFG) during the tied hands condition compared to the free hands condition. A control study ruled out alternative explanations including muscle tension that might have affected the EEG data. Our findings provide new insight on how body postural manipulations impact on perceptual tasks and intrinsic brain activity.
Relationships between soil seed bank composition and standing vegetation along chronosequences in a tropical dry forest in north-eastern Brazil

Abstract To better understand the role of seed banks in ecological succession of dry forests, we compared similarities between vegetation and seed banks and assessed the relative contributions of seed dispersal and persistence in chronosequences in the Brazilian semi-arid region. To sample the standing vegetation and the seed bank, we collected data in three sites with three successional ages in each one (5 y, 25 y and 45 y). A total of 180 soil samples (three sites × three successional ages × 10 plots × two components) were collected. The composition of the seed bank was assessed by the seedling emergence method. Of 166 species identified in the standing vegetation, only 50 (30.1%) were also present in the seed bank, resulting in low similarity (Jaccard index = 0.02–0.21) and reflecting the rarity of woody species and the dominance of annuals (71% of richness). The relative importance of seed persistence and seed dispersal to seed banks composition were balanced in most cases (difference was not rejected in four out six comparisons). Those results suggest that seed banks in tropical dry forests are largely the result of high dispersal rates and the persistence of allochthonous annual species that contribute to decoupling seed bank and vegetation composition.
Construction of Simplified Microbial Consortia to Degrade Recalcitrant Materials Based on Enrichment and Dilution-to-Extinction Cultures

The capacity of microbes degrading recalcitrant materials has been extensively explored from environmental remediation to industrial applications. Although significant achievements were obtained with single strains, focus is now going toward the use of microbial consortia because of advantages in terms of functional stability and efficiency. While consortia assembly attempts were made from several known single strains, another approach consists in obtaining consortia from complex environmental microbial communities in search for novel microbial species, genes and functions. However, assembling efficient microbial consortia from complex environmental communities is far from trivial due to large diversity and biotic interactions at play. Here we propose a strategy containing enrichment and dilution-to-extinction cultures to construct simplified microbial consortia (SMC) for keratinous waste management, from complex environmental communities. Gradual dilutions were performed from a keratinolytic microbial consortium, and dilution 10−9 was selected to construct a SMC library. Further compositional analysis and keratinolytic activity assays demonstrated that microbial consortia were successfully simplified, without impacting their biodegradation capabilities. These SMC possess promising potential for efficient keratinous valorization. More importantly, this reasoning and methodology could be transferred to other topics involving screening for simplified communities for biodegradation, thus considerably broadening its application scope. Importance Microbial consortia have got more and more attention and extensive applications due to their potential advantages. However, a high diversity of microbes is likely to hide uncontrollable risks in practice specific to novel strains and complicated interaction networks. Exploring a convenient and efficient way to construct simplified microbial consortia is able to broaden the applied scope of microbes. This study presents the approach based on enrichment and dilution-to-extinction cultures, which gain abundance microbial consortia including some without losing efficiency from the enriched functional microbial community. The microbial interactions at the strain level were evaluated by using compositional identification and correlation analysis, which contribute to revealing the roles of microbes in the degradation process of recalcitrant materials. Our findings provide a systematic scheme to achieve optimizing microbial consortia for biodegradation from an environmental sample, could be readily applied to a range of recalcitrant materials management from environmental remediation to industrial applications.
Maximizing viral detection with SIV droplet digital PCR (ddPCR) assays

Highly sensitive detection of HIV-1 nucleic acids is of critical importance for evaluating treatment interventions superimposed on combination antiretroviral therapy (cART) in HIV-1 infected individuals. SIV infection of rhesus macaques models many key aspects of human HIV-1 infection and plays a key role in evaluation of approaches for prevention, treatment and attempted eradication of HIV infection. Here we describe ultrasensitive droplet digital PCR (ddPCR) DNA and RT-ddPCR RNA assays for detecting simian immunodeficiency virus (SIV) on the Raindance ddPCR platform. We demonstrate that RainDance ddPCR can tolerate significantly higher cell DNA input without inhibition on a per reaction basis, exceeding the Bio-Rad ddPCR per-reaction input limit by about 18-fold, effectively increasing viral detection sensitivity by allowing a large quantity of sample to be analyzed in each reaction. In addition, the combination of a high processivity RT enzyme and RainDance ddPCR could overcome inhibition in severely inhibited viral RNA samples. These assays offer valuable tools for assessing low level viral production/replication and strategies for targeting residual virus in the setting of cART suppression of viral replication. The methodologies presented here can be adapted for a broad range of applications where highly sensitive nucleic acid detection is required.
Adapting the Design of Thematic Information for Miniaturised Non-Photorealistic 3D City-Models to the User´s Cognitive Skill of Visual Attention

Non-photorealistic rendering (NPR) applies artistic techniques to computer graphics. Much technology-driven research focuses on the optimisation of rendering methods to reduce computational effort. Only few cognition-based studies investigate the potential of non-photorealism to effectively represent geographic information. Based on psychological characteristics of visual attention and cartographic design principles, we propose a cognitive design approach that aims to support users in processing relevant information in 3D city models on miniaturised displays.
A neuro-evolution method for dynamic resource allocation on a chip multiprocessor

Technology-driven limitations will soon force microprocessor chips to contain multiple processing cores, as the scalability of individual cores peaks while transistor counts continue to increase. To obtain the best performance, flexible management of the on-chip resources, such as cache memory and off-chip bandwidth, is needed. However, the control for the dynamic management of these on-chip resources is difficult to design. In this paper, we propose a method for developing such a controller: evolving a recurrent neural network using the enforced sub-populations algorithm. The method is tested in a trace-based simulation that measures dynamic assignation of a pool of level-two cache banks to a set of processing cores. We present results showing that, when the chip is controlled by the neural network, we obtain a 13% performance improvement over static cache partitioning.
Root-Knot Nematode-Triggered Defense Responses in Arabidopsis thaliana During Early Stages of Parasitism

Author(s): Alves Teixeira, Marcella | Advisor(s): Kaloshian, Isgouhi | Abstract: Root-knot nematodes (Meloidogyne spp., RKN) are plant parasites responsible for great losses in agriculture worldwide. After penetrating host roots they establish feeding sites by modifying a few cells from the pericycle, which become multinucleated and enlarged, known as giant cells. Classical nematology research focuses on the characterization of nematode effectors and plant resistance genes. Therefore, little is known about basal immunity against plant parasitic nematodes. In Chapter One we use Arabidopsis thaliana and M. incognita interaction as a model system to investigate plant perception of parasitic nematodes. We show that RKNs can be perceived by plants irrespective of possible damage caused during migration and this perception relies on canonical immunity signaling partners. In addition, we show that RKN perception by Arabidopsis is mediated by BAK1-dependent and independent pathways. To best characterize the transcriptional responses induced by RKN in Arabidopsis roots we performed RNAseq analysis, which is described in Chapter Two. RNAseq analysis revealed induction of several genes 24h after inoculation with RKN in both wild type plants and bak1-5 mutant roots. To identify candidate nematode receptors, RNAseq data was searched for genes that were upregulated upon RKN inoculation and encoded proteins with predicted membrane localization and kinase domains. Screening Arabidopsis with mutations on a few of these mutants allowed identification of a negative regulator of immunity against RKN that has elevated basal levels of defense marker genes and respond to elicitor treatment with stronger and faster ROS burst. Interestingly, this negative regulator belongs to a family of proteins that has not been extensively characterized, the G-type lectin receptor kinases (G-LecRKs). The Chapter Three shows an update on the characterization of Arabidopsis G-LecRKs as well as the first characterization of tomato G-LecRKs by using a methodology well established for characterization of other lectin receptor kinases family. Our analysis shows an expansion of G-LecRKs family in tomato as compared to Arabidopsis and organization of genes in clusters throughout each species genome. Motif enrichment analysis shows conservation of motifs among members of G-LecRKS of Arabidopsis as well as among members of Arabidopsis, tomato and the previously characterized rice G-LecRKs.
A framework for the analysis and evaluation of software development methodologies based on formal, intrinsic and pragmatic criteria

At present, there are a substantial number of software development methodologies in use. This research proposes a framework, based on Van Belle's (2003) framework for the analysis of Enterprise Models, to analyse, evaluate and compare software development methodologies using a set of criteria based on three dimensions (formal, intrinsic and pragmatic). The formal dimension is concerned with structural aspects of methodology process models (formal) such as methodology process model size, complexity and modularity. The intrinsic view is concerned with the inherent meaning of methodologies as described in their reference material and is composed of criteria such as methodology support for project management and verification and validation techniques. Finally, the pragmatic view is concerned with the contextual aspects of methodologies, or aspects which cannot be assessed purely on the information contained within the reference material, such as methodology situationality and flexibility. A thorough review of the relevant literature is provided to describe the formation of the proposed framework. The theory and context of methodologies is also discussed, along with the reasons for and against their use and the main methodological paradigms which form the basis of most modern software development methodologies. The proposed framework is validated using a number of popular and well-known software development methodologies, specifically: Structured Systems Analysis and Design Methodology (SSADM), Object-Oriented Analysis and Design (OOAD), the Microsoft Solutions Framework (MSF), the Rational Unified Process (RUP), Extreme Programming (XP) and Feature-Driven Development (FDD). The results of the analysis supported the proposed framework with the majority of the criteria being both applicable to the domain and the measures for the criteria being satisfactory and valid. Page 3 Un ive rsi ty of Ca pe To wn
Molecular typing revealed the emergence of pvl-positive sequence type 22 methicillin-susceptible Staphylococcus aureus in Urumqi, Northwestern China

Background Staphylococcus aureus is among the most common causes of health care- and community-associated infections worldwide. The distributions of different S. aureus clones change over time and also vary geographically. The purpose of this study was to determine the molecular type and antimicrobial resistance profiles of clinical S. aureus strains isolated in Urumqi, Northwestern China. Methods A total of 605 clinical S. aureus isolates were collected from Xinjiang Military General Hospital, in Urumqi. Protein A-encoding (spa) typing, multilocus sequence typing, staphylococcal chromosomal cassette mec typing, Panton-Valentine leucocidin (pvl) gene detection, and antimicrobial resistance profiling were performed. Results Among these strains, 271 isolates (44.7%) were methicillin-resistant S. aureus (MRSA) and 334 (55.3%) were methicillin-susceptible S. aureus (MSSA). The MRSA strains consisted of 22 spa types and 14 sequence types (STs). ST239-MRSA-III-t030 (73.1%, 198/271) and ST59-MRSA-IV-t437 (11.8%, 32/271) were the most common, and ST22-MRSA-IV-t309 was the rarest (2.02%, 6/271). The MSSA strains consisted of 93 spa types and 29 STs. ST22, ST121, ST398, ST5, ST7, ST188, and ST15 were the main MSSA STs, and ST22-MSSA-t309 was most common (26.0%, 87/334). The pvl gene was present in 20.3% of all S.aureus strains, and 80.8% (88/99) of ST22-MSSA strains harbored the pvl gene. A total of 85.7% pvl-positive ST22-MSSA strains were spa t309 (85/99), and 87.5% of pvl-positive ST22-MSSA strains were from abscesses or wounds (skin and soft tissue infections). All ST239-MRSA strains were resistant to gentamicin (GEN), levofloxacin (LEV), ciprofloxacin (CIP), moxifloxacin (MXF), rifampicin (RIF), and tetracycline (TET). Among the ST59-MRSA strains, over 70.0% were resistant to erythromycin (ERY), clindamycin (CLI), and TET. ST22-MSSA remained susceptible to most antibiotics, but was resistant to PEN (97.0%), ERY (57.6%), and CLI (15.2%). Conclusion Our major results indicated that the antimicrobial resistance profiles and pvl genes of S. aureus isolates from Urumqi were closely associated with clonal lineage. ST239-MRSA-III-t030 and pvl-positive ST22-MSSA-t309 were the most common clones in this region of Northwestern China.
The Rabbit Muscle Phosphofructokinase Gene: Six Types ofmRNAs Are Tissue-Specifically Expressed by Multiple Promoters and Alternative Splicing.

ix LITERATURE REVIEW . 1 SECTION I Tissue-specific expression of six types of rabbit muscle phosphofructokinase mRNAs by multiple promoters and alternative splicing . 46 SECTION II Primer extension at high temperature by Thermus thermophilus DNA polymerase . 92 CONCLUSIONS AND FUTURE STUDIES. 105 REFERENCES . 116 APPENDIX Restriction enzyme map of the 5' flanking region of the rabbit muscle phosphofructokinase gene.124 VITA . 136
Prevalence and genotyping of Trichomonas gallinae in Riyadh, Saudi Arabia

Trichomonas gallinae is a single-celled protozoan parasite and causative agent of trichomonosis. Trichomonosis is a disease with a worldwide distribution, and has recently been highlighted as a pandemic threat to several wild bird species. The aim of this study is to investigate the prevalence and genotypic diversity of Trichomonas gallinae in Riyadh, Saudi Arabia. A total of 273 oral swab samples from birds were collected and tested for T. gallinae infection, and the overall prevalence of Trichomonas gallinae in these samples was 26.4% (72 of 273). We compared the rates of infections with T. gallinae between wild and domestic pigeons and found that the infection was significantly higher in domestic pigeons; a finding which should be considered by the Ministry of Environment, Water and Agriculture of Saudi Arabia when evaluating the role of poultry markets in the transmission of trichomonosis. Sequence analyses of the internal transcribed spacer (ITS) region indicated genetic variation in these parasite strains, as found in the samples collected. Among 48 sequences 15 different ribotypes were found, 12 of which were novel, and 3 of which were previously-described ribotypes: ribotype A, C, and II. This study demonstrates the diversity of T. gallinae strains in Saudi Arabian birds for the first time, and revealed that ribotypes A and C are predominant among Riyadh birds.
Chemical control of a CRISPR-Cas9 acetyltransferase

Lysine acetyltransferases (KATs) play a critical role in the regulation of transcription and other genomic functions. However, a persistent challenge is the development of assays capable of defining KAT activity directly in living cells. Towards this goal, here we report the application of a previously reported dCas9-p300 fusion as a transcriptional reporter of KAT activity. First we benchmark the activity of dCas9-p300 relative to other dCas9-based transcriptional activators, and demonstrate its compatibility with second generation short guide RNA architectures. Next, we repurpose this technology to rapidly identify small molecule inhibitors of acetylation-dependent gene expression. These studies validate a recently reported p300 inhibitor chemotype, and reveal a role for p300’s bromodomain in dCas9-p300-mediated transcriptional activation. Comparison with other CRISPR-Cas9 transcriptional activators highlights the inherent ligand tuneable nature of dCas9-p300 fusions, suggesting new opportunities for orthogonal gene expression control. Overall, our studies highlight dCas9-p300 as a powerful tool for studying gene expression mechanisms in which acetylation plays a causal role, and provide a foundation for future applications requiring spatiotemporal control over acetylation at specific genomic loci.