Miracle-dz/UniFAR-FTUs huggingface dataset:
Fatigue, Sleep, and Autoimmune and Related Disorders

Profound and debilitating fatigue is the most common complaint reported among individuals with autoimmune disease, such as systemic lupus erythematosus, multiple sclerosis, type 1 diabetes, celiac disease, chronic fatigue syndrome, and rheumatoid arthritis. Fatigue is multi-faceted and broadly defined, which makes understanding the cause of its manifestations especially difficult in conditions with diverse pathology including autoimmune diseases. In general, fatigue is defined by debilitating periods of exhaustion that interfere with normal activities. The severity and duration of fatigue episodes vary, but fatigue can cause difficulty for even simple tasks like climbing stairs or crossing the room. The exact mechanisms of fatigue are not well-understood, perhaps due to its broad definition. Nevertheless, physiological processes known to play a role in fatigue include oxygen/nutrient supply, metabolism, mood, motivation, and sleepiness—all which are affected by inflammation. Additionally, an important contributing element to fatigue is the central nervous system—a region impacted either directly or indirectly in numerous autoimmune and related disorders. This review describes how inflammation and the central nervous system contribute to fatigue and suggests potential mechanisms involved in fatigue that are likely exhibited in autoimmune and related diseases.
In silico Analysis Reveals Distribution of Quorum Sensing Genes and Consistent Presence of LuxR Solos in the Pandoraea Species

The most common quorum sensing (QS) system in Gram-negative bacteria consists of signaling molecules called N-acyl-homoserine lactones (AHLs), which are synthesized by an enzyme AHL synthase (LuxI) and detected by a transcriptional regulator (LuxR) that are usually located in close proximity. However, many recent studies have also evidenced the presence of LuxR solos that are LuxR-related proteins in Proteobacteria that are devoid of a cognate LuxI AHL synthase. Pandoraea species are opportunistic pathogens frequently isolated from sputum specimens of cystic fibrosis (CF) patients. We have previously shown that P. pnomenusa strains possess QS activity. In this study, we examined the presence of QS activity in all type strains of Pandoraea species and acquired their complete genome sequences for holistic bioinformatics analyses of QS-related genes. Only four out of nine type strains (P. pnomenusa, P. sputorum, P. oxalativorans, and P. vervacti) showed QS activity, and C8-HSL was the only AHL detected. A total of 10 canonical luxIs with adjacent luxRs were predicted by bioinformatics from the complete genomes of aforementioned species and publicly available Pandoraea genomes. No orphan luxI was identified in any of the genomes. However, genes for two LuxR solos (LuxR2 and LuxR3 solos) were identified in all Pandoraea genomes (except two draft genomes with one LuxR solo gene), and P. thiooxydans was the only species that harbored no QS-related activity and genes. Except the canonical LuxR genes, LuxIs and LuxR solos of Pandoraea species were distantly related to the other well-characterized QS genes based on phylogenetic clustering. LuxR2 and LuxR3 solos might represent two novel evolutionary branches of LuxR system as they were found exclusively only in the genus. As a few luxR solos were located in close proximity with prophage sequence regions in the genomes, we thus postulated that these luxR solos could be transmitted into genus Pandoraea by transduction process mediated by bacteriophage. The bioinformatics approach developed in this study forms the basis for further characterization of closely related species. Overall, our findings improve the current understanding of QS in Pandoraea species, which is a potential pharmacological target in battling Pandoraea infections in CF patients.
Comprehensive Profiling of Gene Copy Number Alterations Predicts Patient Prognosis in Resected Stages I–III Lung Adenocarcinoma

Background: Lung adenocarcinoma (LUAD) possesses a poor prognosis with a low 5-year survival rate even for stages I-III resected patients, it is thus critical to understand the determinants that affect the survival and discover new potentially prognostic biomarkers. Somatic copy number alterations (CNAs) are major source of genomic variations driving tumor evolution, CNAs screening may identify prognostic biomarkers. Methods: Oncoscan MIP array was used to analyze the patterns of CNAs on formalin fixed paraffin embedded(FFPE) tumor specimens from 163 consecutive stage I-III resected LUAD patients, 145 out of which received platinum-based adjuvant chemotherapy. Results: Of the 163 patients, 91(55.8%) were recurred within 3 years after surgery. The most common aberrations in our cohort were 1q, 5p, 5q, 7p, 8q, 14p, 16p, 17q, 20q for copy number gains and 8p, 9p, 13p, 16q, 18q for losses. The GISTIC2 analysis produced 45 amplification peaks and 40 deletion peaks, involving some reported genes TERT, EGFR, MYC, CCND1, CDK4, MDM2, ERBB2, NKX2-1, CCNE1, and CDKN2A, most of which were consistent with TCGA database. The amplifications of 12p12.1 (CMAS, GOLT1B, YS2, LDHB, RECQL, ETNK1, IAPP, PYROXD1, KRAS) and KDM5A were correlated with worse prognosis in our cohort, this result was further validated in 506 LUAD patients from TCGA. In addition, 163 patients could be well-classified into five groups, and the clinical outcomes were significantly different based on threshold copy number at reoccurring alteration peaks. Among the 145 patients who received adjuvant chemotherapy, focal amplification of ERBB2 and deletion of 4q34.3 were found to be specific in relapsed patients, this result was validated in an independent group of Imielinski et al., demonstrating these two CNAs may contribute to resected LUAD recurrence after adjuvant chemotherapy. Conclusion: This study suggests that CNAs profiling may be a potential prognostic classifier in resected LAUD patients. Amplifications of 12p12.1 and KDM5A might be prognostic biomarkers for LUAD, and amplification of ERBB2 and deletion of 4q34.3 predicted early relapse after adjuvant chemotherapy. These novel findings may provide implication for better implementation of precision therapy for lung cancer patients.
Attention Allocation to Financial Information: The Role of Color and Impulsivity Personality Trait

Background In order to raise the level of investor’s protection, the European Commission has recently introduced the key investor information document (KIID), a standard, plainly worded, and consumer-friendly document which should provide individuals with essential information for their investment decisions. KIID layout has been delineated relying on results from focus groups, surveys and telephone interviews, ignoring the reliable, and unbiased insights offered by neuroscientific approaches. Aim The current study aims to elucidate the patterns of eye movements in the early phases of information acquisition during the reading of financial disclosure documents, disentangling the independent role of color and impulsivity at modulating attention distribution toward the different sources of financial information. Materials and Methods Oculomotor behavior was monitored in eighty-one healthy adults through the eye tracking technology (SMI REDn Scientific 60 Hz). An ecological protocol exploiting KIIDs was developed to control for several individual variables, through delivering standard visual stimuli based on official financial documents. Participants performed a passive exploration task (with the only specific instruction of visually exploring the document), followed by an active task where they were asked to rate the financial attractiveness of the products, as low, medium or high. The Barratt impulsiveness scale (BIS-11) was administered to each participant, to score such personality trait. Results Attention distribution over the different information sources, included in the KIIDs, has been quantified and found to be independently modulated by both color and impulsivity, with a greater role of the former over the latter. The addition of either red or blue information to some KIID’s sections increases attention allocation toward the whole document, compared to the usual black and white version. BIS-11 total scores were inversely related to the first and average fixation duration in the neutral, though not in the colored condition. Discussion Bottom-up, stimulus-related mechanisms of attention allocation influence information acquisition during the reading of financial prospectuses to the point that the increased attention induced by color compensates for individual impulsivity. Such evidence should be considered by regulators when devising the disclosure documents in order to increase investors’ protection.
The Mediating Role of Romantic Attachment in the Relationship Between Attachment to Parents and Aggression

Background A secure attachment style could promote more intimacy in romantic relationships, while an insecure attachment style could be correlated with less positive romantic relationships in adulthood. Numerous studies have noted that a secure attachment to parents was correlated with lower levels of aggression, whereas insecure attachments were associated with higher levels of aggression. We aimed to investigate the role of the attachment system as a mediator of the expression of aggressiveness during adolescence. Specifically, we considered that the attachment to parents and peers could influence one’s attachment to a romantic partner. Methods We empirically tested whether there were relationships of parent and peer attachment on aggressiveness mediated by romantic attachment style. Participants of the study included 411 students. Results Results indicated that for males an insecure father-child attachment style seems to be associated with higher levels of anxiety and avoidance in romantic attachments and then with aggressiveness. For females, an insecure mother-child attachment style seems to be associated with higher levels of aggressiveness. Conclusion The attachment to parents and to peers plays a key role in defining romantic attachment according to gender, and these dimensions in turn tend to affect the levels of aggressiveness.
17β-Estradiol Regulates Glucose Metabolism and Insulin Secretion in Rat Islet β Cells Through GPER and Akt/mTOR/GLUT2 Pathway

Aims: To explore the molecular mechanism by which 17β-estradiol (estrogen 2, E2) regulates glucose transporter 2 (GLUT2) and insulin secretion in islet β cells through G protein-coupled estrogen receptor (GPER) via Akt/mTOR pathway. Methods: SPF-grade SD male rats were used to establish an in vivo type 2 diabetes model treated with E2. Rat insulinoma cells (INS-1) were cultured in normal or high glucose media with or without E2. Immunofluorescence double staining was used to detect GPER, GLUT2, insulin, and glucagon immunolocalization in rat islet tissues. Western blot was used to detect GPER, Akt, mTOR, and GLUT2 protein immunocontent. Real-time PCR detected Slc2a2 and glucose kinase (GK) content, and ELISA was used to detect insulin levels. Glucose uptake, GK activity and pyruvate dehydrogenase (PDH) activity were analyzed with glucose detection, GK activity and PDH activity assay kit. Results: Immunofluorescence double staining confocal indicated that E2 treatment up-regulated expression levels of GPER, GLUT2, and insulin, while down-regulated glucagon. Western blot results revealed E2 increased GPER, Akt/mTOR pathway, and GLUT2 protein immunocontent. Real-time PCR showed E2 elevated Slc2a2, GK content. Moreover, E2 improved insulin secretion, glucose uptake, GK activity, and PDH activity. Conclusion: Our findings indicated that exogenous E2 up-regulated GPER via the Akt/mTOR pathway to increase GLUT2 protein content and insulin secretion in islet β cells.
Unsupervised Learning on Resistive Memory Array Based Spiking Neural Networks

Spiking Neural Networks (SNNs) offer great potential to promote both the performance and efficiency of real-world computing systems, considering the biological plausibility of SNNs. The emerging analog Resistive Random Access Memory (RRAM) devices have drawn increasing interest as potential neuromorphic hardware for implementing practical SNNs. In this article, we propose a novel training approach (called greedy training) for SNNs by diluting spike events on the temporal dimension with necessary controls on input encoding phase switching, endowing SNNs with the ability to cooperate with the inevitable conductance variations of RRAM devices. The SNNs could utilize Spike-Timing-Dependent Plasticity (STDP) as the unsupervised learning rule, and this plasticity has been observed on our one-transistor-one-resistor (1T1R) RRAM devices under voltage pulses with designed waveforms. We have also conducted handwritten digit recognition task simulations on MNIST dataset. The results show that the unsupervised SNNs trained by the proposed method could mitigate the requirement for the number of gradual levels of RRAM devices, and also have immunity to both cycle-to-cycle and device-to-device RRAM conductance variations. Unsupervised SNNs trained by the proposed methods could cooperate with real RRAM devices with non-ideal behaviors better, promising high feasibility of RRAM array based neuromorphic systems for online training.
CLP1, a Novel Plant Homeo Domain Protein, Participates in Regulating Cellulase Gene Expression in the Filamentous Fungus Trichoderma reesei

The stringent regulatory network of cellulase gene expression in the filamentous fungus Trichoderma reesei involves multiple transcriptional regulators. However, identification and mechanistic investigation of these regulators are still insufficient. Here, we identified a novel transcriptional regulator, CLP1, a plant homeo domain (PHD) Protein that participates in regulating T. reesei cellulase gene expression. Phylogenetic analyses demonstrated that CLP1 homologs are widely distributed in filamentous fungi including Trichoderma, Penicillium, Fusarium, Neurospora, and Aspergillus species. We demonstrated that CLP1 is a nuclear protein and lack of CLP1 significantly impaired the induced expression of cellulase genes. ChIP experiments showed CLP1 binding to the cellulase gene promoters specifically under cellulose conditions and compromised XYR1 occupancy on the same promoters in the absence of CLP1 at the early induction stage. XYR1 overexpression fully rescued the defect in cellulase production but not the defect in conidia formation in the clp1 null mutant. Further analysis showed that the PHD is required for the CLP1 appropriate subcellular localization as well as the induced cellulase gene expression and conidiation. Taken together, these data demonstrated an important role of CLP1 in the regulation of cellulase and xylanase gene expression in T. reesei.
The Secretion of Streptomyces monbaraensis Transglutaminase From Lactococcus lactis and Immobilization on Porous Magnetic Nanoparticles

Microbial transglutaminase (MTG) from Streptomyces mobaraensis is an important enzyme widely applied in food processing for the improvement of protein properties by catalyzing the cross-linking of proteins. In this work we aimed at improving the production and enabling an easy and efficient purification process from culture supernatants. Thus, recombinant vectors, with either a constitutive promoter (Pp5) or an inducible promoter (PnisA), controlling the expression of the MTG gene fused to the signal peptide of Usp45 (SPusp45) were constructed and then expressed in Lactococcus lactis. After purification, 43.5 ± 0.4 mg/L mature MTG-6His was obtained. It displayed 27.6 ± 0.5 U/mg enzymatic activity cross-linking soy protein isolate effectively. The purified mature MTG was immobilized with magnetic porous Fe3O4 nanoparticles, which improved its activity up to 29.1 ± 0.4 U/mg. The immobilized MTG maintained 67.2% of the initial activity after being recycled for 10 times. The high production and secretion of functional S. mobaraensis MTG from L. lactis and the magnetic immobilized MTG-6His onto Fe3O4 nanoparticles reported in this study would have potential industrial applications.
Major Challenges of Systems-of-Systems with Cloud and DevOps – A Financial Experience Report

The term Systems-of-Systems (SoS) refers to a complex system that comprises other systems (the constituent systems), which have operational and managerial independence, geographical distribution, emergent behavior, and evolutionary development processes. DevSecOps (or SecDevOps) offers an approach to guide the implementation of IT Processes, which in turn may support the integration of a cloud environment to a systems-of-systems environment, incorporating information security practices, as well as fostering collaboration between both development and operation teams. It also aims to promote automation of IT processes so that the development of applications and / or services is fast and secure. However, there is a lack of detail in the process definitions to guide the implementation and use of DevSecOps in a Systems-of-Systems environment, especially when it is intended to merge cloud computing into pre-existing conventional infrastructures. In this context, this paper aims at describe the main actions, concerns and lessons learned, during planning and implementation phases, about IT Processes and IT Governance Model to transform an IT traditional environment into Systems-of-Systems environment, considering DevSecOps standards in a large Brazilian financial institution. It will show how IT Processes and IT Governance Model should be changed for incorporating a Cloud environment to a SoS. For doing so, we proposed the use of DevOps techniques as a means to reduce development time without to affect the quality and information security.
BIM Sim/3D: Multi-Agent Human Activity Simulation in Indoor Spaces

Smart buildings are a prevalent example of cyberphysical systems: embedded with sensors, they emit a continuous data stream based on which algorithms are being developed to infer the occupants' activities in order to control the building's ambience to improve the occupants' comfort and safety, and to reduce the building's energy consumption. This type of sensor-fusion-for-occupant-activity-analysis research requires large data sets; however, the security and privacy concerns around sharing data about people's activities impedes the collection, curation, and sharing of such data sets. One solution to this issue would be the creation of a human-activity simulator for generating synthetic, yet realistic, data sets. In this paper, we describe our human-activity simulator as a component in our general framework for evaluating activity-recognition methods for indoor spaces. Our simulator, developed in Unity3D, uses the Building Information Model (BIM) of the space as the context in which to simulate multiple agents, with different abilities and tasks. We conclude with a reflection of the pros and cons of our simulator design and implementation and discuss areas for future research.
NEAR-DUPLICATE VIDEO DETECTION EXPLOITING NOISE RESIDUAL TRACES

Video phylogeny research about joint analysis of correlated video sequences has shown the possibility of developing interesting forensic applications. As an example, it is possible to study the provenance of near-duplicate (ND) video sequences, i.e., videos generated from the same original one through content preserving transformations. To perform this kind of analysis, accurate detection of ND videos is paramount. In this paper, we propose an algorithm for ND video detection and clustering in a challenging setup. Specifically, we analyze a scenario in which many videos, depicting the same event, are recorded by different users. This situation is critical as non-ND videos acquired from very close viewpoints run the risk of being incorrectly detected as ND. The proposed approach leverages on robust hashing properties and the concept of sensor noise traces.
The relevance of application domains in empirical findings

The term 'software ecosystem' refers to a collection of software systems that are related in some way. Researchers have been using different levels of aggregation to define an ecosystem: grouping them by a common named project (e.g., the Apache ecosystem); or considering all the projects contained in online repositories (e.g., the GoogleCode ecosystem). In this paper we propose a definition of ecosystem based on application domains: software systems are in the same ecosystem if they share the same application domain, as described by a similar technological scope, context or objective. As an example, all projects implementing networking capabilities to trade Bitcoin and other virtual currencies can be considered as part of the same "cryptocurrency" ecosystem. Utilising a sample of 100 Java software systems, we derive their application domains using the Latent Dirichlet Allocation (LDA) approach. We then evaluate a suite of object-oriented metrics per ecosystem, and test a null hypothesis: 'the OO metrics of all ecosystems come from the same population'. Our results show that the null hypothesis is rejected for most of the metrics chosen: the ecosystems that we extracted, based on application domains, show different structural properties. From the point of view of the interested stakeholders, this could mean that the health of a software system depends on domain-dependent factors, that could be common to the projects in the same domain-based ecosystem.
A review and comparison of multi-view 3D reconstruction methods

ABSTRACT 3D reconstruction from multiple views is well studied, fundamental, yet a challenging problem in the field of computer vision. There is a large variety of approaches available in the literature. The methods use different representations for input scene/object and may provide different kinds of outputs. Some methods model entire scene as voxel-set where as some use level sets or polygon mesh representation. Output may be either volume or surface representing the reconstructed object/scene. Some methods work in image space where as some methods work in object space. These methods are developed to offer a good compromise between computation speed, computation complexity and accuracy along with feasibility in implementation. Selection of a particular method depends on the requirements of application and availability of required resources. Though, earlier reviews are available in the literature, fast advances in this field demand latest review. The paper presents a review and comparison of latest multi-view 3D reconstruction methods. This will help researchers to understand state of the art in this field.
Slaughterhouse survey for detection of bovine viral diarrhea infection among beef cattle in Kyushu, Japan

Bovine viral diarrhea virus (BVDV) footprint has spread across the globe and is responsible for one of the most economically important diseases in cattle. In Japan, some regional surveillance and preventive measures to control bovine viral diarrhea (BVD) have been implemented. However, BVDV infection is poorly understood in cattle industries, and there is no systematic BVD surveillance system and control program. Kyushu is the center for raising beef cattle in Japan. Therefore, this study aimed to determine the BVDV infection using a slaughterhouse survey among beef cattle in Kyushu, Japan. A total of 1,075 blood samples were collected at two regional slaughterhouses in Miyazaki prefecture from December 2015 to June 2016. Antigen ELISA was used for detection of BVDV antigen in blood samples. Two samples showed positive results (2/1,075; 0.18%). BVDV RNA was extracted from positive blood samples; the sequence was determined and analyzed by the neighbor-joining method for construction of the phylogenetic tree. Phylogenetic analysis based on the 5’-UTR revealed that the two positive samples were grouped into the same subtype BVDV-1b in the BVDV-1 genotype, but the infected cattle belonged to two different farms. In conclusion, this is the first study to identify the presence of BVDV in a slaughterhouse survey in Kyushu. These findings suggest that a slaughterhouse survey is a useful tool for developing a surveillance system for monitoring infectious diseases in cattle.