Miracle-dz/UniFAR-FTUs huggingface dataset:
Pediatric Functional Neuroimaging: Practical Tips and Pearls.

OBJECTIVE. Functional MRI (fMRI) is clinically used for localization of eloquent cortex before surgical intervention, most commonly motor and language function in patients with tumors or epilepsy. In the pediatric population, special considerations for fMRI relate to limited examination tolerance, small head size, developing anatomy and physiology, and diverse potential abnormalities. In this article, we will highlight pearls and pitfalls of clinical pediatric fMRI including blood oxygenation level-dependent (BOLD) imaging principles, patient preparation, study acquisition, data postprocessing, and examination interpretation. CONCLUSION. Clinical fMRI is indicated for presurgical localization of eloquent cortex in patients with tumors, epilepsy, or other neurologic conditions and requires a solid understanding of technical considerations and data processing. In children, special approaches are needed for patient preparation as well as study design, acquisition, and interpretation. Radiologists should be cognizant of developmental neuroanatomy, causes of neuropathology, and capacity for neuroplasticity in the pediatric population.
Speech-Language pathologists’ decisions when designing an aided AAC display for a compilation case study of a beginning communicator

Abstract Purpose The current study sought to identify decisions speech-language pathologists (SLPs) make and their rationale for those decisions when designing an AAC display for a hypothetical school-aged child who was a beginning communicator. Augmentative and alternative communication (AAC) displays support communicative interactions for children who are unable to use spoken language to meet their communication needs. Children who are at the early stages of learning language, often termed beginning or emerging communicators, may rely heavily on the AAC display to support comprehension and expression. Thus, it is important for speech-language pathologists (SLPs) to design a display that facilitates beginning communicators’ communication development. Methods This paper reports on the answers related to a specific case study presented in an online survey completed by 77 SLPs with experience in AAC. Results Data illustrated design decisions driven by child-specific characteristics and informed by research regarding type of layout, representation, and the importance of various design features. Conclusions Suggestions for future research are provided, including identifying goals and communicative functions best supported by different types of displays, clinicians’ challenges/successes growing a system with the child, and determining the importance of symbol arrangement and organisation in communicative tasks by AAC users. Implications for Rehabilitation Identification of current practices reported by speech-language pathologists given a case study to develop and implement future research. A gap between research and practice suggests the need for better dissemination and application of research supporting the inclusion of people engaged in the event depicted in a visual scene display. Foundations for future research to provide guidance regarding best design of and communication goals supported by visual scene displays and grid-based displays.
Hepatitis C Virus Translation Regulation

Translation of the hepatitis C virus (HCV) RNA genome is regulated by the internal ribosome entry site (IRES), located in the 5’-untranslated region (5′UTR) and part of the core protein coding sequence, and by the 3′UTR. The 5′UTR has some highly conserved structural regions, while others can assume different conformations. The IRES can bind to the ribosomal 40S subunit with high affinity without any other factors. Nevertheless, IRES activity is modulated by additional cis sequences in the viral genome, including the 3′UTR and the cis-acting replication element (CRE). Canonical translation initiation factors (eIFs) are involved in HCV translation initiation, including eIF3, eIF2, eIF1A, eIF5, and eIF5B. Alternatively, under stress conditions and limited eIF2-Met-tRNAiMet availability, alternative initiation factors such as eIF2D, eIF2A, and eIF5B can substitute for eIF2 to allow HCV translation even when cellular mRNA translation is downregulated. In addition, several IRES trans-acting factors (ITAFs) modulate IRES activity by building large networks of RNA-protein and protein–protein interactions, also connecting 5′- and 3′-ends of the viral RNA. Moreover, some ITAFs can act as RNA chaperones that help to position the viral AUG start codon in the ribosomal 40S subunit entry channel. Finally, the liver-specific microRNA-122 (miR-122) stimulates HCV IRES-dependent translation, most likely by stabilizing a certain structure of the IRES that is required for initiation.
Architecture Reconstruction Guidelines, 2nd Edition

Abstract : Architecture reconstruction is the process of obtaining the "as-built" architecture of an implemented system from the existing legacy system. For this process, tools are used to extract information about the system that will assist in building successive levels of abstraction. Although generating a useful representation is not always possible, a successful reconstruction results in an architectural representation that aids in reasoning about the system. This recovered representation is most often used as a basis for redocumenting the architecture of an existing system if the documentation is out of date or nonexistent, and can be used to check the "as-built" architecture against the "as-designed" architecture. The architectural representation can also be used as a starting point for reengineering the system to a new desired architecture. Finally, the representation can be used to help identify components for reuse or to help establish a software product line. This report describes the process of architecture reconstruction using the Architecture Reconstruction and Mining (ARMIN) tool developed by the Carnegie Mellon(registered) Software Engineering Institute and the Robert Bosch Corporation. Guidelines are presented for reconstructing the architectural representations of existing systems. Most of these guidelines are not specific to ARMIN, can be used with other tools, and are useful even if the architecture reconstruction is carried out manually.
A newly identified Leishmania IF4E-interacting protein, Leish4E-IP2, modulates the activity of cap-binding protein paralogs

Abstract Translation of most cellular mRNAs in eukaryotes proceeds through a cap-dependent pathway, whereby the cap-binding complex, eIF4F, anchors the preinitiation complex at the 5′ end of mRNAs and regulates translation initiation. The requirement of Leishmania to survive in changing environments can explain why they encode multiple eIF4E (LeishIF4Es) and eIF4G (LeishIF4Gs) paralogs, as each could be assigned a discrete role during their life cycle. Here we show that the expression and activity of different LeishIF4Es change during the growth of cultured promastigotes, urging a search for regulatory proteins. We describe a novel LeishIF4E-interacting protein, Leish4E-IP2, which contains a conserved Y(X)4LΦ IF4E-binding-motif. Despite its capacity to bind several LeishIF4Es, Leish4E-IP2 was not detected in m7GTP-eluted cap-binding complexes, suggesting that it could inhibit the cap-binding activity of LeishIF4Es. Using a functional assay, we show that a recombinant form of Leish4E-IP2 inhibits the cap-binding activity of LeishIF4E-1 and LeishIF4E-3. Furthermore, we show that transgenic parasites expressing a tagged version of Leish4E-IP2 also display reduced cap-binding activities of tested LeishIF4Es, and decreased global translation. Given its ability to bind more than a single LeishIF4E, we suggest that Leish4E-IP2 could serve as a broad-range repressor of Leishmania protein synthesis.
Effects of Indoor Air Purifiers on Children with Asthma

Purpose To evaluate the effects of air purifiers on the concentrations of indoor air pollutants and on asthma control in children. Materials and Methods In this randomized crossover trial, daily use of an air purifier filter was compared with a matched placebo with the filter off. Thirty elementary school students who had asthma were enrolled and randomly allocated to one of two groups. The primary endpoints were changes in indoor air quality, asthma severity, lung function, airway inflammatory, urine microbiome, and phthalate after the installation of air purifiers. PM2.5 and CO2 were measured as indoor air pollutants. Asthma severity was assessed in terms of both symptom and medication scores acquired using a daily questionnaire. The higher the score, the better the symptom or the less frequent the use of medication. Peak expiratory flow rate and fractional exhaled nitric oxide were also measured. Results The mean age of the enrolled patients was 9.2±1.98 years. The mean concentration of PM2.5 was 17.0 µg/m3 in the filter-off condition, but significantly lower at 9.26 µg/m3 in the filter-on condition. Medication scores were 6.9 for the filter-off and 7.12 for the filter-on conditions, reflecting a statistically significant decrease in the frequency of medications used during air purifier operation. Bacterial richness, as determined using the Chao 1 index, was markedly lower in the filter-on than the filter-off condition. Conclusion This study suggests that air purifiers benefit medication burden in children with asthma by reducing PM2.5 levels.
Willingness to use PrEP among female university students in Lesotho

Oral pre-exposure prophylaxis (PrEP) for HIV-negative individuals at high risk was introduced in Lesotho in April 2016. To assess the feasibility and acceptability of PrEP in Lesotho and to study the attitudes and beliefs around HIV risk and prevention measures among young women, between September and December 2016 we asked 302 female university students at fourteen higher education institutions in Lesotho about their sexual behavior, experiences of sexual coercion and abuse, HIV risk perception, willingness to use PrEP, as well as their attitudes toward condom use and self-administration of daily medications. Overall, 57.3% of the sample reported perceiving themselves at risk of acquiring HIV and 32.1% reported being strongly willing to use PrEP if it were available in their community. In a multivariate mediation analysis, perceived HIV risk was associated with 11.5 percentage points increase in likelihood of using PrEP (p = 0.041). Multiple concurrent sexual partnership was associated with 16.1 percentage points increase in likelihood of self-perceived HIV risk (p = 0.007), while having sexual partners in polygamous relationships was associated with 17.8 percentage points increase in likelihood of self-perceived HIV risk (p = 0.002) and the mediated indirect effect accounted for 18.2% of its total effect. Those who reported strong adherence to antibiotics were 23.1 percentage points more likely to express willingness to use PrEP than those who did not (p = 0.004), and those who reported to dislike condoms were 19.1 percentage points more likely to be willing to use PrEP than those who did not report aversion to condom use: these effect were direct and not mediated by HIV risk perception. Intimate partner violence (IPV) in the network of peers was also directly associated with willingness to use PrEP and its effect was not significantly mediated by HIV risk perception: those who had friends who experienced intimate partner violence were 14.9 percentage points more likely to be willing to use PrEP than those who did not report IPV in their network of peers (p = 0.009). These findings support the inclusion of individuals with multiple concurrent sexual partners among the key populations for PrEP provision and confirm that willingness to use PrEP is not solely driven by HIV risk perception. They also indicate that the presence of IPV in peer networks is related to one’s willingness to use PrEP. PrEP service provision may generate synergies with IPV prevention programs when offered within this framework.
The Effect of Integrating Genomic Information into Genetic Evaluations of Chinese Merino Sheep

Simple Summary Genetic improvement of wool production and quality traits in fine-wool sheep is an appealing option for enhancing the market value of wool products. We estimated genetic parameters and the accuracies of estimated breeding values for various wool production and quality traits in fine-wool sheep using pedigree-based best linear unbiased prediction (PBLUP) and single-step genomic best linear unbiased prediction (ssGBLUP) strategies. ssGBLUP performed slightly better than PBLUP for the studied traits. Therefore, the single-step genetic evaluation method could be successfully implemented in genomic evaluations of fine-wool sheep and the prediction of future breeding values in young Merino sheep as part of an early preselection strategy in the near future. Abstract Genomic evaluations are a method for improving the accuracy of breeding value estimation. This study aimed to compare estimates of genetic parameters and the accuracy of breeding values for wool traits in Merino sheep between pedigree-based best linear unbiased prediction (PBLUP) and single-step genomic best linear unbiased prediction (ssGBLUP) using Bayesian inference. Data were collected from 28,391 yearlings of Chinese Merino sheep (classified in 1992–2018) at the Xinjiang Gonaisi Fine Wool Sheep-Breeding Farm, China. Subjectively-assessed wool traits, namely, spinning count (SC), crimp definition (CRIM), oil (OIL), and body size (BS), and objectively-measured traits, namely, fleece length (FL), greasy fleece weight (GFW), mean fiber diameter (MFD), crimp number (CN), and body weight pre-shearing (BWPS), were analyzed. The estimates of heritability for wool traits were low to moderate. The largest h2 values were observed for FL (0.277) and MFD (0.290) with ssGBLUP. The heritabilities estimated for wool traits with ssGBLUP were slightly higher than those obtained with PBLUP. The accuracies of breeding values were low to moderate, ranging from 0.362 to 0.573 for the whole population and from 0.318 to 0.676 for the genotyped subpopulation. The correlation between the estimated breeding values (EBVs) and genomic EBVs (GEBVs) ranged from 0.717 to 0.862 for the whole population, and the relative increase in accuracy when comparing EBVs with GEBVs ranged from 0.372% to 7.486% for these traits. However, in the genotyped population, the rank correlation between the estimates obtained with PBLUP and ssGBLUP was reduced to 0.525 to 0.769, with increases in average accuracy of 3.016% to 11.736% for the GEBVs in relation to the EBVs. Thus, genomic information could allow us to more accurately estimate the relationships between animals and improve estimates of heritability and the accuracy of breeding values by ssGBLUP.
Cryptographically Secure Pseudo-Random Number Generator IP-Core Based on SHA2 Algorithm †

In the context of growing the adoption of advanced sensors and systems for active vehicle safety and driver assistance, an increasingly important issue is the security of the information exchanged between the different sub-systems of the vehicle. Random number generation is crucial in modern encryption and security applications as it is a critical task from the point of view of the robustness of the security chain. Random numbers are in fact used to generate the encryption keys to be used for ciphers. Consequently, any weakness in the key generation process can potentially leak information that can be used to breach even the strongest cipher. This paper presents the architecture of a high performance Random Number Generator (RNG) IP-core, in particular a Cryptographically Secure Pseudo-Random Number Generator (CSPRNG) IP-core, a digital hardware accelerator for random numbers generation which can be employed for cryptographically secure applications. The specifications used to develop the proposed project were derived from dedicated literature and standards. Subsequently, specific architecture optimizations were studied to achieve better timing performance and very high throughput values. The IP-core has been validated thanks to the official NIST Statistical Test Suite, in order to evaluate the degree of randomness of the numbers generated in output. Finally the CSPRNG IP-core has been characterized on relevant Field Programmable Gate Array (FPGA) and ASIC standard-cell technologies.
Security Architecture for Defining and Enforcing Security Profiles in DLT/SDN-Based IoT Systems

Despite the advantages that the Internet of Things (IoT) will bring to our daily life, the increasing interconnectivity, as well as the amount and sensitivity of data, make IoT devices an attractive target for attackers. To address this issue, the recent Manufacturer Usage Description (MUD) standard has been proposed to describe network access control policies in the manufacturing phase to protect the device during its operation by restricting its communications. In this paper, we define an architecture and process to obtain and enforce the MUD restrictions during the bootstrapping of a device. Furthermore, we extend the MUD model with a flexible policy language to express additional aspects, such as data privacy, channel protection, and resource authorization. For the enforcement of such enriched behavioral profiles, we make use of Software Defined Networking (SDN) techniques, as well as an attribute-based access control approach by using authorization credentials and encryption techniques. These techniques are used to protect devices’ data, which are shared through a blockchain platform. The resulting approach was implemented and evaluated in a real scenario, and is intended to reduce the attack surface of IoT deployments by restricting devices’ communication before they join a certain network.
Lactobacillus garii sp. nov., isolated from a fermented cassava product

A novel Gram-positive, catalase negative, rod-shaped strain, FI11369T, was isolated from gari, a traditional West African fermented food derived from cassava. Based on 16S rRNA gene sequence similarity, the closest type strains were Lactobacillus xiangfangensis LMG 26013T (99.4 % similarity), Lactobacillus plajomi NBRC 107333T (99.1 %), Lactobacillus paraplantarum DSM 10667T (99.1 %), Lactobacillus pentosus DSM 20314T (99.0 %), Lactobacillus plantarum subsp. plantarum ATCC 14917T (99.0 %), Lactobacillus modestisalitolerans NBRC 107235T (98.9 %), Lactobacillus plantarum subsp. argentoratensis DSM 16365T (98.9 %) and Lactobacillus daowaiensis NCIMB 15183T (98.8 %). The genome of strain FI11369T was sequenced and the average nucleotide identity (ANI) was compared with its closest relatives. ANI analysis showed that the closest relative, L. xiangfangensis DSM 27103T, had only a 82.4 % similarity. The main fatty acids of FI11369T were saturated C16 : 0 (18.2 %), unsaturated C18 : 1 ω9c (43.8 %) and cyclopropane C19 : 0 cyclo (ω10c and/or ω6; 22.5 %). Based on the genotypic and phenotypic data obtained in this study, a novel Lactobacillus species, Lactobacillus garii sp. nov., with the type strain FI11369T (=NCIMB 15148=DSM 108249), is proposed.
MrDNA: a multi-resolution model for predicting the structure and dynamics of DNA systems

Abstract Although the field of structural DNA nanotechnology has been advancing with an astonishing pace, de novo design of complex 3D nanostructures and functional devices remains a laborious and time-consuming process. One reason for that is the need for multiple cycles of experimental characterization to elucidate the effect of design choices on the actual shape and function of the self-assembled objects. Here, we demonstrate a multi-resolution simulation framework, mrdna, that, in 30 min or less, can produce an atomistic-resolution structure of a self-assembled DNA nanosystem. We demonstrate fidelity of our mrdna framework through direct comparison of the simulation results with the results of cryo-electron microscopy (cryo-EM) reconstruction of multiple 3D DNA origami objects. Furthermore, we show that our approach can characterize an ensemble of conformations adopted by dynamic DNA nanostructures, the equilibrium structure and dynamics of DNA objects constructed using off-lattice self-assembly principles, i.e. wireframe DNA objects, and to study the properties of DNA objects under a variety of environmental conditions, such as applied electric field. Implemented as an open source Python package, our framework can be extended by the community and integrated with DNA design and molecular graphics tools.
Olfactory Influences on Visual Categorization: Behavioral and ERP Evidence

Abstract Visual stimuli often dominate nonvisual stimuli during multisensory perception. Evidence suggests higher cognitive processes prioritize visual over nonvisual stimuli during divided attention. Visual stimuli should thus be disproportionally distracting when processing incongruent cross-sensory stimulus pairs. We tested this assumption by comparing visual processing with olfaction, a “primitive” sensory channel that detects potentially hazardous chemicals by alerting attention. Behavioral and event-related brain potentials (ERPs) were assessed in a bimodal object categorization task with congruent or incongruent odor–picture pairings and a delayed auditory target that indicated whether olfactory or visual cues should be categorized. For congruent pairings, accuracy was higher for visual compared to olfactory decisions. However, for incongruent pairings, reaction times (RTs) were faster for olfactory decisions. Behavioral results suggested that incongruent odors interfered more with visual decisions, thereby providing evidence for an “olfactory dominance” effect. Categorization of incongruent pairings engendered a late “slow wave” ERP effect. Importantly, this effect had a later amplitude peak and longer latency during visual decisions, likely reflecting additional categorization effort for visual stimuli in the presence of incongruent odors. In sum, contrary to what might be inferred from theories of “visual dominance,” incongruent odors may in fact uniquely attract mental processing resources during perceptual incongruence.
Discovery of chemicals to clear or indicate amyloid aggregates by targeting memory-impairing anti-parallel Aβ dimers.

Amyloid-β (Aβ) oligomers are implicated in Alzheimer disease (AD) pathogenesis. However, their unstable nature and heterogeneous state disrupts elucidation of their explicit role in AD progression, impeding the development of tools targeting soluble Aβ oligomers. To address such obstacles, we designed and synthesized parallel and anti-parallel variants of Aβ(1-40) dimers and characterized their pathogenic properties in AD models. We found anti-parallel dimers induced cognitive impairments with increased amyloidogenesis and cytotoxicity, and subsequently developed a screening platform by immobilizing this dimer variant on 96-well-plates. Through screening, we identified two FDA-approved drugs, Oxytetracycline and Sunitinib, which were able to dissociate Aβ oligomers and plaques to monomers in 5XFAD transgenic mice. In addition, we discovered a fluorescent chemical, Astrophloxine, that could detect aggregated Aβ in brain tissue and cerebrospinal fluid samples of AD mice. Our screening platform provides a stable and homogeneous environment permitting isolated observations of Aβ interactions with dimer-specific molecules.