Miracle-dz/UniFAR-FTUs huggingface dataset:
Analysis of mutational dynamics at the DMPK (CTG)n locus identifies saliva as a suitable DNA sample source for genetic analysis in myotonic dystrophy type 1

Genotype-to-phenotype correlation studies in myotonic dystrophy type 1 (DM1) have been confounded by the age-dependent, tissue-specific and expansion-biased features of somatic mosaicism of the expanded CTG repeat. Previously, we showed that by controlling for the confounding effects of somatic instability to estimate the progenitor allele CTG length in blood DNA, age at onset correlations could be significantly improved. To determine the suitability of saliva DNA as a source for genotyping, we used small pool-PCR to perform a detailed quantitative study of the somatic mutational dynamics of the CTG repeat in saliva and blood DNA from 40 DM1 patients. Notably, the modal allele length in saliva was only moderately higher in saliva and not as large as previously observed in most other tissues. The lower boundary of the allele distribution was also slightly higher in saliva than it was in blood DNA. However, the progenitor allele length estimated in blood explained more of the variation in age at onset than that estimated from saliva. Interestingly, although the modal allele length was slightly higher in saliva, the overall degree of somatic variation was typically lower than in blood DNA, revealing new insights into the tissue-specific dynamics of somatic mosaicism. These data indicate that saliva constitutes an accessible, non-invasive and suitable DNA sample source for performing genetic studies in DM1.
Bone Marrow Stromal Cells Promote Skilled Motor Recovery and Enhance Contralesional Axonal Connections After Ischemic Stroke in Adult Mice

Background and Purpose— We tested the effect of bone marrow stromal cells (BMSCs) on neuronal remodeling of the corticospinal tract originating from the contralesional cortex in mice subjected to unilateral pyramidotomy (PT) followed by middle cerebral artery occlusion (MCAO). Methods— Adult mice with transgenic yellow fluorescent protein labeling in the corticospinal tract were subjected to right hemispheric PT and right permanent or sham MCAO. One day later, the mice were treated intravenously with BMSCs or phosphate-buffered saline. A Foot-Fault test and a single pellet-reaching test were performed before surgery, 3 days after MCAO, and weekly thereafter. Pseudorabies virus-614-monomeric red fluorescent protein was injected into the left forelimb flexor muscles 28 days after surgery (4 days before euthanasia). The brain and cervical cord were processed for fluorescent microscopy to detect red fluorescent protein and yellow fluorescent protein labeling, respectively. Results— Significant functional improvements were evident in PT-MCAO mice treated with BMSCs (n=9) compared with phosphate-buffered saline-treated mice (n=9, P<0.05), but not in mice with PT-sham MCAO treated with either phosphate-buffered saline (n=9) or BMSCs (n=10). Furthermore, in PT-MCAO mice, both corticospinal tract axonal density in the denervated side of the cervical gray matter and red fluorescent protein-labeled pyramidal neurons in the left intact cortex were significantly increased compared with PT-sham MCAO mice (P<0.05). BMSCs significantly enhanced both corticospinal tract density and red fluorescent protein labeling in PT-MCAO mice (P<0.05) only. The behavioral outcome was highly correlated with corticospinal tract density and red fluorescent protein labeling. Conclusions— BMSCs amplify stroke-induced contralesional neuronal remodeling, which contributes to motor recovery after stroke.
Genome‐wide microRNA screening reveals miR‐582‐5p as a mesenchymal stem cell‐specific microRNA in subchondral bone of the human knee joint

Emerging evidence suggests that microRNAs (miRNAs) may be pathologically involved in osteoarthritis (OA). Subchondral bone (SCB) sclerosis is accounted for the knee osteoarthritis (KOA) development and progression. In this study, we aimed to screen the miRNA biomarkers of KOA and investigated whether these miRNAs regulate the differentiation potential of mesenchymal stem cells (MSCs) and thus contributing to SCB. We identified 48 miRNAs in the blood samples in KOA patients (n = 5) through microarray expression profiling detection. After validation with larger sample number, we confirmed hsa‐miR‐582‐5p and hsa‐miR‐424‐5p were associated with the pathology of SCB sclerosis. Target genes prediction and pathway analysis were implemented with online databases, indicating these two candidate miRNAs were closely related to the pathways of pluripotency of stem cells and pathology of OA. Surprisingly, mmu‐miR‐582‐5p (homology of hsa‐miR‐582‐5p) was downregulated in osteogenic differentiation and upregulated in adipogenic differentiation of mesenchymal progenitor C3H10T1/2 cells, whereas mmu‐mir‐322‐5p (homology of hsa‐miR‐424‐5p) showed no change through the in vitro study. Supplementing mmu‐miR‐582‐5p mimics blocked osteogenic and induced adipogenic differentiation of C3H10T1/2 cells, whereas silencing of the endogenous mmu‐miR‐582‐5p enhanced osteogenic and repressed adipogenic differentiation. Further mechanism studies showed that mmu‐miR‐582‐5p was directly targeted to Runx2. Mutation of putative mmu‐miR‐582‐5p binding sites in Runx2 3′ untranslated region (3′UTR) could abolish the response of the 3′UTR‐luciferase construct to mmu‐miR‐582‐5p supplementation. Generally speaking, our data suggest that miR‐582‐5p is an important biomarker of KOA and is able to regulate osteogenic and adipogenic differentiation of MSCs via targeting Runx2. The study also suggests that miR‐582‐5p may play a crucial role in SCB sclerosis of human KOA.
Energy-efficient broadcast and multicast trees for reliable wireless communication

We define energy-efficient broadband and multicast schemes for reliable communication in multi-hop wireless networks. Unlike previous techniques, the choice of neighbors in the broadband and multicast trees in these schemes, are based not only on the link distance, but also on the error rates associated with the link. Our schemes can be implemented using both positive and negative acknowledgement based reliable broadcast techniques in the link layer. Through simulations, we show that our scheme achieves up to 45% improvement over previous schemes on realistic 100-node network topologies. A positive acknowledgment based implementation is preferred. Our simulations show that the additional benefits of a positive acknowledgement based implementation is marginal (1-2%). Therefore a negative acknowledgement based implementation of our schemes is equally applicable in constructing energy-efficient reliable and multicast data delivery paths.
Ferret brain possesses young interneuron collections equivalent to human postnatal migratory streams

The human early postnatal brain contains late migratory streams of immature interneurons that are directed to cortex and other focal brain regions. However, such migration is not observed in rodent brain, and whether other small animal models capture this aspect of human brain development is unclear. Here, we investigated whether the gyrencephalic ferret cortex possesses human‐equivalent postnatal streams of doublecortin positive (DCX+) young neurons. We mapped DCX+ cells in the brains of ferrets at P20 (analogous to human term gestation), P40, P65, and P90. In addition to the rostral migratory stream, we identified three populations of young neurons with migratory morphology at P20 oriented toward: (a) prefrontal cortex, (b) dorsal posterior sigmoid gyrus, and (c) occipital lobe. These three neuronal collections were all present at P20 and became extinguished by P90 (equivalent to human postnatal age 2 years). DCX+ cells in such collections all expressed GAD67, identifying them as interneurons, and they variously expressed the subtype markers SP8 and secretagogin (SCGN). SCGN+ interneurons appeared in thick sections to be oriented from white matter toward multiple cortical regions, and persistent SCGN‐expressing cells were observed in cortex. These findings indicate that ferret is a suitable animal model to study the human‐relevant process of late postnatal cortical interneuron integration into multiple regions of cortex.
Online resource mapping for SDN network hypervisors using machine learning

The visualization of Software-Defined Networks (SDN) allows multiple tenants to share the same physical infrastructure and to use their own SDN controllers. SDN virtualization is achieved through an SDN network hypervisor that operates between the tenants' controllers and the SDN infrastructure. In order to provide performance guarantees, resource mapping is required for both data plane as well as control plane for each virtual SDN network. In the context of SDN virtualization, the control plane resources include the network hypervisor, which needs to be assigned to guarantee the performance for each tenant. In previous work, the hypervisor resource mapping is based on offline benchmarks that measure the hypervisor resource consumption against the control plane work load, e.g., control plane message rate. These offline benchmarks vary across different hypervisor implementations, e.g., single or multi-threaded, and depend on the capabilities of the deployed hardware platform, e.g., the used CPU. We propose an online approach based on machine learning techniques to determine the mapping of hypervisor resources to the control workload at runtime. This concept is already successfully applied in the context of self-configuring networks. We propose three models to estimate hypervisor resources and compare them for two SDN hypervisor implementations, namely FlowVisor and OpenVirteX. We show through measurements on a real virtualized SDN infrastructure that resource mappings can be learned on runtime with insignificant error margins.
Draft Genome Sequence of Enterobacter sp. Strain A8, a Carbazole-Degrading Bacterium

We present here the draft genome sequence of a carbazole-degrading Enterobacter species. The draft genome sequence will provide insight into various genes involved in the degradation of carbazole and other related aromatic compounds. ABSTRACT We present here the draft genome sequence of a carbazole-degrading Enterobacter species. The draft genome sequence will provide insight into various genes involved in the degradation of carbazole and other related aromatic compounds.
Long-term blood pressure trajectories and incident atrial fibrillation in women and men: the Tromsø Study

Abstract Aims To explore sex-specific associations between long-term individual blood pressure (BP) patterns and risk of incident atrial fibrillation (AF) in the general population. Methods and results Blood pressure was measured in 8376 women and 7670 men who attended at least two of the three population-based Tromsø Study surveys conducted in 1986–87, 1994–95, and 2001. Participants were followed for incident AF throughout 2013. Latent mixed modelling was used to identify long-term trajectories of systolic BP and hypertension. Cox regression was used to estimate associations between the identified trajectories and incident AF. Elevated systolic BP throughout the exposure period (1986–2001) independently and differentially increased risk of AF in women and men. In women, having elevated systolic BP trajectories doubled AF risk compared to having persistently low levels, irrespective of whether systolic BP increased, decreased, or was persistently high over time, with hazard ratios of 1.88 (95% confidence interval 1.37–2.58), 2.32 (1.61–3.35), and 1.94 (1.28–2.94), respectively. In men, those with elevated systolic BP that continued to increase over time had a 50% increased AF risk: 1.51 (1.09–2.10). When compared to those persistently normotensive, women developing hypertension during the exposure period, and women and men with hypertension throughout the exposure period had 1.40 (1.06–1.86), 2.75 (1.99–3.80), and 1.36 (1.10–1.68) times increased risk of AF, respectively. Conclusion Long-term BP and hypertension trajectories were associated with increased incidence of AF in both women and men, but the associations were stronger in women.
Encoding cultures in robot emotion representation

Cultural differences may influence interactions between humans with different social norms and cultural traits, incurring different emotional and behavioral responses. The same applies to human-robot interaction (HRI). We believe that controlling robot emotions based on the cultural context can help robots adapt to humans from culturally diverse backgrounds. Such culturally aligned robots are expected to be easily accepted by humans as part of daily life. In this paper, we aim at investigating the role of culture in representing robot emotions which are injected by humans during its early stage of development and subject to change through their own experience thereafter. Several public data sets of pictures labeled with affective ratings by Indian, American, and European subjects are presented to social humanoid Pepper robots. The result shows that robots can learn to behave socially in alignment with an individual's cultural background. Moreover, we have demonstrated that robots under the effect of different cultures can generate different behavioral responses to the same stimuli, which is considered one of the most important issues in socially assitive robotics.
Learning Component-Level Sparse Representation for Image and Video Categorization

A novel component-level dictionary learning framework that exploits image/video group characteristics based on sparse representation is introduced in this paper. Unlike the previous methods that select the dictionaries to best reconstruct the data, we present an energy minimization formulation that jointly optimizes the learning of both sparse dictionary and component-level importance within one unified framework to provide a discriminative and sparse representation for image/video groups. The importance measures how well each feature component represents the group property with the dictionary. Then, the dictionary is updated iteratively to reduce the influence of unimportant components, thus refining the sparse representation for each group. In the end, by keeping the top K important components, a compact representation is obtained for the sparse coding dictionary. Experimental results on several public image and video data sets are shown to demonstrate the superior performance of the proposed algorithm compared with the-state-of-the-art methods.
Prevalence and risk factors of postpartum depression within one year after birth in urban slums of Dhaka, Bangladesh

Postpartum depression (PPD) is a serious pubic health concern and known to have the adverse effects on mother’s perinatal wellbeing; and child’s physical and cognitive development. There were limited literatures on PPD in Bangladesh, especially in urban slum context. The aim of this study was to assess the burden and risk factors of PPD among the urban slum women. A cross-sectional study was conducted between November-December 2017 in three urban slums on 376 women within first 12 months of postpartum. A validated Bangla version of Edinburgh Postnatal Depression Scale was used to measure the depression status. Respondent’s socio-economic characteristics and other risk factors were collected with structured validated questionaire by trained interviewers. Unadjusted Prevalence Ratio (PR) and Adjusted Prevalence Ratio (APR) were estimated with Generalized Linear Model (GLM) and Generalized Estimating Equation (GEE) respectively to identify the risk factors of PPD. The prevalence of PPD was 39.4% within first 12 months following the child birth. Job involvement after child delivery (APR = 1.9, 95% CI = 1.1, 3.3), job loss due to pregnancy (APR = 1.5, 95% CI = 1.0, 2.1), history of miscarriage or still birth or child death (APR = 1.4, 95% CI = 1.0, 2.0), unintended pregnancy (APR = 1.8, 95% CI = 1.3, 2.5), management of delivery cost by borrowing, selling or mortgaging assets (APR = 1.3, 95% CI = 0.9, 1.9), depressive symptom during pregnancy (APR = 2.5, 95% CI = 1.7, 3.8) and intimate partner violence (APR = 2.0, 95% CI = 1.2, 3.3), were identified as risk factors. PPD was not associated with poverty, mother in law and any child related factors. The burden of postpartum depression was high in the urban slum of Bangladesh. Maternal mental health services should be integrated with existing maternal health services. Research is required for the innovation of effective, low cost and culturally appropriate PPD case management and preventive intervention in urban slum of Bangladesh.
DISAPPEARANCE OF THE PROGENITOR OF SUPERNOVA iPTF13bvn

Supernova (SN) iPTF13bvn in NGC 5806 was the first Type Ib SN to have been tentatively associated with a progenitor in pre-explosion images. We performed deep ultraviolet (UV) and optical Hubble Space Telescope observations of the SN site ∼740 days after explosion. We detect an object in the optical bands that is fainter than the pre-explosion object. This dimming is likely not produced by dust absorption in the ejecta; thus, our finding confirms the connection of the progenitor candidate with the SN. The object in our data is likely dominated by the fading SN, implying that the pre-SN flux is mostly due to the progenitor. We compare our revised pre-SN photometry with previously proposed models. Although binary progenitors are favored, models need to be refined. In particular, to comply with our deep UV detection limit, any companion star must be less luminous than a late-O star or substantially obscured by newly formed dust. A definitive progenitor characterization will require further observations to disentangle the contribution of a much fainter SN and its environment.
Molecular Analysis as an Aid To Assess the Public Health Risk of Non-O157 Shiga Toxin-Producing Escherichia coli Strains

ABSTRACT Shiga toxin-producing Escherichia coli (STEC) strains are commensal bacteria in cattle with high potential for environmental and zoonotic transmission to humans. Although O157:H7 is the most common STEC serotype, there is growing concern over the emergence of more than 200 highly virulent non-O157 STEC serotypes that are globally distributed, several of which are associated with outbreaks and/or severe human illness such as hemolytic-uremic syndrome (HUS) and hemorrhagic colitis. At present, the underlying genetic basis of virulence potential in non-O157 STEC is unknown, although horizontal gene transfer and the acquisition of new pathogenicity islands are an expected origin. We used seropathotype classification as a framework to identify genetic elements that distinguish non-O157 STEC strains posing a serious risk to humans from STEC strains that are not associated with severe and epidemic disease. We report the identification of three genomic islands encoding non-LEE effector (nle) genes and 14 individual nle genes in non-O157 STEC strains that correlate independently with outbreak and HUS potential in humans. The implications for transmissible zoonotic spread and public health are discussed. These results and methods offer a molecular risk assessment strategy to rapidly recognize and respond to non-O157 STEC strains from environmental and animal sources that might pose serious public health risks to humans.
Trypanosoma cruzi Subverts Host Cell Sialylation and May Compromise Antigen-specific CD8+ T Cell Responses*

Upon activation, cytotoxic CD8+ T lymphocytes are desialylated exposing β-galactose residues in a physiological change that enhances their effector activity and that can be monitored on the basis of increased binding of the lectin peanut agglutinin. Herein, we investigated the impact of sialylation mediated by trans-sialidase, a specific and unique Trypanosoma transglycosylase for sialic acid, on CD8+ T cell response of mice infected with T. cruzi. Our data demonstrate that T. cruzi uses its trans-sialidase enzyme to resialylate the CD8+ T cell surface, thereby dampening antigen-specific CD8+ T cell response that might favor its own persistence in the mammalian host. Binding of the monoclonal antibody S7, which recognizes sialic acid-containing epitopes on the 115-kDa isoform of CD43, was augmented on CD8+ T cells from ST3Gal-I-deficient infected mice, indicating that CD43 is one sialic acid acceptor for trans-sialidase activity on the CD8+ T cell surface. The cytotoxic activity of antigen-experienced CD8+ T cells against the immunodominant trans-sialidase synthetic peptide IYNVGQVSI was decreased following active trans-sialidase- mediated resialylation in vitro and in vivo. Inhibition of the parasite's native trans-sialidase activity during infection strongly decreased CD8+ T cell sialylation, reverting it to the glycosylation status expected in the absence of parasite manipulation increasing mouse survival. Taken together, these results demonstrate, for the first time, that T. cruzi subverts sialylation to attenuate CD8+ T cell interactions with peptide-major histocompatibility complex class I complexes. CD8+ T cell resialylation may represent a sophisticated strategy to ensure lifetime host parasitism.
A variant of group search optimizer for global optimization

Group search optimizer (GSO) is a stochastic, population-based optimization technique that has shown better performance as for global searching when optimizing multimodal benchmarks. However, it suffers from poor convergence because of its producer-scrounger model, which makes it unable to get a reliable estimiator for evolution path. In order to enhance the local search ability without impairing the global seach ability of GSO, this paper proposes a variant of group search optimizer (VGSO), which develops a producer-organizer model whereby group members are assumed to search for opportunities of either ‘finding’ (producing) or ‘learning’ (organization). This model enables VGSO to achieve a good trade-off between its exploration and exploitation abilities. A comprehensive experimental study is conducted on a set of benchmark functions and a practical optimization problem. Comparison results show that VGSO obtains a promising performance on these optimization problems.
Creative dialogue: talk for thinking in the classroom

Published in 2010 this book utilises research that is both longitudinal and contemporary, in an accessible manner, that whilst not presenting an answer to the succession challenge, it does provide the reader with a detailed introduction and overview of the key issues faced in looking at the succession challenge. The book’s organisation is a key strength allowing the reader to follow a journey of understanding, or to access individual chapters in isolation. The references used are relevant and offer pertinent further reading for the researcher. This book will appeal to a wide audience, from the casual reader through to the international researcher looking for an introduction to the literature available on the succession challenge.