Miracle-dz/UniFAR-FTUs huggingface dataset:
Learning-Based multilabel random walks for image segmentation containing translucent overlapped objects

Supervised image segmentation methods usually start with information extracted from the learning phase to separate an image into non-overlapping regions. We have used user input information or seeds in our previous work to segment partially overlapped translucent regions. However providing a lot of seeds might sometimes be too time consuming that might make the method perform poorly or not work at all. Machine learning algorithms consist of two major phases: learning phase where the information will be generated based on the data, and test phase where the generated information will be used to improve the performance of the method. In previous work user guided labels were used as hard seeds in the RW algorithm. In this paper we extend our previous work to be able to segment multilabel translucent overlapped objects using soft seed information. We first map each segment as a class on a 25D manifold in the learning phase. Then the probability of assigning each of the image pixels to the segments, data term, is obtained by calculating the geodesic distance between the pixels' features and these classes on the manifold. This data term is then used as soft seeds in the RW algorithm instead of user predefined labels. Experimental results on synthetic images show the strength of our proposed method comparing to our previous algorithm with more than 95% segmentation accuracy.
Digital technologies and musical participation for people with intellectual disabilities

Research on the aspirations of people with intellectual disabilities documents the importance of alternative zones of inclusion where they can assert their own definitions of ability and normality. This stands in contrast to assumptions concerning technology and disability that position technology as ‘normalizing’ the disabled body. This paper reports on the role of a digital music jamming tool in providing access to creative practice by people with intellectual disabilities. The tool contributed to the development of a spatio-temporal zone to enable aesthetic agency within and beyond the contexts of deinstitutionalized care. The research identifies the interactions between tools, individuals and groups that facilitated participants’ agency in shaping the form of musical practice. Furthermore, we document the properties of emergent interaction − supported by a tool oriented to enabling music improvisation − as potentially resisting assumptions regarding normalization.
Offshore Landslide Hazard Curves From Mapped Landslide Size Distributions

We present a method to calculate landslide hazard curves along offshore margins based on size distributions of submarine landslides. The method utilizes 10 different continental margins that were mapped by high‐resolution multibeam sonar with landslide scar areas measured by a consistent Geographic Information System procedure. Statistical tests of several different probability distribution models indicate that the lognormal model is most appropriate for these siliciclastic environments, consistent with an earlier study of the U.S. Atlantic margin (Chaytor et al., 2009, https://doi.org/10.1016/j.margeo.2008.08.007). Parameter estimation is performed using the maximum likelihood technique, and confidence intervals are determined using likelihood profiles. Pairwise comparison of size distributions for the 10 margins indicates that the U.S. Atlantic and Queen Charlotte margins are different than most other margins. These margins represent end‐members, with the U.S. Atlantic margin having the highest mean scar area and the Queen Charlotte margin the lowest. We demonstrate that empirical, offshore landslide hazard curves can be developed from the landslide size distributions, if the duration of mapped landslide activity is known. This study indicates that the shape parameter of the size distribution is similar among all 10 margins, and thus, the shape of the hazard curves is also similar. Significant differences in hazard curves among the margins are therefore related to differences in mean sizes and, potentially, differences in the duration of landslide activity.
Revisiting the question of limited genetic variation within Schistosoma japonicum

Abstract Recent electrophoretic data have indicated that Schistosoma japonicum in mainland China may be a species complex, with the existence of a cryptic species being predicted from the analysis of schistosome populations from Sichuan province. To investigate the Sichuan form of S. japonicum, 4.9 kbp of mitochondrial DNA from each of three samples of the parasite from China (two from Sichuan and one from Hunan) and one from Sorsogon in the Philippines were amplified, sequenced and characterized. The sequence data were compared with those from the related South-east Asian species of S. mekongi (Khong Island, Laos) and S. malayensis (Baling, Malaysia) and that from S. japonicum from Anhui (China). At both the nucleotide and amino-acid levels, the variation among the five S. japonicum samples was limited (<1%). This was consistent with the conclusions drawn from previous molecular studies, in which minimal variation among S. japonicum populations was also detected. In contrast, S. mekongi and S. malayensis, species recognized as separate but closely related, differ from each other by about 10%, and each differs by 25%-26% from S. japonicum. Phylogenetic trees provided a graphic representation of these differences, showing all S. japonicum sequences to be very tightly clustered and distant from S. mekongi and S. malayensis, the last two being clearly distinct from each other. The results thus indicate no significant intraspecific genetic variation among S. japonicum samples collected from different geographical areas and do not support the idea of a distinct form in Sichuan.
Development of Exon Skipping Therapies for Duchenne Muscular Dystrophy: A Critical Review and a Perspective on the Outstanding Issues

Duchenne muscular dystrophy (DMD) is a rare, severe, progressive muscle-wasting disease leading to disability and premature death. Patients lack the muscle membrane-stabilizing protein dystrophin. Antisense oligonucleotide (AON)-mediated exon skipping is a therapeutic approach that aims to induce production of partially functional dystrophins. Recently, an AON targeting exon 51 became the first of its class to be approved by the United States regulators [Food and Drug Administration (FDA)] for the treatment of DMD. A unique aspect of the exon-skipping approach for DMD is that, depending on the size and location of the mutation, different exons need to be skipped. This challenge raises a number of questions regarding the development and regulatory approval of those individual compounds. In this study, we present a perspective on those questions, following a European stakeholder meeting involving academics, regulators, and representatives from industry and patient organizations, and in the light of the most recent scientific and regulatory experience.
Novel back-biased UTBB lateral SCR for FDSOI ESD protections

For the first time, a Lateral SCR (Silicon Controlled Rectifier) with Ultra-Thin Body and Buried Oxide (UTBB) is experimentally demonstrated. This device is dedicated to Electro-Static Discharge (ESD) protection and has been designed and fabricated with 28 nm Fully Depleted SOI technology. A new control technique is proposed: the use of back-gate biasing. Characteristics such as low leakage, controllable triggering (as a function of back gate voltage and ground-plane type), and device geometry are explored. We discuss several configurations (floating or locked P-base) and show promising results in terms of ESD protection performance.
Biotechnology and Bioengineering

Funding information Ministry of Science and Technology, Grant/ Award Number: MOST 103‐2221‐E‐002 ‐210 Abstract Microenvironmental factors including physical and chemical cues can regulate stem cells as well as terminally differentiated cells to modulate their biological function and differentiation. However, one of the physical cues, the substrate’s dimensionality, has not been studied extensively. In this study, the flow‐focusing method with a microfluidic device was used to generate gelatin bubbles to fabricate highly ordered three‐dimensional (3D) scaffolds. Rat H9c2 myoblasts were seeded into the 3D gelatin bubble‐based scaffolds and compared to those grown on 2D gelatin‐coating substrates to demonstrate the influences of spatial cues on cell behaviors. Relative to cells on the 2D substrates, the H9c2 myoblasts were featured by a good survival and normal mitochondrial activity but slower cell proliferation within the 3D scaffolds. The cortical actin filaments of H9c2 cells were localized close to the cell membrane when cultured on the 2D substrates, while the F‐actins distributed uniformly and occupied most of the cell cytoplasm within the 3D scaffolds. H9c2 myoblasts fused as multinuclear myotubes within the 3D scaffolds without any induction but cells cultured on the 2D substrates had a relatively lower fusion index even differentiation medium was provided. Although there was no difference in actin α 1 and myosin heavy chain 1, H9c2 cells had a higher myogenin messenger RNA level in the 3D scaffolds than those of on the 2D substrates. This study reveals that the dimensionality influences differentiation and fusion of myoblasts.
PIK3CA Mutations and PTEN Loss Correlate with Similar Prognostic Factors and Are Not Mutually Exclusive in Breast Cancer

Purpose: The phosphatidylinositol 3′-kinase/Akt pathway is frequently altered in breast cancer. PTEN, a phosphatase that opposes the effect of phosphatidylinositol 3′-kinase, can be mutated or lost, whereas the PIK3CA gene is mutated. These have been proposed as alternative mechanisms, and their clinicalpathology significance is under discussion. In this study, we aimed to explore whether PIK3CA mutations and PTEN loss are mutually exclusive mechanisms, correlate with other known clinicopathologic markers, or have clinical implication in breast cancer. Experimental Design: Exons 9 and 20 of the PIK3CA gene were analyzed in 270 breast tumors, and mutations were detected by single-stranded conformational analysis followed by sequencing. The expression of PTEN was evaluated by immunohistochemistry in 201 tumors. Results: PIK3CA mutations were found in 24% of the tumors and associated with estrogen receptor+ status, small size, negative HER2 status, high Akt1, and high cyclin D1 protein expression. PTEN was negative in 37% of the cases and PTEN loss was associated with PIK3CA mutations (P = 0.0024). Tumors presenting PTEN loss or both alterations were often estrogen receptor+, small in size, and HER2−. PIK3CA mutations predicted for longer local recurrence-free survival. Moreover, PTEN loss by itself or combined with mutated PIK3CA tended to confer radiosensitivity. In addition, the patients with high S-phase fraction had longer recurrence-free survival if they carried mutations in the PIK3CA gene and/or had lost PTEN, whereas the same alterations were associated with shorter recurrence-free survival among patients with low S-phase fraction. Conclusions: PIK3CA mutations and PTEN loss were not mutually exclusive events and associated with similar prognostic factors.
Co-Inactivation of GlnR and CodY Regulators Impacts Pneumococcal Cell Wall Physiology

CodY, a nutritional regulator highly conserved in low G+C Gram-positive bacteria, is essential in Streptococcus pneumoniae (the pneumococcus). A published codY mutant possessed suppressing mutations inactivating the fatC and amiC genes, respectively belonging to iron (Fat/Fec) and oligopeptide (Ami) ABC permease operons, which are directly repressed by CodY. Here we analyzed two additional published codY mutants to further explore the essentiality of CodY. We show that one, in which the regulator of glutamine/glutamate metabolism glnR had been inactivated by design, had only a suppressor in fecE (a gene in the fat/fec operon), while the other possessed both fecE and amiC mutations. Independent isolation of three different fat/fec suppressors thus establishes that reduction of iron import is crucial for survival without CodY. We refer to these as primary suppressors, while inactivation of ami, which is not essential for survival of codY mutants and acquired after initial fat/fec inactivation, can be regarded as a secondary suppressor. The availability of codY - ami + cells allowed us to establish that CodY activates competence for genetic transformation indirectly, presumably by repressing ami which is known to antagonize competence. The glnR codY fecE mutant was then found to be only partially viable on solid medium and hypersensitive to peptidoglycan (PG) targeting agents such as the antibiotic cefotaxime and the muramidase lysozyme. While analysis of PG and teichoic acid composition uncovered no alteration in the glnR codY fecE mutant compared to wildtype, electron microscopy revealed altered ultrastructure of the cell wall in the mutant, establishing that co-inactivation of GlnR and CodY regulators impacts pneumococcal cell wall physiology. In light of rising levels of resistance to PG-targeting antibiotics of natural pneumococcal isolates, GlnR and CodY constitute potential alternative therapeutic targets to combat this debilitating pathogen, as co-inactivation of these regulators renders pneumococci sensitive to iron and PG-targeting agents.
Structural Equation Modeling Modeling (SEM) of Occupational Accidents Size Based on Risk Management Factors; A Field Study in Process Industries

Background: Due to high risks for occupational accidents, process industries are one of the most dangerous industries around the world. Accidents’ size in these industries are influenced by combination of different factors. Objectives: The present study aimed at analyzing and modeling occupational accidents’ size and investigating the role of different risk management factors on accidents’ size in process industries. Methods: This analytical study was carried out on accidents in ten process industries, including petrochemicals, refineries, and chemical industries during eight years (2008 to 2015). Studied data were included variables and factors of risk management systems and information about human injuring accidents. Data analysis and modeling were done based on feature selection by Pearson χ coefficient and structural equation modeling (SEM) approach using statistical software of IBM SPSS AMOS v22.0. Results: Lost working days (LWD) as index of accident size was estimated 197.42 ± 111.06 days. Results of feature selection and SEM approach showed that LWD was affected by different factors such as safety and health (S and H) training, risk management, and risk control, and its indicator variables (P < 0.05). Conclusions: The findings implied that structural equation modeling is a reliable and applicable accidents analysis method. Furthermore, the results should be considered to prevent and reduce occupational accidents’ size in process industries.
Cognitive Predictors of Improvements in Adults’ Spoken Word Recognition Six Months after Cochlear Implant Activation

This study investigated whether cognitive measures obtained prior to cochlear implant surgery activation could predict improvements in spoken word recognition in adult cochlear implant recipients 6 months after activation. In addition to noncognitive factors identified by previous studies (i.e. younger age, shorter duration of hearing loss), the present results indicated that improvement in spoken word recognition was associated with higher verbal learning scores and better verbal working memory. Contrary to expectation, neither general cognitive ability nor processing speed was significantly correlated with outcome at 6 months. Multiple regression analyses revealed that a combination of verbal learning scores and lip-reading skill accounted for nearly 72% of the individual differences in improvement in spoken word recognition (i.e. the variance in spoken word recognition scores at 6 months that remained unexplained after controlling for baseline spoken word recognition scores). These findings have relevance for research on auditory processing with cochlear implants as well as implications for clinical interventions.
FIXED-b ASYMPTOTICS FOR SPATIALLY DEPENDENT ROBUST NONPARAMETRIC COVARIANCE MATRIX ESTIMATORS

This paper develops a method for performing inference using spatially dependent data. We consider test statistics formed using nonparametric covariance matrix estimators that account for heteroskedasticity and spatial correlation (spatial HAC). We provide distributions of commonly used test statistics under “fixed-b” asymptotics, in which HAC smoothing parameters are proportional to the sample size. Under this sequence, spatial HAC estimators are not consistent but converge to nondegenerate limiting random variables that depend on the HAC smoothing parameters, the HAC kernel, and the shape of the spatial region in which the data are located. We illustrate the performance of the “fixed-b” approximation in the spatial context through a simulation example.
Dedifferentiation of caudate-cortical connectivity is linked to reduced D1 dopamine receptor availability and poorer memory function in aging

Decreasing integrity of striato-cortical circuits has been highlighted as an important determinant of declines in flexible, higher-order cognition in older age. Here, leveraging multi-modal (fMRI, PET) neuroimaging data from a large adult lifespan sample, we demonstrate older age to be associated with less specific functional coupling between the caudate and cortical association networks. This age-related dedifferentiation of caudate- cortical connectivity was present during both rest and an active working memory task, and predicted poorer short and long-term memory performance with older age. Notably, reduced striatal and prefrontal dopamine D1-like receptor (D1DR) availability was associated with less specific caudate-cortical coupling across the lifespan and accounted for age-related variation in this measure. These findings highlight decreased dopaminergic neuromodulation as one factor contributing to differences in striato-cortical function, and memory performance, with older age.
Autonomic Nervous System activity correlates with peak experiences induced by DMT and predicts increases in wellbeing

Non-ordinary states of consciousness induced by psychedelics can be accompanied by so-called ‘peak experiences’, characterized at the emotional level by their intensity and positive valence. These experiences are strong predictors of positive outcomes following psychedelic-assisted therapy, and it is therefore important to better understand their biology. Despite growing evidence that the autonomic nervous system (ANS) plays an important role in mediating emotional experiences, its involvement in the psychedelic experience is poorly understood. The aim of this study was to investigate to what extant changes in the relative influence of the sympathetic (SNS) and parasympathetic nervous systems (PNS) over cardiac activity may reflect the subjective experience induced by the short-acting psychedelic N,N-Dimethyltryptamine (DMT). We derived measures of SNS and PNS activity from the electrocardiogram data of 17 participants (11 males, 6 females, mean age = 33.8 y, SD = 8.3) while they received either DMT or placebo. Results show that the joint influence of SNS and PNS (‘sympatho-vagal coactivation’) over cardiac activity was robustly correlated with participants ratings of ‘Spiritual Experience’ and ‘Insightfulness’ during the DMT experience, while also being related to improved wellbeing scores two weeks after the session. In addition, we found that the state of balance between the two ANS branches (‘sympatho-vagal balance’) before DMT injection predicted scores of ‘Insightfulness’ during the DMT experience. These findings demonstrate the important involvement of the ANS in psychedelic-induced peak experiences and may pave the way to the development of biofeedback-based tools to enhance psychedelic-therapy. Significance statement Psychedelics can give rise to intense positive subjective experiences - aligned with Maslow’s notion of ‘peak experiences’ - that can have a positive and enduring impact on mental health. Understanding how these experiences relate to peripheral physiology before and during the acute effects of psychedelics is an important object of enquiry, as it may help advance the therapeutic use of these compounds. In this study, we demonstrate that specific peripheral states computed from heart rate activity recordings predicted and correlated with acute peak experiences and increases in wellbeing. These findings have implications for the relationship between peripheral physiology and altered states of consciousness. Moreover, they highlight a putative marker of physiological ‘readiness’ prior the psychedelic experience that could predict therapeutically relevant mechanisms that might be modified to improve mental health outcomes in psychedelic-therapy.
GWAS-informed data integration and non-coding CRISPRi screen illuminate genetic etiology of bone mineral density

Over 1,100 independent signals have been identified with genome-wide association studies (GWAS) for bone mineral density (BMD), a key risk factor for mortality-increasing fragility fractures; however, the effector gene(s) for most remain unknown. Informed by a variant-to-gene mapping strategy implicating 89 non-coding elements predicted to regulate osteoblast gene expression at BMD GWAS loci, we executed a single-cell CRISPRi screen in human fetal osteoblast 1.19 cells (hFOBs). The BMD relevance of hFOBs was supported by heritability enrichment from cross-cell type stratified LD-score regression involving 98 cell types grouped into 15 tissues. 24 genes showed perturbation in the screen, with four (ARID5B, CC2D1B, EIF4G2, and NCOA3) exhibiting consistent effects upon siRNA knockdown on three measures of osteoblast maturation and mineralization. Lastly, additional heritability enrichments, genetic correlations, and multi-trait fine-mapping revealed that many BMD GWAS signals are pleiotropic and likely mediate their effects via non-bone tissues that warrant attention in future screens.
Evaluating the position of the uncal apex as a predictor of episodic memory across the adult lifespan

Structural decline of the hippocampus occurs in heterogeneous patterns across its spatial extent, and is an important determinant of episodic memory dysfunction in aging. However, evidence indicate that the anatomical landmark uncal apex, used to demarcate anterior and posterior hippocampal subregions, changes position as the hippocampus atrophies. This emphasizes a risk of misclassifying gray matter into the incorrect subregion when using standard demarcation methods, contributing to over- and underestimation of age effects on anterior and posterior hippocampal volume. Yet, it remains unexplored whether inter-individual differences in uncal apex position predict episodic memory performance in itself. Here, we manually identified the uncal apex in anatomical MRI data from a healthy adult-lifespan sample (n=180; 20-79 years), assessed age differences in its position, and associations with word recollection performance. Increasing age was linked to a more anteriorly located uncal apex (retracting ∼0.041 mm/year). Importantly, a more anterior uncal apex position was linked to lower memory performance. Whereas anterior hippocampal volume remained stable with increasing age, posterior volume displayed non-linear decline with an infliction point at approximately 45 years. Neither anterior nor posterior hippocampal volumes predicted memory performance, but the ratio of posterior to anterior volume showed a significant association with memory when taking the position of the uncal apex into account. These results indicate that uncal apex position may provide an estimate of hippocampal integrity sensitive to inter-individual differences in memory, independent of limitations associated with different segmentation methods.