Miracle-dz/UniFAR-FTUs huggingface dataset:
Hybrid algorithm for multi artifact removal from single channel EEG

Electroencephalogram (EEG) signals recorded from the ambulatory systems are mostly contaminated by various artifacts like, electrooculogram (EOG), motion artifacts (MA) and electrocardiogram (ECG) artifacts. These artifacts limit the accuracy in further analysis of EEG in practise. So far, several existing methods have been proposed with the combination of decomposition techniques and independent component analysis (ICA) to remove single artifacts and only few methods to remove multiple artifacts from the single channel EEG. As improperly denoised EEG signals can result in wrong diagnosis, in this work, Singular Spectrum Analysis (SSA) and ICA are jointly combined with Generalized Moreau Envelope Total Variation (GMETV) technique to simultaneously remove combinations of different artifacts from single channel EEG. In this work, the SSA is used to decompose the contaminated single channel EEG, while the ICA is employed to separate the various hidden sources as independent components (ICs). Although the ICA is adequate in source separation, there is still, some essential EEG signal data appearing as artifact in the IC. Hence, eliminating this would allow EEG signal information to be lost. The GMETV approach is proposed in this paper, to estimate the actual artifacts in order to address these issues. The estimated actual artifacts are subtracted from the artifact ICs providing the residue of wanted component of EEG. This residue is added back to the remaining ICs, to obtain the denoised EEG. Simulation results demonstrated that the proposed technique performs better compared to the existing techniques. The Relative Root Mean Square Error (RRMSE) is reduced by 12.02% and 7.22% compared to SSA-ICA and SSA-ICA-thresholding respectively. Similarly, the Correlation Coefficient (CC) is increased by 21.48% and 8.25% with respect to SSA-ICA and SSA-ICA-thresholding respectively.
Genome-wide proximity between RNA polymerase and DNA topoisomerase I supports transcription in Streptococcus pneumoniae

Streptococcus pneumoniae is a major cause of disease and death that develops resistance to multiple antibiotics. DNA topoisomerase I (TopoI) is a novel pneumococcal drug target. TopoI is the sole type-I pneumococcal topoisomerase that regulates supercoiling homeostasis in this bacterium. In this study, a direct in vitro interaction between TopoI and RNA polymerase (RNAP) was detected by surface plasmon resonance. To understand the interplay between transcription and supercoiling regulation in vivo, genome-wide association of RNAP and TopoI was studied by ChIP-Seq. RNAP and TopoI were enriched at the promoters of 435 and 356 genes, respectively. Higher levels of expression were consistently measured in those genes whose promoters recruit both RNAP and TopoI, in contrast with those enriched in only one of them. Both enzymes occupied a narrow region close to the ATG codon. In addition, RNAP displayed a regular distribution throughout the coding regions. Likewise, the summits of peaks called with MACS tool, mapped around the ATG codon in both cases. However, RNAP showed a broader distribution towards ATG-downstream positions. Remarkably, inhibition of RNAP with rifampicin prevented the localization of TopoI at promoters and, vice versa, inhibition of TopoI with seconeolitsine prevented the binding of RNAP to promoters. This indicates a functional interplay between RNAP and TopoI. To determine the molecular factors responsible for RNAP and TopoI co-recruitment, we looked for DNA sequence motifs. We identified a motif corresponding to a -10-extended promoter for TopoI and for RNAP. Furthermore, RNAP was preferentially recruited to genes co-directionally oriented with replication, while TopoI was more abundant in head-on genes. TopoI was located in the intergenic regions of divergent genes pairs, near the promoter of the head-on gene of the pair. These results suggest a role for TopoI in the formation/stability of the RNAP-DNA complex at the promoter and during transcript elongation.
Ride to cell wall: Arabidopsis XTH11, XTH29 and XTH33 exhibit different secretion pathways and responses to heat and drought stress

Summary The xyloglucan endotransglucosylase/hydrolases (XTHs) are enzymes involved in cell wall assembly and growth regulation, cleaving and re‐joining hemicellulose chains in the xyloglucan–cellulose network. Here, in a homologous system, we compare the secretion patterns of XTH11, XTH33 and XTH29, three members of the Arabidopsis thaliana XTH family, selected for the presence (XTH11 and XTH33) or absence (XTH29) of a signal peptide, and the presence of a transmembrane domain (XTH33). We show that XTH11 and XTH33 reached, respectively, the cell wall and plasma membrane through a conventional protein secretion (CPS) pathway, whereas XTH29 moves towards the apoplast following an unconventional protein secretion (UPS) mediated by exocyst‐positive organelles (EXPOs). All XTHs share a common C‐terminal functional domain (XET‐C) that, for XTH29 and a restricted number of other XTHs (27, 28 and 30), continues with an extraterminal region (ETR) of 45 amino acids. We suggest that this region is necessary for the correct cell wall targeting of XTH29, as the ETR‐truncated protein never reaches its final destination and is not recruited by EXPOs. Furthermore, quantitative real‐time polymerase chain reaction analyses performed on 4‐week‐old Arabidopsis seedlings exposed to drought and heat stress suggest a different involvement of the three XTHs in cell wall remodeling under abiotic stress, evidencing stress‐, organ‐ and time‐dependent variations in the expression levels. Significantly, XTH29, codifying the only XTH that follows a UPS pathway, is highly upregulated with respect to XTH11 and XTH33, which code for CPS‐secreted proteins.
Phosphorylation of the androgen receptor at Ser81 is co‐sustained by CDK1 and CDK9 and leads to AR‐mediated transactivation in prostate cancer

Androgen receptor (AR) is the principal molecule in prostate cancer (PCa) etiology and therapy. AR re‐activation still remains a major challenge during treatment of castration‐resistant prostate cancer (CRPC) tumors that relapse after castration therapies. Recent reports have indicated the enrichment of Ser81‐phosphorylated AR (pS81) in the nucleus of CRPC cells, and CDK1 and CDK9 as the kinases phosphorylating AR at S81. In the current study we showed that pS81 is preferentially localized in the nucleus in both rapid biopsy metastatic CRPC samples and PCa xenografts, and nuclear pS81 localization is correlated with AR transactivation in tumor xenografts. Chromatin immunoprecipitation (ChIP) analysis demonstrated an alignment of S81 phosphorylation and AR‐mediated transactivation with the chromatin locus openness. Moreover, pS81‐specific ChIP‐Seq showed a disproportional occupancy of pS81 on AR‐activated promoters, while 3C‐ChIP assays further indicated an enrichment of pS81 at the PSA enhancer‐promoter loop, a known AR activating hub. In the latter, CDK9 was shown to modulate the transactivation of the AR and RNA Pol II. Indeed, ChIP and re‐ChIP assays also confirmed that AR‐dependent activation of the PSA enhancer and promoter mediated by pS81 was coupled with activation of Pol II and the pTEFb complex. Mechanistically, we determined that CDK1 and CDK9 sustained the pS81 AR modification in the soluble and chromatin‐bound fractions of PCa cells, respectively. Finally, we demonstrated that CDK1 activity was maintained throughout the cell cycle, and that CDK1 inhibitors restored androgen sensitivity in CRPC tumor cells. Based on these findings, CDK1 and CDK9 could be targeted as pS81 kinases in patients with CRPC, either alone or in conjunction with direct AR antagonists.
COVID-19, time to oneself, and loneliness: Creativity as a resource

Abstract Objectives Physical distancing to reduce the spread of the coronavirus disease 2019 has increased alone time, with unintended mental health ramifications including increased loneliness, which may be particularly detrimental for older adults. We investigated time-varying associations between daily time to oneself and loneliness, and the role of everyday creativity as a resource. Methods 126 adults aged 18-84 completed online questionnaires including a 10-day daily diary module, during which they self-reported alone time, everyday creativity, and loneliness. Data were analyzed using multilevel models, controlling for study day, participation date, gender, and relationship status. Results Greater average amounts of alone time were associated with greater loneliness, an association that was stronger in old age. In a daily context, individuals reported feeling lonelier on days when they had more time to themselves than usual. This within-person association was weaker with older age. Everyday creativity did not moderate alone time-loneliness associations. However, holding time to oneself constant, participants felt less lonely and less bothered by alone time on days when they were more creative than usual. Discussion Participating in creative behaviors (e.g., pursuing arts and crafts) might be linked with reduced loneliness. Intervention studies are needed to investigate whether fostering creativity could help promote mental well-being in times when people, especially older adults, are vulnerable to loneliness and associated health risks.
Maximum A Posteriori Approximation of Hidden Markov Models for Proportional Sequential Data Modeling With Simultaneous Feature Selection

One of the pillar generative machine learning approaches in time series data study and analysis is the hidden Markov model (HMM). Early research focused on the speech recognition application of the model with later expansion into numerous fields, including video classification, action recognition, and text translation. The recently developed generalized Dirichlet HMMs have proven efficient in proportional sequential data modeling. As such, we focus on investigating a maximum a posteriori (MAP) framework for the inference of its parameters. The proposed approach differs from the widely deployed Baum–Welch through the placement of priors that regularizes the estimation process. A feature selection paradigm is also integrated simultaneously in the algorithm. For validation, we apply our proposed approach in the classification of dynamic textures and the recognition of infrared actions.
Oncological safety of therapeutic ‘nipple-sparing mastectomy’ followed by reconstruction: a systematic review

Abstract Background Breast cancer (BC) treatment traditionally consisted of radical and often mutilating surgery. Advances in the field of BC have led to new remedies, enabling the paradigm shift from radical to conservative surgery. New treatments such as nipple-sparing mastectomy (NSM) are becoming more popular, aiming to improve both oncological and aesthetic outcomes. However, evidence confirming the oncological safety of NSM is currently lacking, hindering its application. This systematic review sought to analyze NSM’s oncological safety as an alternative to conventional mastectomy (CM). Patients and methods A systematic review was performed, respecting the PRISMA guidelines. Pubmed, Embase, and Web of Science databases were consulted and searched for keywords: ‘nipple-sparing mastectomy’ and ‘mammaplasty’, or combinations of synonyms. Only original studies published between 2000 and 2020 reporting tumor recurrence and/or survival rates with a minimum of 5-year follow-up were included. Results From the 1675 unique records found, 14 studies were included, amounting to 5980 female BC patients who underwent NSM plus reconstruction. Included studies described either only ductal carcinoma in situ (DCIS, n = 1), only invasive BC (n = 3) or DCIS and invasive BC (n = 10). The most recurrent oncological metrics were 5-year local recurrence (0–10%), locoregional recurrence (0–7.4%), distant recurrence (1.6–15.6%), and overall survival rate (93.1–100%). Conclusion Based on long-term low BC recurrences and high survival rates, NSM is perceived to be non-inferior to CM from an oncological perspective. This identifies NSM plus reconstruction to be a safe curative treatment. Further studies should aim to elicit clear and applicable selection criteria in order to maximize NSM's potential.
High molecular weight sodium hyaluronate improves survival of syndecan-1-deficient septic mice by inhibiting neutrophil migration

We investigated the role of endothelial glycocalyx and its component syndecan-1 protein in the pathophysiology of sepsis-induced vascular hyper-permeability and examined the therapeutic effects of high-molecular-weight sodium hyaluronate (HMW-SH). Methods Sepsis was induced by cotton smoke inhalation followed by intranasal administration of Pseudomonas aeruginosa in female (> 6 months) Balb/c and syndecan-1 knockout mice. Survival of mice, lung capillary endothelial glycocalyx integrity, lung water content, and vascular hyper-permeability were determined with or without HMW-SH treatment in these mice. Effects of HMW-SH on endothelial permeability and neutrophil migration were tested in in vitro setting. Results In septic wildtype mice, we found a severely damaged pulmonary microvascular endothelial glycocalyx and elevated levels of shed syndecan-1 in the circulation. These changes were associated with significantly increased pulmonary vascular permeability. In septic syndecan-1 knockout mice, extravascular lung water content was higher, and early death was observed. The administration of HMW-SH significantly reduced mortality and lung water content in septic syndecan-1 knockout mice, but not in septic wildtype mice. In in vitro setting, HMW-SH inhibited neutrophil migration and reduced cultured endothelial cell permeability increases. However, these effects were reversed by the addition of recombinant syndecan-1 ectodomain. Conclusions HMW-SH reduced lung tissue damage and mortality in the absence of syndecan-1 protein, possibly by reducing vascular hyper-permeability and neutrophil migration. Our results further suggest that increased shed syndecan-1 protein levels are linked with the inefficiency of HMW-SH in septic wildtype mice.
Symbiont switching and trophic mode shifts in Orchidaceae

Summary Mycorrhizal fungi are central to the biology of land plants. However, to what extent mycorrhizal shifts – broad evolutionary transitions in root‐associated fungal symbionts – are related to changes in plant trophic modes remains poorly understood. We built a comprehensive DNA dataset of Orchidaceae fungal symbionts and a dated plant molecular phylogeny to test the hypothesis that shifts in orchid trophic modes follow a stepwise pattern, from autotrophy over partial mycoheterotrophy (mixotrophy) to full mycoheterotrophy, and that these shifts are accompanied by switches in fungal symbionts. We estimate that at least 17 independent shifts from autotrophy towards full mycoheterotrophy occurred in orchids, mostly through an intermediate state of partial mycoheterotrophy. A wide range of fungal partners was inferred to occur in the roots of the common ancestor of this family, including ‘rhizoctonias’, ectomycorrhizal, and wood‐ or litter‐decaying saprotrophic fungi. Phylogenetic hypothesis tests further show that associations with ectomycorrhizal or saprotrophic fungi were most likely a prerequisite for evolutionary shifts towards full mycoheterotrophy. We show that shifts in trophic mode often coincided with switches in fungal symbionts, suggesting that the loss of photosynthesis selects for different fungal communities in orchids. We conclude that changes in symbiotic associations and ecophysiological traits are tightly correlated throughout the diversification of orchids.
Distinct fiber-specific white matter reductions pattern in early- and late-onset Alzheimer’s disease

Background: The underlying white matter impairment in patients with early and late-onset Alzheimer’s disease (EOAD and LOAD) is still unclear, and this might due to the complex AD pathology. Methods: We included 31 EOAD, 45 LOAD, and 64 younger, 46 elder controls in our study to undergo MRI examinations. Fiber density (FD) and fiber bundle cross-section (FC) were measured using fixel-based analysis based on diffusion weighted images. On whole brain and tract-based level, we compared these parameters among different groups (p<0.05, FWE corrected). Moreover, we verified our results in another independent dataset using the same analyses. Results: Compared to young healthy controls, EOAD had significantly lower FD in the splenium of corpus callosum, limbic tracts, cingulum bundles, and posterior thalamic radiation, and higher FC in the splenium of corpus callosum, dorsal cingulum and posterior thalamic radiation. On the other hand, LOAD had lower FD and FC as well. Importantly, a similar pattern was found in the independent validation dataset. Among all groups, both the FD and FC were associated with cognitive function. Furthermore, FD of fornix column and body, and FC of ventral cingulum were associated with composite amyloid and tau level (r=-0.34 and -0.53, p<0.001) respectively. Conclusions: EOAD and LOAD were characterized by distinct white matter impairment patterns, which may be attributable to their different neuropathologies.
Blocking glutamate mGlu5 receptors with the negative allosteric modulator CTEP improves disease course in SOD1G93A mouse model of amyotrophic lateral sclerosis

The pathogenesis of amyotrophic lateral sclerosis (ALS) is not fully clarified, although excessive glutamate (Glu) transmission and the downstream cytotoxic cascades are major mechanisms for motor neuron death. Two metabotropic glutamate receptors (mGlu1 and mGlu5) are overexpressed in ALS and regulate cellular disease processes. Expression and function of mGlu5 receptors are altered at early symptomatic stages in the SOD1G93A mouse model of ALS and knockdown of mGlu5 receptors in SOD1G93A mice improved disease progression.
Psychiatric risk and resilience: Plasticity genes and positive mental health

The at‐risk mental state (ARMS) for psychosis has long played a key role in diathesis‐stress models of schizophrenia. More recent studies, however, have called for extending the boundaries of the ARMS construct beyond attenuated psychosis in nonhelp‐seeking samples to include not only other vulnerability indicators but also protective factors related to genotype, mental health, personality, and cognition.
The growing repertoire of genetic tools for dissecting chlamydial pathogenesis.

Multiple species of obligate intracellular bacteria in the genus Chlamydia are important veterinary and/or human pathogens. These pathogens all share similar biphasic developmental cycles and transition between intracellular vegetative reticulate bodies and infectious elementary forms, but vary substantially in their host preferences and pathogenic potential. A lack of tools for genetic engineering of these organisms has long been an impediment to the study of their biology and pathogenesis. However, the refinement of approaches developed in C. trachomatis over the last ten years, and adaptation of some of these approaches to other Chlamydia spp. in just the last few years, has opened exciting new possibilities for studying this ubiquitous group of important pathogens.
Zoonotic tuberculosis knowledge and practices among cattle handlers in selected districts of Bangladesh

We assessed zoonotic tuberculosis (zTB) knowledge and prevention and control practices of 404 cattle handlers via a survey in three dairy-intensive districts of Bangladesh. Most respondents were aged 30–49 (52%) and male (95%). Almost all (99%) recognized the important public health burden of tuberculosis in Bangladesh, however, most (58%) had inadequate knowledge about zTB transmission to humans. Inappropriate practices such as: not using protective equipment (98%); smoking, drinking or eating food whilst working with cattle (69%); and sharing the same premises with animals (83%) were identified. Cattle handlers educated at secondary or higher levels were 2.82- (95% CI: 1.59–5.10) and 5.15 times (95% CI: 1.74–15.20) more likely to have adequate knowledge of control and prevention activities compared to those with no formal education. Those who had reared animals for 1–5 years were 2.67 times (95% CI: 1.44–4.91) more likely to have adequate knowledge, compared to those who reared animals for >15 years. Cattle handlers with a monthly incomes of 10,000–20,000 taka were significantly (Odds Ratio = 0.36, 95% CI: 0.14–0.92) less likely to have adequate knowledge compared to those with monthly incomes <10,000 taka. Cattle handlers with high school or higher education were 6.98 times (95% CI: 2.47–19.71) more likely to use appropriate zTB control and prevention practices compared to those without formal education. Those who had reared animals for 1–5 years, 6–10 years and 11–15 years were 2.72- (95% CI: 1.42–5.24), 2.49- (95% CI: 1.29–4.77) and 2.86 times (95% CI: 1.13–7.23) more likely to apply appropriate practices compared to those who reared animals for >15 years. Overall, education, duration of cattle rearing and monthly income predicted zTB knowledge and practices. There is an urgent need to educate those at high-risk of zTB transmission on issues including the handling of infected animals, and general hygiene. A One Health approach, to support the Sustainable Development Goals and the End TB strategy, appears to be the way forward.
EFFECT OF WATER QUALITY ON DESTRUCTION OF ODOR CAUSING SUBSTANCES DURING OZONATION PROCESSES

In this study the odor causing substances from four surface waters, namely trans-1,10dimethyl-trans-9-decalol (GSM) and 2-methylisoborneol (2-MIB) were ozonated at a range of ozone doses. Five organic fractions, including humic acid, fulvic acid, hydrophobic neutral, hydrophilic acid, and hydrophilic neutral, were extracted/isolated from source water and ozonated in synthetic waters. The surface waters containing more dissolved organic carbon, highly hydrophobic organics and specific ultra-violet absorbance (SUVA) value exhibited a high ozone demand, and the destruction of GSM and 2-MIB was significantly higher than the water containing low hydrophobic organic content and SUVA value at all ozone doses. Furthermore, the results of ozonation of synthetic waters indicated the degradation rate was significantly higher in the organic fraction with the highest aromaticity, phenolic groups, and SUVA. Ozonation in rich algae containing water shows that ozone or OH radical also destructed the algal cell, caused excretion of extracellular organic matter (EOM) to the bulk phase, with results showing a competing effect between EOM and odor causing substances.