Miracle-dz/UniFAR-FTUs huggingface dataset:
Multiple Intraspecific Variations of Mitochondrial Genomes in the Green-Tide Forming Alga, Ulva compressa Linnaeus (Ulvophyceae, Chlorophyta)

To gain further insights into intraspecific evolution of Ulva mitochondrial genomes, the mitogenomes of three morphotypes of the green-tide forming alga, Ulva compressa Linnaeus from China and United States, were sequenced and compared with the available data from Ulvophyceae. The U. compressa mitogenomes displayed substantial genome size variation at intraspecific level ranging from 61,700 to > 66,587 bp, due to different acquisitions of foreign DNA fragments, gain or loss of both group I and II introns, and non-coding intergenic spacer regions. The U. compressa mitogenomes harbored variable gene content ranging from 69 genes (including orfs) in Uco1 to 76 in Uco5, and contained different intron content from 4 introns in Uco3 and Uco4 to 7 in Uco1. A total of 63 genes and only two group IB introns (intron cox1-1107 and cox1-1125) were shared by these five mitogenomes. The U. compressa mitogenomes accumulated many more inverted repeat (IR) elements, ranging from 45 in Uco1 to 88 in Uco2, than that of the other Ulva species (3–34). A locally collinear block of eight genes (rps11-rps19-rps4-rpl16-trnR-trnQ-trnE-trnS) with the size of 3,631 bp has been inverted only in Uco1 indicating that the rearrangement event happened after its divergence from Uco2–5 and might be related to a specific IR element. The majority of the common genes (~76%) displayed high identity (>98%) among these five mitogenomes, while some low values were observed in six genes mainly due to duplication and insertion/deletion mutations of small DNA fragments. Our study presented the first case of multiple intraspecific variations in ulvophycean mitogenomes, and indicated that the mitogenome will be a valuable tool for understanding the native or non-indigenous nature of the cosmopolitan Ulva species.
Establishment of a Jaw Fibrosarcoma Patient-Derived Xenograft and Evaluation of the Tumor Suppression Efficacy of Plumbagin Against Jaw Fibrosarcoma

Background: Head and neck fibrosarcoma is a rare malignant tumor, accounting for about 1% of all head and neck tumors. It can also occur in the jaw bone, for which surgical resection is the main treatment but the recurrence rate is high and the prognosis is usually poor. Due to the lack of models mimicking the biological characteristics of the tumor, there is little progress in the research of the pathogenesis and treatment of fibrosarcoma. Therefore, there is an urgent need to explore a high-fidelity model that can reflect the biological characteristics of fibrosarcoma for the sake of improving the therapeutic outcome and prognosis, and preventing recurrence. Patient-derived xenografts (PDX) may more accurately reflect the human disease, and is an attractive platform to study disease biology and develop treatments and biomarkers. In this study we describe the establishment of jaw fibrosarcoma PDX models and compare PDX tumors to those of human origin. Methods: Tumor biopsies from a patient with jaw fibrosarcoma were implanted in immunodeficient mice. Primary and PDX tumors were characterized extensively by histology, immunohistochemistry and humanized identification. Based on the finding of our previous preliminary research that plumbagin had an anti-tumor effect against head and neck cancer, we used this model in the present study to evaluate the anti-tumor effect of plumbagin on jaw fibrosarcoma. Results: The established PDX model maintained the histological and immunohistochemical characteristics of the primary tumor. Plumbagin significantly inhibited the tumor growth in the jaw fibrosarcoma PDX model. Conclusion: We successfully established a PDX model of jaw fibrosarcoma and demonstrated that this PDX model preserved the important molecular characteristics of the human primary tumor, thus providing a powerful tool for treatment research and new drug development of jaw fibrosarcoma. In addition, plumbagin was found to have an inhibitory effect on the growth of PDX modeled jaw fibrosarcoma, which provides a preliminary research basis for its clinical application.
A look at throat singing

Throat singing enables a singer to sing simultaneous with two,three and four voices. The main sound is generated by the vocal cords and other flexible structures like false cords, arytenoid cartilages, aryepiglottic folds and epiglottic root are vibrated to cause throat singing. The spectral analysis of the three samples of throat singing depicts peaks and valleys at the same frequencies with some large differences in the sound level at same frequency. Among the three distinct peaks observed, the first peak is due to the vibration of the vocal cords, corresponding to the fundamental frequency. The second peak is the harmonic of the first whereas the third peak represents the independant vibrations of the structures other than vocal cords.
Secreted Chaperones in Neurodegeneration

Protein homeostasis, or proteostasis, is a combination of cellular processes that govern protein quality control, namely, protein translation, folding, processing, and degradation. Disruptions in these processes can lead to protein misfolding and aggregation. Proteostatic disruption can lead to cellular changes such as endoplasmic reticulum or oxidative stress; organelle dysfunction; and, if continued, to cell death. A majority of neurodegenerative diseases involve the pathologic aggregation of proteins that subverts normal neuronal function. While prior reviews of neuronal proteostasis in neurodegenerative processes have focused on cytoplasmic chaperones, there is increasing evidence that chaperones secreted both by neurons and other brain cells in the extracellular – including transsynaptic – space play important roles in neuronal proteostasis. In this review, we will introduce various secreted chaperones involved in neurodegeneration. We begin with clusterin and discuss its identification in various protein aggregates, and the use of increased cerebrospinal fluid (CSF) clusterin as a potential biomarker and as a potential therapeutic. Our next secreted chaperone is progranulin; polymorphisms in this gene represent a known genetic risk factor for frontotemporal lobar degeneration, and progranulin overexpression has been found to be effective in reducing Alzheimer’s- and Parkinson’s-like neurodegenerative phenotypes in mouse models. We move on to BRICHOS domain-containing proteins, a family of proteins containing highly potent anti-amyloidogenic activity; we summarize studies describing the biochemical mechanisms by which recombinant BRICHOS protein might serve as a therapeutic agent. The next section of the review is devoted to the secreted chaperones 7B2 and proSAAS, small neuronal proteins which are packaged together with neuropeptides and released during synaptic activity. Since proteins can be secreted by both classical secretory and non-classical mechanisms, we also review the small heat shock proteins (sHsps) that can be secreted from the cytoplasm to the extracellular environment and provide evidence for their involvement in extracellular proteostasis and neuroprotection. Our goal in this review focusing on extracellular chaperones in neurodegenerative disease is to summarize the most recent literature relating to neurodegeneration for each secreted chaperone; to identify any common mechanisms; and to point out areas of similarity as well as differences between the secreted chaperones identified to date.
Genetic Diversity and Phylogeography of Thottapalayam thottimvirus (Hantaviridae) in Asian House Shrew (Suncus murinus) in Eurasia

Murid and cricetid rodents were previously believed to be the principal reservoir hosts of hantaviruses. Recently, however, multiple newfound hantaviruses have been discovered in shrews, moles, and bats, suggesting a complex evolutionary history. Little is known about the genetic diversity and geographic distribution of the prototype shrew-borne hantavirus, Thottapalayam thottimvirus (TPMV), carried by the Asian house shrew (Suncus murinus), which is widespread in Asia, Africa, and the Middle East. Comparison of TPMV genomic sequences from two Asian house shrews captured in Myanmar and Pakistan with TPMV strains in GenBank revealed that the Myanmar TPMV strain (H2763) was closely related to the prototype TPMV strain (VRC66412) from India. In the L-segment tree, on the other hand, the Pakistan TPMV strain (PK3629) appeared to be the most divergent, followed by TPMV strains from Nepal, then the Indian-Myanmar strains, and finally TPMV strains from China. The Myanmar strain of TPMV showed sequence similarity of 79.3–96.1% at the nucleotide level, but the deduced amino acid sequences showed a high degree of conservation of more than 94% with TPMV strains from Nepal, India, Pakistan, and China. Cophylogenetic analysis of host cytochrome b and TPMV strains suggested that the Pakistan TPMV strain was mismatched. Phylogenetic trees, based on host cytochrome b and cytochrome c oxidase subunit I genes of mitochondrial DNA, and on host recombination activating gene 1 of nuclear DNA, suggested that the Asian house shrew and Asian highland shrew (Suncus montanus) comprised a species complex. Overall, the geographic-specific clustering of TPMV strains in Asian countries suggested local host-specific adaptation. Additional in-depth studies are warranted to ascertain if TPMV originated in Asian house shrews on the Indian subcontinent.
Purification of Rubisco activase from rice.

Rubisco 1. 5-bisphosphate carboxylase/oxygenase activase was purified from rice leaves by 35% ammonium sulfate fraction, DEAE-cellulose and Mono Q chromatography. SDS-PAGE electrophore- togram showed that Rubisco activase (RCA) was composed of 45 kD and 41 kD subunits. ATP was neces- sary to maintain Rubisco activase activity. Maximal activity of the enzyme was obtained with ATP 1. 5 mmol/L.
How to Do Things with Words: A Bayesian Approach

Communication changes the beliefs of the listener and of the speaker. The value of a communicative act stems from the valuable belief states which result from this act. To model this we build on the Interactive POMDP (IPOMDP) framework, which extends POMDPs to allow agents to model others in multi-agent settings, and we include communication that can take place between the agents to formulate Communicative IPOMDPs (CIPOMDPs). We treat communication as a type of action and therefore, decisions regarding communicative acts are based on decision-theoretic planning using the Bellman optimality principle and value iteration, just as they are for all other rational actions. As in any form of planning, the results of actions need to be precisely specified. We use the Bayes’ theorem to derive how agents update their beliefs in CIPOMDPs; updates are due to agents’ actions, observations, messages they send to other agents, and messages they receive from others. The Bayesian decision-theoretic approach frees us from the commonly made assumption of cooperative discourse – we consider agents which are free to be dishonest while communicating and are guided only by their selfish rationality. We use a simple Tiger game to illustrate the belief update, and to show that the ability to rationally communicate allows agents to improve efficiency of their interactions.
Vocational Profile and Correlates of Employment in People With Schizophrenia: The Role of Avolition

Objective Employment was associated with recovery in individuals with schizophrenia. Our study aimed to delineate the vocational profile and investigate factors associated with likelihood of employment in individuals with schizophrenia. Materials and Methods 276 community dwelling outpatients with schizophrenia were recruited; 274 completed the Positive and Negative Syndrome Scale (PANSS) and Brief Negative Symptom Scale (BNSS). Information on employment status, work outcomes and demographics were collected. Occupation was coded in accordance with the Singapore standard occupational classification. Either BNSS Motivation and Pleasure (MAP) and Emotional Expressivity (EE) or BNSS five-factor (Anhedonia, Asociality, Avolition, Blunted Affect, Alogia) were examined with PANSS factors and demographics in logistic regression with employment status and working full-time as outcome variables. Results One-hundred and twenty-seven (46.01%) participants were employed; 65 (51.18%) worked full-time. In the model with BNSS MAP-EE, MAP (OR=0.897, CI=0.854-0.941) and presence of physical comorbidity (OR=0.533, CI=0.304-0.937) were associated with reduced likelihood of employment; female sex (OR=0.286, CI=0.128 - 0.637) was associated with working part-time. In the model with BNSS five-factor, Avolition (OR=0.541, CI=0.440-0.666), and PANSS Positive (OR=0.924, CI=0.855-0.997) were associated with reduced likelihood of employment; female sex (OR=0.289, CI=0.126 - 0.662) and Avolition (OR=0.644, CI=0.475 - 0.872) were associated with working part-time. Discussion Our study described the vocational profile and correlates of employment in a developed urban Asian country. Negative symptoms, particularly MAP and Avolition, positive symptoms, and physical comorbidity reduced an individual’s likelihood of employment, while female sex and Avolition were associated with working part-time. Efforts to identify and address these factors are necessary to encourage employment in individuals with schizophrenia.
A phase separation in a protonated layered nickel titanate to form Ni-doped anatase/rutile TiO2 nanocomposite with efficient visible-light responsive photocatalytic activity

ABSTRACT We report a simple methodology for the preparation of an efficient visible-light responsive TiO2 photocatalyst through acid treatment of a lepidocrocite-type layered nickel cesium titanate (Cs0.7Ti1.65Ni0.35O4) for interlayer protonation and subsequent calcination at different temperatures (400–600°C) to induce structural transformation. The Ni-doped anatase/rutile nanocomposite possessing a morphology similar to that of protonated layered nickel titanate is obtained at all calcination temperatures. The sample obtained at 600°C exhibits the highest visible-light responsive photocatalytic activity for decomposition of the aqueous methylene blue dye under visible-light (λ > 420 nm) irradiation. The activity is 14 times higher than that of P25 (standard TiO2 photocatalyst) modified with Ni2+ and 3 times higher than that of NiTiO3 (visible-light responsive photocatalyst). The efficient visible-light responsive photocatalytic activity is ascribable to the visible-light absorption ability of the TiO2 phase owing to Ni-doping. Also, an efficient electron transfer across anatase–rutile interfaces for inhibition of charge recombination could be responsible for the activity. This methodology is a new route for efficient visible-light responsive photocatalysts based on TiO2 doped with various elemental species. This is because lepidocrocite-type layered titanates are available in a variety of chemical compositions. GRAPHICAL ABSTRACT
Tolerance and Persistence of Pseudomonas aeruginosa in Biofilms Exposed to Antibiotics: Molecular Mechanisms, Antibiotic Strategies and Therapeutic Perspectives

Pseudomonas aeruginosa biofilm-related infections are difficult to treat with antibiotics. Along the different layers of the biofilm, the P. aeruginosa population is heterogeneous, exhibiting an extreme ability to adapt his metabolic activity to the local microenvironment. At the deepest layers of the biofilm is a subset of dormant cells, called persister cells. Though antimicrobial failure might be multifactorial, it is now demonstrated that these persister cells, genetically identical to a fully susceptible strain, but phenotypically divergent, are highly tolerant to antibiotics, and contribute to antimicrobial failure. By eradicating susceptible, metabolically active cells, antibiotics bring out pre-existing persister cells. The biofilm mode of growth creates microenvironment conditions that activate stringent response mechanisms, SOS response and toxin-antitoxin systems that render the bacterial population highly tolerant to antibiotics. Using diverse, not standardized, models of biofilm infection, a large panel of antibiotic regimen has been evaluated. They demonstrated that biofilm growth had an unequal impact of antibiotic activity, colistin and meropenem being the less impacted antibiotics. Different combination and sequential antimicrobial therapies were also evaluated, and could be partially efficient, but none succeeded in eradicating persister cells, so that non-antibiotic alternative strategies are currently under development. This article reviews the molecular mechanisms involved in antibiotic tolerance and persistence in P. aeruginosa biofilm infections. A review of the antimicrobial regimen evaluated for the treatment of P. aeruginosa biofilm infection is also presented. While tremendous progress has been made in the understanding of biofilm-related infections, alternative non-antibiotic strategies are now urgently needed.
Longitudinal study of cognitive function in glioma patients treated with modern radiotherapy techniques and standard chemotherapy

Abstract Introduction: Cognitive function is an important outcome measure in patients with brain tumor, providing information about the patient’s clinical situation, treatment effects and possible progressive disease. The aim of this longitudinal study was to evaluate effects of the currently used radiation and chemotherapy treatment on cognitive function and to investigate associations between cognitive function at baseline and progression as well as overall survival. Methods: 32 patients newly diagnosed with malignant glioma were evaluated at baseline with CNS Vital Signs (CNS-VS), a computerized standardized neuropsychological test battery, prior to arc-based radiotherapy and concomitant chemotherapy with Temozolomide. CNS-VS measures the cognitive functions known to be affected in patients with brain tumor, covering nine cognitive domains. Follow-up cognitive evaluations were performed in 26 patients after 3.5 months and in 13 patients 1 year after treatment start. Results: Overall cognitive scores were lower in the studied patient cohort at baseline compared to standardized domain scores. At 3.5 months follow-up cognitive functioning was slightly decreased, but only in 1/9 cognitive domains – visual memory – where significant changes were found compared to baseline test results. Similarly, at 12 months follow-up no significant changes in cognitive test results were seen compared to baseline examination, except for a decrease in the visual memory domain. In relation to early progression, the most significant cognitive deficits were dysfunctional visual memory and low executive functioning at baseline. Low executive function at baseline correlated most significantly with shorter overall survival. Conclusion: The present study suggests that the currently used arc-based radiotherapy and chemotherapy might affect cognitive function less negatively than previously described during treatment and in the first year after treatment in malignant glioma patients. In general, a high cognitive test score at baseline was associated with longer time to progression and with longer survival.
Sensitivity of OFDM and FBMC to Interference

This paper gives a comparison between the well-known Orthogonal Frequency-Division Multiplexing (OFDM) and the Filter Bank Multicarrier (FBMC) modulation regarding their capability to cope with external interferers. This is especially interesting for communication networks in which due to the network design, a collision or crosstalk of additional signals may occur. It will be shown under which conditions FBMC performs better and under which conditions OFDM continues to show better results. Nevertheless, the results show that FBMC is a promising candidate as a reliable physical layer technique particularly in asynchronous wireless communication networks for industrial sensors, where a simple retransmission of the signal may not be desired due to latency requirements.
Effect of Insulin on Expression of LDLR, SREBP-2 and Cell Proliferation in Chang (normal) Liver Cells

Low-density lipoprotein receptor (LDLR) maintains lipid metabolism and its expression is regulated by Sterol Regulatory Element Binding proteins (SREBPs). This study was designed to investigate the effect of insulin, a mitogen on LDLR, SREBP-2 receptor expression and cell proliferation. Insulin was found to have a stimulatory effect on the expression of LDLR and its transcription factor SREBP-2. Fluorescent dye (Dil) labelling assay revealed significantly increased uptake of Dil-LDL in the presence of insulin. Insulin also showed increased rate of cell replication. These findings suggested that LDLR expression is enhanced in the presence of insulin, which in turn results in increased uptake of LDL into the cells causing increased cell proliferation. The elevated expression of SREBP-2 indicated the influence of insulin on the transcription of genes responsible for increased expression and activity of LDLR.Keywords: LDL receptor, SREBP-2, Atherosclerosis, LDL uptake and BrdUrd Assay.
Combining Angiodysplasia Classification and Segmentation on Capsule Endoscopy Images Using Attentional AlbuNet

Wireless capsule endoscopy is a useful method for physicians to retrieve images in gastro patients trying to segment bleeding or lesion areas called "angiodysplasia". There were prior successes of the deep learning approach that solely focused on the lesion images. However, most frames in endoscopy videos are non-lesions. Thus, they incorrectly segmented angiodysplasia in non-lesion images. In this paper, we introduce a method to take a classification of lesion/non-lesion images into consideration of the segmentation framework. We propose to combine classification and segmentation using two approaches: (i) cascading model and (ii) joint model with various joint loss calculations. Also, the segmentation model is employed from the winner of our previous work called "Attentional AlbuNet". The experiment was conducted on two angiodysplasia datasets from MICCAI 2017 and 2018. The results show that our joint model outperforms the traditional segmentation model. It can improve performance in both classification and segmentation tasks. For the classification, it can almost perfectly classify lesion images from non-lesion images. For the segmentation task, it achieves dice of 92.16% and 71.54% on MICCAI 2017 and 2018 datasets, consecutively.
Effects of Membrane Directed Neurotoxicants on the Contractile Activity of Cultured Skeletal Muscle Cells

The effects of the sodium channel toxins saxitoxin, veratridine, deltamethrin and Anemonia sulcata toxin II on the spontaneous contractile activity of cultured rat skeletal muscle cells, were investigated. In addition, the influence of the external concentrations of K+ and Ca2+ ions was studied. The results indicate that the spontaneous contractility of cultured muscle cells is a suitable endpoint for assessing subtle alterations in the electrical properties of excitable membranes, and for quantifying in vitro the potency of neurotoxicants acting on the excitable membranes of nerve and muscle cells.