Miracle-dz/UniFAR-FTUs huggingface dataset:
Epistasis between synonymous and nonsynonymous mutations in Dictyostelium discoideum ammonium transporter amtA drives functional complementation in Saccharomyces cerevisiae

Role of Horizontal Gene Transfer (HGT) in evolution transcends across the three domains of life. Ammonium transporters are present in all species and therefore offer an excellent paradigm to study protein evolution following HGT. While investigating HGT through complementation assay, we observed that synonymous and nonsynonymous mutations follow an epistastic relationship. As a proxy for HGT, we attempted to complement a mep1mep2mep3Δ strain of S. cerevisiae (triple deletion strain) which cannot grow on ammonium as a sole nitrogen source below a concentration of 3 mM, with amtA of D. discoideum. As the wild type amtA did not complement, we isolated two mutant derivatives of amtA that complemented the triple deletion strain of S. cerevisiae. amtA M1 bears three nonsynonymous and two synonymous substitutions and these substitutions are necessary for its functionality. amtA M2 bears two nonsynonymous and one synonymous substitution, all of which are necessary for functionality. These mutants were then studied at phenotypic, cell biological, and biochemical level. Interestingly, AmtA M1 transports ammonium but does not confer toxicity to methylamine while AmtA M2 transports ammonium as well as confers methylamine toxicity, demonstrating functional diversification. Based on the results presented, we suggest that protein evolution cannot be fathomed by studying nonsynonymous and synonymous substitutions separately. This is because, protein evolution entails an interaction between synonymous and nonsynonymous substitution, which seems to have gone unnoticed thus far. Above observations have significant implications in various facets of biological processes and are discussed in detail. Highlights Ammonium transporters (Amts) from bacteria to humans complement in yeast AmtA of D. discoideum does not complement yeast defective for ammonium uptake Synonymous & nonsynonymous mutations are essential for AmtA functionality in yeast Conformational differences underlie functionality & functional diversification Protein evolution entails interaction of synonymous & nonsynonymous mutations
Inhibition of mutant IDH1 promotes cycling of acute myeloid leukemia stem cells

Acute myeloid leukemias (AML) are comprised of multiple cell types with distinct capabilities to propagate the disease and resist therapy. Approximately 20% of AML patients carry gain- of-function mutations in IDH1 or IDH2 that result in over-production of the onco-metabolite 2-HG. Although IDH inhibitors can induce complete morphological remission, almost all patients eventually relapse. Analysis of clinical samples suggests that a population of IDH mutant cells is able to persist during treatment eventually acquiring 2-HG independence and drug resistance. Herein we characterized the molecular and cellular responses to the clinical IDH1 inhibitor AG-120 at high resolution using a novel multi-allelic mouse model of IDH1 mutant AML. We demonstrate that AG-120 exerts cell type-dependent effects on leukemic cells promoting delayed disease regression. Although IDH1 inhibition alone was not able to fully eradicate the disease, we uncovered that it increases cycling of rare leukemic stem cells and triggers transcriptional upregulation of the pyrimidine salvage pathway. Accordingly, AG-120 sensitized IDH1 mutant AML to azacitidine with the combination of AG-120 and azacitidine showing vastly improved efficacy in vivo. Our data highlight the impact of non- genetic heterogeneity on treatment response and provide mechanistic rationale for a drug combination that is being tested in clinical trials. STATEMENT OF SIGNIFICANCE Inhibition of mutant IDH1 in AML is insufficient to eliminate the disease but promotes proliferation of quiescent leukemic stem cells. Our data provide a mechanistic explanation for the observed synergy between IDH inhibitors and azacitidine and suggest that IDH inhibitors may also synergize with other drugs that preferentially target actively dividing cells.
Evaluasi pelaksanaan blended learning di SMK TI Udayana menggunakan model CSE-UCLA

Penelitian ini bertujuan untuk memperoleh tingkat efektivitas pelaksanaan blended learning di SMK TI Udayana ditinjau dari beberapa komponen evaluasi yaitu system assessment, program planning, program implementation, program improvement, dan program certification. Metode penelitian yang digunakan dalam penelitian ini adalah studi evaluatif, dengan menggunakan model evaluasi CSE-UCLA (Center for the Study of Evaluation- University of California in Los Angeles). Subjek penelitian terdiri dari: kepala sekolah, guru, siswa, dan tim pengelola blended learning. Hasil penelitian menunjukkan bahwa rata-rata tingkat efektivitas pada komponen system assessment sebesar 86,7% sehingga termasuk kategori tinggi, rata-rata tingkat efektivitas pada komponen program planning sebesar 85,6% sehingga termasuk kategori tinggi, rata-rata tingkat efektivitas pada komponen program implementation sebesar 87,5% sehingga termasuk kategori tinggi, rata-rata tingkat efektivitas pada komponen program improvement sebesar 88,5% sehingga termasuk kategori tinggi, dan rata-rata tingkat efektivitas pada komponen program certification sebesar 88,9% sehingga termasuk kategori tinggi. Kata kunci: evaluasi, blended learning, CSE-UCLA EVALUATION OF BLENDED LEARNING AT SMK TI UDAYANA USING CSE-UCLA MODEL Abstract This study aimed to obtain the level of effectiveness of blended learning implementation at SMK TI Udayana in terms of some of the evaluation components such as: system assessment, program planning, program implementation, program improvement, and program certification. The method used in this study is an evaluative study, using CSE-UCLA (Center for the Study of Evaluation- University of California in Los Angeles) evaluation model. The research subjects consisted of: headmaster, teachers, students and the management team of blended learning. The results showed that the average level of effectiveness on the system assessment component amounted to 86.7% that includes high category, the average level of effectiveness on the program planning component amounted to 85.6% that includes high category, the average level of effectiveness on the program implementation component amounted to 87.5% that includes high category, the average level of effectiveness on the program improvement component amounted to 88.5% that includes high category, the average level of effectiveness on the program certification component amounted to 88.9% that includes high category. Keywords: evaluation, blended learning, CSE-UCLA
Computational Analysis of Effects of Clot Length on Acute Ischemic Stroke Recanalization under Different Cyclic Aspiration Loading Conditions

Acute ischemic stroke, the second leading cause of death worldwide, results from occlusion of a cerebral artery by a blood clot. Application of cyclic aspiration using an aspiration catheter is a current therapy for the removal of lodged clots. In this study, we perform finite element simulations to analyze deformation of long clots, having length to radius ratio of 2 to 10, which corresponds to clot-length of 2.85–14.25 mm, under peak-to-peak cyclic aspiration pressures of 10 to 50mmmHg, and frequencies of 0.5, 1 and 2 Hz. Our computational system comprises of a nonlinear viscoelastic solid clot, a hyperelastic artery, and a nonlinear viscoelastic cohesive zone, the latter modeling the clot–artery interface. We observe that clots having length-to-radius ratio approximately greater than two separate from the inner arterial surface somewhere between the axial and distal ends, irrespective of the cyclic aspiration loading conditions. The stress distribution within the clot shows large tensile stresses in the clot interior, indicating the possibility of simultaneous fragmentation of the clot. Thus, this study shows us the various failure mechanisms simultaneously present in the clot during cyclic aspiration. Similarly, the stress distribution within the artery implies a possibility of endothelial damage to the arterial wall near the end where the aspiration pressure is applied. This framework provides a foundation for further investigation to clot fracture and adhesion characterization.
A formalism for sequential estimation of neural membrane time constant and input–output curve towards selective and closed-loop transcranial magnetic stimulation

Objective. To obtain a formalism for real-time concurrent sequential estimation of neural membrane time constant and input–output (IO) curve with transcranial magnetic stimulation (TMS). Approach. First, the neural membrane response and depolarization factor, which leads to motor evoked potentials with TMS are analytically computed and discussed. Then, an integrated model is developed which combines the neural membrane time constant and IO curve. Identifiability of the proposed integrated model is discussed. A condition is derived, which assures estimation of the proposed integrated model. Finally, sequential parameter estimation (SPE) of the neural membrane time constant and IO curve is described through closed-loop optimal sampling and open-loop uniform sampling TMS. Without loss of generality, this paper focuses on a specific case of commercialized TMS pulse shapes. The proposed formalism and SPE method are directly applicable to other pulse shapes. Main results. The results confirm satisfactory estimation of the membrane time constant and IO curve parameters. By defining a stopping rule based on five times consecutive convergence of the estimation parameters with a tolerances of 0.01, the membrane time constant and IO curve parameters are estimated with 82 TMS pulses with absolute relative estimation errors (AREs) of less than 4% with the optimal sampling SPE method. At this point, the uniform sampling SPE method leads to AREs up to 16%. The uniform sampling method does not satisfy the stopping rule due to the large estimation variations. Significance. This paper provides a tool for real-time closed-loop SPE of the neural time constant and IO curve, which can contribute novel insights in TMS studies. SPE of the membrane time constant enables selective stimulation, which can be used for advanced brain research, precision medicine and personalized medicine.
The neural response at the fundamental frequency of speech is modulated by word-level acoustic and linguistic information

Spoken language comprehension requires rapid and continuous integration of information, from lower-level acoustic to higher-level linguistic features. Much of this processing occurs in the cerebral cortex. Its neural activity exhibits, for instance, correlates of predictive processing, emerging at delays of a few hundred milliseconds. However, the auditory pathways are also characterized by extensive feedback loops from higher-level cortical areas to lower-level ones as well as to subcortical structures. Early neural activity can therefore be influenced by higher-level cognitive processes, but it remains unclear whether such feedback contributes to linguistic processing. Here, we investigated early speech-evoked neural activity that emerges at the fundamental frequency. We analyzed EEG recordings obtained when subjects listened to a story read by a single speaker. We identified a response tracking the speaker’s fundamental frequency that occurred at a delay of 11 ms, while another response elicited by the high-frequency modulation of the envelope of higher harmonics exhibited a larger magnitude and longer latency of about 18 ms. Subsequently, we determined the magnitude of these early neural responses for each individual word in the story. We then quantified the context-independent frequency of each word and used a language model to compute context-dependent word surprisal and precision. The word surprisal represented how predictable a word is, given the previous context, and the word precision reflected the confidence about predicting the next word from the past context. We found that the word-level neural responses at the fundamental frequency were predominantly influenced by the acoustic features: the average fundamental frequency and its variability. Amongst the linguistic features, only context-independent word frequency showed a weak but significant modulation of the neural response to the high-frequency envelope modulation. Our results show that the early neural response at the fundamental frequency is already influenced by acoustic as well as linguistic information, suggesting top-down modulation of this neural response.
Gαq modulates the energy metabolism of osteoclasts

Introduction The bacterial protein toxin Pasteurella multocida toxin (PMT) mediates RANKL-independent osteoclast differentiation. Although these osteoclasts are smaller, their resorptive activity is high which helps in efficient destruction of nasal turbinate bones of pigs. Methods The proteome of bone marrow-derived macrophages differentiated into osteoclasts with either RANKL or PMT was analysed. The results were verified by characterizing the metabolic activity using Seahorse analysis, a protein translation assay, immunoblots, real-time PCR as well as flow cytometry-based monitoring of mitochondrial activity and ROS production. A Gαq overexpression system using ER-Hoxb8 cells was used to identify Gαq-mediated metabolic effects on osteoclast differentiation and function. Results PMT induces the upregulation of metabolic pathways, which included strong glycolytic activity, increased expression of GLUT1 and upregulation of the mTOR pathway. As OxPhos components were expressed more efficiently, cells also displayed increased mitochondrial respiration. The heterotrimeric G protein Gαq plays a central role in this hypermetabolic cell activation as it triggers mitochondrial relocalisation of pSerSTAT3 and an increase in OPA1 expression. This seems to be caused by a direct interaction between STAT3 and OPA1 resulting in enhanced mitochondrial respiration. Overexpression of Gαq mimicked the hypermetabolic phenotype observed for PMT-induced osteoclasts and resulted in higher glycolytic and mitochondrial activity as well as increased bone resorptive activity. In addition, rheumatoid arthritis (RA) patients showed an increase in GNAQ expression, especially in the synovial fluid. Discussion Our study suggests that Gαq plays a key role in PMT-induced osteoclastogenesis. Enhanced expression of GNAQ at the site of inflammation in RA patients indicates its pathophysiological relevance in the context of inflammatory bone disorders.
Assessing the importance of resistance, persistence and hyper-mutation for antibiotic treatment success with stochastic modelling

Antimicrobial resistance poses a rising threat to global health, making it crucial to understand the routes of bacterial survival during antimicrobial treatments. Treatment failure can result from genetic or phenotypic mechanisms, which diminish the effect of antibiotics. By assembling empirical data, we find that, for example, Pseudomonas aeruginosa infections in cystic fibrosis patients frequently contain persisters, transiently non-growing and antibiotic-refractory subpopulations, and hyper-mutators, mutants with elevated mutation rates and thus higher probability of genetic resistance emergence. Resistance, persistence and hyper-mutation dynamics are difficult to disentangle experimentally. Hence, we use stochastic population modelling and deterministic fitness calculations of bacterial evolution under antibiotic treatment to investigate how genetic resistance and phenotypic mechanisms affect treatment success. We find that treatment failure is caused by resistant mutants at lower antibiotic concentrations (with high final bacterial numbers), but by persistence phenotypes at higher antibiotic concentrations (with low final bacterial numbers). Facilitation of resistance occurs through hyper-mutators during treatment, but through persistence only after treatment is discontinued, which allows for persisters to resume growth and evolve resistance in the absence of antibiotics. Our findings highlight the time- and concentration-dependence of different bacterial mechanisms to escape antibiotic killing, which should be considered when designing ‘resistance-proof’ antimicrobial treatments.
Thalamic bursting and the role of timing and synchrony in thalamocortical signaling in the awake mouse

The thalamus controls transmission of sensory signals from periphery to cortex, ultimately shaping perception. Despite this significant role, dynamic thalamic gating and the consequences for downstream cortical sensory representations have not been well studied in the awake brain. We optogenetically modulated the ventro-posterior medial thalamus in the vibrissa pathway of the awake mouse, and measured spiking activity in the thalamus, and activity in primary somatosensory cortex (S1) using extracellular electrophysiology and genetically encoded voltage imaging. Thalamic hyperpolarization significantly enhanced thalamic sensory-evoked bursting, yet surprisingly the S1 cortical response was not amplified, but instead timing precision was significantly increased, spatial activation more focused, and there was an increased synchronization of cortical inhibitory neurons. A thalamocortical network model implicates the modulation of precise timing of feedforward thalamic population spiking, presenting a highly sensitive, timing-based gating of sensory signaling to cortex.
Fecal immunoglobulin A (IgA) and its subclasses in systemic lupus erythematosus patients are nuclear antigen reactive and this feature correlates with gut permeability marker levels

Systemic lupus erythematosus (SLE) is characterized by the production of anti-nuclear autoantibodies. Here, for the first time, we show that the abundances of gut permeability marker Zonulin and IgA1- and IgA2-subclasses are significantly higher in the fecal samples of SLE patients compared to HCs. Importantly, IgA-total, IgA1- and IgA2-subclasses from SLE patients showed higher nAg reactivity titers. Notably, we found that not only the nuclear antigen (nAg) reactive fecal IgA1:IgA2 ratio is higher in SLE patients, but also the abundance and nAg reactivity of fecal IgA and subclasses, IgA1 particularly, correlate with the fecal levels of Zonulin, which is produced primarily in the small intestine. These observations suggest that higher amounts of nAg-reactive IgA are produced, particularly, in the proximal gut as indicated by higher IgA1:IgA2 abundance and nAg reactivity ratios and correlation of these features with the Zonulin levels.
Selective Hydrogenation of 5-Hydroxymethylfurfural to 2,5-Dimethylfuran Over Popcorn-Like Nitrogen-Doped Carbon-Confined CuCo Bimetallic Catalyst

A new type of biomass-based liquid fuel, 2,5-dimethylfuran (DMF), has attracted significant attention owing to its unique physical properties and carbon neutrality. It can be obtained from the hydrogenation of 5-hydroxymethylfurfural (HMF), an important biomass platform compound. In this study, we developed a nitrogen-doped carbon-confined CuCo bimetallic catalyst with a popcorn-like structure for the selective hydrogenation of HMF with high efficiency and adequate stability. Under optimized conditions, 100% HMF conversion and 93.7% DMF selectivity were achieved. The structure of the catalyst was characterized using XRD, XPS, SEM, and TEM. It was observed that carbon spheres, which were covered by nitrogen-doped carbon nanotubes, uniformly formed, while metal particles were confined in the nitrogen-doped carbon nanotubes. The popcorn-like structure exhibited a larger surface area and provided more contact sites, while the confined metal particles were the main active sites. The synergistic effect between Cu and Co was beneficial for DMF selectivity.
Epidemiology and Clinical Characteristics of Human Coronaviruses-Associated Infections in Children: A Multi-Center Study

Background Human coronaviruses (HCoVs) are associated with upper respiratory tract infections. Although studies have analyzed the clinical and epidemiological characteristics of HCoV-associated infections, no multi-center studies have been conducted in Korean children. We aimed to describe the epidemiology and clinical characteristics of HCoV-associated infection in children. Methods We retrospectively reviewed medical records of children in whom HCoVs were detected using multiplex reverse transcriptase-polymerase chain reaction amplification in five centers from January 2015 to December 2019. Results Overall, 1,096 patients were enrolled. Among them, 654 (59.7%) patients were male. The median age was 1 year [interquartile range (IQR), 0–2 years]. HCoVs were identified mainly in winter (55.9%). HCoV-229E, HCoV-OC43, and HCoOV-NL63 were detected mainly in winter (70.9, 55.8, and 57.4%, respectively), but HCoV-HKU1 was mainly identified in spring (69.7%). HCoV-OC43 (66.0%) was detected most frequently, followed by HCoV-NL63 (33.3%), and HCoV-229E (7.7%). Two different types of HCoVs were co-detected in 18 samples, namely. Alphacoronavirus-betacoronavirus co-infection (n = 13) and, alphacoronavirus-alphacoronavirus co-infection (n = 5). No betacoronavirus-betacoronavirus co-infection was detected. Patients were diagnosed with upper respiratory tract infection (41.4%), pneumonia (16.6%), acute bronchiolitis (15.5%), non-specific febrile illness (13.1%), croup (7.3%), and acute gastroenteritis (5.1%). There were 832 (75.9%) hospitalized patients with a median duration of hospitalization of 4 days (IQR, 3–5 days); 108 (9.9%) patients needed supplemental oxygen with 37 (3.4%) needing high-flow nasal cannula or mechanical ventilation. There were no deaths. Conclusion HCoV-associated infections exhibit marked seasonality with peaks in winter. Patients with lower respiratory tract infection, a history of prematurity, or underlying chronic diseases may progress to a severe course and may need oxygen therapy.
Airway Microbiota in Patients With Synchronous Multiple Primary Lung Cancer: The Bacterial Topography of the Respiratory Tract

Microbes and microbiota dysbiosis are correlated with the development of lung cancer; however, the airway taxa characteristics and bacterial topography in synchronous multiple primary lung cancer (sMPLC) are not fully understood. The present study aimed to investigate the microbiota taxa distribution and characteristics in the airways of patients with sMPLC and clarify specimen acquisition modalities in these patients. Using the precise positioning of electromagnetic navigation bronchoscopy (ENB), we analyzed the characteristics of the respiratory microbiome, which were collected from different sites and using different sampling methods. Microbiome predictor variables were bacterial DNA burden and bacterial community composition based on 16sRNA. Eight non-smoking patients with sMPLC in the same pulmonary lobe were included in this study. Compared with other sampling methods, bacterial burden and diversity were higher in surface areas sampled by bronchoalveolar lavage (BAL). Bacterial topography data revealed that the segment with sMPLC lesions provided evidence of specific colonizing bacteria in segments with lesions. After taxonomic annotation, we identified 4863 phylotypes belonging to 185 genera and 10 different phyla. The four most abundant specific bacterial community members detected in the airway containing sMPLC lesions were Clostridium, Actinobacteria, Fusobacterium, and Rothia, which all peaked at the segments with sMPLC lesions. This study begins to define the bacterial topography of the respiratory tract in patients with sMPLC and provides an approach to specimen acquisition for sMPLC, namely BAL fluid obtained from segments where lesions are located.