Miracle-dz/UniFAR-FTUs huggingface dataset:
Differential binding cell-SELEX: method for identification of cell specific aptamers using high throughput sequencing

Aptamers have evolved as a viable alternative to antibodies in recent years. High throughput sequencing (HTS) has revolutionized the aptamer research by increasing the number of reads from few using Sanger sequencing to millions of reads using HTS approach. Despite the availability and advantages of HTS compared to Sanger sequencing there are only 50 aptamer HTS sequencing samples available on public databases. HTS data for aptamer research are mostly used to compare sequence enrichment between subsequent selection cycles. This approach does not take full advantage of HTS because enrichment of sequences during selection can be due to inefficient negative selection when using live cells. Here we present differential binding cell-SELEX (systematic evolution of ligands by exponential enrichment) workflow that adapts FASTAptamer toolbox and bioinformatics tool edgeR that is mainly used for functional genomics to achieve more informative metrics about the selection process. We propose fast and practical high throughput aptamer identification method to be used with cell-SELEX technique to increase successful aptamer selection rate against live cells. The feasibility of our approach is demonstrated by performing aptamer selection against clear cell renal cell carcinoma (ccRCC) RCC-MF cell line using RC-124 cell line from healthy kidney tissue for negative selection.
Impact of the COVID-19 lockdown on digital device-related ocular health

Purpose: Since the declaration of the lockdown due to COVID-19, the usage of digital devices has gone up across the globe, resulting in a challenge for the visual systems of all ages. The purpose of this study is to assess the impact of the lockdown on digital device usage, and consequently, the ocular surface health implications and circadian rhythm abnormalities related to digital eye strain. Methods: An open online survey was sent through various social media platforms and was open for a period of 2 weeks. Results: A total of 407 usable responses were obtained; the average age of respondents was 27.4 years. Typically, 93.6% of respondents reported an increase in their screen time since the lockdown was declared. The average increase in digital device usage was calculated at about 4.8 ± 2.8 h per day. The total usage per day was found to be 8.65 ± 3.74 hours. Sleep disturbances have been reported by 62.4% of people. Typically, 95.8% of respondents had experienced at least one symptom related to digital device usage, and 56.5% said that the frequency and intensity of these symptoms increased since the lockdown was declared. Conclusion: The study highlighted the drastic increase in use of digital devices after the initiation of the COVID-19 lockdown, and along with it, the slow deterioration of ocular health across all age groups. Awareness about prevention of digital eye strain should be stressed, and going forward, measures to bring these adverse effects to a minimum should be explored.
One year period of invasive pneumococcal disease in children from a tertiary care hospital in Turkey in the post-vaccine era

ABSTRACT The incidence of invasive pneumococcal disease (IPD) has decreased after pneumococcal conjugate vaccine used; however, a breakthrough infection may still be seen after vaccination. In this study, eight pediatric inpatients and nine episodes with IPD in our center were included. Their age and gender, diagnoses, facilitating factors, the status of immunization and the antibiotic resistance of Pneumococci, serotypes of Pneumococci were noted. The isolates were subjected to disc susceptibility tests for penicillin, macrolides, and fluoroquinolones, according to the guidelines of the Clinical and Laboratory Standards Institute. Of the vaccinated seven cases, four of them (57.1%) developed IPD which their serogroups were in vaccine content. It was observed that all four cases in question had an underlying facilitating factor. Pneumococcal antibiotic susceptibility is also crucial. Three of nine isolates (33.4%) were resistant, and one isolate (11.2%) was intermediate susceptible to penicillin. Six of the nine isolates (66.7%) had macrolide resistance in our investigation. Invasive pneumococcal infections with serogroups that exist in pneumococcal conjugate vaccine content may occur in vaccinated individuals.
Variants c.677 C>T, c.1298 A>C in MTHFR, and c.66 A>G in MTRR Affect the Occurrence of Recurrent Pregnancy Loss in Chinese Women

Objective: Although genetic variants of key enzymes in the folic acid-methionine metabolic circulation, including methylenetetrahydrofolate reductase (MTHFR) and methionine synthase reductase (MTRR) were thought to be related to the risk of recurrent pregnancy loss (RPL), the results of recent studies have been inconsistent. Therefore, the present retrospective case–control study was designed to explore whether the variants c.66A>G in MTRR and c.677C>T and c.1298A>C in MTHFR are associated with the susceptibility of RPL in Southeast Chinese women. Materials and Methods: In total, samples from 237 RPL patients and 618 healthy controls were collected and genotyped by fluorescent quantitative polymerase chain reaction. The frequencies of the variants were calculated and compared between the two groups. The relative risk of the various genotypes was further determined by calculating the odds ratio (OR) at a 95% confidence interval (CI). Results: A significant positive correlation was observed between the variants MTHFR c.677C>T, MTHFR c.1298A>C, MTRR c.66A>G, and RPL susceptibility (MTHFR c.677C>T, OR = 0.74, 95% CI = 0.58–0.95, p = 0.02; MTHFR c.1298A>C, OR = 1.39, 95% CI = 1.09–1.77, p = 0.008; MTRR c.66A>G, OR = 1.38, 95% CI = 1.10–1.73, p = 0.006). Further analysis of the genotypic distributions of the three variants between the two groups showed that the MTHFR c.677C>T heterozygote was associated with lower RPL risk, while the MTHFR c.1298A>C variant and MTRR c.66A>G heterozygote were correlated with higher RPL risk (dominant model, MTHFR c.677C>T, OR = 0.70, 95% CI = 0.52–0.95, p = 0.02; MTHFR c.1298A>C, OR = 1.39, 95% CI = 1.03–1.88, p = 0.032; MTRR c.66A>G, OR = 1.62, 95% CI = 1.20–2.19, p = 0.002). Conclusion: MTHFR c.677C>T and c.1298A>C and MTRR c.66A>G were associated with RPL in Southeast Chinese women.
Role of AT1G72910, AT1G72940, and ADR1-LIKE 2 in Plant Immunity under Nonsense-Mediated mRNA Decay-Compromised Conditions at Low Temperatures

Nonsense-mediated mRNA decay (NMD) removes aberrant transcripts to avoid the accumulation of truncated proteins. NMD regulates nucleotide-binding, leucine-rich repeat (NLR) genes to prevent autoimmunity; however, the function of a large number of NLRs still remains poorly understood. Here, we show that three NLR genes (AT1G72910, AT1G72940, and ADR1-LIKE 2) are important for NMD-mediated regulation of defense signaling at lower temperatures. At 16 °C, the NMD-compromised up-frameshift protein1 (upf1) upf3 mutants showed growth arrest that can be rescued by the artificial miRNA-mediated knockdown of the three NLR genes. mRNA levels of these NLRs are induced by Pseudomonas syringae inoculation and exogenous SA treatment. Mutations in AT1G72910, AT1G72940, and ADR1-LIKE 2 genes resulted in increased susceptibility to Pseudomonas syringae, whereas their overexpression resulted in severely stunted growth, which was dependent on basal disease resistance genes. The NMD-deficient upf1 upf3 mutants accumulated higher levels of NMD signature-containing transcripts from these NLR genes at 16 °C. Furthermore, mRNA degradation kinetics showed that these NMD signature-containing transcripts were more stable in upf1 upf3 mutants. Based on these findings, we propose that AT1G72910, AT1G72940, and ADR1-LIKE 2 are directly regulated by NMD in a temperature-dependent manner and play an important role in modulating plant immunity at lower temperatures.
Using Discrete Multiphysics Modelling to Assess the Effect of Calcification on Hemodynamic and Mechanical Deformation of Aortic Valve

This study proposes a 3D particle-based (discrete) multiphysics approach for modelling calcification in the aortic valve. Different stages of calcification (from mild to severe) were simulated, and their effects on the cardiac output were assessed. The cardiac flow rate decreases with the level of calcification. In particular, there is a critical level of calcification below which the flow rate decreases dramatically. Mechanical stress on the membrane is also calculated. The results show that, as calcification progresses, spots of high mechanical stress appear. Firstly, they concentrate in the regions connecting two leaflets; when severe calcification is reached, then they extend to the area at the basis of the valve.
Releasing a Toolkit and Comparing the Performance of Language Embeddings Across Various Spoken Language Identification Datasets

In this paper, we propose a software toolkit for easier end-to-end training of deep learning based spoken language identiﬁ-cation models across several speech datasets. We apply our toolkit to implement three baseline models, one speaker recognition model, and three x-vector architecture variations, which are trained on three datasets previously used in spoken language identiﬁcation experiments. All models are trained separately on each dataset (closed task) and on a combination of all datasets (open task), after which we compare if the open task training yields better language embeddings. We begin by training all models end-to-end as discriminative classiﬁers of spectral features, labeled by language. Then, we extract language embedding vectors from the trained end-to-end models, train separate Gaussian Naive Bayes classiﬁers on the vectors, and compare which model provides best language embeddings for the back-end classiﬁer. Our experiments show that the open task condition leads to improved language identiﬁcation performance on only one of the datasets. In addition, we discovered that increasing x-vector model robustness with random frequency channel dropout signiﬁcantly reduces its end-to-end classiﬁcation performance on the test set, while not affecting back-end classiﬁ-cation performance of its embeddings. Finally, we note that two baseline models consistently outperformed all other models.
Exploring the Use of an Artificial Accent of English to Assess Phonetic Learning in Monolingual and Bilingual Speakers

We designed a production experiment to explore the relatively controversial phenomenon of the bilingual advantage. Our focus is on an understudied aspect of bilingual cognition, specifically phonetic learning. We presented 36 participants (17 monolinguals and 19 early bilinguals) living in New York City with an artificially constructed accent of English, differing in four ways from Standard American English. More precisely, the novel accent included a vocalic change (diphthongization of the open-mid front unrounded vowel), consonantal change (tapping of intervocalic liquids), syllable structure change (epenthesis in voiceless s-clusters) and suprasegmental change (a novel intonation pattern in tag questions). After recording their baseline accents, the participants first completed a training task, in which they listened to and then directly imitated sentences heard in the novel accent, and then a testing task, in which they were asked to read the baseline sentences in the accent they had just learned in the absence of any audio prompts. In this paper, we present acoustic results with diphthongization and tag question intonation. Our findings replicate the previously observed bilingual advantage in phonetic learning across the board and extend it to novel learning circumstances.
Predictive current control in electrical drives: an illustrated review with case examples using a five‐phase induction motor drive with distributed windings

The industrial application of electric machines in variable-speed drives has recently grown thanks to the development of microprocessors and power converters. Although three-phase machines constitute the most common case, the interest of the research community is also focused on multiphase machines with more than three phases. The principal reason lies in the exploitation of their advantages such as reliability, better current distribution among phases or lower current harmonic in the converter, to name a few. Nevertheless, multiphase drive applications require the development of complex controllers to regulate the torque (or speed) and flux of the machine. In this regard, predictive current controllers have appeared as a viable alternative due to an easy formulation and high flexibility to incorporate different control objectives. It is found, however, that these controllers face some peculiarities and limitations in their use that require attention. This work attempts to tackle the predictive current control technique as a viable alternative for the regulation of multiphase drives, paying special attention to the development of the control technique and the discussion of the benefits and limitations. Case examples with experimental results using a symmetrical five-phase induction machine with distributed windings are included to this end.
BMI1 Roles in Cancer Stem Cells and Its Association with MicroRNAs Dysregulation in Cancer: Emphasis on Colorectal Cancer

Context: Colorectal cancer (CRC) is among the most common cancers in the world. Despite the existence of different treatment strategies such as chemoradiation and surgery, CRC therapy still remains a significant challenge as a result of the existence of cancer stem cells (CSCs). Evidence Acquisition: This review is comprised of research and review studies published in valid databases such as PubMed, ScienceDirect, Medline, Google Scholar, and Scopus, using the following keywords: BMI1, cancer stem cell, microRNA, and colorectal cancer. Results: BMI1 (B cell-specific Moloney murine leukemia virus integration site 1) is a key component of polycomb repressor complex 1 (PRC1) and plays a significant role in CSCs self-renewal in various types of cancer including CRC. It has been proven that BMI1, in association with deregulated microRNAs (miRNAs), can promote cell cycle progression as well as epithelial to mesenchymal transition (EMT) in cancer. Conclusions: BMI1 is a colon stem cell marker that is up-regulated in colon CSCs and can be taken as a promising target for CRC therapy. This review describes the role of BMI-1 in the self-renewal of CSCs and EMT in association with miRNA dysregulation (with emphasis on CRC).
Dopaminergic signalling is necessary, but not sufficient for cued fear memory destabilisation

Pharmacological targeting of memory reconsolidation is a promising therapeutic strategy for the treatment of fear memory-related disorders. However, the success of reconsolidation-based approaches depends upon the effective destabilisation of the fear memory by memory reactivation. Here, we show that the nootropic nefiracetam stimulates tone fear memory destabilisation to facilitate reconsolidation disruption by the glucocorticoid receptor antagonist mifepristone. Moreover, the enhancing effect of nefiracetam was dependent upon dopamine D1 receptor activation, although direct D1 receptor agonism was not sufficient to facilitate destabilisation. Finally, while the combined treatment with nefiracetam and mifepristone did not confer fear-reducing effects under conditions of extinction learning, there was some evidence that mifepristone reduces fear expression irrespective of memory reactivation parameters. Therefore, the use of combination pharmacological treatment to stimulate memory destabilisation and impair reconsolidation has potential therapeutic benefits, without risking a maladaptive increase of fear.
Targeting Periodic Solutions of Chaotic Systems

Abstract: A linear augmentation method for stabilizing chaotic systems around unstable fixed points [Sharma et al, Phys. Rev. E. , 83, 67201 (2011)] is extended to stabilize chaotic oscillators in a desired periodic state around a chosen target point. The chaotic system attains a periodic orbit with desired frequency around a chosen center of rotation that can be controlled by variation of the coupling parameters of the augmented systems. The dynamical properties of the controlled systems, verified using Lyapunov exponent, show transition from chaotic to periodic state through a boundary crisis route, and near the transition points the systems posses mutistability.
Identifying phenological functional types in savanna trees

Savannas are notable for the varied patterns of leaf display in the tree layer. Characterising this variation, and assessing the range of phenological strategies apparent in savanna ecosystems will be helpful for understanding savanna tree life-histories and their response to global change. We recorded leaf phenological metrics on a monthly basis for 28 woody species for one year in a semi-arid savanna at Nylsvley Nature Reserve, South Africa. Using these metrics four plant functional types were described: (1) evergreen species, which retained full canopy throughout the year; (2) semi-evergreen species, which lost a significant amount of canopy during the dry season, but not less than 60%; (3) obligate deciduous species in which the canopy was leafless for about 3 months during the dry season; and (4) rain-stimulated species, in which canopy flushing was driven by rainfall patterns. Of the 28 species, 18% were evergreen, 18% obligate deciduous, 32% semi-evergreen and 32% were rain-stimulated species. These results confirm that phenological strategies are variable in savannas, and highlight that there are numerous cues controlling the timing of leaf out and leaf drop. By defining distinct phenological strategies we can predict which plant functional types will have phenological cues that will be vulnerable to shifting climates.
Selenium oxidation and removal by ion exchange

Strong-base anion exchange was evaluated as a process for the removal of trace quantities of selenium from groundwater. The efficiency of the process was found to be dependent on the oxidation state of selenium, with the selenate anion (Se(VI)) having a greater affinity for the anion-exchange resin than selenite or biselenite anions (Se(IV)). An analytical method was developed to measure the concentrations of Se(IV) and Se(VI) (i.e., to determine the speciation of selenium) at trace concentrations in groundwater. The oxidation of Se(IV) to Se(VI) at trace concentration in groundwater was studied with this new analytical method.
Distinct functional classes of excitatory neurons in mouse V1 are differentially modulated by learning and task engagement

Learning can cause significant changes in neural responses to relevant stimuli, in addition to modulation due to task engagement. However, it is not known how different functional types of excitatory neurons contribute to these changes. To address this gap, we performed two-photon calcium imaging of excitatory neurons in layer 2/3 of mouse primary visual cortex before and after learning of a visual discrimination. We found that excitatory neurons show striking diversity in the temporal dynamics of their response to visual stimuli during the behavior, and based on this we classified them into transient, sustained, and suppressed groups. Notably, these functionally defined cell classes exhibit different visual stimulus selectivity and modulation by locomotion, and were differentially affected by training condition. In particular, we observed a decrease in the number of transient neurons responsive during behavior after learning, while both transient and sustained cells showed an increase in modulation due to task engagement after learning. The identification of functional diversity within the excitatory population, with distinct changes during learning and task engagement, provides insight into the cortical pathways that allow context-dependent neural representations.
Microenvironments to regulate cellular behavior for neural development and regeneration

IV Zusammenfassung . V Motivation and Scope of this Thesis . 1 1. Background and Introduction . 4 1.1 The guiding cues at the natural extracellular microenvironment . 5 1.2 Biomaterial parameters relevant for neuronal migration . 6 1.3 Biomaterial designs to support directional neurite extension . 10 1.3. 1 Neural growth on patterns of cell adhesive ligands . 11 1.3. 2 Topographical cues for guiding neurite extension . 13 1.3. 3 Guided neurite growth by rigidity patterns . 23 1.3. 4 Directed growth on “living scaffolds” . 24 1.3. 5 Guiding neurite extension by light and photoactivatable biomaterials . 25 2. Microenvironments to trigger migration and somal translocation in cortical neurons . 27 2.
Food as Coronavirus Prophylaxis

The global human coronavirus-2 epidemic requires rapid response, and the scientists are searching for prevention and treatment. The epidemiologic data collected during the epidemic show that in China COVID-19 has a lethality rate of 3.5% versus 1.19% in Japan; or 4.9% in Italy versus 0% in Germany, as of March 2nd , there may be many reasons for these differences in lethality, and diet may be one of them. COVID-19 is a β-coronavirus, like SARS and MERS, and the spread resembles the 2003 and 2012 epidemics from the same family of virus. The finding of the COVID-19 receptor angiotensin-converting enzyme 2 (ACE2) permits to repurpose drugs used for its inhibition. Herein we explored natural drugs that have shown to inhibit ACE2 and CD26 and prevented MERS and COVID-19 cellular entry. We propose a diet rich in niacin (vitamin B3) and berberine as prophylaxis for COVID-19 and β-coronavirus infections.
Comparative Analysis of Antibacterial Activity of Ciprofloxacin and Homeopathic Mother Tincture

Objective: The aim of this study was to evaluate and compare in vitro antibacterial effects of ciprofloxacin and homeopathic mother tinctures.Methods: All the experimental homeopathic mother tinctures were donated by Masood Homeopathic Pharmaceuticals, Pakistan. Among tested bacteria, Escherichia coli (014) and Bacillus subtilis (143) were taken in the form of standard culture agar from the First Fungal Culture Bank of Pakistan (FCBP), Institute of Agricultural Sciences (IAGS), the University of Punjab, Lahore and Pseudomonas aeruginosa (ATCC 9027) and Staphylococcus aureus (ATCC 6538) were taken from American Type Culture Collection (ATCC). Ciprofloxacin (standard antibiotic) 1mg/ml was taken as positive control and 70% alcohol was taken as negative control. Homeopathic mother tinctures were checked for their antibacterial activity against four bacterial strains (Bacillus subtilis, Escherichia coli, Pseudomonas aeruginosa, and Staphylococcus aureus) through agar well diffusion method.Results: Ciprofloxacin expressed maximum activity against Pseudomonas aeruginosa among all tested bacteria. All tested mother tinctures expressed more or less antibacterial activity against Staphylococcus aureus with maximum activity of Eucalyptus globulus (zone of inhibition 21.7 mm). Eight out of ten mother tinctures expressed activity against Escherichia coli with maximum activity of Eucalyptus globulus (zone of inhibition 17 mm). Nine out of ten homeopathic mother tinctures expressed significant antibacterial activity against Pseudomonas aeruginosa with maximum activity of Hydrastis canadensis (zone of inhibition 28 mm). Similarly, nine out of ten homeopathic mother tinctures expressed significant antibacterial activity against Bacillus subtilis with maximum activity of Hydrastis canadensis (zone of inhibition 26 mm). Conclusion: Hence, concluded that homeopathic mother tinctures showed antibacterial potential.