Miracle-dz/UniFAR-FTUs huggingface dataset:
FAM35A co-operates with REV7 to coordinate DNA double-strand break repair pathway choice

DNA double-strand breaks (DSBs) can be repaired by two major pathways: non-homologous end-joining (NHEJ) and homologous recombination (HR). DNA repair pathway choice is governed by the opposing activities of 53BP1, in complex with its effectors RIF1 and REV7, and BRCA1. However, it remains unknown how the 53BP1/RIF1/REV7 complex stimulates NHEJ and restricts HR to the S/G2 phases of the cell cycle. Using a mass spectrometry (MS)-based approach, we identify 11 high-confidence REV7 interactors and elucidate the role of a previously undescribed factor, FAM35A/SHDL2, as a novel effector of REV7 in the NHEJ pathway. FAM35A depletion impairs NHEJ-mediated DNA repair and compromises antibody diversification by class switch recombination (CSR) in B-cells. FAM35A accumulates at DSBs in a 53BP1-, RIF1- and REV7-dependent manner and antagonizes HR by limiting DNA end resection. In fact, FAM35A is part of a larger complex composed of REV7 and another previously uncharacterized protein, C20orf196/SHDL1, which promotes NHEJ and limits HR. Together, these results establish FAM35A as a novel effector of REV7 in controlling the decision-making process during DSB repair.
Overview of multicarrier CDMA

The authors present an overview of new multiple access schemes based on a combination of code division and multicarrier techniques, such as multicarrier code-division multiple access (MC-CDMA), multicarrier direct sequence CDMA (multicarrier DS-CDMA), and multitone CDMA (MT-CDMA).
Determination and diagnostic value of CA9 mRNA in peripheral blood of patients with oral leukoplakia

Abstract Background: Oral leukoplakia is one of the most common oral premalignant disorder. The classical evaluation through tissue biopsy is not always valid to evaluate the risk of malignization. Material and methods: RT-qPCR was performed on 47 blood samples (21 patients with leukoplakia, 2 with oral squamous cell carcinoma (OSCC), and 24 healthy patients) and on 11 tissue samples (3 leukoplakia, 4 OSCC, and 4 samples of healthy tissue). Results: There are significant differences in expression between the different groups (F = 4.057, p = .006). The Duncan post hoc test shows that the only group that differentiates is the tumour tissue. Using Wilcoxon test, different covariables of patients with leukoplakia were analysed with respect to the group of healthy patients and no significant differences were observed. Conclusions: The diagnostic route through liquid biopsy has not been conclusive in this study, but there are significant differences in the levels analysed in the different tissue samples.
Privacy Preservation by Disassociation TR-IMIS-2011-1

In this work, we focus on the preservation of user privacy in the publication of sparse multidimensional data. Existing works protect the users’ sensitive information by generalizing or suppressing quasi identifiers in the original data. In many real world cases, neither generalization nor the distinction between sensitive and non-sensitive items is appropriate. For example, web search query logs contain millions of terms that are very hard to categorize as sensitive or non sensitive. At the same time, a generalization-based anonymization would remove the most valuable information in the dataset; the original terms. Motivated by this problem, we propose an anonymization technique termed disassociation that preserves the original terms but hides the fact that two or more different terms appear in the same record. Up to now, such techniques were used to sever the link between quasiidentifiers and sensitive values in settings with a clear distinction between these types of values. Our proposal generalizes these techniques for sparse multidimensional data, where no such distinction holds. We protect the users’ privacy by disassociating combinations of terms that can act as quasi-identifiers from the rest of the record or by disassociating the constituent terms, so that the identifying combination cannot be accurately recognized. To this end, we present an algorithm that anonymizes the data by first clustering them and then locally disassociating identifying combinations of terms. We analyze the attack model and extend the km-anonymity guaranty to the aforementioned setting. We empirically evaluate our method on real and synthetic datasets.
Long-term community change through multiple rapid transitions in a desert rodent community

While studies increasingly document long-term change in community composition, whether long-term change occurs gradually or via rapid reorganization events remains unclear. We used Latent Dirichlet Allocation (LDA) and a change-point model to examine the long-term dynamics of a desert rodent community undergoing compositional change over a 38-year span. Our approach detected three rapid reorganization events, where changes in the relative abundances of dominant and rare species occurred, and a separate period of increased variance in the structure of the community. These events coincided with time periods—possibly related to climate events—where the total abundance of rodents was extremely low. There are a variety of processes that could link low abundance events with a higher probability of rapid ecological transitions, including higher importance of stochastic processes (i.e., competitive interactions or priority effects) and the removal of structuring effects of competitive dominants or incumbent species. Continued study of the dynamics of community change will provide important information not only on the processes structuring communities, but will also provide guidance for forecasting how communities will undergo change in the future.
Round off Error propagation in simulation of RC circuit Subtitle: Simulation of RC circuit

Electrical devices often use RC, LC or RLC circuit to design power amplifiers, filters and mixers etc. Complex iterative algorithms are used for the simulation of these circuits. This paper illustrates numerical experiments on growth of rounding off error in simulation of simple RC circuit using fourth order Runge-Kutta method (RK) and the Runge-Kutta-Fehlberg with adaptive step size control method (RKF). Our analysis indicates that in simulations with RK method, round off error grows ~ 80% with 10-15 iterations and ~96-98% within 100 iterations with different step sizes and double precision. In the simulations with RKF method round off error grows to 70% with 10-20 iterations and ~80% within 100 iterations. It does not exceed 80% for 1000 of iterations for single and double precision. This indicates that growth of round off error in RKF method is less and it should be used to minimize round off error. Keywords—Simulation of RC circuit, Round off error, Runge Kutta methods
Disruption of the KH1 domain of Fmr1 leads to transcriptional alterations and attentional deficits in rats

Fragile X Syndrome (FXS) is a neurodevelopmental disorder caused by mutations in the FMR1 gene. FXS is a leading monogenic cause of autism spectrum disorder (ASD) and inherited intellectual disability (ID). In most cases, the mutation is an expansion of a microsatellite (CGG triplet), which leads to suppressed expression of the fragile X mental retardation protein (FMRP), an RNA-binding protein involved in multiple aspects of mRNA metabolism. Interestingly, we found that the previously published Fmr1 knockout rat model of FXS expresses a transcript with an in-frame deletion of a K-homology (KH) domain, KH1. KH domains are RNA-binding domains of FMR1 and several of the few, known point mutations associated with FXS are found within them. We observed that this deletion leads to medial prefrontal cortex (mPFC)-dependent attention deficits, similar to those observed in FXS, and to alterations in transcriptional profiles within the mPFC, which mapped to two weighted gene coexpression network analysis modules. We demonstrated that these modules are conserved in human frontal cortex, are enriched for known FMRP targets and for genes involved in neuronal and synaptic processes, and that one is enriched for genes that are implicated in ASD, ID, and schizophrenia. Hub genes in these conserved modules represent potential targets for FXS. These findings provide support for a prefrontal deficit in FXS, indicate that attentional testing might be a reliable cross-species tool for investigating the pathophysiology of FXS and a potential readout for pharmacotherapy testing, and identify dysregulated gene expression modules in a relevant brain region. Significance Statement The significance of the current study lies in two key domains. First, this study demonstrates that deletion of the Fmrp-KH1 domain is sufficient to cause major mPFC-dependent attention deficits in both males and females, like those observed in both individuals with FXS and in knockout mouse models for FXS. Second, the study shows that deletion of the KH1 domain leads to alterations in the transcriptional profiles within the medial prefrontal cortex (mPFC), which are of potential translational value for subjects with FXS. These findings indicate that attentional testing might be a reliable cross-species tool for investigating the pathophysiology of FXS and a potential readout for pharmacotherapy testing and also highlight hub genes for follow up.
Data-driven modeling of cholinergic modulation of neural microcircuits: bridging neurons, synapses, and network states

Neuromodulators, such as acetylcholine (ACh), control information processing in neural microcircuits by regulating neuronal and synaptic physiology. Computational models and simulations enable predictions on the potential role of ACh in reconfiguring network states. As a prelude into investigating how the cellular and synaptic effects of ACh collectively influence emergent network dynamics, we developed a data-driven framework incorporating phenomenological models of the anatomy and physiology of cholinergic modulation of the neocortex. The first-draft models were integrated into a biologically detailed tissue model of neocortical microcircuitry to predict how ACh affects different types of neurons and synapses, and consequently alters global network states. Preliminary simulations not only corroborate the long-standing notion that ACh desynchronizes network activity, but also reveal a potentially finegrained control over a spectrum of neocortical states. We show that low levels of ACh, such as those during sleep, drive microcircuit activity into slow oscillations and network synchrony, whereas high ACh concentrations, such as those during wakefulness, govern fast oscillations and network asynchrony. In addition, network states modulated by ACh levels shape spike-time cross-correlations across distinct neuronal populations in strikingly different ways. These effects are likely due to the differential regulation of neurons and synapses caused by increasing levels of ACh that enhances cellular excitability by increasing neuronal activity and decreases the efficacy of local synaptic transmission by altering neurotransmitter release probability. We conclude by discussing future directions to refine the biological accuracy of the framework, which will extend its utility and foster the development of hypotheses to investigate the role of neuromodulation in neural information processing.
Visualizing Media Bias through Twitter

Traditional media outlets are known to report political news in a biased way, potentially affecting the political beliefs of the audience and even altering their voting behaviors. Therefore, tracking bias in everyday news and building a platform where people can receive balanced news information is important. We propose a model that maps the news media sources along a dimensional dichotomous political spectrum using the co-subscriptions relationships inferred by Twitter links. By analyzing 7 million follow links, we show that the political dichotomy naturally arises on Twitter when we only consider direct media subscription. Furthermore, we demonstrate a real-time Twitter-based application that visualizes an ideological map of various media sources.
Marine Fe-oxidizing Zetaproteobacteria: Historical, ecological, and genomic perspectives

The Zetaproteobacteria are a class of bacteria typically associated with marine Fe oxidizing environments. First discovered in the hydrothermal vents at Loihi Seamount, Hawaii, they have become model organisms for marine microbial Fe oxidation. In addition to deep sea and shallow hydrothermal vents, Zetaproteobacteria are found in coastal sediments, other marine subsurface environments, steel corrosion biofilms, as well as saline terrestrial aquifers and springs. Isolates from a range of environments all grow by Fe oxidation. Their success lies partly in their microaerophily, which enables them to compete with abiotic Fe oxidation at the low O2 concentrations common to Fe(II)-rich oxic/anoxic transition zones. Also, Zetaproteobacteria make a variety of biomineral morphologies as a repository for Fe(III) waste, and as attachment structures. To determine the known diversity of the Zetaproteobacteria, we have used 16S rRNA gene sequences to define 59 operational taxonomic units (OTUs), at 97% similarity. While some Zetaproteobacteria taxa appear to be cosmopolitan, various habitats enrich for different sets of Zetaproteobacteria. OTU networks show that certain Zetaproteobacteria co-exist, sharing compatible niches. These niches may correspond with adaptations to O2, H2, and nitrate availability, based on genomic analyses. Also, a putative Fe oxidation gene has been found in diverse Zetaproteobacteria taxa, suggesting that the Zetaproteobacteria evolved as specialists in Fe oxidation. In all, culture, genomic, and environmental studies suggest that Zetaproteobacteria are widespread, and therefore have a broad influence on marine and saline terrestrial Fe cycling.
Heterologous Expression of Pseudomonas putida Methyl-Accepting Chemotaxis Proteins Yields Escherichia coli Chemotactic to Aromatic Compounds

Escherichia coli, commonly used in chemotaxis studies, is attracted mostly by amino acids, sugars and peptides. We envisioned modifying chemotaxis specificity of E. coli by expressing heterologous chemoreceptors from Pseudomonas putida enabling attraction either to toluene or benzoate. The mcpT gene encoding the type 40H methyl-accepting chemoreceptor for toluene from Pseudomonas putida MT53 and the pcaY gene for the type 40H receptor for benzoate and related molecules from P. putida F1 were expressed from the trg promoter on a plasmid in motile wild-type E. coli MG1655. E. coli cells expressing McpT accumulated in chemoattraction assays to sources with 60–200 μM toluene; less strongly than the response to 100 μM serine, but statistically significantly stronger than to sources without any added attractant. An McpT-mCherry fusion protein was detectably expressed in E. coli and yielding weak but distinguishable membrane and polar foci in 1% of cells. E. coli expressing PcaY showed weak attraction to 0.1–1 mM benzoate but 50–70% of cells localized the PcaY-mCherry fusion to their membrane. We conclude that implementing heterologous receptors in the E. coli chemotaxis network is possible and, upon improvement of the compatibility of the type 40H chemoreceptors, may bear interest for biosensing. IMPORTANCE Bacterial chemotaxis might be harnessed for the development of rapid biosensors, in which chemical availability is deduced from cell accumulation to chemoattractants over time. Chemotaxis of Escherichia coli has been well-studied, but the bacterium is not attracted to chemicals of environmental concern, such as aromatic solvents. We show here that heterologous chemoreceptors for aromatic compounds from Pseudomonas putida at least partly functionally complement the E. coli chemotaxis network, yielding cells attracted to toluene or benzoate. Complementation was still inferior to native chemoattractants like serine, but our study demonstrates the potential for obtaining selective sensing for aromatic compounds in E. coli.
Desynchronizing to be faster? Perceptual- and attentional-modulation of brain rhythms in sub-millisecond scale

Neural oscillatory signals has been associated with many high-level functions (e.g. attention and working memory), because they reflect correlated behaviors of neural population that would facilitate the information transfer in the brain. On the other hand, a decreased power of oscillation (event-related desynchronization or ERD) has been associated with an irregular state in which many neurons behave in an uncorrelated manner. In contrast to this view, here we show that the human ERD is linked to the increased regularity of oscillatory signals. Using magnetoencephalography, we found that presenting a visual stimulus not only induced the ERD of alpha (8-13 Hz) and beta (13-30 Hz) rhythms in the contralateral visual cortex but also reduced the mean and variance of their inter-peak intervals (IPIs). This indicates that the suppressed alpha/beta rhythms became faster (reduced mean) and more regular (reduced variance) during visual stimulation. The same changes in IPIs, especially those of beta rhythm, were observed when subjects allocated their attention to a contralateral visual field. Those results revealed a new role of the ERD and further suggested that our brain regulates and accelerates a clock for neural computations by actively inducing the desynchronization in task-relevant regions.
Weather and climate monitoring for food risk management

Food insecurity represents one of the main indicators of the poverty level of a country and can breed a strong dependence on foreign aid with a strong slowdown of the national economy. African arid and semi‐arid areas are characterised by food precariousness and their agricultural activity is strongly dependent on the extreme climatic conditions that affect the available water supply. This situation has led to the need to develop new tools for the prediction and the management of crisis. The characterisation of climate and the identification of anomalies, the monitoring of weather conditions and their influence on crops, short and medium range weather forecasts and long‐term climate predictions are among the most powerful tools to predict, in as short a time as possible, crises due to the absence or delay of rainfall season. Meteorological information can also be used as an input to agrometeorological models applied for crisis prevention or for its management during the growing season when the crops are already present. In this paper, a review of these tools is made and some operational products presented. Copyright © 2006 Royal Meteorological Society
The importance of integrating flash cards as a visual tool inprove the retention of the meaning of verbs in the students of the ninth year of basic education

We have focused this project on the use of flashcards with activities that the English teachers can use in the teaching-learning process. These activities are created not only to present new vocabulary, and practice pronunciation, but also to call the attention of the students to participate in class using the verbs. The use of flashcards helps teachers to introduce a new word through an image and that image is about any vocabulary word and in this case is about verbs. Moreover, Andrew Cohen mentions some advantages of the flashcards. The main is that flashcardsengage a mental faculty known as active recall which is a principle of efficient learning, which claims the need to actively stimulate memory. Also there are three types of learners, kinesthetic learners who learn by doing, auditory learners learn by listening and visual learners learn by looking. All of them are important and the activities presented in this project will help to introduce the verbs in ninth year of basic education to visual learners achieving a long-term retention.
TLR3-TRIF pathway activation by Neospora caninum RNA enhances infection control

Neospora caninum is a protozoan parasite closely related to Toxoplasma gondii and has been studied for causing neuromuscular disease in dogs and abortions in cattle. It is recognized as the major cause of economic losses in bovine products. In that sense, this study aimed to evaluate the role of TLR3-TRIF dependent resistance against N. caninum infection. We observed that TLR3−/− and TRIF−/− mice presented higher parasite burden, increased inflammatory lesions and reduced production of IL-12p40, TNF, IFN-γ, and NO. Differently from T. gondii, N. caninum tachyzoites and its RNA recruited TLR3 and IRF3 to the parasitophorous vacuole (PV). We observed that N. caninum upregulated the expression of TRIF in macrophages, which by its turn upregulated IFN-α and IFN-β in the presence of the parasite. Furthermore, TRIF−/− infected macrophages produced lower levels of IL-12p40 and IFN-α replacement was able to completely restore the production of this key cytokine. Our results have shown that TLR3-TRIF signaling pathway enhances resistance against N. caninum infection, since it improves Th1 immune responses that control parasitism and tissue inflammation, which are hallmarks of the disease.
Biokimia dan Teknologi Farmasi: Desain Obat dan Vaksin dengan Pendekatan Biomedis Molekular

Perkembangan ilmu biokimia telah membuka cakrawala baru dengan dikembangkannya teknologi farmasi dengan pendekatan skala molekul. Dimenangkannya hadiah Nobel kimia tahun 2013 oleh peneliti Komputasi Kimia/Bioinformatika telah menunjukkan bahwa metode in silico molecular dynamics, homology modeling,dan molecular docking telah berperan penting dalam teknologi farmasi modern. Kedepannya, data hasil komputasi tersebut dapat digunakan untuk pengembangan personalized medicine. Artikel ulasan ini bertujuan untuk mengkaji peran penting biomedis molecular dalam teknologi farmasi modern.