Miracle-dz/UniFAR-FTUs huggingface dataset:
Cancer-specific CTCF binding facilitates oncogenic transcriptional dysregulation

Background The three-dimensional genome organization is critical for gene regulation and can malfunction in diseases like cancer. As a key regulator of genome organization, CCCTC-binding factor (CTCF) has been characterized as a DNA-binding protein with important functions in maintaining the topological structure of chromatin and inducing DNA looping. Among the prolific binding sites in the genome, several events with altered CTCF occupancy have been reported as associated with effects in physiology or disease. However, hitherto there is no comprehensive survey of genome-wide CTCF binding patterns across different human cancers. Results To dissect functions of CTCF binding, we systematically analyze over 700 CTCF ChIP-seq profiles across human tissues and cancers and identify cancer-specific CTCF binding patterns in six cancer types. We show that cancer-specific lost and gained CTCF binding events are associated with altered chromatin interactions, partially with DNA methylation changes, and rarely with sequence mutations. While lost bindings primarily occur near gene promoters, most gained CTCF binding events exhibit enhancer activities and are induced by oncogenic transcription factors. We validate these findings in T cell acute lymphoblastic leukemia cell lines and patient samples and show that oncogenic NOTCH1 induces specific CTCF binding and they cooperatively activate expression of target genes, indicating transcriptional condensation phenomena. Conclusions Specific CTCF binding events occur in human cancers. Cancer-specific CTCF binding can be induced by other transcription factors to regulate oncogenic gene expression. Our results substantiate CTCF binding alteration as a functional epigenomic signature of cancer.
Lifetime and 12 months cannabis use and disorders among soldiers residing in a military community in Nigeria

ABSTRACT Objective: The main aim of the study was to determine the lifetime and 12 months prevalence of cannabis use and cannabis use disorder (CUD) and their correlates among a military population in Nigeria. Method: Military officers (N = 223) were interviewed in this descriptive cross-sectional study. The Composite International Diagnostic Interview 7.0 was used to generate data on prevalence of cannabis use and to obtain the diagnosis of CUD. Results: Prevalence of lifetime cannabis was 13.5%, 12 months (6.8%), lifetime cannabis abuse (4.9%), lifetime cannabis dependence (0.9%), lifetime CUD (5.8%), and 12-month CUD (2.2%). Predictors at 95% CI of lifetime cannabis use include: elementary education OR = 2.23 (1.13–5.23), Hausa ethnicity/Fulani OR = 2.30, (1.34–5.82), minority tribes OR = 1.33 (1.12–3.66), ever received disciplinary action OR = 1.77, (1.19–5.64), ever deployed to operational areas OR = 1.12 (1.02–3.21), and ever injured in combat OR = 2.45, (1.39–7.41); and predictors of 12 months cannabis use include: elementary education OR = 1.78 (1.09–4.62), Hausa/Fulani ethnicity OR = 2.06 (1.27–533), the minority tribes OR = 1.42 (1.08–4.58), and ever injured in combat OR = 1.79 (1.04–5.21). Conclusion: Certain workplace factors, similar to other parts of the world, were associated with cannabis use in the Nigerian military.
Point-spread Function Estimation for Adaptive Optics Imaging of Astronomical Extended Objects

This paper focuses on point-spread function (PSF) estimation for astronomical images containing only single extended objects captured by adaptive optics systems. The problem is very different from, and much more challenging than, PSF estimation with point-like source images. We propose a new PSF estimation framework based on deep-learning technology. In this framework, PSFs can be estimated “end-to-end” using the original degraded images. Moreover, such a framework can precisely address different sources of blur without requiring accurate prior information about the PSF, image or imaging system. Therefore, the method is practical. We test the proposed method on both simulated and real data, and the favorable results show that the method is valid and performs much better than classical methods do.
Me, Myself, and My Thoughts: The Influence of Brooding and Reflective Rumination on Depressive Symptoms in Athletes in the United Kingdom

Individual differences in vulnerability to depression are still underexplored in athletes. We tested the influence of different brooding and reflective rumination profiles (i.e., repetitive thought processes in response to low/depressed mood) on the odds of experiencing clinically relevant depressive symptoms in competitive athletes (N = 286). The Patient Health Questionnaire–9 and the Ruminative Responses Scale–short form were utilized to measure depression and rumination, respectively. Compared to athletes with a low brooding/reflection profile, athletes with a high brooding/reflection profile had significantly higher odds of experiencing clinical levels of depressive symptoms (OR = 13.40, 95% CI = 3.81–47.11). A high reflection/low brooding profile was not, however, related to increased odds of depressive symptoms. Future research could extend our findings by exploring determinants of ruminative tendencies, especially brooding, in athletes. Furthermore, psychological interventions targeting rumination could be examined as a potential prevention and treatment approach to tackling depressive symptoms in athletes.
Standard Deviation Characterization of a Small Size Reverberation Chamber by Using Full-wave Simulation and E-Field Probe

Reverberation Chamber (RC) is a new type of measurement equipment used in electromagnetic compatibility and antenna tests and capable to produce an almost uniform electric filed inside a Working Volume (WV). In this paper, the field uniformity of an actual small size RC is studied. At first, the mode density of the chamber which should be larger than unity is investigated. In the next step, the Standard Deviation (SD) of a small size RC, as a field uniformity criterion is investigated in an existing RC. A highly detailed three-dimensional model of chamber including its stirrers, antenna, WV, and its door create to verify the field uniformity of a RTS60 reverberation chamber. The removal of reverberation chamber’s stirrers shows that they have a direct effect on the uniformity of field. As the stirrer moves during the test, the effect of three different position of stirrer on the field uniformity is investigated. The transmission antenna, as an important component of these rooms, is simulated and investigated separately. The reflection coefficient of that antenna fit the working frequency band of the chamber. In a real scenario, the SD of the chamber is measured by using an electric field probe. A comparison between the simulation and measurement also is done in order to confirm the uniformity of the electric fields.
Characterization of Fatty Acids in Cereals and Oilseeds from the Republic of Serbia by Gas Chromatography – Mass Spectrometry (GC/MS) with Chemometrics

Abstract This study investigates the potential of fatty acid profiles of various industrial crops to discriminate them based on their botanical origin. All of the analyzed plants were grown on experimental fields at Rimski Šančevi, Republic of Serbia. Cereal samples (corn, wheat, barley, and oat) were milled into flour and lipid fractions were extracted using n-hexane. Lipid fractions of oilseed samples (rape, flax, safflower, and pumpkin) were obtained by mechanical pressing. The fatty acids present in lipid fractions, were derivatized into corresponding volatile methyl esters (FAMEs) and determined on a gas chromatography/mass spectrometry instrument (GC-MS). Peaks of eluting compounds were simultaneously identified using mass spectra libraries, giving a match quality of over 90%. The peaks of molecular ions of methyl esters of 9 dominant fatty acids were extracted, and their abundances used to create numerical matrices for further data processing. Chemometric multivariate data analysis tools—principal component analysis (PCA), cluster analysis (CA), principal coordinate analysis (PCoA) and linear discriminant analysis (LDA), were used to extract significant variables, visualize discriminations, and classify between analyzed plant samples. The applied tools demonstrated separations of analyzed cereals in three groups: corn, oat and the samples of small grains—wheat and barley. In the case of oilseeds a clear separation between all four plant species was obtained. This work represents a new concept of the application of fatty acid analysis in developing authentication methods for industrial crops and their staple food products.
Robust algorithm of Clustering for the Detection of Hidden Variables in Bayesian Networks

In machine learning there are tree principal areas where the computer is able to learn, the ﬁrst one is supervised learning, the second one is unsupervised learning and the third one learning by reinforcement. On the ﬁrst appears something that the literature calls the ”learning problem” where they study the most common scenes in relationship to the data and the model, in this paper we purpose a modiﬁcation of the MS-EM algorithm that estimated a hidden variable from incomplete data in a scene where the model is unknown, and this algorithm is able to get a Bayesian network that explains the presence and relationship of the hidden variable and the dataset.
Impulsivity and impulse control disorders in pregnancy

ABSTRACT OBJECTIVE: We investigate the relationship between impulsivity and impulse control disorders (ICDs) in pregnancy. We claim that women with unplanned pregnancies are more impulsive and have a higher frequency of ICDs. METHODS: We perform a study on the 152 pregnant women who applied to Haydarpaşa Numune Training and Research Hospital Obstetrics outpatient clinic for routine follow-up. The participants are informed about the content of the study and their consents are taken. Socio-demographic characteristics of the participants are recorded. ICDs and impulsivity are assessed by Minnesota Impulse Control Disorders Interview Scale and Barrat Impulsivity Scale (BIS). RESULTS: ICD was present in 11.8% of the pregnant women (n = 18) before gestation and 9.2% (n = 14) during gestation. The motor and total impulsivity scores of those diagnosed with ICD during and before pregnancy were higher than those without ICD. The most common ICD during and before pregnancy was compulsive buying (3.3%). The relationship between pregnancy trimester and BIS score is insignificant. CONCLUSION: The motor and total impulsivity scores of those diagnosed with ICD before and during pregnancy were higher than scores of those not having ICD. It is well-known that ICDs cause not only pschiatric comorbidity but also illegal or high-risk behaviours, interpersonal, social, and economical problems. Thus, early recognition and treatment of ICDs in pregnancies will have a positive effect on both mothers’ and babies’ health.
Patients with Abdominal Aortic Aneurysm Demonstrate Higher Levels of Non-cholesterol Sterol Markers of Endogenous Cholesterol Synthesis

Aims: To establish the levels of selected non-cholesterol sterols in patients with abdominal aortic aneurysm (AAA) and to compare them with levels in non-AAA patients treated for lipid metabolism disorder. To compare the levels of high-sensitivity C-reactive protein (hs-CRP) and Lp-PLA 2 – inflammation markers in the same group of patients. Study Design: A total of 58 AAA patients indicated for elective surgical procedure and 20 non-AAA patients in the control group treated for lipid metabolism disorder were examined. Methodology: Lathosterol (Lat), desmosterol (Des), lanosterol (Lan), campesterol (Cam) and sitosterol (Sit) were analysed with the use of GC/MS in fasting plasma of patients with AAA and cholesterol synthesis in AAA patients are higher compared with those in non-AAA patients treated for lipid metabolism disorder. Higher hs-CRP levels in AAA patients show increased inflammatory activity compared with the control group.
A shape-gain approach for vector quantization based on flat tori

In this paper we present a vector quantization framework for Gaussian sources which combines a spherical code on layers of flat tori and the shape and gain technique. The basic concepts of spherical codes in tori layers are reviewed and two constructions are presented for the shape by exploiting the \begin{document}$ k/2 $\end{document} -dimensional lattices \begin{document}$ D_{k/2} $\end{document} and \begin{document}$ A^{*}_{k/2} $\end{document} as its pre-image. A scalar quantizer is optimized for the gain by using the Lloyd-Max algorithm for a given rate. The computational complexity of the quantization process is dominated by the lattice decoding process, which is linear for the \begin{document}$ D_{k/2} $\end{document} lattice and quadratic for the \begin{document}$ A^{*}_{k/2} $\end{document} lattice. The proposed quantizer is described in details and some numerical results are presented in terms of the SNR as a function of the quantization rate, in bits per dimension. The results show that the quantizer designed from the \begin{document}$ D_4 $\end{document} lattice outperform previous records when the rate is equal to 1 bit per dimension. These quantizer also outperform the quantizers designed from the dual lattice \begin{document}$ A^{*} $\end{document} for all rates tested. In general the two proposed frameworks perform within 2 dB of the rate distortion function, which may be a good trade-off considering their low computational complexity.
The role of primary healthcare in the management of work-related DED in the Netherlands

Dry eye disease (DED), and especially work-related dry eye, has an increasing incidence, and is expected to become a significant public health problem, with the increasing age until retirement, and the effect of the modern, digital, working environment causing higher visual demands. The indoor environment and more demanding, eye-related tasks, are risks factors for the development of dry eye symptoms, leading to DED at these workplaces. The current management for diagnosed DED is strongly pharmaceutical-based, and research looking at solutions towards better functioning and well-being of DED patients is rare. There is also a lack of evidence about the role of healthcare professionals in DED management. A substantial proportion of office workers surveyed experienced mild/moderate dry eye symptoms, and that while these were experienced more at work than at home, they had a negative impact on daily activities at work and after work, interfering with their social life. There is a lack of in-depth knowledge in dry eye diagnosis and management in all primary healthcare professionals surveyed and education is needed in management of work-related dry eye; there is a need for a specialised DED optometrist, with a recognised qualification; inter-professional cooperation should be promoted through better communication pathways; OHPs and optometrists should work together at the association level to develop clinical care guidelines; and a chronic care pathway in DED should be developed as part of the Dutch Government healthcare reforms.
Phylogenetic comparative methods are problematic when applied to gene trees with speciation and duplication nodes: correcting for biases in testing the ortholog conjecture

This repository contains “manuscript_dunn. RData” file, which is reproduced by using the files and scripts of Dunn et al. (Dunn CW, Zapata F, Munro C, Siebert S, Hejnol A (2018) Pairwise comparisons across species are problematic when analyzing functional genomic data. Proc Natl Acad Sci U S A 115: E409–E417. doi:10.1073/pnas.1707515115). In this repository, we also supplied “Data_TMRR_latest. rda” file, containing the results generated by using our own scripts. Our scripts are available on GitHub: https://github.com/tbegum/Testing_the_ortholog_conjecture.
Role of Proteomics in the Study of Trypanosoma cruzi Biology

Proteomics is the science that studies the proteome, which corresponds to the global expression of proteins at a given time under determined conditions. In the last 20 years, proteomics has emerged as a powerful tool that has allowed the study of proteins that are expressed in the cell under normal or altered conditions as well as post-translational modifications, such as phosphorylation, glycosidation, acetylation, and methylation, among others. In this chapter, we present the main contributions of proteomics to the knowledge of Trypanosoma cruzi biology . Proteomes of all T. cruzi life cycle stages, secretomes/exoproteomes, post-translational modifications such as phosphorylation or acetylation and immunomes, interactomes, and glycomes are described. The role of proteomics in the identification of new chemotherapeutic targets and potential vaccine candidates will also be discussed. to the intracellular superoxide and in and them. These observations indicate that protein expression focused on increased motility and control of macrophage-derived free radicals may represent a survival and persistence strategy developed by TcI isolates T. cruzi trypsin and Lys C. The peptides are subjected to a cleaning phase, and the peptides can be labeled using techniques such as ICAT, ITRAQ , and SILAC or not be labeled, using label-free quantification (LFQ ). Finally, the samples are subjected to a ultrahigh-pressure liquid chromatography (UHPLC) associated to mass spectrometry (MS). The information obtained is submitted to bioinformatics analysis using software such as MaxQuant (or others), for quantitative proteomics analysis, and then by Andromeda to obtain the sequence of the peptides in the different databases and Perseus (or others) to obtain classifications, proteomics interactions, post-transductional modifications, and metabolic pathways.
Fault‐tolerant FOC for five‐phase SPMSM with non‐sinusoidal back EMF

A fault-tolerant field-oriented control (FOC) is proposed for five-phase surface-mounted permanent magnet synchronous motor (SPMSM) with non-sinusoidal back electromotive force under single-phase open-circuit fault. On the basis of the concept of preserving the circular rotation of fundamental magnetic motive force and PM flux linkage, the decoupled model of five-phase SPMSM under single-phase open-circuit fault is derived. To suppress the torque ripples caused by third-harmonic content of PM flux linkage, the closed-form solution of current references with zero-torque pulsation in the synchronous coordinate is presented. Then, the presented solution is used for obtaining optimum current references to achieve minimum stator winding losses and maximum available torque while satisfying the zero-torque-pulsation constraint. The optimal current references generation method is simple and is suitable for real-time implementation. The experimental results confirm that the proposed method can effectively suppress the torque ripples and produce lower stator winding losses as well as wider-torque operation range compared with traditional fault-tolerant FOC method.
Production of indigenous vegetables and livelihood of farmers in Nigeria–Canada vegetable project

ABSTRACT Many indigenous vegetables are generally underutilized across different cultures, but they remain alternatives to exotic vegetables that often are expensive. This study investigated effects of participation in indigenous vegetable production on livelihood of farmers. Multistaged sampling was used to collect data from 222 vegetable farmers sampled from using a semi-structured questionnaire. Principal component analysis and endogenous switching regression (ESR) were employed for analysis. The ESR accounted for heterogeneity in the decision to participate or not, and for unobservable characteristics of farmers and their farms. Principal component analysis indicated 44.44% of respondents are low-level participants in production of indigenous vegetables (<4). Participation in the Nigeria–Canada vegetable project (NiCanVeg) increased household income; however, the impact of participation on income was smaller for households that participated, than those that did not. The impact of the NiCanVeg project on livelihood of participants was negative. For a project to have positive significant effects on livelihood, household characteristics of participants should be considered in its implementation.
Output feedback control for an underactuated benchmark system with bounded torques

In this paper, we consider the stabilization of the translational oscillator with a rotational actuator (TORA) system. Existing control methods for the TORA system are developed on the basis of the assumptions that full state feedback is available, and the actuator can supply control torques with any bounded amplitudes or system parameters are exactly known. In order to relax these assumptions, an amplitude‐saturated output feedback controller is proposed for the TORA system. Compared with existing control methods, the proposed method exhibits four remarkable features: free of plant parameters, bounded amplitude, output feedback, and unwinding behavior prevention. Specifically, the passivity of the TORA system is analyzed first. Then, a constructive energy‐like function is introduced and a corresponding amplitude‐saturated output feedback control law for the TORA system is proposed on the basis of the constructed energy‐like function. Lyapunov‐based analysis and LaSalle's invariance principle are used to prove the boundedness and convergence of the closed‐loop signals. Finally, numerical simulations with comparisons to previous reported methods are implemented to demonstrate the superior performance of the proposed method.
Klasifikasi Berita Hoax Dengan Menggunakan Metode Naive Bayes

Hoaxes contain false news or non-sourced news. Today, hoaxes are very widely spread through internet media. The development of information technology that has so quickly triggered the spread of hoax information through the internet has become uncontrolled. So we need an intelligent system that can classify hoax news content that is spread through internet media. The hoax classification process can be done through the preprocessing stage then weighting the word and classification using naive bayes. Measurements were made using the 10-ford cross validation method. The results obtained from these measurements, it is known that the value of fold 6 has the highest accuracy, which is equal to 85.28% which is classified as relevant documents as much as 307 and irrelevant as much as 53 or an error rate of 14.72%. While the average value based on hoax news and true news value precision 0.896 and recall 0.853