Miracle-dz/UniFAR-FTUs huggingface dataset:
Reconstruction of Complex Networks Under Missing and Spurious Noise Without Prior Knowledge

The problem of network reconstruction under missing and spurious interactions has attracted widespread interests, for it currently appears in a myriad of contexts. However, the existing methods require assuming that prior knowledge is known, which is not always available in realistic situations. The approach of stochastic block models (SBMs) can overcome this limitation, but it is very time-consuming and liable to trap in a local optimum. Specifically, we have to passively wait for several days or longer when it is applied to relatively big networks. In this paper, we study the heuristic mechanism of SBM and reveal that its greedy strategy may lead to the drop of the solution speed and optimality. Accordingly, we propose a novel network reconstruction method, called enhanced SBM (ESBM), with the assistance of the simulated annealing mechanism. By comparing ESBM with SBM in both synthetic and real networks, the experimental results suggest that the reconstructed network’s global properties of the ESBM can be closer to those of the true network than those of the SBM. Furthermore, the ESBM can flexibly adjust the convergence time according to the actual speed demands. We are surprised to find that, by slightly sacrificing the prediction accuracy, the calculation speed of ESBM can be more than ten times faster than that of SBM. Our results may also shed light on maximum-likelihood methods for large-scale networks’ reconstruction.
SARS‐CoV‐2 spike protein enhances MAP4K3/GLK‐induced ACE2 stability in COVID‐19

ACE2 on epithelial cells is the SARS‐CoV‐2 entry receptor. Single‐cell RNA‐sequencing data derived from two COVID‐19 cohorts revealed that MAP4K3/GLK‐positive epithelial cells were increased in patients. SARS‐CoV‐2‐induced GLK overexpression in epithelial cells was correlated with COVID‐19 severity and vesicle secretion. GLK overexpression induced the epithelial cell‐derived exosomes containing ACE2; the GLK‐induced exosomes transported ACE2 proteins to recipient cells, facilitating pseudovirus infection. Consistently, ACE2 proteins were increased in the serum exosomes from another COVID‐19 cohort. Remarkably, SARS‐CoV‐2 spike protein‐stimulated GLK, and GLK stabilized ACE2 in epithelial cells. Mechanistically, GLK phosphorylated ACE2 at two serine residues (Ser776, Ser783), leading to the dissociation of ACE2 from its E3 ligase UBR4. Reduction in UBR4‐induced Lys48‐linked ubiquitination at three lysine residues (Lys26, Lys112, Lys114) of ACE2 prevented its degradation. Furthermore, SARS‐CoV‐2 pseudovirus or live virus infection in humanized ACE2 mice induced GLK and ACE2 protein levels, and ACE2‐containing exosomes. Collectively, ACE2 stabilization by SARS‐CoV‐2‐induced MAP4K3/GLK may contribute to the pathogenesis of COVID‐19.
Spectrally Efficient QAM-FBMC System Using FTN Scheme with Block-Wise Interleaved Filters

In this paper, we propose a new quadrature amplitude modulation (QAM) based filter bank multi-carrier (FBMC) system using faster-than-Nyquist (FTN) scheme with block-wise interleaved filters. The proposed QAM-FBMC system can be implemented by block transform processing to have well-localization in time and frequency domains. The proposed QAM-FBMC system does not have time and frequency overheads such as cyclic prefix (CP), tail and guard band. In addition, the FTN scheme is applied to boost the spectral efficiency. Also, the proposed QAM-FBMC system can compensate interference more effectively using maximum likelihood sequence equalization in frequency domain. Simulation results shows the better bit error rate performances at high signal-to-noise ratios than the CP-OFDM systems. Therefore, the proposed QAM-FBMC system can achieve high spectral efficiency by reduction of time and frequency overheads and the FTN signaling.
Population Dynamics of Wide Compatibility System and Evaluation of Intersubspecific Hybrids by indica-japonica Hybridization in Rice

The exploitation of heterosis through intersubspecific hybridisation between indica and japonica has been a major breeding target in rice, but is marred by the cross incompatibility between the genomes. Wide compatibility (WC) is a triallelic system at the S5 locus on chromosome 6 that ensures the specificity of hybridisation within and between indica and japonica. The S5n allele that favours intercrossing is sparsely distributed in the rice gene pool and therefore warrants identification of diverse WC sources to develop superior intersubspecific hybrids. In this study, we have identified several novel WC sources through the marker-assisted screening of a large set of 950 rice genotypes. Seventeen percent of the genotypes carried S5n, which fell into two subpopulations. The WC genotypes showed wide phenotypic and genotypic variability, including both indica and japonica lines. Based on phenotypic performance, the WC varieties were grouped into three clusters. A subset of 41 WC varieties was used to develop 164 hybrids, of which WC/japonica hybrids showed relative superiority over WC/indica hybrids. The multilocation evaluation of hybrids indicated that hybrids derived from WC varieties, such as IRG137, IRG143, OYR128, and IRGC10658, were higher yielding across all the three different locations. Most of the hybrids showed the stability of performance across locations. The identified diverse set of wide compatible varieties (WCVs) can be used in the development of intersubspecific hybrids and also for parental line development in hybrid rice breeding.
Quantitation of MicroRNA-155 in Human Cells by Heterogeneous Enzyme-Linked Oligonucleotide Assay Coupled with Mismatched Catalytic Hairpin Assembly Reaction

In the present work, we describe the development of a chemiluminescent enzyme-linked oligonucleotide assay coupled with mismatched catalytic hairpin assembly (mCHA) amplification for the quantitative determination of microRNA-155. To improve its sensitivity, a polymerase-free mCHA reaction was applied as an isothermal amplification method. The detection limit of the proposed assay was 400 fM. In addition, the high specificity of the assay was demonstrated. The proposed assay allowed assessment of the content of microRNA-155 in human cancer lines such as HepG2, Caco2, MCF7, and HeLa. The quantitation of microRNA-155 was performed after purification of short RNAs (less than 200 nt) from cell lysates since a high matrix effect was observed without this pre-treatment. The results of the quantitative determination of the microRNA content in cells were normalized using nematode microRNA-39, the concentration of which was determined using a heterogeneous assay developed by us using a strategy identical to that of the microRNA-155 assay.
Prevalence and predictors of anemia among pregnant women in Ethiopia: Systematic review and meta-analysis

Background In Ethiopia limited information is available regarding the prevalence and predictors of anemia in pregnancy. This systematic review and meta-analysis estimated the pooled prevalence of anemia among pregnant women in Ethiopia and also identified its predictors. Materials and methods The published primary studies were searched in the following electronic databases; PubMed/Medline, Google scholars, AJOL, and EMBASE. All primary studies published from 01/01/2010 to 30/05/2020 and written in English language were included without restriction on study setting and design. Critical appraisal of all available articles was done and extracted data was analyzed using STATA software version 14. The pooled prevalence of anemia was presented using a forest plot. The I2 statistical test for heterogeneity, and the Egger’s and Begg’s tests for publication bias were used. The relative risk was used to assess the association of predictor variables with anemia. Result After screening 274 articles, sixty studies were included in the analysis. The pooled prevalence of anemia among pregnant women was 26.4(95% CI: 23.1, 29.6). Sub-group analysis showed higher pooled prevalence from community-based studies than institutional-based studies. Factors that were protective against maternal anemia included urban residence, formal education and smaller family size. Short birth interval and not having antenatal care (ANC) are associated with a higher risk of maternal anemia. Women with low dietary diversity [RR: 2.61(95% CI, 1.85, 3.68)], mid-upper arm circumference (MUAC) less than 23 cm [RR: 2.35(95% CI, 1.53, 3.68)] and those not taking iron-folic acid [RR: 1.53(95% CI: 1.30, 1.81)] also had a higher risk of anemia. Conclusion Almost one in four pregnant women in Ethiopia had anemia. Being literate, living in urban areas with small family size and adequate birth spacing, as well as good dietary diversity are associated with a lower risk of anemia in pregnancy. Registration number (ID: CRD42020211054).
Novel Trends in Hydrogel Development for Biomedical Applications: A Review

Nowadays, there are still numerous challenges for well-known biomedical applications, such as tissue engineering (TE), wound healing and controlled drug delivery, which must be faced and solved. Hydrogels have been proposed as excellent candidates for these applications, as they have promising properties for the mentioned applications, including biocompatibility, biodegradability, great absorption capacity and tunable mechanical properties. However, depending on the material or the manufacturing method, the resulting hydrogel may not be up to the specific task for which it is designed, thus there are different approaches proposed to enhance hydrogel performance for the requirements of the application in question. The main purpose of this review article was to summarize the most recent trends of hydrogel technology, going through the most used polymeric materials and the most popular hydrogel synthesis methods in recent years, including different strategies of enhancing hydrogels’ properties, such as cross-linking and the manufacture of composite hydrogels. In addition, the secondary objective of this review was to briefly discuss other novel applications of hydrogels that have been proposed in the past few years which have drawn a lot of attention.
Impulse Noise Suppression for Single-Carrier Coded Systems by Monte Carlo Expectation Maximization

An efficient approach to alleviating performance loss caused by unknown (non-stationary) impulse noise, which is typically sparse and whose statistics are difficult to model accurately, was made possible in power line communications systems when the clipping operation is properly implemented. As reported in numerous papers, the clipping threshold, which impacts system performance profoundly, is closely related with the probability of impulse occurrence and the strength of the background noise. This paper first highlights that the least-absolute-shrinkage-and-selection-operator (LASSO) algorithm, aimed at estimating the regularization parameter $\lambda$ and sparse vector of regression coefficients, can be interpreted as an effective clipping operation. Subsequently, a hybrid of the Bayesian LASSO and the maximum a posteriori algorithm using the Monte Carlo expectation maximization (MCEM) is proposed to simultaneously estimate the regularization parameter and detect the convolutional codeword in single-carrier coded systems subject to the impulse noise. Moreover, by exploiting information exchangeable between those two aforementioned entities, a novel termination rule on the EM iteration stage is devised. Numerical results attest the efficacy of the proposed scheme, despite a lack of statistical knowledge on impulse noise models.
Clinical phenotype of adult‐onset liver disease in patients with variants in ABCB4 , ABCB11 , and ATP8B1

Variants in ATP8B1, ABCB11, and ABCB4 underlie the most prevalent forms of progressive familial intrahepatic cholestasis. We aim to describe variants in these genes in a cohort of patients with adult‐onset liver disease, and explore a genotype–phenotype correlation. Patients with onset of liver disease aged above 18 who underwent sequencing of cholestasis genes for clinical purposes over a 5‐year period were identified. Bioinformatic analysis of variants was performed. Liver histology was evaluated in patients with variants. Of the 356 patients tested, at least one variant was identified in 101 (28.4%): 46 ABCB4, 35 ABCB11, and 28 ATP8B1. Patients with ABCB4 variants had chronic liver disease (71.7%) and pregnancy‐associated liver dysfunction (75%), with a younger age of onset in more severe genotypes (p = 0.046). ABCB11 variants presented with pregnancy‐associated liver dysfunction (82.4%) and acute/episodic cholestasis (40%), with no association between age of onset and genotype severity. ATP8B1 variants were associated with chronic liver disease (75%); however, they were commonly seen in patients with an alternate etiology of liver disease and variants were of low predicted pathogenicity. In adults with suspected genetic cholestasis, variants in cholestasis genes were frequently identified and were likely to contribute to the development of liver disease, particularly ABCB4 and ABCB11. Variants were often in heterozygous state, and they should no longer be considered recessive Mendelian traits. Sequencing cholestasis genes in selected patients with adult‐onset disease should be considered, with interpretation in close collaboration with histopathologists and geneticists.
Patient-Important Outcomes Other Than Mortality in Contemporary ICU Trials: A Scoping Review

OBJECTIVES: Randomized clinical trials (RCTs) conducted in adult ICU patients increasingly include patient-important outcomes other than mortality. This comes with challenges regarding outcome choices/definitions, handling of deceased patients and missing data in analyses, and choices of effect measures and statistical methods due to complex distributions. This scoping review aimed to characterize how these challenges are handled in relevant contemporary RCTs. DATA SOURCES: We systematically searched 10 selected journals for RCTs conducted primarily in adult ICU patients published between 1 January 2018 and 5 May 2022 reporting at least one patient-important outcome other than mortality, including “days alive without”…-type outcomes, functional/cognitive/neurologic outcomes, health-related quality of life (HRQoL) outcomes, and ordinal/other outcomes. STUDY SELECTION: Abstracts and full-texts were assessed independently and in duplicate by two reviewers. DATA EXTRACTION: Data were extracted independently and in duplicate by two reviewers using predefined and pilot-tested extraction forms and subsequently categorized to facilitate analysis. DATA SYNTHESIS: We included 687 outcomes from 167 RCTs, with 32% of RCTs using a patient-important outcome other than mortality as a (co-)primary outcome, most frequently “days alive without”…-type outcomes. Many different functional/cognitive/neurologic (103) and HRQoL (29) outcomes were reported. Handling of deceased patients varied, with analyses frequently restricted to survivors only for functional/cognitive/neurologic (62%) and HRQoL (89%) outcomes. Follow-up was generally longer and missing data proportions higher for functional/cognitive/neurologic and HRQoL outcomes. Most outcomes were analyzed using nonparametric tests (31%), linear regression/t tests (27%), chi-square–like tests (12%), and proportional odds logistic regression (9%), often without presentation of actual treatment effects estimates (38%). CONCLUSIONS: In this sample of RCTs, substantial variation in practice and suboptimal methodological choices were observed. This calls for increased focus on standardizing outcome choices and definitions, adequate handling of missing data and deceased patients in analyses, and use of statistical methods quantifying effect sizes.
Association analyses of host genetics, root-colonizing microbes, and plant phenotypes under different nitrogen conditions in maize

The root-associated microbiome (rhizobiome) affects plant health, stress tolerance, and nutrient use efficiency. However, it remains unclear to what extent the composition of the rhizobiome is governed by intraspecific variation in host plant genetics in the field and the degree to which host plant selection can reshape the composition of the rhizobiome. Here, we quantify the rhizosphere microbial communities associated with a replicated diversity panel of 230 maize (Zea mays L.) genotypes grown in agronomically relevant conditions under high N (+N) and low N (-N) treatments. We analyze the maize rhizobiome in terms of 150 abundant and consistently reproducible microbial groups and we show that the abundance of many root-associated microbes is explainable by natural genetic variation in the host plant, with a greater proportion of microbial variance attributable to plant genetic variation in -N conditions. Population genetic approaches identify signatures of purifying selection in the maize genome associated with the abundance of several groups of microbes in the maize rhizobiome. Genome-wide association study was conducted using the abundance of microbial groups as rhizobiome traits, and n=622 plant loci were identified that are linked to the abundance of n=104 microbial groups in the maize rhizosphere. In 62/104 cases, which is more than expected by chance, the abundance of these same microbial groups was correlated with variation in plant vigor indicators derived from high throughput phenotyping of the same field experiment. We provide comprehensive datasets about the three-way interaction of host genetics, microbe abundance, and plant performance under two N treatments to facilitate targeted experiments toward harnessing the full potential of root-associated microbial symbionts in maize production.
Foot Plantar Pressure Distribution Modeling Based On Image Processing

Several factors have been associated with the distribution of plantar foot pressure, including: (i) the body weight, (ii) age, (iii) foot structure and (iv) standing / walking strategy. It is predicted that the biomechanics of the foot is influenced by the structure of the foot. The objective of this study was to obtain the plantar pressure distribution model of the foot using custom image processing algorithms upon the images captured by a commercial plantar pressure measurement machine, the EMED-X. The study involved the participation and data collection from 79 human subjects, ranging from age 20–60 years old. This model can be analysed further to be used as a predictor for the formation of foot ulceration in certain subjects.
Long-Term Exposure to Ozone and Fine Particulate Matter and Risk of Premature Coronary Artery Disease: Results from Genetics of Atherosclerotic Disease Mexican Study

Simple Summary Epidemiological studies have identified associations between fine particulate matter (with an aerodynamic diameter of less than 2.5 μm (PM2.5)) and ozone exposure with cardiovascular disease; however, studies linking ambient air pollution and premature coronary artery disease (pCAD) in Latin America are nonexistent. We leveraged data from the Genetics of Atherosclerotic Disease (GEA) Mexican study to address the question of the extent to which long-term exposure to ozone and PM2.5 exposure was associated with the risk of pCAD. We showed for the first time a higher risk of pCAD associated with 1 ppb increase in ozone (1-year, 2-year, 3-year, and 5-year) and 5μg/m3 of PM2.5 (5-year) compared to controls. This study provides evidence that ozone and PM2.5 may be a modifiable risk factor for pCAD. Abstract (1) Background: Epidemiological studies have identified associations between fine particulate matter (PM2.5) and ozone exposure with cardiovascular disease; however, studies linking ambient air pollution and premature coronary artery disease (pCAD) in Latin America are non-existing. (2) Methods: Our study was a case–control analysis nested in the Genetics of Atherosclerotic Disease (GEA) Mexican study. We included 1615 participants (869 controls and 746 patients with pCAD), recruited at the Instituto Nacional de Cardiología Ignacio Chávez from June 2008 to January 2013. We defined pCAD as history of myocardial infarction, angioplasty, revascularization surgery or coronary stenosis > 50% diagnosed before age 55 in men and age 65 in women. Controls were healthy individuals without personal or family history of pCAD and with coronary artery calcification equal to zero. Hourly measurements of ozone and PM2.5 from the Atmospheric Monitoring System in Mexico City (SIMAT in Spanish; Sistema de Monitero Atmosférico de la Ciudad de México) were used to calculate annual exposure to ozone and PM2.5 in the study participants. (3) Results: Each ppb increase in ozone at 1-year, 2-year, 3-year and 5-year averages was significantly associated with increased odds (OR = 1.10; 95% CI: 1.03–1.18; OR = 1.17; 95% CI: 1.05–1.30; OR = 1.18; 95% CI: 1.05–1.33, and OR = 1.13; 95% CI: 1.04–1.23, respectively) of pCAD. We observed higher risk of pCAD for each 5 µg/m3 increase only for the 5-year average of PM2.5 exposure (OR = 2.75; 95% CI: 1.47–5.16), compared to controls. (4) Conclusions: Ozone exposure at different time points and PM2.5 exposure at 5 years were associated with increased odds of pCAD. Our results highlight the importance of reducing long-term exposure to ambient air pollution levels to reduce the burden of cardiovascular disease in Mexico City and other metropolitan areas.
Culturally Adapting Evidence on Dementia Prevention for Ethnically Diverse Communities: Lessons Learnt from co-design

ABSTRACT Objectives 40% of dementia cases can be prevented by addressing 12 lifestyle factors. These risk factors have increased presence in ethnic minorities, yet dementia prevention messages have not reached these communities. This article investigates the experience of co-designing a dementia prevention animated film with 9 ethnic groups in Australia. Methods Evidence-based recommendations were adapted through an iterative process involving workshops with a stakeholder advisory committee and nine focus groups with 104 participants from the Arabic-, Hindi-, Tamil-, Cantonese-, Mandarin-, Greek-, Italian-, Spanish-, and Vietnamese-speaking communities. Data were analyzed using the Normalization Process Theory. Results Cultural adaptation involves consideration of the mode of delivery, imagery and tone of the resource being developed; ensuring cultural adequacy; anticipating the need of the end-users; and managing linguistic challenges associated with working across multiple languages. Conclusions Learnings from this co-design process offer valuable insights for researchers and program developers who work with ethnic minority groups. Clinical Implications • Adaptation across cultures and languages is a negotiation not a consensus building exercise • Linguistic adaptation requires consideration of the education levels, and linguistic and intergenerational preferences of community members • Co-designing across multiple languages and cultures risks “flattening out” key aspects of cultural specificity.
Electrodeposited Magnetic Nanowires with Radial Modulation of Composition

In the last few years, magnetic nanowires have gained attention due to their potential implementation as building blocks in spintronics applications and, in particular, in domain-wall- based devices. In these devices, the control of the magnetic properties is a must. Cylindrical magnetic nanowires can be synthesized rather easily by electrodeposition and the control of their magnetic properties can be achieved by modulating the composition of the nanowire along the axial direction. In this work, we report the possibility of introducing changes in the composition along the radial direction, increasing the degrees of freedom to harness the magnetization. In particular, we report the synthesis, using template-assisted deposition, of FeNi (or Co) magnetic nanowires, coated with a Au/Co (Au/FeNi) bilayer. The diameter of the nanowire as well as the thickness of both layers can be tuned at will. In addition to a detailed structural characterization, we report a preliminary study on the magnetic properties, establishing the role of each layer in the global collective behavior of the system.