Miracle-dz/UniFAR-FTUs huggingface dataset:
Markov chains improve the significance computation of overlapping genome annotations

Motivation Genome annotations are a common way to represent genomic features such as genes, regulatory elements or epigenetic modifications. The amount of overlap between two annotations is often used to ascertain if there is an underlying biological connection between them. In order to distinguish between true biological association and overlap by pure chance, a robust measure of significance is required. One common way to do this is to determine if the number of intervals in the reference annotation that intersect the query annotation is statistically significant. However, currently employed statistical frameworks are often either inefficient or inaccurate when computing p-values on the scale of the whole human genome. Results We show that finding the p-values under the typically used “gold” null hypothesis is 𝒩𝒫-hard. This motivates us to reformulate the null hypothesis using Markov chains. To be able to measure the fidelity of our Markovian null hypothesis, we develop a fast direct sampling algorithm to estimate the p-value under the gold null hypothesis. We then present an open-source software tool MCDP that computes the p-values under the Markovian null hypothesis in 𝒪 (m2 + n) time and 𝒪 (m) memory, where m and n are the numbers of intervals in the reference and query annotations, respectively. Notably, MCDP runtime and memory usage are independent from the genome length, allowing it to outperform previous approaches in runtime and memory usage by orders of magnitude on human genome annotations, while maintaining the same level of accuracy. Availability The software is available at https://github.com/fmfi-compbio/mc-overlaps. All data for reproducibility are available at https://github.com/fmfi-compbio/mc-overlaps-reproducibility
Using soybean historical field trial data to study genotype by environment variation and identify mega-environments with the integration of genetic and non-genetic factors

Soybean (Glycine max (L.) Merr. ) provides plant-based protein for global food production and is extensively bred to create cultivars with greater productivity in distinct environments. Plant breeders evaluate new soybean genotypes using multi-environment trials (MET). The application of MET assumes that trial locations provide representative environmental conditions that cultivars are likely to encounter when grown by farmers. In addition, MET are important to depict the patterns of genotype by environment interactions (GEI). To evaluate GEI for soybean seed yield and identify mega-environments (ME), a retrospective analysis of 39,006 data points from experimental soybean genotypes evaluated in preliminary and uniform field trials conducted by public plant breeders from 1989-2019 was considered. ME were identified from phenotypic information from the annual trials, geographic, soil, and meteorological records at the trial locations. Results indicate that yield variation was mostly explained by location and location by year interactions. The static portion of the GEI represented 26.30% of the total yield variance. Estimates of variance components derived from linear mixed models demonstrated that the phenotypic variation due to genotype by location interaction effects was greater than genotype by year interaction effects. A trend analysis indicated a two-fold increase in the genotypic variance between 1989-1995 and 1996-2019. Furthermore, the heterogeneous estimates of genotypic, genotype by location, genotype by year, and genotype by location by year variances, were encapsulated by distinct probability distributions. The observed target population of environments can be divided into at least two and at most three ME, thereby suggesting improvements in the response to selection can be achieved when selecting directly for clustered (i.e., regions, ME) versus selecting across regions. Clusters obtained using phenotypic data, latitude, and soil variables plus elevation, were the most effective. In addition, we published the R package SoyURT which contains the data sets used in this work. 2 Highlights Mega-environments can be identified with phenotypic, geographic, and meteorological data. Reliable estimates of variances can be obtained with proper analyses of historical data. Genotype by location was more important than genotype by year variation for seed yield. The trend in genotype by environment variances was captured in probability distributions.
Base station polarization-sensitive adaptive antenna for mobile radio

An attractive alternative to combat desired-signal fading and suppress co-channel interference in a mobile radio environment is to use a base station adaptive antenna with polarization-sensitive elements. This paper describes the design of a four-crossed-dipole adaptive array in which polarization discrimination is used to separate the desired signal from both directional and non-directional wave interference. In contrast to previous work, mutual coupling has been included in the evaluation of the array performance, using the method of moments. Further, computer simulation shows that the performance of the adaptive antenna is improved in the presence of a flat-backed corner reflector. <<ETX>>
An Electric Load Forecasting Scheme for University Campus Buildings Using Artificial Neural Network and Support Vector Regression

Since the electricity is produced and consumed simultaneously, predicting the electric load and securing affordable electric power are necessary for reliable electric power supply. In particular, a university campus is one of the highest power consuming institutions and tends to have a wide variation of electric load depending on time and environment. For these reasons, an accurate electric load forecasting method that can predict power consumption in real-time is required for efficient power supply and management. Even though various influencing factors of power consumption have been discovered for the educational institutions by analyzing power consumption patterns and usage cases, further studies are required for the quantitative prediction of electric load. In this paper, we build an electric load forecasting model by implementing and evaluating various machine learning algorithms. To do that, we consider three building clusters in a campus and collect their power consumption every 15 minutes for more than one year. In the preprocessing, features are represented by considering periodic characteristic of the data and principal component analysis is performed for the features. In order to train the electric load forecasting model, we employ both artificial neural network and support vector machine. We evaluate the prediction performance of each forecasting model by 5-fold cross-validation and compare the prediction result to real electric load.
A NOVEL MICROSTRIP-TO-WAVEGUIDE TRANSITION USING ELECTROMAGNETIC BANDGAP STRUCTURE

A novel microstrip-to-waveguide transition using mushroom-like electromagnetic bandgap (EBG) structure is proposed. The transition consists of a waveguide terminated with a mushroomlike EBG structure fabricated on a conductor-backed dielectric substrate and a strip probe inserted into the waveguide. The mushroom-like EBG structure can replace a quarter-wavelength waveguide back-short used in the conventional probe-type transitions. The transition has been designed on a single layered dielectric substrate by placing the EBG patches and the strip probe on the same surface of the substrate. The fabricated microstrip-to-waveguide transition has achieved a good performance with return loss greater than 15 dB over a bandwidth of 5% in the Ka-band.
Special Issue on EMC in the Near-Field: Theory, Measurements, and Applications Foreword

The papers in this special issue focus on theory, measurements, and applications for electromagnetics in near-field. Numerous electromagnetic compatibility (EMC) problems occur in the near-field (NF) where far-field (FF) concepts, measurement techniques, and equipment may not provide correct insight and solutions. The ability to identify near-field effects when assessing EMC problems is important to both researchers and practitioners alike. Applications of advanced technologies, which are characterized by new materials and rapidly increasing frequencies, in different civil, industrial, and military areas highlight the importance of NF techniques. This issue examines recent research on NF theoretical approaches, computational models, and measurement techniques in light of EMC goals.
InGaAs tunnel FET with sub-nanometer EOT and sub-60 mV/dec sub-threshold swing at room temperature

InGaAs homojunction Tunnel FET devices are demonstrated with sub-60 mV/dec Sub-threshold Swing (SS) measured in DC. A 54 mV/dec SS is achieved at 100 pA/μm over a drain voltage range of 0.2–0.5 V. The SS remains sub-60 mV/dec over 1.5 orders of magnitude of current at room temperature. Trap-Assisted Tunneling (TAT) is found to be negligible in the device evidenced by low temperature dependence of the transfer characteristics. Equivalent Oxide Thickness (EOT) is found to play the major role in achieving sub-60 mV/dec performance. The EOT of the demonstrated devices is 0.8 nm.
Pediatric Preventive Care in Middle-High Resource Countries—The Padova Chart for Health in Children

Importance The Padova Chart for Health in Children (PCHC) aims to gather the evidence of healthcare promotion and protection for chidren and adolescents (i.e., aged <18 y) into a single document in order to guide families, healthcare providers and social actors on healthy choices. No more than 2% of Europeans and North Americans aged <30 y have a healthy lifestyle. This, together with metabolic and brain plasticity during childhood, creates the ideal opportunity to implement preventive strategies. Guided interventions promoting healthy lifestyle in children and families therefore have a key role in abating the unprecedented pandemic of non-communicable diseases (NCDs) in adulthood. Observations The PCHC is divided into four sections: nutrition, cardiovascular health, respiratory health, and mental and social health. Each section is structured in an ALICE approach (assessment, lobbying, intervention, call-for-action, evaluation): assessment of necessity, describing relevance to healthcare; lobbying to identify those who can effect the proposed interventions; interventions involving family, school and peers; a call-for-action to define priorities among the proposed interventions; and objective evaluation measures that can be applied on a population basis. Conclusions and Relevance Interventions promoting health in childhood require joint action from multiple institutional, local and family representatives, with the shared goal of promoting health across the entire age group. These lifestyle interventions have the potential to change the lifetime risk trajectory for NCDs.
Does the E-Commerce City Pilot Reduce Environmental Pollution? Evidence From 265 Cities in China

In order to promote the healthy and rapid development of e-commerce, China launched the construction of National E-commerce Demonstration Cities in 2009. This paper presents a feasible road to achieving sustainable development through the new urban development model. The paper employs the data of 265 cities in China from 2007 to 2016 as a research sample and uses the multiperiod difference-in-difference method to test the impact of National E-commerce Demonstration Cities pilots on urban environmental pollution. The basic result shows that urban environmental pollution is reduced by about 17.5% on average after becoming pilot cities, and the National E-commerce Demonstration Cities policy significantly reduces urban environmental pollution. We adopt a series of robustness tests, and all tests show that the basic result is still robust. Moreover, heterogeneity tests show that the pollution reduction effect of the National E-commerce Demonstration Cities policy in big cities is stronger than in small- and mid-sized cities, and there is no significant difference between the eastern cities and mid-western cities. The pollution reduction effect of the National E-commerce Demonstration Cities policy is more significant in cities with high human capital, low fiscal expenditure, and high information infrastructure. The empirical results of the spatial Dubin model show that the pilot city has no significant spatial spillover to neighboring cities. In the era of rapid development of e-commerce, this study provides a reference for developing countries to improve the urban environment and achieve sustainable development by using the new urban development model integrating e-commerce and urbanization.
Bradykinin-Induced Sensitization of Transient Receptor Potential Channel Melastatin 3 Calcium Responses in Mouse Nociceptive Neurons

TRPM3 is a calcium-permeable cation channel expressed in a range of sensory neurons that can be activated by heat and the endogenous steroid pregnenolone sulfate (PS). During inflammation, the expression and function of TRPM3 are both augmented in somatosensory nociceptors. However, in isolated dorsal root ganglion (DRG) neurons application of inflammatory mediators like prostaglandins and bradykinin (BK) inhibit TRPM3. Therefore, the aim of this study was to examine the effect of preceding activation of cultured 1 day old mouse DRG neurons by the inflammatory mediator BK on TRPM3-mediated calcium responses. Calcium signals were recorded using the intensity-based dye Fluo-8. We found that TRPM3-mediated calcium responses to PS were enhanced by preceding application of BK in cells that responded to BK with a calcium signal, indicating BK receptor (BKR) expression. The majority of cells that co-expressed TRPM3 and BKRs also expressed TRPV1, however, only a small fraction co-expressed TRPA1, identified by calcium responses to capsaicin and supercinnamaldehyde, respectively. Signaling and trafficking pathways responsible for sensitization of TRPM3 following BK were characterized using inhibitors of second messenger signaling cascades and exocytosis. Pharmacological blockade of protein kinase C, calcium–calmodulin-dependent protein kinase II and diacylglycerol (DAG) lipase did not affect BK-induced sensitization, but inhibition of DAG kinase did. In addition, release of calcium from intracellular stores using thapsigargin also resulted in TRPM3 sensitization. Finally, BK did not sensitize TRPM3 in the presence of exocytosis inhibitors. Collectively, we show that preceding activation of DRG neurons by BK sensitized TRPM3-mediated calcium responses to PS. Our results indicate that BKR-mediated activation of intracellular signaling pathways comprising DAG kinase, calcium and exocytosis may contribute to TRPM3 sensitization during inflammation.
Comparison of Risk of Target Organ Damage in Different Phenotypes of Arterial Stiffness and Central Aortic Blood Pressure

Objectives The aim of this study was to explore the risk of target organ damage (TOD) in different groups based on carotid-femoral pulse wave velocity (cfPWV) and central aortic blood pressure (CBP) in different populations. Methods The study cohort was divided into four groups according to the status of cfPWV and CBP [Group (cfPWV/CBP): high cfPWV and high CBP; Group (cfPWV): high cfPWV and normal CBP; Group (CBP): normal cfPWV and high CBP; Group (control): normal cfPWV and normal CBP]. TOD was determined by the assessment of carotid intima-media thickness (CIMT) abnormality, chronic kidney disease (CKD), microalbuminuria, and left ventricular hypertrophy (LVH). Results A total of 1,280 patients (mean age 53.14 ± 12.76 years, 64.1% male patients) were recruited in this study. Regarding Group (control) as reference, LVH was significantly higher in Group (cfPWV) and Group (CBP) [OR 2.406, 95% CI (1.301–4.452), P < 0.05; OR 2.007, 95% CI (1.335–3.017), P < 0.05]; microalbuminuria was significantly higher in Group (cfPWV/CBP) and Group (CBP) [OR 3.219, 95% CI (1.630–6.359), P < 0.05; OR 3.156, 95% CI (1.961–5.079), P < 0.05]. With age stratified by 60 years, the risk of CKD was significantly higher in Group (cfPWV/CBP) [OR 4.019, 95% CI (1.439–11.229), P < 0.05]. Conclusion Different phenotypes based on the status of cfPWV and CBP were associated with different TOD. Individuals with both cfPWV and CBP elevated have a higher risk of microalbuminuria.
Transdiagnostic Cognitive-Behavioral Therapy for Depression and Anxiety Disorders in Cardiovascular Disease Patients: Results From the CHAMPS Pilot-Feasibility Trial

Objective The aim of the Cardiovascular Health in Anxiety and Mood Problems Study (CHAMPS) is to pilot the Unified Protocol (UP) for the transdiagnostic treatment of depression and anxiety disorders in patients recently hospitalized for cardiovascular diseases (CVDs) and evaluate the feasibility. Methods The present study is a controlled, block randomized pragmatic pilot-feasibility trial incorporating qualitative interview data, comparing UP (n = 9) with enhanced usual care (EUC, n = 10). Eligible trial participants had a recent CVD-cause admission and were above the severity threshold for depression or anxiety denoted by Patient Health Questionnaire (PHQ-9) total scores ≥10 and/or Generalized Anxiety Disorder (GAD-7) total scores ≥7 respectively on two occasions, and met criteria for one or more depression or anxiety disorders determined by structured clinical interview. Study outcomes were analyzed as intention-to-treat using linear mixed models and qualitative interview data were analyzed with content analysis. Results Quantitative and qualitative measured indicated acceptability of the transdiagnostic CBT intervention for CVD patients with depression or anxiety disorders. Satisfaction with UP was comparable to antidepressant therapy and higher than general physician counseling. However, there were difficulties recruiting participants with current disorders and distress on two occasions. The UP was associated with a reduction in total number of disorders determined by blinded raters. Linear mixed models indicated that a significantly greater reduction in anxiety symptoms was evident in the UP group by comparison to the EUC group (GAD-7, p between groups = 0.011; Overall Anxiety Severity and Impairment Scale, p between groups = 0.013). Results favored the UP group by comparison to EUC for change over 6 months on measures of physical quality of life and harmful alcohol use. There was no difference between the two groups on changes in depression symptoms (PHQ-9), stress, metacognitive worry beliefs, physical activity, or adherence. Discussion In conclusion, this feasibility trial indicates acceptability of transdiagnostic CBT intervention for CVD patients with depression or anxiety disorders that is tempered by difficulties with recruitment. Larger trials are required to clarify the efficacy of transdiagnostic depression and anxiety disorder CBT in populations with CVDs and depressive or anxiety disorders. Clinical Trial Registration https://www.australianclinicaltrials. gov.au/anzctr/trial/ACTRN12615000555550, identifier: ACTRN12615000555550.
Axon Guidance Molecules in the Islets of Langerhans

The islets of Langerhans, responsible for regulating blood glucose in vertebrates, are clusters of endocrine cells distributed throughout the exocrine pancreas. The spatial architecture of the different cell types within the islets controls cell-cell communication and impacts their ability to collectively regulate glucose. Islets rely on a range of chemotactic and adhesive cues to establish and manage intercellular relationships. Growing evidence indicates that axon guidance molecules such as Slit-Robo, Semaphorin-Neuropilin, Ephrin-Eph, and Netrins, influence endocrine progenitors’ cell migration to establish correct architecture during islet morphogenesis, as well as directly regulating physical cell-cell communication in the mature islet to coordinate hormone secretion. In this mini-review, we discuss what is known and not yet known about how axon guidance molecules contribute to islet morphogenesis and function.
A Novel Hyaluronic Acid-Black Rice Anthocyanins Nanocomposite: Preparation, Characterization, and Its Xanthine Oxidase (XO)-Inhibiting Properties

To promote the normal metabolism of human uric acid, high-performance hyaluronic acid-black rice anthocyanins (HAA) nanocomposite particles were successfully prepared by a simple crosslinking method as a novel xanthine oxidase inhibitor. Its structure and properties were characterized by scanning electron microscopy (SEM), transmission electron microscopy (TEM), Fourier transform infrared spectrometry (FT-IR), and X-ray diffraction (XRD). SEM and TEM electron microscopy showed an obvious double-layer spherical structure with a particle size of ~298 nm. FT-IR and XRD analysis confirmed that black rice anthocyanins (ATC) had been successfully loaded into the hyaluronic acid (HA) structure. Nanocomposite particles (embedded form) showed higher stability in different environments than free black rice ATC (unembedded form). In addition, the preliminary study showed that the inhibition rate of the nanocomposite particles on Xanthine oxidase (XO) was increased by 40.08%. These results indicate that HAA nanocomposite particles can effectively improve black rice ATC's stability and activity, creating an ideal new material for inhibiting XO activity that has a broad application prospect.
Analysis of Scattering Angle Sampling by Multi-Angle Imaging Polarimeters for Different Orbit Geometries

Per the 2017–2027 Decadal Survey for Earth Science and Applications from Space, many resources are being dedicated to identifying the most cost-effective and appropriate space-based approaches to aid in answering important questions related to the roles of aerosols, clouds, convection, and precipitation within the climate system. This includes developing advanced space-based multi-angle polarimetric imagers for observing aerosols and clouds. The information content with respect to aerosol and cloud properties of such instruments partly depends on the observed range of scattering angles. Factors influencing the sampled scattering angle range include orbit geometry, solar, and viewing angle geometry and swath width. The focus of this research is to gain better insight into how each of these factors influence the scattering angle range sampled by different polarimeter platforms. Based on calculations of example precessing and sun-synchronous orbits, we conclude that the maximum observed scattering angles vary primarily with local equator crossing time (LCT) and location across the swath, while the minimum observed scattering angles vary primarily with LCT and latitude. The altitude and inclination of a precessing orbit determines the length of cycles occurring in LCT and thus in the scattering angle sampling statistics. For a nominal polarimeter with a 57° swath width in an orbit with 65.5° inclination, scattering angle ranges that are suitable for aerosol and cloud remote sensing are sampled somewhere across the swath at most covered latitudes roughly 54% of days throughout the year. Unfavorable scattering angles are observed on days where the orbit is near the terminator and LCT are early in the morning or late in the evening, when solar zenith angles are generally not suited for remote sensing. Decreasing the instrument’s swath width to 7° primarily decreases the maximum observed scattering angle, and therefore limits the range of crossing times for which a large range of scattering angles are observed. In addition, the fraction of days throughout the year with favorable scattering angles decreases to roughly 37%. These calculations will aid in the development of next-generation observing systems using combinations of instrument platforms in different orbits, as well for other missions such as those using cubesats.