Miracle-dz/UniFAR-FTUs huggingface dataset:
Benchmarking Long-Read Assemblers for Genomic Analyses of Bacterial Pathogens Using Oxford Nanopore Sequencing

Oxford Nanopore sequencing can be used to achieve complete bacterial genomes. However, the error rates of Oxford Nanopore long reads are greater compared to Illumina short reads. Long-read assemblers using a variety of assembly algorithms have been developed to overcome this deficiency, which have not been benchmarked for genomic analyses of bacterial pathogens using Oxford Nanopore long reads. In this study, long-read assemblers, namely Canu, Flye, Miniasm/Racon, Raven, Redbean, and Shasta, were thus benchmarked using Oxford Nanopore long reads of bacterial pathogens. Ten species were tested for mediocre- and low-quality simulated reads, and 10 species were tested for real reads. Raven was the most robust assembler, obtaining complete and accurate genomes. All Miniasm/Racon and Raven assemblies of mediocre-quality reads provided accurate antimicrobial resistance (AMR) profiles, while the Raven assembly of Klebsiella variicola with low-quality reads was the only assembly with an accurate AMR profile among all assemblers and species. All assemblers functioned well for predicting virulence genes using mediocre-quality and real reads, whereas only the Raven assemblies of low-quality reads had accurate numbers of virulence genes. Regarding multilocus sequence typing (MLST), Miniasm/Racon was the most effective assembler for mediocre-quality reads, while only the Raven assemblies of Escherichia coli O157:H7 and K. variicola with low-quality reads showed positive MLST results. Miniasm/Racon and Raven were the best performers for MLST using real reads. The Miniasm/Racon and Raven assemblies showed accurate phylogenetic inference. For the pan-genome analyses, Raven was the strongest assembler for simulated reads, whereas Miniasm/Racon and Raven performed the best for real reads. Overall, the most robust and accurate assembler was Raven, closely followed by Miniasm/Racon.
Two-dimensional detector software: From real detector to idealised image or two-theta scan

Abstract Detector systems introduce distortions into acquired data. To obtain accurate angle and intensity information, it is necessary to calibrate, and apply corrections. Intensity non-linearity, spatial distortion, and non-uniformity of intensity response, are the primary considerations. It is better to account for the distortions within scientific analysis software, but often it is more practical to correct the distortions to produce ‘idealised’ data. Calibration methods and software have been developed for single crystal diffraction experiments, using both approaches. For powder diffraction experiments the additional task of converting a two-dimensional image to a one-dimensional spectrum is used to allow Rietveld analysis. This task may be combined with distortion correction to produce intensity information and error estimates. High-pressure experiments can introduce additional complications and place new demands on software. Flexibility is needed to be able to integrate different angular regions se.
Population Genetics of Odontarrhena (Brassicaceae) from Albania: The Effects of Anthropic Habitat Disturbance, Soil, and Altitude on a Ni-Hyperaccumulator Plant Group from a Major Serpentine Hotspot

Albanian taxa and populations of the genus Odontarrhena are most promising candidates for research on metal tolerance and Ni-agromining, but their genetic structure remains unknown. We investigated phylogenetic relationships and genetic differentiation in relation to distribution and ploidy of the taxa, anthropic site disturbance, elevation, soil type, and trace metals at each population site. After performing DNA sequencing of selected accessions, we applied DNA-fingerprinting to analyze the genetic structure of 32 populations from ultramafic and non-ultramafic outcrops across Albania. Low sequence divergence resulted in poorly resolved phylograms, but supported affinity between the two diploid serpentine endemics O. moravensis and O. rigida. Analysis of molecular variance (AMOVA) revealed significant population differentiation, but no isolation by distance. Among-population variation was higher in polyploids than in diploids, in which genetic distances were lower. Genetic admixing at population and individual level occurred especially in the polyploids O. chalcidica, O. decipiens, and O. smolikana. Admixing increased with site disturbance. Outlier loci were higher in serpentine populations but decreased along altitude with lower drought and heat stress. Genetic variability gained by gene flow and hybridization at contact zones with “resident” species of primary ultramafic habitats promoted expansion of the tetraploid O. chalcidica across anthropogenic sites.
Can Moderate Levels of Organic Selenium in Dairy Cow Feed Naturally Enrich Dairy Products?

Simple Summary Milk and dairy products, such as cheese and yogurt, can be useful sources of selenium-enriched products to increase human Se intake. We studied the effect of dairy cow feed supplementation with inorganic plus organic Se on milk yield, and on the Se enrichment of milk and dairy products to obtain naturally enriched products. Two groups of lactating cows were assigned to two feeding treatments, both with 0.240 mg Se/kg of ration dry matter: One was supplemented with inorganic Se, the other with a 60/40 ratio of inorganic Se/organic Se. The results showed that the inclusion of inorganic plus organic Se did not affect the yield or basic chemical composition of milk; however, the Se content of milk was higher with inorganic plus organic Se supplementation. Cheese from cows fed inorganic plus organic Se had a higher Se content, although this effect was not observed for yogurt. At a moderate level in the diet, sodium selenite plus Se yeast may be more effective than only inorganic Se, increasing the Se concentration in milk and cheese. Abstract This work studied the effect of dairy cow ration supplementation with inorganic plus organic Se on metabolic status, milk yield, and the quality of milk and dairy products, especially its Se content. Twenty multiparous Holstein Friesian lactating cows were assigned to two feeding treatments. The cows were fed with 22.5 kg dry matter (DM) of total mixed ration (11.75 kg DM of forage plus 10.75 kg DM of concentrate) by head. There were two different concentrates with the same Se content (0.240 mg/kg of ration DM) but with different Se sources: The control (CON) was supplemented with inorganic Se (sodium selenite); and the other (IOSe) was supplemented with sodium selenite plus organic Se (Sel-Plex®), at 0.144 and 0.096 mg Se/kg of ration DM, respectively. The results indicated that, in general, the IOSe treatment did not modify the metabolic profile, and even decreased the total oxidant status (p < 0.05) and did not lead to a deterioration of quality and yield of milk. However, milk and cheese from IOSe had higher Se content (an increase of 29.7% and 38.2%, respectively) than CON (p < 0.01), but this effect was not observed in yogurt. In general, physical or sensorial parameters of cheeses did not show differences between treatments. Moderate inorganic plus organic Se supplementation may be more effective than inorganic Se, increasing the Se content in milk and cheese, without causing a deterioration in quality or productive parameters.
Psychological pain and depression: it’s hard to speak when it hurts

Abstract Objective To investigate the neuropsychological features of depressed patients reporting high level of psychological pain. Methods Sixty-two inpatients were included and divided into two groups according to the level of psychological pain assessed by a Likert scale. Cognitive abilities were assessed using the Trail Making Test, the Stroop test, and Verbal Fluency Test (semantic and phonemic verbal fluency). Univariate and multivariate analyses were performed to determine neuropsychological factors associated with a high level of psychological pain. Results The median level of psychological pain was 8/10. High level of psychological pain was associated with poor phonemic verbal fluency performance in men (p = 0.009), but not in women, even after controlling for confounding factors (age, level of depression, anxiety). Groups did not differ on the Trail Making Test, the Stroop test, or the semantic verbal fluency measure. Conclusion Psychological pain is a specific clinical entity that should be considered to be more significant than just a symptom of depression. High level of psychological pain appears to be associated with a deficit of phonemic verbal fluency in depressed men. This finding could help to target psychotherapeutic treatments and improve screening. Key points Patients with high psychological pain do not differ on the Trail Making Test, the Stroop Test or the Sematic Verbal Fluency Measure to patients with low psychological pain High psychological pain is associated with a deficit in phonemic verbal fluency in depressed men Future research should aim to clarify gender differences in psychological pain in participants with and without major depressive disorder, as well as explore the complex relationship between cognition and the different forms of pain (psychological, physical and psychosomatic)
Modeling Ankle Torque and Stiffness Induced by Functional Electrical Stimulation

Functional electrical stimulation (FES) is commonly used for individuals with neuromuscular impairments to generate muscle contractions. Both joint torque and stiffness play important roles in maintaining stable posture and resisting external disturbance. However, most previous studies only focused on the modulation of joint torque using FES while ignoring the joint stiffness. A model that can simultaneously modulate both ankle torque and stiffness induced by FES was investigated in this study. This model was composed of four subparts including an FES-to-activation model, a musculoskeletal geometry model, a Hill-based muscle-tendon model, and a joint stiffness model. The model was calibrated by the maximum voluntary contraction test of the tibialis anterior (TA) and gastrocnemius medial (GAS) muscles. To validate the model, the estimated torque and stiffness by the model were compared with the measured torque and stiffness induced by FES, respectively. The results showed that the proposed model can estimate torque and stiffness with electrically stimulated TA or/and GAS, which was significantly correlated to the measured torque and stiffness. The proposed model can modulate both joint torque and stiffness induced by FES in the isometric condition, which can be potentially extended to modulate the joint torque and stiffness during FES-assisted walking.
Maternal Education Level and Excessive Recreational Screen Time in Children: A Mediation Analysis

There is increasing recognition of the adverse health consequences of excessive recreational screen time (RST) in children and adolescents. Early interventions that aim to reduce RST are crucial, but there are some controversies about which individual and parental variables affect RST in children. The aim of this study was to determine the relationship of parental education level with RST in children and early adolescents and to identify mediators of these relationships. This cross-sectional study examined a sample of children (2–14 year-old) who attended routine childcare visits in primary health care centers in Spain (n = 402; 53.7% males; mean age: 7 ± 4 year-old). A self-reported questionnaire was given to the parents to assess sociodemographic data, parental education, the home media environment, and RST in children. Separate analysis was performed for two age groups (2–6 year-old and 6–14 year-old). Path analysis, an application of structural equation modeling, was used to analyze the data. Fitty three percent of the children had excessive RST (≥2 h/day). The maternal education level, eating lunch/dinner in front of a TV, presence of a background TV, and the amount of parental TV viewing had significant associations with excessive RST in both age groups. For the younger group, the maternal education level had direct and indirect effects on RST (total effect: β = −0.29, p < 0.01). For the older group, maternal education level only had a significant indirect effect on RST, and this was mediated by the presence of a background TV and the time of parental TV viewing (total indirect effect: β = −0.11, p < 0.01). A higher maternal education level appears to be associated with certain environmental factors or habits that prevent excessive RST.
River state classification combining patch-based processing and CNN

This paper proposes a method for classifying the river state (a flood risk exists or not) from river surveillance camera images by combining patch-based processing and a convolutional neural network (CNN). Although CNN needs much training data, the number of river surveillance camera images is limited because flood does not frequently occur. Also, river surveillance camera images include objects that are irrelevant to the flood risk. Therefore, the direct use of CNN may not work well for the river state classification. To overcome this limitation, this paper develops patch-based processing for adjusting CNN to the river state classification. By increasing training data via the patch segmentation of an image and selecting patches that are relevant to the river state, the adjustment of general CNNs to the river state classification becomes feasible. The proposed patch-based processing and CNN are developed independently. This yields the practical merits that any CNN can be used according to each user’s purposes, and the maintenance and improvement of each component of the whole system can be easily performed. In the experiment, river state classification is defined as the following problems using two datasets, to verify the effectiveness of the proposed method. First, river images from the public dataset called Places are classified to images with Muddy labels and images with Clear labels. Second, images from the river surveillance camera in Nagaoka City, Japan are classified to images captured when the government announced heavy rain or flood warning and the other images.
Mechanical Energy Expenditure at Lumbar Spine and Lower Extremity Joints During the Single-Leg Squat Is Affected by the Nonstance Foot Position

Supplemental Digital Content is Available in the Text. Abstract Hirsch, SM, Chapman, CJ, Frost, DM, and Beach, TAC. Mechanical energy expenditure at lumbar spine and lower extremity joints during the single-leg squat is affected by the nonstance foot position. J Strength Cond Res 36(9): 2417–2426, 2022—Previous research has shown that discrete kinematic and kinetic quantities during bodyweight single-leg squat (SLS) movements are affected by elevated foot positioning and sex of the performer, but generalizations are limited by the high-dimensional data structure reported. Using a 3D inverse dynamical linked-segment model, we quantified mechanical energy expenditure (MEE) at each joint in the kinetic chain, the total MEE (sum of MEE across aforesaid joints), and the relative contribution of each joint to total MEE during SLSs performed with elevated foot positioned beside stance leg (SLS-Side), and in-front of (SLS-Front) and behind (SLS-Back) the body. Total MEE differed between SLS variations (p = 0.002), with the least amount observed in the SLS-Back (effect size [ES] = 0.066–0.069). Approximately 50% of total MEE was contributed by the knee joint in each SLS variation, whereas MEE at the ankle, hip, and lumbar spine (in absolute and relative terms) varied complexly as a function of the elevated foot position. Total MEE (p = 0.0192, ES = 0.852) and the absolute MEE at the knee and spine was greater in men across the SLS variations performed (p = 0.025–0.036, ES = 0.715–0.766), but only the lumbar spine contribution to total MEE was larger in men across all SLS variations (p = 0.045, ES = 0.607). Otherwise, there were no other sex-specific responses observed. Biomechanically, SLS movements are generally “knee-dominant,” but changing elevated foot position effectively redistributes MEE among other joints in the linkage. Consistent with the previous conclusions reached based on discrete kinematic and kinetic data, not all SLSs are equal.
Ionospheric Phase Compensation for InSAR Measurements Based on the Faraday Rotation Inversion Method

The ionospheric error can significantly affect the synthetic aperture radar (SAR) signals, particularly in the case of L band and lower frequency SAR systems. The ionospheric distortions are mixed with terrain and ground deformation signals, lowering the precision of the interferometric measurements. Moreover, it is often difficult to detect the small-scale ionospheric structure due to its rapid changes and may have more influence on ionospheric phase compensation for InSAR measurements. In this paper, we present a Faraday rotation (FR) inversion method and corresponding procedure to compensate the ionospheric error for SAR interferograms and to detect the variations of small-scale ionospheric disturbances. This method retrieves the absolute total electron content (TEC) based on the FR estimation and corrects the ionospheric error for synthetic aperture radar interferometry (InSAR) measurements by transforming the differential TEC into the ionospheric phase. In two selected study cases, located in high latitude and equatorial regions where ionospheric disturbances occur frequently, we test the method using the Phased Array L-band Synthetic Aperture Radar (PALSAR) full-polarimetric SAR images. Our results show that the proposed procedure can effectively compensate the ionospheric phase. In order to validate the results, we present the results of ionospheric phase compensation based on the split-spectrum method as a comparison to the proposed method. To analyze the ability of our proposed method in detecting small-scale ionospheric disturbances, TEC derived from FR estimation are also compared with those derived from the global ionosphere maps (GIM). Our research provides a robust choice for the correction of ionospheric error in SAR interferograms. It also provides a powerful tool to measure small-scale ionospheric structure.
Evaluation of Orthorexia Nervosa and Symptomatology Associated with Eating Disorders among European University Students: A Multicentre Cross-Sectional Study

The objectives of the present study were to (1) evaluate prevalence of orthorexia nervosa (ON) in university students in Spain and Poland, (2) assess differences in ON and eating disorder (ED) pathology in both samples and (3) examine the relationship between ON and ED symptoms among Spanish and Polish university students. Eight hundred and sixty university students participated in the present study (Mage = 21.17 ± 3.38; MBMI = 22.57 ± 3.76). The Spanish and Polish samples comprised 485 and 375 students, respectively. The Düsseldorf Orthorexia Scale and the Eating Disorder Inventory were used in the present study. ON prevalence rates of 2.3% and 2.9%, respectively, are found in the Spanish and Polish samples. Compared to Polish students, Spanish university students reported increased drive for thinness and lower body dissatisfaction, lower level of ineffectiveness and lower level of interpersonal distrust. ON was positively related to drive for thinness, bulimia, body dissatisfaction, perfectionism interoceptive awareness (in both Spanish and Polish students) and ineffectiveness (in Spanish students). Our findings suggest that ON significantly overlaps with ED symptoms, which is in line with recent studies. Longitudinal studies are needed to assess how ON develops in a sample of young adults and whether it develops in isolation of or in parallel with ED pathology.
Similarities between bovine and human germline development revealed by single-cell RNAseq.

The germ cell lineage ensures the creation of new individuals and perpetuates the genetic information across generations. Primordial germ cells are pioneers of gametes and exist transiently during development until they differentiate into oogonia in females, or spermatogonia in males. Little is known about the molecular characteristics of primordial germ cells in cattle. By performing single-cell RNA-sequencing, quantitative real-time PCR, and immunofluorescence analyses of fetal gonads between 40 and 90 days of fetal age, we evaluated the molecular signatures of bovine germ cells at the initial stages of gonadal development. Our results indicate that at 50 days of fetal age, bovine primordial germ cells were in the early stages of development, expressing genes of early primordial germ cells, including transcriptional regulators of human germline specification (e.g. SOX17, TFAP2C, and PRDM1). Bovine and human primordial germ cells also share expression of KIT, EPCAM, ITGA6, and PDPN genes coding for membrane-bound proteins, and an asynchronous pattern of differentiation. Additionally, the expression of members of Notch, Nodal/Activin, and BMP signaling cascades in the bovine fetal ovary, suggests that these pathways are involved in the interaction between germ cells and their niche. Results of this study provide insights into the mechanisms involved in the development of bovine primordial germ cells and put in evidence similarities between the bovine and human germline.
A Diffusion Model Approach for Understanding the Impact of 17 Interventions on the Race Implicit Association Test

Performance on implicit measures reflects construct-specific and nonconstruct-specific processes. This creates an interpretive issue for understanding interventions to change implicit measures: Change in performance could reflect changes in the constructs of interest or changes in other mental processes. We reanalyzed data from six studies (N = 23,342) to examine the process-level effects of 17 interventions and one sham intervention to change race implicit association test (IAT) performance. Diffusion models decompose overall IAT performance (D-scores) into construct-specific (ease of decision-making) and nonconstruct-specific processes (speed–accuracy trade-offs, non-decision-related processes like motor execution). Interventions that effectively reduced D-scores changed ease of decision-making on compatible and incompatible trials. They also eliminated differences in speed–accuracy trade-offs between compatible and incompatible trials. Non-decision-related processes were affected by two interventions only. There was little evidence that interventions had any long-term effects. These findings highlight the value of diffusion modeling for understanding the mechanisms by which interventions affect implicit measure performance.