Miracle-dz/UniFAR-FTUs huggingface dataset:
Mutual Information as a Performance Measure for Binary Predictors Characterized by Both ROC Curve and PROC Curve Analysis

The predictive receiver operating characteristic (PROC) curve differs from the more well-known receiver operating characteristic (ROC) curve in that it provides a basis for the evaluation of binary diagnostic tests using metrics defined conditionally on the outcome of the test rather than metrics defined conditionally on the actual disease status. Application of PROC curve analysis may be hindered by the complex graphical patterns that are sometimes generated. Here we present an information theoretic analysis that allows concurrent evaluation of PROC curves and ROC curves together in a simple graphical format. The analysis is based on the observation that mutual information may be viewed both as a function of ROC curve summary statistics (sensitivity and specificity) and prevalence, and as a function of predictive values and prevalence. Mutual information calculated from a 2 × 2 prediction-realization table for a specified risk score threshold on an ROC curve is the same as the mutual information calculated at the same risk score threshold on a corresponding PROC curve. Thus, for a given value of prevalence, the risk score threshold that maximizes mutual information is the same on both the ROC curve and the corresponding PROC curve. Phytopathologists and clinicians who have previously relied solely on ROC curve summary statistics when formulating risk thresholds for application in practical agricultural or clinical decision-making contexts are thus presented with a methodology that brings predictive values within the scope of that formulation.
Indirect Vibration of the Upper Limbs Alters Transmission Along Spinal but Not Corticospinal Pathways

The aim of this study was to investigate whether indirect upper limb vibration (ULV) modulates transmission along spinal and corticospinal pathways that control the human forearm. All measures were assessed under CONTROL (no vibration) and ULV (30 Hz; 0.4 mm displacement) conditions while participants maintained a small contraction of the right flexor carpi radialis (FCR) muscle. To assess spinal pathways, Hoffmann reflexes (H-reflexes) elicited by stimulation of the median nerve were recorded from FCR with motor response (M-wave) amplitudes matched between conditions. An H-reflex conditioning paradigm was also used to assess changes in presynaptic inhibition by stimulating the superficial radial (SR) nerve (5 pulses at 300Hz) 37 ms prior to median nerve stimulation. Cutaneous reflexes in FCR elicited by stimulation of the SR nerve at the wrist were also recorded. To assess corticospinal pathways, motor evoked potentials (MEPs) elicited by transcranial magnetic stimulation of the contralateral motor cortex were recorded from the right FCR and biceps brachii (BB). ULV significantly reduced H-reflex amplitude by 15.7% for both conditioned and unconditioned reflexes (24.0±15.7 vs 18.4±11.2 % Mmax; p<0.05). Middle latency cutaneous reflexes were also significantly reduced by 20.0% from CONTROL (−1.50 ± 2.1 % Mmax) to ULV (−1.73 ± 2.2 % Mmax; p<0.05). There was no significant effect of ULV on MEP amplitude (p>0.05). Therefore, ULV inhibits cutaneous and H-reflex transmission without influencing corticospinal excitability of the forearm flexors suggesting increased presynaptic inhibition of afferent transmission as a likely mechanism. A general increase in inhibition of spinal pathways with ULV may have important implications for improving rehabilitation for individuals with spasticity (SCI, stroke, MS, etc).
Integrated characterization of SARS-CoV-2 genome, microbiome, antibiotic resistance and host response from single throat swabs

The ongoing coronavirus disease 2019 (COVID-19) pandemic, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection, poses a severe threat to humanity. Rapid and comprehensive analysis of both pathogen and host sequencing data is critical to track infection and inform therapies. In this study, we performed unbiased metatranscriptomic analysis of clinical samples from COVID-19 patients using a recently developed RNA-seq library construction method (TRACE-seq), which utilizes tagmentation activity of Tn5 on RNA/DNA hybrids. This approach avoids the laborious and time-consuming steps in traditional RNA-seq procedure, and hence is fast, sensitive, and convenient. We demonstrated that TRACE-seq allowed integrated characterization of full genome information of SARS-CoV-2, putative pathogens causing coinfection, antibiotic resistance, and host response from single throat swabs. We believe that the integrated information will deepen our understanding of pathogenesis and improve diagnostic accuracy for infectious diseases.
Synergistic Information Transfer in the Global System of Financial Markets

Uncovering dynamic information flow between stock market indices has been the topic of several studies which exploited the notion of transfer entropy or Granger causality, its linear version. The output of the transfer entropy approach is a directed weighted graph measuring the information about the future state of each target provided by the knowledge of the state of each driving stock market index. In order to go beyond the pairwise description of the information flow, thus looking at higher order informational circuits, here we apply the partial information decomposition to triplets consisting of a pair of driving markets (belonging to America or Europe) and a target market in Asia. Our analysis, on daily data recorded during the years 2000 to 2019, allows the identification of the synergistic information that a pair of drivers carry about the target. By studying the influence of the closing returns of drivers on the subsequent overnight changes of target indexes, we find that (i) Korea, Tokyo, Hong Kong, and Singapore are, in order, the most influenced Asian markets; (ii) US indices SP500 and Russell are the strongest drivers with respect to the bivariate Granger causality; and (iii) concerning higher order effects, pairs of European and American stock market indices play a major role as the most synergetic three-variables circuits. Our results show that the Synergy, a proxy of higher order predictive information flow rooted in information theory, provides details that are complementary to those obtained from bivariate and global Granger causality, and can thus be used to get a better characterization of the global financial system.
Adipogenesis in post-weanling pigs fed conjugated linoleic acid

Adipogenesis in Post-Weanling Pigs Fed Conjugated Linoleic Acid. (August 2004) Vanessa Lynn Adams, B.S., Texas A&M University Chair of Advisory Committee: Dr. Stephen B. Smith The effects of conjugated linoleic acid (CLA) on lipogenesis and preadipocyte proliferation in young pigs were evaluated in two separate experiments. The first compared dietary effects of linoleic acid, beef tallow, and CLA on composition, lipogenesis, and DNA synthesis. Eighteen pigs weaned at 17 d of age were allotted randomly to corn-based diets supplemented with 1.5% corn oil, 1.5% tallow, or 1.5% CLA. The second experiment evaluated the effects of CLA included with diets high in polyunsaturated fat or beef tallow. Twenty-four pigs weaned at 17 d of age were allotted randomly to one of four corn-based diets supplemented with: 15% corn oil, 12% corn oil + 3% CLA, 15% tallow, and 12% tallow + 3% CLA. The piglets in both trials were fed a basal diet for 7 d and their respective diet for 35 d. [U-C]Glucose incorporation into total lipids was (experiment 1): 10.64, 11.04, 13.64; (experiment 2): 21.15, 17.54, 21.34, and 19.52 nmol/(10 cells per h) for subcutaneous (s.c.) adipose tissue from corn oil, tallow, CLA; corn oil, corn oil + CLA, tallow, and tallow + CLA-fed piglets, respectively. Tritiated thymidine incorporation into DNA was not different in s.c. adipocytes across treatment groups, but was 5,581, 2,794, 6,573, and 3,760 dpm/(10 cells per h) in s.c. stromal vascular cells from corn oil, corn oil + CLA, tallow, and tallow + CLA-fed piglets, respectively (CLA main effect p<0.034). Additionally, there
In Vivo Brain Glutathione is Higher in Older Age and Correlates with Mobility

Brain markers of oxidative damage increase with advancing age. In response, brain antioxidant levels may also increase with age, although this has not been well investigated. Here we used edited magnetic resonance spectroscopy to quantify endogenous levels of glutathione (GSH, one of the most abundant brain antioxidants) in 37 young (mean: 21.8 (2.5) years; 19 F) and 23 older adults (mean: 72.8 (8.9) years; 19 F). Accounting for age-related atrophy, we identified higher frontal and sensorimotor GSH levels for the older compared to the younger adults. For the older adults only, higher sensorimotor (but not frontal) GSH was correlated with poorer balance, gait, and manual dexterity. This suggests a regionally-specific relationship between higher brain oxidative stress levels and motor performance declines with age. We suggest these findings reflect a compensatory upregulation of GSH in response to increasing brain oxidative stress with normal aging. Together, these results provide insight into age differences in brain antioxidant levels and implications for motor function.
A 6-year lidar survey reveals enhanced rockwall retreat and modified rockfall magnitudes/frequencies in deglaciating cirques

Abstract. Cirque erosion contributes significantly to mountain denudation and is a key element of glaciated mountain topography. Despite long-standing efforts, rates of rockwall retreat and the proportional contributions of low-, mid- and high-magnitude rockfalls have remained poorly constrained. Here, a unique, terrestrial-lidar-derived rockfall inventory (2011–2017) of two glaciated cirques in the Hohe Tauern range, Central Alps, Austria, is analysed. The mean cirque wall retreat rate of 1.9 mm a −1 ranks in the top range of reported values and is mainly driven by enhanced rockfall from the lowermost, freshly deglaciated rockwall sections. Retreat rates are significantly elevated over decades subsequent to glacier downwasting. Elongated cirque morphology and recorded cirque wall retreat rates indicate headward erosion is clearly outpacing lateral erosion, most likely due to the cataclinal backwalls, which are prone to large dip-slope failures. The rockfall magnitude–frequency distribution – the first such distribution derived for deglaciating cirques – follows a distinct negative power law over 4 orders of magnitude. Magnitude–frequency distributions in glacier-proximal and glacier-distal rockwall sections differ significantly due to an increased occurrence of large rockfalls in recently deglaciated areas. In this paper, the second of two companion pieces, we show how recent climate warming shapes glacial landforms, controls spatiotemporal rockfall variation in glacial environments and indicates a transient signal with decadal-scale exhaustion of rockfall activity immediately following deglaciation crucial for future hazard assessments.
IL-37 exerts therapeutic effects in experimental autoimmune encephalomyelitis through the receptor complex IL-1R5/IL-1R8

Background: Interleukin 37 (IL-37), a member of IL-1 family, broadly suppresses inflammation in many pathological conditions by acting as a dual-function cytokine in that IL-37 signals via the extracellular receptor complex IL1-R5/IL-1R8, but it can also translocate to the nucleus. However, whether IL-37 exerts beneficial actions in neuroinflammatory diseases, such as multiple sclerosis, remains to be elucidated. Thus, the goals of the present study were to evaluate the therapeutic effects of IL-37 in a mouse model of multiple sclerosis, and if so, whether this is mediated via the extracellular receptor complex IL-1R5/IL-1R8. Methods: We used a murine model of MS, the experimental autoimmune encephalomyelitis (EAE). We induced EAE in three different single and double transgenic mice (hIL-37tg, IL-1R8 KO, hIL-37tg-IL-1R8 KO) and wild type littermates. We also induced EAE in C57Bl/6 mice and treated them with various forms of recombinant human IL-37 protein. Functional and histological techniques were used to assess locomotor deficits and demyelination. Luminex and flow cytometry analysis were done to assess the protein levels of pro-inflammatory cytokines and different immune cell populations, respectively. qPCRs were done to assess the expression of IL-37, IL-1R5 and IL-1R8 in the spinal cord of EAE, and in blood peripheral mononuclear cells and brain tissue samples of MS patients. Results: We demonstrate that IL-37 reduces inflammation and protects against neurological deficits and myelin loss in EAE mice by acting via IL1-R5/IL1-R8. We also reveal that administration of recombinant human IL-37 exerts therapeutic actions in EAE mice. We finally show that IL-37 transcripts are not up-regulated in peripheral blood mononuclear cells and in brain lesions of MS patients, despite the IL-1R5/IL-1R8 receptor complex is expressed. Conclusions: This study presents novel data indicating that IL-37 exerts therapeutic effects in EAE by acting through the extracellular receptor complex IL-1R5/IL-1R8, and that this protective physiological mechanism is defective in MS individuals. IL-37 may therefore represent a novel therapeutic avenue for the treatment of MS with great promising potential.
Sequence of Trypanosoma cruzi reference strain SC43 nuclear genome and kinetoplast maxicircle confirms a strong genetic structure among closely related parasite discrete typing units.

Chagas disease is a zoonotic, parasitic, vector-borne neglected tropical disease that affects the lives of over 6 million people throughout the Americas. Trypanosoma cruzi, the causative agent, presents extensive genetic diversity. Here we report the genome sequence of reference strain SC43cl1, a hybrid strain belonging to the TcV discrete typing unit (DTU). The assembled diploid genome was 79 Mbp in size, divided into 1,236 contigs with an average coverage reaching x180. There was extensive synteny of SC43cl1 genome with closely related TcV and TcVI genomes, with limited sequence rearrangements. TcVI genomes included several expansions not present in TcV strains. Comparative analysis of both nuclear and kinetoplast sequences clearly separated TcV from TcVI strains, which strongly supports the current DTU classification.
The Complete Plastome Sequence Of Penstemon fruticosus (Pursh) Greene (Plantaginaceae)

Abstract The genus Penstemon is an emerging model for the study of continental adaptive radiation. We report here the first complete plastome sequence for this genus. The P. fruticosus (shrubby, or brush penstemon) plastome is 152,704 bp in length with a quadripartite structure consisting of a large single-copy region (83,693 bp) and a small single-copy region (17,820 bp) that are separated by two inverted repeats (25,594 bp). The plastome contained 24 tRNA genes, 8 rRNA genes, and 83 protein-coding genes for a total of 115 unique genes. Phylogenetic analysis of whole chloroplast sequences shows that the nearest relatives of P. fruticosus are the Plantago and Veronica genera in the Plantaginaceae family.
Rejecting Muslim or Christian religious practices in five West European countries: a case of discriminatory rejection?

ABSTRACT Rejection of Muslim religious practices in West European societies is typically explained by prejudicial feelings towards Muslims as a group. However, although people can oppose Muslim religious practices because they feel negatively towards Muslims as a group, they might also have more general reasons for doing so. By simultaneously considering multiple religious acts (wearing religious symbols and following religious education in public schools) and multiple religious actors (Muslims and Christians), we theoretically differentiate between individuals who apply a double-standard by rejecting Muslim but not Christian religious practices (discriminatory rejection) and those who reject practices independently of the religious group engaged in them (equal rejection). Among majority members in five West European countries, the findings support the existence of equal rejection next to discriminatory rejection with both patterns of responses having different associations with people's prejudices towards Muslim, their endorsement of civil liberties and secular values, and their religious affiliation.
Proposal of a Conditioning Activity Model on Sprint Swimming Performance

This study aimed to propose a conditioning activity (CA) model to stimulate improvement on neuromuscular responses, mechanical parameters and for the 50-m freestyle swimming. Thirteen male swimmers (19 ± 3 years and performances of 77% in relation to World Championship records) performed four CA protocols followed by a maximum performance in the 50-m freestyle. In the first protocol (P1) swimmers performed a standard warm-up (∼15 min); in the second protocol (P2) lunges (3 × 85% of the one-repetition maximum); in the third (P3) pull-ups (3 maximum repetitions) and box jumps 40 cm high and 60 cm deep (1 × 5 with 10% of the corporal weight); and in the fourth protocol (P4) a combination of exercises from the second and third protocols. CA protocols had no effect on the standard warm-up. However, P2 performance (27.01 ± 1.25 s) was similar to P1 (27.01 ± 1.18 s) and presented higher positive effects in mechanical parameters for the swim start performance in comparison to other protocols, contributing to improvements in the 50-m freestyle. In addition, turnaround time also had a negative effect, mainly in P3 (3.12 ± 0.28 s), signaling the improvement of this variable in all protocols (P1: 3.30 ± 0.38 s; P2: 3.17 ± 0.30 s; P4: 3.17 ± 0.34 s). P2 (after: 80 ± 11%; before: 82.7 ± 9.9%) and P3 (after: 82.7 ± 9.9%; before: 85.1 ± 9.7%) presented a possible positive effect on the percentage of voluntary activation in relation to P1 (after: 79.3 ± 10.7%; before: 76.3 ± 12%). In conclusion, the proposed conditioning activity protocols were not efficient for performance improvement in the 50-m freestyle compared to the standard model and seem to specifically influence each phase of the event.
Screen Time and Executive Function in Toddlerhood: A Longitudinal Study

Technology is pervasive in homes with young children. Emerging evidence that electronic screen-based media use has adverse effects on executive functions may help explain negative relations between media use and early academic skills. However, longitudinal investigations are needed to test this idea. In a sample of 193 British toddlers tracked from age 2 to 3 years, we test concurrent and predictive relations between screen use and children’s executive function. We find no concurrent association between screen use and executive function; however, screen time at age 2 is negatively associated with the development of executive functions in toddlerhood from age 2 to 3, controlling for a range of covariates including verbal ability. Implications for parenting, education, and pediatric recommendations are discussed.
On the probabilistic modeling of fake news (hoax) persistency in online social networks and the role of debunking and filtering

Understanding the dynamics of information diffusion, including spreading of fake news, hoaxes, and generally, misinformation/disinformation, has become crucial in post‐truth societies. The paper focuses on the probability that a hoax originated at a given time will continue to spread indefinitely in online social networks; a minimalistic model based on the theory of branching processes is devised, which only considers the basic possible reactions that users can have after reading a post whose content is a hoax, that is, to share it further, to ignore it, or to try to debunk it. The analysis of the resulting dynamics shows that ignoring is indeed not sufficient to stop the spreading, not even if most people do so. More active counter‐measures are needed; in particular, the proposed model formally describes the ways in which retractions and debunking posts, cultural/educational initiatives, and content moderation policies (including filtering) by Internet companies, can impact on the persistency probability of hoaxes and generally fake news.
Evaluation of Indoor and Outdoor Aquaculture Systems as Alternatives to Harvesting Hemolymph From Random Wild Capture of Horseshoe Crabs

This study evaluated two approaches to the aquaculture of Limulus polyphemus with the ultimate goal of harvesting Limulus amebocyte lysate (LAL) at an industrial scale. To monitor Horseshoe crabs (HSCs), a combination of physical, biochemical and cellular components were examined for HSC cohorts in an indoor recirculating aquaculture system (RAS) and an outdoor on-bottom pen culture system (PCS) over a 6-month period. The metrics included body weight, hemocyanin (Hc) concentration, amebocyte density, and LAL reactivity. In addition, a simulated biomedical bleeding event (extracting 30% of the total hemolymph volume) was performed to assess the impact on physiochemical properties of the hemolymph and amebocytes. Overall, the HSCs fared better in the RAS compared to the PCS, with higher rebound kinetics with respect to Hc, amebocyte density, LAL reactivity, and with 100% survival in the RAS cohort. Further, hemolymph reinfusion (after amebocyte removal) was shown to improve HSC recovery time. In summary, outcomes of this research show that a RAS, coupled with adequate nutrition and monitoring can provide HSCs with a suitable environment for sustainable hemolymph extraction and year-round LAL production.
Leveraging a Domain Ontology in (Neural) Learning from Heterogeneous Data

Injecting domain knowledge into a neural learner to alleviate reliance on high-quality data and improve explainability is a rapidly expanding research trend. While most of the effort focused on regular topology formats such as sequences and grids, we consider graph datasets. Moreover, instead of knowledge graph (KG) embedding that underlies the majority of graph- centered methods, we propose a dedicated pattern mining-based approach. As our patterns are ontologically-generalized, they achieve multiple objectives: domain knowledge infusion, generalization capacity enhancement, interpretability, etc.
PARMAP: A Pan-Genome-Based Computational Framework for Predicting Antimicrobial Resistance

Antimicrobial resistance (AMR) has emerged as one of the most urgent global threats to public health. Accurate detection of AMR phenotypes is critical for reducing the spread of AMR strains. Here, we developed PARMAP (Prediction of Antimicrobial Resistance by MAPping genetic alterations in pan-genome) to predict AMR phenotypes and to identify AMR-associated genetic alterations based on the pan-genome of bacteria by utilizing machine learning algorithms. When we applied PARMAP to 1,597 Neisseria gonorrhoeae strains, it successfully predicted their AMR phenotypes based on a pan-genome analysis. Furthermore, it identified 328 genetic alterations in 23 known AMR genes and discovered many new AMR-associated genetic alterations in ciprofloxacin-resistant N. gonorrhoeae, and it clearly indicated the genetic heterogeneity of AMR genes in different subtypes of resistant N. gonorrhoeae. Additionally, PARMAP performed well in predicting the AMR phenotypes of Mycobacterium tuberculosis and Escherichia coli, indicating the robustness of the PARMAP framework. In conclusion, PARMAP not only precisely predicts the AMR of a population of strains of a given species but also uses whole-genome sequencing data to prioritize candidate AMR-associated genetic alterations based on their likelihood of contributing to AMR. Thus, we believe that PARMAP will accelerate investigations into AMR mechanisms in other human pathogens.