Miracle-dz/UniFAR-FTUs huggingface dataset:
Biomedical Knowledge Graphs Construction From Conditional Statements

Conditions play an essential role in biomedical statements. However, existing biomedical knowledge graphs (BioKGs) only focus on factual knowledge, organized as a flat relational network of biomedical concepts. These BioKGs ignore the conditions of the facts being valid, which loses essential contexts for knowledge exploration and inference. We consider both facts and their conditions in biomedical statements and proposed a three-layered information-lossless representation of BioKG. The first layer has biomedical concept nodes, attribute nodes. The second layer represents both biomedical fact and condition tuples by nodes of the relation phrases, connecting to the subject and object in the first layer. The third layer has nodes of statements connecting to a set of fact tuples and/or condition tuples in the second layer. We transform the BioKG construction problem into a sequence labeling problem based on a novel designed tag schema. We design a Multi-Input Multi-Output sequence labeling model (MIMO) that learns from multiple input signals and generates proper number of multiple output sequences for tuple extraction. Experiments on a newly constructed dataset show that MIMO outperforms the existing methods. Further case study demonstrates that the BioKGs constructed provide a good understanding of the biomedical statements.
Identification of Novel Genomic Regions and Superior Alleles Associated with Zn Accumulation in Wheat Using a Genome-Wide Association Analysis Method

Micronutrient deficiencies, and especially zinc (Zn) deficiency, pose serious health problems to people who mainly depend on cereal-based diets. Here, we performed a genome-wide association study (GWAS) to detect the genetic basis of the Zn accumulation in wheat (Triticum aestivum L.) grains with a diversity panel of 207 bread wheat varieties. To uncover authentic quantitative trait loci (QTL) controlling Zn accumulation, the varieties were planted in three locations. In total, 29 unique loci associated with Zn grain accumulation were identified. Notably, seven non-redundant loci located on chromosomes 1B, 3B, 3D, 4A, 5A, 5B, and 7A, were detected at least in two environments. Of these quantitative trait loci (QTL), six coincided with known QTL or genes, whereas the highest effect QTL on chromosome 3D identified in this study was not reported previously. Searches of public databases revealed that the seven identified QTL coincided with seven putative candidate genes linked to Zn accumulation. Among these seven genes, NAC domain-containing protein gene (TraesCS3D02G078500) linked with the most significant single nucleotide polymorphism (SNP) AX-94729264 on chromosome 3D was relevant to metal accumulation in wheat grains. Results of this study provide new insights into the genetic architecture of Zn accumulation in wheat grains.
Glycogen Utilization during Running: Intensity, Sex, and Muscle-Specific Responses

ABSTRACT Purpose This study aimed to quantify net glycogen utilization in the vastus lateralis (VL) and gastrocnemius (G) of male (n = 11) and female (n = 10) recreationally active runners during three outdoor training sessions. Methods After 2-d standardization of carbohydrate intakes (6 g·kg−1 body mass per day), glycogen was assessed before and after 1) a 10-mile road run (10-mile) at lactate threshold, 2) 8 × 800-m track intervals (8 × 800 m) at velocity at V˙O2max, and 3) 3 × 10-min track intervals (3 × 10 min) at lactate turnpoint. Results Resting glycogen concentration was lower in the G of female compared with males (P < 0.001) runners, although no sex differences were apparent in the VL (P = 0.40). Within the G and VL of male runners, net glycogen utilization differed between training sessions where 10 miles was greater than both track sessions (all comparisons, P < 0.05). In contrast, net glycogen utilization in female runners was not different between training sessions in either muscle (all comparisons, P > 0.05). Net glycogen utilization was greater in male than in female runners in both VL (P = 0.02) and G (P = 0.07) during the 10-mile road run. With the exception of male runners during the 3 × 10-min protocol (P = 0.28), greater absolute glycogen utilization was observed in the G versus the VL muscle in both male and female runners and during all training protocols (all comparisons, P < 0.05). Conclusion Data demonstrate that 1) prolonged steady-state running necessitates a greater glycogen requirement than shorter but higher-intensity track running sessions, 2) female participants display evidence of reduced resting muscle glycogen concentration and net muscle glycogen utilization when compared with male participants, and 3) net glycogen utilization is higher in the G muscle compared with the VL.
Physical, Biochemical, and Neuromuscular Responses to Repeated Sprint Exercise in Eumenorrheic Female Handball Players: Effect of Menstrual Cycle Phases

Abstract Graja, A, Kacem, M, Hammouda, O, Borji, R, Bouzid, MA, Souissi, N, and Rebai, H. Physical, biochemical, and neuromuscular responses to repeated sprint exercise in eumenorrheic female handball players: effect of menstrual cycle phases. J Strength Cond Res 36(8): 2268–2276, 2022—Very few studies have been interested in the relationship between ovarian hormones and physiological function in female athletes. The aim of this study was to assess the effect of menstrual phases (MP) on physical, neuromuscular, and biochemical responses after repeated sprint exercise (RSE) in female handball players. Ten eumenorrheic athletes (22.5 ± 1.5 years, 1.70 ± 0.04 m) participated in 3 study visits (follicular phase [FP], luteal phase [LP], and premenstrual phase [PMP]). During each MP, they performed 20 × 5-second cycle sprints interspersed with 25 seconds of rest. Maximal voluntary contraction (MVC) tests of the knee extensor muscles at 90° of knee flexion were performed before and after RSE. Peak force and electromyography (EMG) signals were measured during the MVC tests. Blood samples were collected before and 3 minutes after each session. The percentage of decrement in peak power output over the 20 × 5-second cycle test (i.e., fatigue index) calculated between sprints 1 and 20 decreased significantly during PMP (−43.3% ± 5.7%) but not in LP (−39.2% ± 7.7%) compared with FP (−32.44% ± 6.3%) (p < 0.05). Moreover, no significant difference was found between MP in all frequency components of EMG before RSE (p > 0.05). Maximal voluntary contraction, neuromuscular efficiency, and median frequency values of vastus lateralis and rectus femoris were significantly decreased in PMP compared with FP and LP (p < 0.05). Creatine kinase (CK) levels were significantly higher in PMP compared with FP and LP after RSE (p < 0.05). These findings suggest that RSE induces more peripheral fatigue associated with muscle damage in PMP. This might be attributable to hormonal variation across MP. Therefore, FP seems to be the right time for intense training to improve strength performance.
Serum 24S-hydroxycholesterol predicts long-term brain structural and functional outcomes after hypoxia-ischemia in neonatal mice

The major pathway of brain cholesterol turnover relies on its hydroxylation into 24S-hydroxycholesterol (24S-HC) using brain-specific cytochrome P450 46A1 (CYP46A1). 24S-HC produced exclusively in the brain normally traverses the blood-brain barrier to enter the circulation to the liver for excretion; therefore, the serum 24S-HC level is an indication of cholesterol metabolism in the brain. We recently reported an upregulation of CYP46A1 following hypoxia-ischemia (HI) in the neonatal mouse brain and a correlation between serum 24S-HC levels and acute brain damage. Here, we performed a longitudinal study to investigate whether the serum 24S-HC concentrations predict long-term brain structural and functional outcomes. In postnatal day 9 mice subjected to HI, the serum 24S-HC levels increased at 6 h and 24 h after HI and correlated with the infarct volumes measured histologically or by T2-weighted MRI. The 24 h levels were associated with white matter volume loss quantified by MBP immunostaining and luxol fast blue staining. The animals with higher serum 24S-HC at 6 h and 24 h corresponded to those with more severe motor and cognitive deficits at 35-40 days after HI. These data suggest that 24S-HC could be a novel and early blood biomarker for severity of neonatal HI brain damage and associated functional impairments.
Dietary Advanced Glycation End-products (AGE) and Risk of Breast Cancer in the Prostate, Lung, Colorectal and Ovarian Cancer Screening Trial (PLCO)

Advanced glycation end-products (AGEs) are implicated in the pathogenesis of several chronic diseases including cancer. AGEs are produced endogenously but can also be consumed from foods. AGE formation in food is accelerated during cooking at high temperatures. Certain high fat or highly processed foods have high AGE values. The objective of the study was to assign and quantify Nε-carboxymethyl-lysine (CML)-AGE content in food and investigate the association between dietary AGE intake and breast cancer risk in the Prostate, Lung, Colorectal and Ovarian Cancer Screening Trial. The study included women enrolled in the intervention arm who were cancer-free at baseline and completed a baseline questionnaire and food frequency questionnaire (DQX). CML-AGE values were assigned and quantified to foods in the DQX using a published AGE database. Cox proportional hazards models were used to estimate the hazard ratios (HR) and 95% confidence intervals (CI) of breast cancer among all women, and stratified by race/ethnicity, invasiveness of disease, and hormone receptor status. After a median 11.5 years of follow-up, 1,592 women were diagnosed with breast cancer. Higher CML-AGE intake was associated with increased risk of breast cancer among all women (HRQ5VSQ1, 1.30; 95% CI, 1.04–1.62; Ptrend = 0.04) and in non-Hispanic white women (HRT3VST1, 1.21; 95% CI, 1.02–1.44). Increased CML-AGE intake was associated with increased risk of in situ (HRT3VST1, 1.49; 95% CI, 1.11–2.01) and hormone receptor–positive (HRT3VST1, 1.24; 95% CI, 1.01–1.53) breast cancers. In conclusion, high intake of dietary AGE may contribute to increased breast cancer.
Super‐beacons: Open‐source probes with spontaneous tuneable blinking compatible with live‐cell super‐resolution microscopy

Localization based super-resolution microscopy relies on the detection of individual molecules cycling between fluorescent and non-fluorescent states. These transitions are commonly regulated by high-intensity illumination, imposing constrains to imaging hardware and producing sample photodamage. Here, we propose single-molecule self-quenching as a mechanism to generate spontaneous photoswitching independent of illumination. To demonstrate this principle, we developed a new class of DNA-based open-source Super-Resolution probes named Super-Beacons, with photoswitching kinetics that can be tuned structurally, thermally and chemically. The potential of these probes for live-cell friendly Super-Resolution Microscopy without high-illumination or toxic imaging buffers is revealed by imaging Interferon Inducible Transmembrane proteins (IFITMs) at sub-100nm resolutions.
Sparse Data-Driven Learning for Effective and Efficient Biomedical Image Segmentation.

Sparsity is a powerful concept to exploit for high-dimensional machine learning and associated representational and computational efficiency. Sparsity is well suited for medical image segmentation. We present a selection of techniques that incorporate sparsity, including strategies based on dictionary learning and deep learning, that are aimed at medical image segmentation and related quantification. Expected final online publication date for the Annual Review of Biomedical Engineering, Volume 22 is June 4, 2020. Please see http://www.annualreviews. org/page/journal/pubdates for revised estimates.
Post-Cardiotomy Parasternal Nerve Block with Bupivacaine May Be Associated with Reduced Post-Operative Opioid Use in Children: A Retrospective Cohort Study

Postoperative pain treatment affects immediate and long-term outcomes in children undergoing cardiac surgery. Opioids, as part of multimodal analgesia, are effective in treating pain, however, they can be disadvantageous due to adverse side effects. Therefore, we assessed whether the local anesthetic bupivacaine as a parasternal nerve block in children post-cardiac surgery is an effective adjunct to pain management. This was a retrospective cohort study of all patients who underwent cardiothoracic surgery via median sternotomy at a large children’s hospital between November 2011 and February 2014 with and without bupivacaine following the introduction of perioperative bupivacaine in late 2012 on a single unit. 62 out of 148 patients (age 3–17 years) who received bupivacaine demonstrated decreased postoperative opioid use. Within one day of surgery, patients who received bupivacaine required, on average, 0.57 mg/kg (95% CI, 0.46 to 0.68) of total morphine equivalent compared to 0.93 mg/kg (95% CI, 0.80 to 1.06) for patients who did not receive bupivacaine. This difference was statistically significant after adjusting for potential confounders (p-value = 0.002). Length of stay and intubation were shorter on average among patients who received bupivacaine, but these differences were not statistically significant after adjusting for potential confounders. The study results seem to suggest that the perioperative administration of bupivacaine may reduce opioid usage among children post-cardiotomy.
Affective Well‐Being, Rumination, and Positive Reappraisal among People Living with HIV: A Measurement‐Burst Diary Study

Background Changes of affective well‐being are usually analysed either as longitudinal processes or as daily fluctuations. We used a three‐burst diary study to combine these perspectives. Method The participants were 211 patients with a diagnosis of HIV infection. In three bursts with 6‐month intervals, they completed an online diary for five consecutive days, which gives 15 days of measurements. They evaluate affective well‐being (positive and negative affect), stress associated with a central hassle, and coping (rumination and positive reappraisal). Results Higher daily stress coupled with higher rumination was related to lower well‐being. For positive reappraisal, the picture was more complex. First, its interaction with daily stress had an effect on negative, but not on positive, affect. Second, this effect was significant only at the first burst. Conclusions These results suggest a stable debilitating effect of daily rumination, but a limited and diminishing beneficial effect of daily positive reappraisal among people living with HIV. As such, they do not confirm the view that positive reappraisal sustains affective well‐being during chronic health conditions. This may inform stress management interventions for PLWH, which are now increasingly taking the form of mobile applications, adapted to the daily lives of patients in their natural environment.
Disability discrimination and well-being in the United Kingdom: a prospective cohort study

Objectives Disability discrimination is linked with poorer well-being cross-sectionally. The aim of this study was to explore prospective associations between disability discrimination and well-being. Design Prospective cohort study. Setting The United Kingdom Household Longitudinal Study. Participants Data were from 871 individuals with a self-reported physical, cognitive or sensory disability. Primary outcome measures Depression was assessed in 2009/10. Psychological distress, mental functioning, life satisfaction and self-rated health were assessed in 2009/10 and 2013/14. Results Data were analysed using linear and logistic regression with adjustment for age, sex, household income, education, ethnicity and impairment category. Perceived disability discrimination was reported by 117 (13.4%) participants. Cross-sectionally, discrimination was associated with depression (OR=5.40, 95% CI 3.25 to 8.97) fair/poor self-rated health (OR=2.05; 95% CI 1.19 to 3.51), greater psychological distress (B=3.28, 95% CI 2.41 to 4.14), poorer mental functioning (B=−7.35; 95% CI −9.70 to −5.02) and life satisfaction (B=−1.27, 95% CI −1.66 to −0.87). Prospectively, discrimination was associated with increased psychological distress (B=2.88, 95% CI 1.39 to 4.36) and poorer mental functioning (B=−5.12; 95% CI −8.91 to −1.34), adjusting for baseline scores. Conclusions Perceived disability-related discrimination is linked with poorer well-being. These findings underscore the need for interventions to combat disability discrimination.
Structure and Dynamics of the Superprotonic Conductor Caesium Hydrogen Sulfate, CsHSO4

We have investigated caesium hydrogen sulfate, CsHSO4, in all three of its ambient pressure phases by total scattering neutron diffraction, inelastic neutron scattering (INS) and Raman spectroscopies and periodic density functional theory calculations. Above 140 °C, CsHSO4 undergoes a phase transition to a superprotonic conductor that has potential application in intermediate temperature fuel cells. Total scattering neutron diffraction data clearly show that all the existing structures of this phase are unable to describe the local structure, because they have either partial occupancies of the atoms and/or non-physical O–H distances. Knowledge of the local structure is crucial because it is this that determines the conduction mechanism. Starting from one of the previous models, we have generated a new structure that has no partial occupancies and reasonable O–H distances. After geometry optimisation, the calculated radial distribution function is in reasonable agreement with the experimental data, as are the calculated and observed INS and Raman spectra. This work is particularly notable in that we have measured INS spectra in the O–H stretch region above room temperature, which is extremely rare. The INS spectra have the enormous advantage that the electrical anharmonicity that complicates the infrared spectra is absent and the stretch modes are plainly seen.
Discordance between the patient’s and physician’s global assessment in rheumatoid arthritis: Data from the REAL study—Brazil

Background Discordance between patient’s global assessment (PtGA) and physician’s global assessment (PhGA) has been described in rheumatoid arthritis (RA). Understanding the reasons for this discrepancy is important in the context of treat-to-target treatment strategy. Objective To assess the determinants of PtGA and PhGA and factors associated with discordance between them. Methods The REAL study included RA patients from Brazilian public health centers. Clinical, laboratory and outcomes measures were collected. PtGA and the PhGA were rated on a visual analog scale and analyzed. Three groups were defined: no discordance (difference between PtGA and PhGA within 3 cm), positive discordance (PtGA exceeding PhGA by >3 cm), and negative discordance (PtGA less than PhGA by >3 cm). Multivariate regression analysis was used to identify determinants of PtGA and PhGA and their discordance. Results 1115 patients (89,4% female, mean age 56.7y and median disease duration of 12.7y) were enrolled. Two factors were associated with PtGA in the final multivariate model: one point increase in the pain scale leads to an increase of 0.62 in PtGA; one point increase in HAQ increases by 9,25 points the PtGA. The factors associated with PhGA were pain scale, number of tender and swollen joints (NTJ and NSJ), positive RF, ESR, HAQ-DI and use of corticosteroids. Discordance between patient and physician was found in 30.52%: positive discordance in 24.6% and negative discordance in 5.92%. An increase of one point in the NSJ was associated with a 12% increase in the chance of negative discordance. The chance of positive discordance increased by 90% and 2% for each unit increased in HAQ-DI and pain scale respectively. Finally, the chance of positive discordance decreased by 3% for each point increased in NTJ and by 15% for each point increased in NSJ. Conclusion In one-third of the assessments, there was disagreement between PtGA and PhGA (a positive discordance was found in 80% of them). Pain and function were determinants for patients to estimate disease activity, while swollen joints was the main factor related to a worse physician’s evaluation. These data show how different can be the perspectives of patients and assistants.
The relationship between maximum tolerance and motor activation during transcutaneous spinal stimulation is unaffected by the carrier frequency or vibration

Transcutaneous spinal stimulation (TSS) is a useful tool to modulate spinal sensorimotor circuits and has emerged as a potential treatment for motor disorders in neurologically impaired populations. One major limitation of TSS is the discomfort associated with high levels of stimulation during the experimental procedure. The objective of this study was to examine if the discomfort caused by TSS can be alleviated using different stimulation paradigms in a neurologically intact population. Tolerance to TSS delivered using conventional biphasic balanced rectangular pulses was compared to two alternative stimulation paradigms: a 5 kHz carrier frequency and biphasic balanced rectangular pulses combined with vibrotactile stimulation. In ten healthy participants, tolerance to TSS was examined using both single‐pulse (0.2 Hz) and continuous (30 Hz) stimulation protocols. In both the single‐pulse and continuous stimulation protocols, participants tolerated significantly higher levels of stimulation with the carrier frequency paradigm compared to the other stimulation paradigms. However, when the maximum tolerable stimulation intensity of each stimulation paradigm was normalized to the intensity required to evoke a lower limb muscle response, there were no statistical differences between the stimulation paradigms. Our results suggest that, when considering the intensity of stimulation required to obtain spinally evoked motor potentials, neither alternative stimulation paradigm is more effective at reducing discomfort than the conventional, unmodulated pulse configuration.
Advances in simultaneous PET/MR for imaging neuroreceptor function

Hybrid imaging using PET/MRI has emerged as a platform for elucidating novel neurobiology, molecular and functional changes in disease, and responses to physiological or pharmacological interventions. For the central nervous system, PET/MRI has provided insights into biochemical processes, linking selective molecular targets and distributed brain function. This review highlights several examples that leverage the strengths of simultaneous PET/MRI, which includes measuring the perturbation of multi-modal imaging signals on dynamic timescales during pharmacological challenges, physiological interventions or behavioral tasks. We discuss important considerations for the experimental design of dynamic PET/MRI studies and data analysis approaches for comparing and quantifying simultaneous PET/MRI data. The primary focus of this review is on functional PET/MRI studies of neurotransmitter and receptor systems, with an emphasis on the dopamine, opioid, serotonin and glutamate systems as molecular neuromodulators. In this context, we provide an overview of studies that employ interventions to alter the activity of neuroreceptors or the release of neurotransmitters. Overall, we emphasize how the synergistic use of simultaneous PET/MRI with appropriate study design and interventions has the potential to expand our knowledge about the molecular and functional dynamics of the living human brain. Finally, we give an outlook on the future opportunities for simultaneous PET/MRI.