Miracle-dz/UniFAR-FTUs huggingface dataset:
Recruitment and Deoxygenation of Selected Respiratory and Skeletal Muscles During Incremental Loading in Stable COPD Patients

PURPOSE: To evaluate changes in oxygenated (O2Hb), deoxygenated (HHb), and total hemoglobin (tHb) of the sternocleidomastoid (SCM), parasternal (PS), biceps (BC), and tibialis anterior (TA) using near-infrared spectroscopy during incremental loading of the inspiratory muscles and the elbow flexors in people with stable chronic obstructive pulmonary disease. METHODS: Fifteen participants with obstructive pulmonary disease were recruited in a repeated-measures crossover design. Near-infrared spectroscopy optodes were applied over the SCM, PS, BC, and TA to measure O2Hb, HHb, and tHb. Participants were randomly assigned to perform incremental inspiratory threshold loading or elbow flexor loading that imposed higher loads every 2 minutes until task failure. At least 1 week later, participants performed the other test. Arterial oxygen saturation (SpO2) was monitored continuously. RESULTS: O2Hb of the main agonist muscles, SCM and BC, decreased compared with the other muscles during inspiratory threshold loading and elbow flexor loading, respectively. SCM O2Hb and BC O2Hb decreased at higher loads compared with baseline. SCM tHb and HHb increased, whereas TA tHb decreased during inspiratory threshold loading. tHb did not change among any muscles during elbow flexor loading. SpO2 did not change from baseline to task failure. CONCLUSIONS: Our data suggest that the SCM was recruited progressively during incremental inspiratory threshold loading; however, O2Hb was not maintained in this muscle. Similarly, O2Hb was not maintained in the biceps during elbow flexor loading. This regional deoxygenation in SCM and BC during incremental loading protocols was not reflected by a decrease in SpO2.
Child maltreatment and allostatic load: Consequences for physical and mental health in children from low-income families

Abstract Child maltreatment and biomarkers of allostatic load were investigated in relation to child health problems and psychological symptomatology. Participants attended a summer research day camp and included 137 maltreated and 110 nonmaltreated low-income children, who were aged 8 to 10 years (M = 9.42) and racially and ethnically diverse; 52% were male. Measurements obtained included salivary cortisol and dehydroepiandosterone, body mass index, waist–hip ratio, and blood pressure; these indicators provided a composite index of allostatic load. Child self-report and camp adult-rater reports of child symptomatology were obtained; mothers provided information on health problems. The results indicated that higher allostatic load and child maltreatment status independently predicted poorer health outcomes and greater behavior problems. Moderation effects indicated that allostatic load was related to somatic complaints, attention problems, and thought problems only among maltreated children. Risks associated with high waist–hip ratio, low morning cortisol, and high morning dehydroepiandosterone also were related to depressive symptoms only for maltreated children. The results support an allostatic load conceptualization of the impact of high environmental stress and child abuse and neglect on child health and behavioral outcomes and have important implications for long-term physical and mental health.
Task-Induced Deactivation from Rest Extends beyond the Default Mode Brain Network

Activity decreases, or deactivations, of midline and parietal cortical brain regions are routinely observed in human functional neuroimaging studies that compare periods of task-based cognitive performance with passive states, such as rest. It is now widely held that such task-induced deactivations index a highly organized ‘default-mode network’ (DMN): a large-scale brain system whose discovery has had broad implications in the study of human brain function and behavior. In this work, we show that common task-induced deactivations from rest also occur outside of the DMN as a function of increased task demand. Fifty healthy adult subjects performed two distinct functional magnetic resonance imaging tasks that were designed to reliably map deactivations from a resting baseline. As primary findings, increases in task demand consistently modulated the regional anatomy of DMN deactivation. At high levels of task demand, robust deactivation was observed in non-DMN regions, most notably, the posterior insular cortex. Deactivation of this region was directly implicated in a performance-based analysis of experienced task difficulty. Together, these findings suggest that task-induced deactivations from rest are not limited to the DMN and extend to brain regions typically associated with integrative sensory and interoceptive processes.
Evolutionary computation for the prediction of secondary protein structures

We have developed an evolutionary computation approach to predict secondary structure motifs using some main amino acid physical-chemical properties. The prediction model will consist of rules that predict both the beginning and the end of the regions corresponding to a secondary structure state conformation (α-helix or β-strand). A study about propensities of each pair of amino acids in capping regions of α-helix and β-strand are also performed with a data set of 12,830 non-homologous and non-redundant protein sequences.
On Pinsker's and Vajda's Type Inequalities for Csiszár's $f$ -Divergences

Let <i>D</i> and <i>V</i> denote respectively Information Divergence and Total Variation Distance. Pinsker's and Vajda's inequalities are respectively <i>D</i> ≥ [ 1/ 2] <i>V</i><sup>2</sup> and <i>D</i> ≥ log[( 2+<i>V</i>)/( 2-<i>V</i>)] - [( 2<i>V</i>)/( 2+<i>V</i>)]. In this paper, several generalizations and improvements of these inequalities are established for wide classes of <;i>f<;/i>-divergences. First, conditions on <i>f</i> are determined under which an <i>f</i>-divergence <i>Df</i> will satisfy <i>Df</i> ≥ <i>cf V</i><sup>2</sup> or <i>Df</i> ≥ <i>c</i><sub>2,</sub><i>f V</i><sup>2</sup> + <i>c</i><sub>4,</sub><i>f V</i><sup>4</sup>, where the constants <i>cf</i>, <i>c</i><sub>2,</sub><i>f</i> and <i>c</i><sub>4,</sub><i>f</i> are best possible. As a consequence, lower bounds in terms of <i>V</i> are obtained for many well known distance and divergence measures, including the χ<sup>2</sup> and Hellinger's discrimination and the families of Tsallis' and Rényi's divergences. For instance, if <i>D</i><sub>(α)</sub> (<i>P</i>||<i>Q</i>) = [α(α-1)]<sup>-1</sup> [∫<i>p</i><sup>α</sup><i>q</i><sup>1-α</sup><i>d</i>μ-1] and ℑ<sub>α</sub> (<i>P</i>||<i>Q</i>) = (α-1)<sup>-1</sup> log[∫<i>p</i><sup>α</sup><i>q</i><sup>1-α</sup><i>d</i>μ] are respectively the relative information of type α and the Rényi's information gain of order α, it is shown that <i>D</i><sub>(α)</sub> ≥ [ 1/ 2] <i>V</i><sup>2</sup> + [ 1/ 72] (α+1)(2-α) <i>V</i><sup>4</sup> whenever -1 ≤ α ≤ 2, α ≠ 0,1 and that ℑ<sub>α</sub> ≥ [( α)/ 2] <i>V</i><sup>2</sup> + [ 1/ 36] α(1 + 5 α- 5 α<sup>2</sup> ) <i>V</i><sup>4</sup> for 0 <; α <; 1. In a somewhat different direction, and motivated by the fact that these Pinsker's type lower bounds are accurate only for small variation (<i>V</i> close to zero), lower bounds for <i>Df</i> which are accurate for both small and large variation (<i>V</i> close to two) are also obtained. In the special case of the information divergence they imply that <i>D</i> ≥ log[ 2/( 2-<i>V</i>)] - [( 2-<i>V</i>)/2] log[( 2+<i>V</i>)/2], which uniformly improves Vajda's inequality.
Impact of high-fat diet on antioxidant status, vascular wall thickening and cardiac function in adult female LDLR–/– mice

Background: Western diet, rich in saturated fatty acids and cholesterol, is associated with increased cardiovascular risk. We thus investigated in female mice the influence of this diet on plasma antioxidant status, vascular wall thickening and cardiac function. Methods and Results: Adult female C57BL/6J wild type (WT) and LDLR–/– mice were fed a normal diet (ND) or a high-fat diet (HFD) for 17 weeks. HFD induced an increase in plasma lipids and vitamin C (Vit C) levels in both groups but at a much higher level in LDLR–/– and a decrease in plasma ascorbyl free radical levels to Vit C ratio (an endogenous oxidative stress index) in LDLR–/–. We only found a slight decrease in circulating antioxidant status evaluated by the Oxygen Radical Absorbance Capacity (ORAC) assay in WT, but not in LDLR–/–. Echocardiography evidenced an increase in arterial wall thickness in aortic arch at atherosclerosis predilection sites in HFD LDLR–/– as compared to ND LDLR–/– and HFD WT. This result was confirmed by histology. Further-more, histological examination of aortic valves showed an increase in atherosclerotic lesions. Our study, using echocardiography, show that chronic HFD does not induce any major modifications of systolic function in the both mice groups. Conclusions: High-fat intake in mice causes serious disturbances in lipid plasma levels associated to variations of circulating antioxidant status due, at least in part, to an increase in Vit C. At this stage, atherosclerotic lesions, observed in aortic arch and valve, do not impair cardiac function in HFD-fed mice.
Halo and Through-Focus Performance of Four Diffractive Multifocal Intraocular Lenses.

PURPOSE To compare, as a function of pupil size, the through-focus performance and halo features of four diffractive intraocular lenses (IOLs). METHODS Three diffractive bifocal IOLs (ReSTOR +2.5 D SV25T0, Tecnis +2.75 D ZKB00, and AT LISA +3.75 D 809M) and a diffractive trifocal IOL (AT LISA tri +3.33 D, +1.66 D 839MP) were tested in vitro in a modified International Organization for Standardization eye model. The modulation transfer function (MTF) at the IOLs' foci was obtained with pupils ranging from 2.0 to 5.0 mm. Through-focus MTF curves (at 50 cycles/mm) were compared among all the IOLs. The halo formation and characteristics were obtained from image analysis. RESULTS The multifocal IOLs studied in this work showed, at their foci, secondary out-of-focus images, which originate halos and whose characteristics depend on the lens design and pupil size. The smallest halo occurred for the distance focus of the SV25T0. The distance and near foci of the SV25T0 yielded, respectively, the best and lowest optical quality among the studied IOLs. The distance focus of the ZKB00, AT LISA, and AT LISA tri were of similar quality, but the near focus of the ZKB00 outperformed the near foci of the rest of the IOLs. The IOLs' optical performance gradually deteriorates as pupil increases. CONCLUSIONS Differences in the design of the diffractive IOLs translate into differences in optical quality at their foci, through-focus performance, and halo features, which can offer further information to surgeons when selecting which IOL to implant.
Assessing the Potential of HPV16 E6 Seroprevalence as a Biomarker for Anal Dysplasia and Cancer Screening—A Systematic Review and Meta-Analysis

Elevated rates of human papillomavirus (HPV)-related anal high-grade squamous intraepithelial lesions (HSIL) and anal cancer (AC) in populations like men who have sex with men (MSM) living with HIV underscore the need for effective screening. While high-resolution anoscopy-guided biopsy is the gold standard, limited provider availability poses a challenge. This has spurred interest in identifying biomarkers for improved AC prevention. Antibodies against HPV16 oncoprotein E6, known as markers for cervical and oropharyngeal cancers, are the focus of the current study. The systematic review and meta-analysis included six studies meeting inclusion criteria, assessing HPV16 E6 seroprevalence in individuals with anal HSIL or AC. A two-step meta-analysis estimated pooled odds ratios and 95% confidence intervals (CI) for HPV16 E6 seroprevalence and HSIL or AC. Pooled prevalence, sensitivity, specificity, and diagnostic odds ratios were also calculated. This meta-analysis revealed a 3.6-fold increased risk of HSIL for HPV16 E6 seropositive individuals, escalating to a 26.1-fold risk increase for AC. Pooled specificity and sensitivity indicated a high specificity (0.99; 95%CI: 0.99, 0.99) but lower sensitivity (0.19; 95%CI: 0.10, 0.34) for HPV16 E6 serostatus as an AC biomarker. In conclusion, while HPV16 E6 seroprevalence demonstrates specificity as a potential biomarker for HPV-related AC, its utility as a standalone screening tool may be limited. Instead, it could serve effectively as a confirmation test, particularly in high-risk populations, alongside other diagnostic methods. Further research is imperative to explore HPV16 E6 seroconversion dynamics and alternative screening algorithms.
Combining micro and macro-modeling in DEVS for computational biology

In computational biology there is an increasing need to combine micro and macro views of the system of interest. Therefore, explicit means to describe micro and macro level and the downward and upward causation that link both are required. Multi-Level-DEVS (or m^-DEVS) supports an explicit description of macro and micro level, information at macro level can be accessed from micro level and vice versa, micro models can be synchronously activated by the macro model and also the micro models can trigger the dynamics at macro level. To link both levels, different methods are combined, to those belong, value coupling, synchronous activations, variable ports, and invariants. The execution semantic of the formalism is given by an abstract simulator and its use is illustrated based on an small extract of the Wnt pathway.
Drug Repositioning via Graph Neural Networks: Identifying Novel JAK2 Inhibitors from FDA-Approved Drugs through Molecular Docking and Biological Validation

The increasing utilization of artificial intelligence algorithms in drug development has proven to be highly efficient and effective. One area where deep learning-based approaches have made significant contributions is in drug repositioning, enabling the identification of new therapeutic applications for existing drugs. In the present study, a trained deep-learning model was employed to screen a library of FDA-approved drugs to discover novel inhibitors targeting JAK2. To accomplish this, reference datasets containing active and decoy compounds specific to JAK2 were obtained from the DUD-E database. RDKit, a cheminformatic toolkit, was utilized to extract molecular features from the compounds. The DeepChem framework’s GraphConvMol, based on graph convolutional network models, was applied to build a predictive model using the DUD-E datasets. Subsequently, the trained deep-learning model was used to predict the JAK2 inhibitory potential of FDA-approved drugs. Based on these predictions, ribociclib, topiroxostat, amodiaquine, and gefitinib were identified as potential JAK2 inhibitors. Notably, several known JAK2 inhibitors demonstrated high potential according to the prediction results, validating the reliability of our prediction model. To further validate these findings and confirm their JAK2 inhibitory activity, molecular docking experiments were conducted using tofacitinib—an FDA-approved drug for JAK2 inhibition. Experimental validation successfully confirmed our computational analysis results by demonstrating that these novel drugs exhibited comparable inhibitory activity against JAK2 compared to tofacitinib. In conclusion, our study highlights how deep learning models can significantly enhance virtual screening efforts in drug discovery by efficiently identifying potential candidates for specific targets such as JAK2. These newly discovered drugs hold promises as novel JAK2 inhibitors deserving further exploration and investigation.
Common Variants at 9p21 and 8q22 Are Associated with Increased Susceptibility to Optic Nerve Degeneration in Glaucoma

Optic nerve degeneration caused by glaucoma is a leading cause of blindness worldwide. Patients affected by the normal-pressure form of glaucoma are more likely to harbor risk alleles for glaucoma-related optic nerve disease. We have performed a meta-analysis of two independent genome-wide association studies for primary open angle glaucoma (POAG) followed by a normal-pressure glaucoma (NPG, defined by intraocular pressure (IOP) less than 22 mmHg) subgroup analysis. The single-nucleotide polymorphisms that showed the most significant associations were tested for association with a second form of glaucoma, exfoliation-syndrome glaucoma. The overall meta-analysis of the GLAUGEN and NEIGHBOR dataset results (3,146 cases and 3,487 controls) identified significant associations between two loci and POAG: the CDKN2BAS region on 9p21 (rs2157719 [G], OR = 0.69 [95%CI 0.63–0.75], p = 1.86×10−18), and the SIX1/SIX6 region on chromosome 14q23 (rs10483727 [A], OR = 1.32 [95%CI 1.21–1.43], p = 3.87×10−11). In sub-group analysis two loci were significantly associated with NPG: 9p21 containing the CDKN2BAS gene (rs2157719 [G], OR = 0.58 [95% CI 0.50–0.67], p = 1.17×10−12) and a probable regulatory region on 8q22 (rs284489 [G], OR = 0.62 [95% CI 0.53–0.72], p = 8.88×10−10). Both NPG loci were also nominally associated with a second type of glaucoma, exfoliation syndrome glaucoma (rs2157719 [G], OR = 0.59 [95% CI 0.41–0.87], p = 0.004 and rs284489 [G], OR = 0.76 [95% CI 0.54–1.06], p = 0.021), suggesting that these loci might contribute more generally to optic nerve degeneration in glaucoma. Because both loci influence transforming growth factor beta (TGF-beta) signaling, we performed a genomic pathway analysis that showed an association between the TGF-beta pathway and NPG (permuted p = 0.009). These results suggest that neuro-protective therapies targeting TGF-beta signaling could be effective for multiple forms of glaucoma.
Body dissatisfaction in women across the lifespan: results of the UNC-SELF and Gender and Body Image (GABI) studies.

To explore age differences in current and preferred silhouette and body dissatisfaction (current - preferred silhouette discrepancy) in women aged 25-89 years using figural stimuli [range: 1 (very small) to 9 (very large)]. Data were abstracted from two online convenience samples (N = 5868). t-tests with permutation-adjusted p-values examined linear associations between mean silhouette scores (current, preferred, discrepancy score) and age with/without stratification by body mass index (BMI). Modal current silhouette was 5; modal preferred silhouette was 4; mean discrepancy score was 1.8. There was no significant association between current silhouette and age, but a positive linear association between preferred silhouette and age remained after stratification by BMI. A significant inverse linear association of silhouette discrepancy score and age was found only prior to stratification by BMI. Body dissatisfaction exists in women across the adult life span and is influenced by BMI.
Kruppel-like factor 15 is a regulator of cardiomyocyte hypertrophy

Cardiac hypertrophy is a common response to injury and hemodynamic stress and an important harbinger of heart failure and death. Herein, we identify the Kruppel-like factor 15 (KLF15) as an inhibitor of cardiac hypertrophy. Myocardial expression of KLF15 is reduced in rodent models of hypertrophy and in biopsy samples from patients with pressure-overload induced by chronic valvular aortic stenosis. Overexpression of KLF15 in neonatal rat ventricular cardiomyocytes inhibits cell size, protein synthesis and hypertrophic gene expression. KLF15-null mice are viable but, in response to pressure overload, develop an eccentric form of cardiac hypertrophy characterized by increased heart weight, exaggerated expression of hypertrophic genes, left ventricular cavity dilatation with increased myocyte size, and reduced left ventricular systolic function. Mechanistically, a combination of promoter analyses and gel-shift studies suggest that KLF15 can inhibit GATA4 and myocyte enhancer factor 2 function. These studies identify KLF15 as part of a heretofore unrecognized pathway regulating the cardiac response to hemodynamic stress.
Tritium Records to Trace Stratospheric Moisture Inputs in Antarctica

Better assessing the dynamic of stratosphere‐troposphere exchange is a key point to improve our understanding of the climate dynamic in the East Antarctica Plateau, a region where stratospheric inputs are expected to be important. Although tritium (3H or T), a nuclide naturally produced mainly in the stratosphere and rapidly entering the water cycle as HTO, seems a first‐rate tracer to study these processes, tritium data are very sparse in this region. We present the first high‐resolution measurements of tritium concentration over the last 50 years in three snow pits drilled at the Vostok station. Natural variability of the tritium records reveals two prominent frequencies, one at about 10 years (to be related to the solar Schwabe cycles) and the other one at a shorter periodicity: despite dating uncertainty at this short scale, a good correlation is observed between 3H and Na+ and an anticorrelation between 3H and δ18O measured on an individual pit. The outputs from the LMDZ Atmospheric General Circulation Model including stable water isotopes and tritium show the same 3H‐δ18O anticorrelation and allow further investigation on the associated mechanism. At the interannual scale, the modeled 3H variability matches well with the Southern Annular Mode index. At the seasonal scale, we show that modeled stratospheric tritium inputs in the troposphere are favored in winter cold and dry conditions.
PPTP: Privacy-Preserving Traffic Padding in Web-Based Applications

Web-based applications are gaining popularity as they require less client-side resources, and are easier to deliver and maintain. On the other hand, web applications also pose new security and privacy challenges. In particular, recent research revealed that many high profile web applications might cause sensitive user inputs to be leaked from encrypted traffic due to side-channel attacks exploiting unique patterns in packet sizes and timing. Moreover, existing solutions, such as random padding and packet-size rounding, were shown to incur prohibitive overhead while still failing to guarantee sufficient privacy protection. In this paper, we first observe an interesting similarity between this privacy-preserving traffic padding (PPTP) issue and another well studied problem, privacy-preserving data publishing (PPDP). Based on such a similarity, we present a formal PPTP model encompassing the privacy requirements, padding costs, and padding methods. We then formulate PPTP problems under different application scenarios, analyze their complexity, and design efficient heuristic algorithms. Finally, we confirm the effectiveness and efficiency of our algorithms by comparing them to existing solutions through experiments using real-world web applications.