Miracle-dz/UniFAR-FTUs huggingface dataset:
As We Were and as We Should Be, Combined Exercise Training in Adults with Schizophrenia: CORTEX-SP Study Part I

ABSTRACT Introduction Given the health benefits and the role of exercise as an anti-inflammatory adjuvant program, this study aimed to determine the effectiveness of a combined exercise program on cardiorespiratory fitness (CRF), body composition, and biochemical levels in adults with schizophrenia (SZ) characterized at baseline as metabolically unhealthy overweight with low CRF. Methods Participants diagnosed with SZ (n = 112, 41.3 ± 10.4 yr, 28.7% women) were randomly assigned into a treatment-as-usual control group (n = 53) or a supervised exercise group (n = 59, 3 d·wk−1). Each combined exercise session consisted of both a low-volume high-intensity interval training (<10 min of high-intensity time per session) and a resistance circuit-training program. All variables were assessed before and after the intervention (20 wk). For the assessment of CRF, a peak cardiopulmonary exercise test on a cycle ergometer was used. Results After the intervention, participants from the exercise group (n = 51) showed increases in CRF (P < 0.001) through peak oxygen uptake (L·min−1; Δ = 17.6%; mL·kg−1·min−1, Δ = 19.6%) and the metabolic equivalent of task (Δ = 19%), with no significant changes (P > 0.05) in body composition and biochemical variables. However, the treatment-as-usual group (n = 38) did not show any significant change in the study variables (P > 0.05). Between-group significant differences (P ≤ 0.05) were observed in CRF, first ventilatory threshold, and heart rate peak after the intervention period, favoring the exercise group. Conclusions This study demonstrated that a supervised combined exercise program in people with SZ helps to maintain body composition values and improve CRF levels. This could lead to an important clinical change in the characterization from metabolically unhealthy overweight to a metabolically healthy overweight population. Hence, exercise should be considered a co-adjuvant program in the treatment of the SZ population.
How do symptoms of each joint contribute to global pain, disease activity and functional disability in rheumatoid arthritis?—A comprehensive association study using a large cohort

Background Established assessment tools for patients with rheumatoid arthritis (RA), including disease activity scores (DASs), disease activity indexes (DAIs), visual analog scales (VASs), and health assessment questionnaires (HAQs), are widely used. However, comparative associations between joint involvement and disease status assessment tools have rarely been investigated. Methods We included a dataset of 4016 patients from a large RA cohort from 2012 to 2019. The tenderness and swelling of each joint were counted as a symptom, with 70 and 68 affected joints throughout the body, respectively. The relative contribution of various joints to the disease status assessment tools, VAS scores, and functional disability indexes was analyzed using multiple regression analysis. Results The wrist showed the most significant contribution overall, especially in DASs and VASs, while the metacarpophalangeal and proximal interphalangeal joints made significant contributions to DASs and DAIs, but not to VASs and HAQs. The shoulder and the elbow significantly contributed to HAQs, but only the shoulder did to the VASs. The knee universally contributed to all of the tools, but the ankle played a minor but important role in most assessment tools, especially in HAQs. Similar but different contribution ratios were found between the sets of DASs, DAIs, VASs, or HAQs. Conclusions Each joint makes a unique contribution to these assessment tools. The improvement or aggravation of symptoms in each joint affects the assessment tools in different manners.
Evaluation of inflammatory cytokines in drug-naïve major depressive disorder: A systematic review and meta-analysis

Objective: Altered levels of peripheral inflammatory and proinflammatory cytokine markers affect the different clinical stages of major depressive disorder (MDD). A concrete understanding of the causal mechanism of MDD is a prerequisite in developing treatment strategies and preventive plans. Here we aimed to conduct an updated systematic review and meta-analysis of studies assessing the association of C-reactive protein (CRP), INF-γ, MCP-1, and TNF-α in the peripheral fluid of drug-naïve MDD patients and healthy controls (HCs). Methods: We extracted articles from PubMed, ProQuest, PsycINFO, Web of Science, and Scopus databases from inception until 14 February 2021, to find relevant studies. In this meta-analysis, we included a total of 23 eligible studies (1,366 MDD patients and 1,342 controls) in the final meta-analysis. The Cochran’s chi-square Q-test and I2-index were applied to measure the heterogeneity and inconsistency of all combined results. We selected a random-effect model during the analysis and measured publication biases using the funnel plot. We performed Bonferroni adjustment for multiple testing. Results: We found a high level of TNF-α in MDD patients than in control subjects Standardized Mean Difference (SMD) with a random-effects model: 1.04, 95% CI: 0.69–1.39, z = 5.84, p < 0.001). The levels of CRP (SMD with a random-effects model: 0.18, 95% CI: −0.85–1.23, z = 0.35, p = 0.73), INF-ɤ (SMD with a random-effects model: −0.05, 95% CI: −2.72–2.62, z = 0.03, p = 0.97), and MCP-1 (SMD with a random-effects model: 0.70, 95% CI: −0.09–1.49, z = 1.73, p = 0.08) were not significantly varies between MDD patients and HCs. Conclusion: The present study findings suggest the upregulated level of peripheral TNF-α but not CRP, INF-γ, and MCP-1 involve in depression. The elevated inflammatory cytokines confirmed the inflammatory state of depression. Therefore, inflammatory cytokines might serve as potential risk assessment markers in MDD.
Excess of nonceruloplasmin serum copper in AD correlates with MMSE, CSF β-amyloid, and h-tau

Objective: To assess whether serum copper in Alzheimer disease (AD) correlates with cognitive scores, β-amyloid, and other CSF markers of neurodegeneration. Methods: The authors studied copper, ceruloplasmin, total peroxide, and antioxidants levels (TRAP) in serum; β-amyloid in plasma; and copper, β-amyloid, h-tau, and P-tau in the CSF of 28 patients with AD and 25 healthy controls, in relation to clinical status. Results: Serum copper (p < 0.0001), peroxides (p = 0.002), a copper fraction unexplained by ceruloplasmin (p < 0.0001), and CSF h-tau (p = 0.001) were increased in AD, whereas serum TRAP (p = 0.03) and CSF β-amyloid were decreased (p < 0.0001). Plasma β-amyloid increased with age in healthy controls (r = 0.6; p = 0.05). CSF markers of AD correlated with serum copper variables. CSF copper was partially dependent on the serum copper fraction unexplained by ceruloplasmin (t = 2.2, p = 0.04). CSF β-amyloid seemed to be related to serum copper (r = −0.46; p = 0.002). Mini-Mental Status Examination scores correlated positively with β-amyloid (r = 0.46, p = 0.002) and inversely with copper unexplained by ceruloplasmin (r = −0.45, p = 0.003). Conclusions: The authors' results confirm the existence of changes in copper component distribution, particularly the copper fraction unexplained by ceruloplasmin and support the hypothesis of a β-amyloid and copper connection in Alzheimer disease.
An amortized approach to non-linear mixed-effects modeling based on neural posterior estimation

Non-linear mixed-effects models are a powerful tool for studying heterogeneous populations in various fields, including biology, medicine, economics, and engineering. However, fitting these models to data is computationally challenging if the description of individuals is complex and the population is large. To address this issue, we propose a novel machine learning-based approach: We exploit neural density estimation based on normalizing flows to approximate individual-specific posterior distributions in an amortized fashion, thereby allowing for an efficient inference of population parameters. Applying this approach to problems from cell biology and pharmacology, we demonstrate its scalability to large data sets in an unprecedented manner. Moreover, we show that it enables accurate uncertainty quantification and extends to stochastic models, which established methods, such as SAEM and FOCEI are unable to handle. Thus, our approach outperforms state-of-the-art methods and improves the analysis capabilities for heterogeneous populations.
Increased tolerance to commonly used antibiotics in a Pseudomonas aeruginosa ex vivo porcine keratitis model

Antibiotics in development are usually tested on rapidly dividing cells in a culture medium and do not reflect the complexity of infections in vivo, while testing in vivo is limited, expensive and ethically concerning. This often results in the development and subsequent prescription of antibiotics only targeting infections in which pathogens are undergoing rapid cell division and in case of persistent infections like keratitis leads to poor clinical outcomes such as impaired vision or loss of an eye. In this study, we demonstrate antibiotic tolerance of Pseudomonas aeruginosa strains PA01 and PA14 using the ex vivo porcine keratitis model in which bacterial physiology more closely mimics infections in vivo than in a culture medium. MBEC and MIC were used as a guideline to establish the concentration of applied antibiotics on tissue. Infected ex vivo porcine corneas were treated with therapeutically relevant concentrations of gentamicin, ciprofloxacin and chloramphenicol. Ciprofloxacin was the most potent across all tests demonstrating a positive correlation with MIC but not MBEC. Nonetheless, the results demonstrated that MIC and MBEC concentrations were not sufficient to clear infection even after 18 hours of continuous exposure to the tested antibiotics reflecting the need for novel antibiotics that can target the persistent subpopulation of these pathogens and the ability of the ex vivo keratitis model to be a relevant platform to identify novel antibiotics with suitable activities. There was a clear visual distinction between corneas infected with cytotoxic strain PA14 and invasive strain PA01. In this study, both strains PA14 and PA01 showed a high level of antibiotic tolerance, which suggests that in clinical settings the treatment approach could be similar regardless of the causative strain. Data summary The authors confirm all supporting data and protocols have been provided within the article or through supplementary data files.
Sample designs and sampling errors for the World Fertility Survey

The paper describes and tabulates sample design characteristics and parameters for 35 national surveys in developing countries conducted under the World Fertility Survey [WFS] programme. Common design features are discussed in relation to the various practical contraints inherent in the basic data collection operation. A procedure for computing sampling errors is outlined and data from selected WFS surveys are used to investigate the pattern of sampling error results across sample subclasses substantive variables and countries. The effects of clustering stsratification and weighting are also studied
Etude de la degradation des etats de surface du sol, par teledetection : analyses spectrales, spatiales et diachroniques

Cette etude presente une nouvelle approche pour la caracterisation des etats de surface du sol, par teledetection. Le role des principaux facteurs du sol est analyse au laboratoire, sur des echantillons varies avec un spectrophotometre. La matiere organique et le fer diminuent la reflectance, le calcaire l'augmente. La couleur est un facteur important pour definir la forme de la courbe spectrale dans le visible. Sur le terrain, on a etudie la relation rugosite-reflectance. L'evolution de surfaces rugueuses a lisses a ete suivie par des mesures radiometriques et des observations macroscopiques sur differents sites. Un modele entre la reflectance et le stade de degradation a ete defini sous des conditions precises d'humidite et d'eclairement. Les diverses relations mises en evidence au laboratoire et sur le terrain permettent de mieux interpreter les images satellitaires et de suivre les phenomenes d'erosion dans le temps
Design and Methodology in the Science of Reading

personal observations. Arguably, observations are only the beginning of scientiﬁ c knowledge. There are times when our observations can lead us to the correct conclusions, but there are other times they can lead us astray. Observations give us ideas about what could possibly be occurring, but from these W hat is the science of reading? The Reading League, in their document “Science of Reading: Deﬁ ning Guide” (TRL, 2022), proposes that “the science of reading is a vast, interdisciplinary body of scientiﬁ cally-based* research about reading and issues related to reading and writing” (p. 11). The asterisk is carrying a lot of weight here. What does it mean for something to be scientiﬁ cally based? It means that the evidence for a claim is weighed by the design and methods used to collect and analyze it, and the claim takes into account the limitations of that evidence. In this paper we will discuss some of the designs and methods used to investigate how children learn to read for understanding and provide a brief history into the use of these designs in reading and educational research.
Adversarial images with downscaling

Most works on adversarial attacks consider small images whose size already ﬁts the model. This paper explores at-tacking large images on classiﬁers with different input sizes. Downscaling is a necessary ﬁrst step to adapt the size of the image to the model that might reform the adversarial signal. This paper studies the possibility of forging adversarial images through different interpolation methods, the distortion of their adversarial signal, and the transferability over other downscaling methods. This paper ﬁnally explores attacking an ensemble model which gathers different resizing interpo-lations to increase the transferability of the attack against a set downscaling kernels.
Comprehensive analysis of Hox gene expression in the amphipod crustacean Parhyale hawaiensis

Hox genes play crucial roles in establishing regional identity along the anterior–posterior axis in bilaterian animals, and have been implicated in generating morphological diversity throughout evolution. Here we report the identification, expression, and initial genomic characterization of the complete set of Hox genes from the amphipod crustacean Parhyale hawaiensis. Parhyale is an emerging model system that is amenable to experimental manipulations and evolutionary comparisons among the arthropods. Our analyses indicate that the Parhyale genome contains a single copy of each canonical Hox gene with the exception of fushi tarazu, and preliminary mapping suggests that at least some of these genes are clustered together in the genome. With few exceptions, Parhyale Hox genes exhibit both temporal and spatial colinearity, and expression boundaries correlate with morphological differences between segments and their associated appendages. This work represents the most comprehensive analysis of Hox gene expression in a crustacean to date, and provides a foundation for functional studies aimed at elucidating the role of Hox genes in arthropod development and evolution. & 2015 Elsevier Inc. All rights reserved.
Power Mismatch and Civil Conflict: An Empirical Investigation

This paper empirically shows that the imbalance between an ethnic group’s political and military power is crucial to understanding the likelihood that such a group engages in a conflict. We develop a novel measure of a group’s military power by combining machine learning techniques with rich data on ethnic group characteristics and outcomes of civil conflicts in Africa and the Middle East. We couple this measure with available indicators of an ethnic group’s political power as well as with a novel proxy based on information about the ethnicity of cabinet members. We find that groups characterized by a higher mismatch between military and political power are between 30% and 50% more likely to engage in a conflict against their government depending on the specification used. We also find that the effects of power mismatch are nonlinear, which is in agreement with the predictions of a simple model that accounts for the cost of conflict. Moreover, our results suggest that high-mismatched groups are typically involved in larger and centrist conflicts. The policy implication is that power-sharing recommendations and institutional design policies for peace should consider primarily the reduction of power mismatches between relevant groups, rather than focusing exclusively on equalizing political power in isolation.
Rapid assessment of mercury-contaminated sites through the Toxic Site Identification Program (TSIP). Colombia

Mercury concentration measurements were compiled from 72 sites located throughout seven departments of Colombia using field information gathered from 2016–2021 by Pure Earth, an international non-profit organization, and secondary information from previously conducted studies. These measurements and other data such as type of contaminated resource (water, soil), resource use (fishing, agricultural, residential, and industrial), estimated at-risk population, and permissible contamination limits were entered into Pure Earth’s Toxic Site Identification Program (TSIP) database. Using information from the TSIP database, the Blacksmith Index, a contaminated site intervention prioritization index, was calculated for all 72 sites. After applying exclusion criteria to the sites for this study, the results show that approximately 55,095 people are affected by mercury contamination in 44 sites. Of these study sites, the site with the highest Blacksmith Index value and therefore, the highest health risk due to mercury contamination, is La Bocana in the department of Valle del Cauca.
Influence of Dietary Energy and Protein Intake on Yield and Composition of Milk in Crossbred Dairy Cows

There are a number of fundamental factors that affects milk components such as genetics, breed, environment, parity, stage of lactation, disease, season and age of the cow. Of all the factors, nutrition offers the most effective means of rapidly altering milk composition. Although, almost all components of milk are subjected to manipulation, the extents are variable. In general, fat percent and the fatty acid profile of milk are most likely to change, whereas lactose is least sensible and protein is intermediate. Again, changes in milk composition are not always obvious. For example, total protein concentration could remain constant, but significant changes could occur in the ratio of casein to non-protein nitrogen. Additionally, the dairy cow is a relatively inefficient converter of dietary nitrogen into milk protein. ThereThe study was carried out on 120 crossbred Holstein × Shahiwal dairy cows for a period of 150 days to quantify the influence of dietary energy and protein intake on yield and composition of milk. Total 12 dairy farms having similar housing systems and holding at least 20 dairy cows in between mid to late lactation were selected for study purposes. The farms were located in the peri-urban and urban areas of Chittagong, Bangladesh. Milk samples were collected from individual cow. Milk from cows having same body condition scoring (BCS) were mixed together to make a composite sample. Chemical analyses of the samples were carried out in triplicate for fat, protein, lactose, total solids (TS), solids not fat (SNF) and ash. Dietary metabolizable energy (ME) and crude protein (CP) intake were measured by analyzing the amount of total mixed ration ingested by the individual cow. Results indicated that, ME intake (MJ/d) significantly (P<0.01) influenced milk yield, milk fat and TS content of milk in crossbred Holstein Friesian dairy cows. Similar to ME, CP intake (g/d) also influenced (P<0.01) milk yield, fat, protein, lactose, TS and ash content of milk. Correlation coefficient matrix indicated that, milk yield was positively correlated with ME and CP intake. However, there was a negative association between ME or CP intake and milk protein, lactose, TS and SNF of milk even though the strength of association was variable. It could therefore be inferred that, adequate dietary ME and CP intake is important to optimize milk yield and milk composition in crossbred Holstein × Shahiwal dairy cows reared under intensive farming systems in tropical regions.
Surface Engineering Methods for Powder Bed Printed Tablets to Optimize External Smoothness and Facilitate the Application of Different Coatings

In a previous attempt to achieve ileo-colonic targeting of bovine intestinal alkaline phosphatase (BIAP), we applied a pH-dependent coating, the ColoPulse coating, directly on powder bed printed (PBP) tablets. However, the high surface roughness necessitated an additional sub-coating layer [Nguyen, K. T. T. , Pharmaceutics 2022]. In this study, we aimed to find a production method for PBP tablets containing BIAP that allows the direct application of coating systems. Alterations of the printing parameters, binder content, and printing layer height, when combined, were demonstrated to create visually less rough PBP tablets. The addition of ethanol vapor treatment further improved the surface’s smoothness significantly. These changes enabled the direct application of the ColoPulse, or enteric coating, without a sub-coating. In vitro release testing showed the desired ileo-colonic release or upper-intestinal release for ColoPulse or enteric-coated tablets, respectively. Tablets containing BIAP, encapsulated within an inulin glass, maintained a high enzymatic activity (over 95%) even after 2 months of storage at 2–8 °C. Importantly, the coating process did not affect the activity of BIAP. In this study, we demonstrate, for the first time, the successful production of PBP tablets with surfaces that are directly coatable with the ColoPulse coating while preserving the stability of the encapsulated biopharmaceutical, BIAP.
Correlated inverse Gaussian frailty models for bivariate survival data

Abstract Frailty models are used in the survival analysis to account for the unobserved heterogeneity in individual risks to disease and death. To analyze the bivariate data on related survival times, the shared frailty models were suggested. Shared frailty models are used despite their limitations. To overcome their disadvantages correlated frailty models may be used. In this paper, we introduce the Inverse Gaussian correlated frailty models with two different baseline distributions namely, the generalized log logistic and the generalized Weibull. We introduce the Bayesian estimation procedure using Markov Chain Monte Carlo (MCMC) technique to estimate the parameters involved in these models. We present a simulation study to compare the true values of the parameters with the estimated values. Also we apply these models to a real life bivariate survival data set of McGilchrist and Aisbett (1991) related to the kidney infection data and a better model is suggested for the data.
Acoustic Analysis of Psychological Stress in a Speech Signal

This master’s thesis deals with the acoustic analysis of psychological stress in a speech signal. The effects of stress on human body, particularly on the respiratory system, serve as a foundation for research into the effect of stress on speech. Acoustic parameters, specifically the fundamental frequency f0, are investigated in relation to stress exposure. The database was created from data collected as part of an experiment at the Faculty of Science at Charles University. The primary goals of this work are to create a stressed speech database, select appropriate acoustic speech features based on previous research, and analyse them. Despite the fact that this thesis is a pilot project, the results show a potential for detecting psychological stress in speech using acoustic parameters, especially f0, and intensity. Preliminary results on vowel [a:] also show promising results for jitter, CPP and CPPs, and mean autocorrelation.