Miracle-dz/UniFAR-FTUs huggingface dataset:
Evaluation of Pathway Activation for a Single Sample Toward Inflammatory Bowel Disease Classification

Since similar complex diseases are much alike in clinical symptoms, patients are easily misdiagnosed and mistreated. It is crucial to accurately predict the disease status and identify markers with high sensitivity and specificity for classifying similar complex diseases. Many approaches incorporating network information have been put forward to predict outcomes, but they are not robust because of their low reproducibility. Several pathway-based methods are robust and functionally interpretable. However, few methods characterize the disease-specific states of single samples from the perspective of pathways. In this study, we propose a novel framework, Pathway Activation for Single Sample (PASS), which utilizes the pathway information in a single sample way to better recognize the differences between two similar complex diseases. PASS can mainly be divided into two parts: for each pathway, the extent of perturbation of edges and the statistic difference of genes caused by a single disease sample are quantified; then, a novel method, named as an AUCpath, is applied to evaluate the pathway activation for single samples from the perspective of genes and their interactions. We have applied PASS to two main types of inflammatory bowel disease (IBD) and widely verified the characteristics of PASS. For a new patient, PASS features can be used as the indicators or potential pathway biomarkers to precisely diagnose complex diseases, discover significant features with interpretability and explore changes in the biological mechanisms of diseases.
Susceptibility of Chicken Embryos, Sheep, Cattle, Pigs, and Chickens to Zika Virus Infection

The susceptibility of sheep, cattle, pigs, chickens and chicken embryos to Zika virus infection was evaluated by experimental inoculation with Zika virus Thailand strain isolated from a Canadian traveler in 2013. The inoculated animals did not develop any clinical signs of disease nor evidence of Zika virus replication in peripheral blood, cerebrospinal fluid and tissues including brain and spinal cord assessed by real-time RT-PCR. Sera were also negative for Zika virus antibodies by Zika virus neutralization assays as well as Zika virus immunoperoxidase staining of Zika infected Vero cells. Chicken embryos were inoculated by different routes including yolk sac (4 day old embryos), chorioallantoic membrane (8 day old embryos), amniotic fluid (8 day old embryos) and intravenous routes (12 day old embryos). Virus replication in chicken embryos was observed in the brain and body tissues following intravenous (IV), yolk sac (YS), chorioallantoic membrane (CAM), and amniotic fluid (AF) inoculation routes. The highest mortality was observed in embryos inoculated via yolk sac. The dead embryos showed diffuse muscular hemorrhages. The yolk sac inoculated chicken embryos showed delayed hatching and displayed neurological signs immediately after hatching. These studies demonstrate that 8 week old sheep, 6 month old cattle, 4 week old pigs, and 4 week old chickens are not susceptible to Zika virus infection when inoculated experimentally and therefore unlikely to pose a risk as Zika virus reservoirs. However, chicken embryos are highly susceptible to Zika virus resulting in clinical disease of chicks after hatching. This study demonstrates that Zika virus has a tropism for embryonic tissue and that chicken embryos can be used as a model to study Zika virus replication and pathogenesis.
Therapeutic Potential of Mesenchymal Stem Cells for Cancer Therapy

Mesenchymal stem cells (MSCs) are among the most frequently used cell type for regenerative medicine. A large number of studies have shown the beneficial effects of MSC-based therapies to treat different pathologies, including neurological disorders, cardiac ischemia, diabetes, and bone and cartilage diseases. However, the therapeutic potential of MSCs in cancer is still controversial. While some studies indicate that MSCs may contribute to cancer pathogenesis, emerging data reported the suppressive effects of MSCs on cancer cells. Because of this reality, a sustained effort to understand when MSCs promote or suppress tumor development is needed before planning a MSC-based therapy for cancer. Herein, we provide an overview on the therapeutic application of MSCs for regenerative medicine and the processes that orchestrates tissue repair, with a special emphasis placed on cancer, including central nervous system tumors. Furthermore, we will discuss the current evidence regarding the double-edged sword of MSCs in oncological treatment and the latest advances in MSC-based anti-cancer agent delivery systems.
The Place and Role of The Father in Early Life

Abstract The present paper is an attempt to create bridges of understanding between the subjective investigation in the psychoanalytic situation and the empirical research concerning a subject not enough explored in its earliest dimensions – the place and role of the father in the first year of the child’s life. As part of a more extensive empirical research on the dynamics of child development in the first year of life, the research presented in this article was built and articulated within the psychodynamic theories of development, it was conducted in the form of a standardized research and generated a series of results that are re-integrated into the psychoanalytic understanding, validating and being validated by psychoanalytic knowledge. The central point of this encounter between the psychodynamic understanding and the results of empirical research is that the father is an active presence in the development of the child from the first year of life, in a formula of internal and external triadic relationship and that one of the most important function of the father in this early stage of life is to facilitate a way for the child to build his own loving and creative relationship with the world.
A Rheo-optical Investigation into the Viscoelastic Moduli of Acidified Milk Gel

Abstract Diffusing wave spectroscopy (DWS) in the backscattering geometry was employed to observe the evolution of the intensity correlation function during the acidification of skimmed milk by gluconic-δ-lactone (GDL). At the stage when the formation of casein particle gel is largely complete the correlation function at shorter decay times reveals the local structural arrest of the casein micelles, whereas at longer delay times it illustrates the hindered slow motion of casein micelle aggregates. We use the principles of the approach suggested by Mason, Gang and Weitz, linking the optically measured mean square displacement, , of the microscopic particles in a dense colloid to its viscoelastic properties, to provide an estimate of the frequency dependent viscoelastic modulus of the acidified milk gel (AMG). We compare the viscoelastic moduli measured by the conventional mechanical rheometry with the optically measured ones. The results of the two different experimental methods are found to be in reasonable agreement.
A note on a property of the Gini coefficient

Abstract The scope of this note is a self-contained presentation of a mathematical method that enables us to give an absolute upper bound for the difference of the Gini coefficients |G(σ1, . . ., σn) − G(γ1, . . . , γn)| , where (γ1, . . . , γn) represents the vector of the gross wages and (σ1, . . . , σn) represents the vector of the corresponding super-gross wages that is used in the Czech Republic for calculating the net wage. Since (as of June 2019) σi = 100 ⎡ 1.34 γi/100⎤, the study of the above difference seems to be somewhat inaccessible for many economists. However, our estimate based on the presented technique implies that the introduction of the super-gross wage concept does not essentially affect the value of the Gini coefficient as sometimes expected.
Profile of coordination motor abilities in elite judokas and badminton players compared to non-athletes

Summary Study aim: To determine the level and internal structure of profiles of coordination motor abilities in elite judokas and badminton players compared to a group of non-athletes. Material and methods: The material for the study was the results collected from 12 competitors of the Polish national badminton team (age: 22.7 ± 4.5), 10 members of the national judo team who represented mean weight categories (age: 23.0 ± 3.3) and 25 non-athletes, who were male university students of the Faculty of Physical Education and Sport (age: 23.0 ± 0.8). The scope of the study included basic somatic features and selected coordination motor abilities measured by means of computer tests. Results: Statistically significant differences between badminton players and judokas were obtained for reaction times (visual, auditory and selective) as well as spatial orientation. In all cases, a higher level was found for badminton players. Furthermore, analysis of differences between badminton players and non-athletes revealed statistically significant differences only for the selective reaction time. A substantial differentiation of the internal structure of the models of coordination motor abilities was obtained. This pattern was particularly noticeable in the group of judokas and badminton players, where the difference between characteristics was ca. 0.76 SD. Substantially smaller differences (0.21 SD) between particular variables included in the coordination profile were found for non-athlete university students. Conclusion: The lower results of the elite judokas show the need for developing the coordination motor abilities during training. The largest reserves are to be found in raising the level of reaction times and spatial orientation.
Essay on Finance-Growth Nexus

Abstract There is a long tradition in literature that banks can play a special role in the propagation of economic fluctuations. Theory suggests many channels through which financial system affects, and is affected by, economic growth. One of the most important empirical studies on this topic shows a strong positive relation between financial development and economic growth. However, the hypothesis that credit expansion is the main development instrument was challenged in the Asian crisis in the second half of the 1990s, and then even more strongly in the crisis after 2008 which was followed by almost a decade of economic stagnation. Development of the banking sector in Southeast European countries in the pre-crisis period was characterized by relatively high credit growth rates and, consequently, with an increase of the credit-to-GDP ratio. Some authors argue that the marginal effect of financial depth on economic growth becomes negative when credit to the private sector reaches about 100% of GDP. Taking into account relatively low level of credit-to-GDP ratio, we may assume that there is still enough room for finance to contribute to economic growth in Southeast European countries.
Melanism as a potential thermal benefit in eastern fox squirrels (Sciurus niger)

Abstract Melanistic fox squirrels (Sciurus niger) have expanded westward and increased in frequency in the Omaha, Nebraska, and Council Bluffs, Iowa, metropolitan areas. The selective advantage of melanism is currently unknown, but thermal advantages have been hypothesized, especially in winter. No difference in metabolic response curves were measured between melanistic (black) and rufus (orange) fox squirrels. When exposed to sunny skies, both melanistic and rufus squirrels had higher surface (skin and fur) temperature as ambient temperatures increased. Melanistic squirrel surface temperatures did not differ when squirrels were exposed to sunny or cloudy skies. However, rufus individuals showed significantly lower increases in surface temperatures when under cloudy skies. During fall months, rufus individuals were about 1.5 times more active throughout the day than melanistic individuals. However, in winter, melanistic fox squirrels were approximately 30% more active in the mornings (before 13:00) compared to rufus squirrels. Pre-winter body condition was higher in melanistic (25.5 ± 1.8 g/cm) compared to rufus (20.30 ± 3.6 g/cm) fox squirrels; however, there were no significant differences between melanistic (22.8 ± 1.4 g/cm) and rufus (23.9 ± 0.8 g/cm) fox squirrel post-winter body condition. The results of this study indicate that melanistic fox squirrels may have a slight winter thermal advantage over rufus fox squirrels by maintaining higher skin temperatures.
The relationship between neck angles and ground reaction forces in schoolchildren during backpack carriage

Summary Study aim: This study aimed to examine the effect of carrying backpacks on neck posture and ground reaction forces (GRFs) and to investigate the relationship between neck angles and GRFs during backpack carriage in schoolchildren. Material and methods: The craniohorizontal angle (CHA), craniovertebral angle (CVA), sagittal shoulder posture (SSP) and GRFs were measured in right-handed schoolchildren (14 male and 12 female) with mean age 10.17 ± 1.15 years during loaded and unloading conditions. The Qualisys motion analysis system with a force plate was used to assess the neck angles and GRFs. Results: During backpack carriage there was a significant increase in the CHA (p = 0.001), significant decrease in the CVA and SSP (p = 0.001, 0.016 respectively), no significant difference in the normalized (scaled to body weight) vertical GRFs (p > 0.05), and a significant increase in the anterior braking and posterior propulsive GRFs (p = 0.035, 0.002 respectively) compared to the unloading condition. While carrying a backpack there was a moderate negative correlation between the SSP and first vertical GRF (r = –0.464) and a strong negative correlation with the second vertical GRF (r = –0.571) and the posterior propulsive GRF (r = –0.587). Conclusion: Carrying a backpack weighing 15% of the child’s body weight changes the head posture and increases the normalized value of the anterior-posterior shear force. During backpack carriage, decreasing the SSP is associated with increasing the load acceptance, thrusting and posterior propulsive forces. Increasing the shearing force may lead to development of postural abnormities. Consequently, the ideal backpack weight should be considered by parents and teachers.
Supporting Information

SI Dataset 1 The codeword files for the compositions in our dataset. The file names are also their unique IDs formatted as “composition (or publication) year composer piece identifier. ” For example, the ID of Beethoven’s Für Elise first publicized in 1867 with catalogue number WoO 59 is “1867 beethoven WoO59. ” We created each file by converting the MIDI file of each piece into a sequence of codewords with the measures marked M. Each codeword consists of the MIDI numbers of the notes being separated by bar notations. For example, the codeword {C3,C4} is shown as 48|60.
Internet of Things and Enhanced Living Environments: Measuring and Mapping Air Quality Using Cyber-physical Systems and Mobile Computing Technologies

This paper presents a real-time air quality monitoring system based on Internet of Things. Air quality is particularly relevant for enhanced living environments and well-being. The Environmental Protection Agency and the World Health Organization have acknowledged the material impact of air quality on public health and defined standards and policies to regulate and improve air quality. However, there is a significant need for cost-effective methods to monitor and control air quality which provide modularity, scalability, portability, easy installation and configuration features, and mobile computing technologies integration. The proposed method allows the measuring and mapping of air quality levels considering the spatial-temporal information. This system incorporates a cyber-physical system for data collection and mobile computing software for data consulting. Moreover, this method provides a cost-effective and efficient solution for air quality supervision and can be installed in vehicles to monitor air quality while travelling. The results obtained confirm the implementation of the system and present a relevant contribution to enhanced living environments in smart cities. This supervision solution provides real-time identification of unhealthy behaviours and supports the planning of possible interventions to increase air quality.
Carrot Genotypes Contrasted by Root Color and Grown under Different Conditions Displayed Differential Pharmacological Profiles in Vascular and Metabolic Cells

Carrots’ genotype and growing conditions influence their potential properties to fight against cardiovascular and metabolic diseases. The present study evaluated the influence of carrot genotypes contrasted by root color (Bolero, Presto, Karotan, Deep Purple, Kintoki and Blanche des Vosges) growing under standard, water-restricted, biotic stress (Alternaria dauci inoculation), and combined stress conditions (water restriction and A. dauci inoculation). The effect of carrots’ polyphenol and carotenoid content was assessed on endothelial and smooth muscle cells, hepatocytes, adipocytes and macrophages functions (oxidative stress, apoptosis, proliferation, lipid accumulation and inflammation). Independently of varieties or growing conditions, all carrot extracts affected vascular cells’ oxidative stress and apoptosis, and metabolic cells’ oxidative stress and lipid accumulation. Three clusters were revealed and displayed beneficial properties mostly for adipocytes function, smooth muscle cells and hepatocytes, and endothelial cells and hepatocytes, respectively. Karotan and Presto varieties exhibited endothelial tropism while Blanche des Vosges targeted adipocytes. Carrots under biotic stress are more efficient in inducing beneficial effects, with the Bolero variety being the most effective. However, extracts from carrots which grew under combined stress conditions had limited beneficial effects. This report underscores the use of certain carrot extracts as potential effective nutraceutical supplements for metabolic diseases.
Working Alliance in Blended Versus Face-to-Face Cognitive Behavioral Treatment for Patients with Depression in Specialized Mental Health Care

This study investigates working alliance in blended cognitive behavioral therapy (bCBT) for depressed adults in specialized mental health care. Patients were randomly allocated to bCBT (n = 47) or face-to-face CBT (n = 45). After 10 weeks of treatment, both patients and therapists in the two groups rated the therapeutic alliance on the Working Alliance Inventory Short-Form Revised (WAI-SR; Task, Bond, Goal, and composite scores). No between-group differences were found in relation to either patient or therapist alliance ratings, which were high in both groups. In the full sample, a moderate positive association was found between patient and therapist ratings on Task (ρ = 0.41, 95% CI 0.20; 0.59), but no significant associations emerged on other components or composite scores. At 30 weeks, within-and between-group associations between alliance and changes in depression severity (QIDS, Quick Inventory of Depressive Symptomatology) were analyzed with linear mixed models. The analyses revealed an association between depression over time, patient-rated alliance, and group (p < 0.001). In face-to-face CBT, but not in bCBT, lower depression scores were associated with higher alliance ratings. The online component in bCBT may have led patients to evaluate the working alliance differently from patients receiving face-to-face CBT only.
Advances in Occurrence, Importance, and Mycotoxin Control Strategies: Prevention and Detoxification in Foods

Mycotoxins are toxic substances that can infect many foods with carcinogenic, genotoxic, teratogenic, nephrotoxic, and hepatotoxic effects. Mycotoxin contamination of foodstuffs causes diseases worldwide. The major classes of mycotoxins that are of the greatest agroeconomic importance are aflatoxins, ochratoxins, fumonisins, trichothecenes, emerging Fusarium mycotoxins, enniatins, ergot alkaloids, Alternaria toxins, and patulin. Thus, in order to mitigate mycotoxin contamination of foods, many control approaches are used. Prevention, detoxification, and decontamination of mycotoxins can contribute in this purpose in the pre-harvest and post-harvest stages. Therefore, the purpose of the review is to elaborate on the recent advances regarding the occurrence of main mycotoxins in many types of important agricultural products, as well as the methods of inactivation and detoxification of foods from mycotoxins in order to reduce or fully eliminate them.
Investigating possible syndemic relationships between structural and drug use factors, sexual HIV transmission and viral load among men of colour who have sex with men in Los Angeles County.

INTRODUCTION AND AIMS Past research investigating syndemic factors and HIV-related outcomes has overlooked the impact of structural conditions on behaviours linked with HIV transmission and disease progression. Given prevalent substance use among our sample, we explored whether four structural conditions indicative of social marginalisation and previously correlated with increased risk for HIV infection demonstrated syndemic (additive/synergistic) effects on: (i) HIV viral suppression; and (ii) self-reported involvement in sexual HIV transmission behaviours among a prospective cohort mostly comprising men of colour who have sex with men (MCSM; i.e. Latino/Hispanic and African American/black men) in Los Angeles County. DESIGN AND METHODS Data were collected between August 2014 and March 2017. The structural conditions of interest were: current unemployment, recent (≤6 months) incarceration history, 'unstable' accommodation (past month) and remote (>6 months) contact with health-care providers. Generalised estimating equations assessed possible additive effects of experiencing multiple structural conditions, and possible synergistic effects on the HIV-related outcomes. RESULTS Of 428 participants, nearly half (49%) were HIV-positive at baseline. Involvement in sexual HIV transmission risk behaviours varied over follow-up (22-30%). Reporting ≥2 structural syndemic conditions was significantly associated with reporting sexual HIV transmission risk behaviours among HIV-negative participants, and detectable viral load among HIV-positive participants. Frequent methamphetamine use was consistently associated with the HIV-related outcomes across the final multivariate models. DISCUSSION AND CONCLUSIONS When developing initiatives to address HIV transmission among marginalised sub-populations including MCSM, we must holistically consider systemic and structural issues (e.g. unemployment and homelessness), especially in the context of prevalent substance use.