Miracle-dz/UniFAR-FTUs huggingface dataset:
Pirfenidone attenuates lung fibrotic fibroblast-mediated fibrotic responses to transforming growth factor-β1

Pirfenidone, an antifibrotic agent used for treatment of idiopathic pulmonary fibrosis (IPF), functions by inhibiting myofibroblast differentiation, which is involved in transforming growth factor (TGF)-β1-induced IPF pathogenesis. However, unlike normal lung fibroblasts, the relationship between pirfenidone responses of TGF-β1-induced human fibrotic lung fibroblasts and lung fibrosis is unknown. Here, we investigated the effect of pirfenidone on the functions of two new targets, collagen triple helix repeat containing protein 1 (CTHRC1) and four-and-a-half LIM domain protein 2 (FHL2), which included fibroblast activity, collagen gel contraction, and migration toward fibronectin. Compared to control lung fibroblasts, pirfenidone restored TGF-β1-stimulated fibroblast-mediated collagen gel contraction, migration, and CTHRC1 release in lung fibrotic fibroblasts. Furthermore, pirfenidone attenuated TGF-β1- and CTHRC1-induced fibroblast activity, bone morphogenic protein-4/Gremlin1 upregulation, and α-smooth muscle actin, fibronectin, and FHL2 downregulation, similar to that observed post-CTHRC1 inhibition. In contrast, FHL2 inhibition suppressed migration and fibronectin expression but did not downregulate CTHRC1. Overall, pirfenidone suppressed fibrotic fibroblast-mediated fibrotic processes via inverse regulation of CTHRC1-induced lung fibroblast activity. Thus, CTHRC1 can be used for predicting pirfenidone response and developing new therapeutic target for lung fibrosis. Summary statement Pirfenidone suppressed TGF-β1-mediated fibrotic processes in fibrotic lung fibroblasts by attenuating CTHRC1 expression, suggesting that CTHRC1 may be a novel therapeutic target for treating patients with lung fibrosis.
Heterochronic shifts and conserved embryonic shape underlie crocodylian craniofacial disparity and convergence

The distinctive anatomy of the crocodylian skull is intimately linked with dietary ecology, resulting in repeated convergence on blunt- and slender-snouted ecomorphs. These evolutionary shifts depend upon modifications of the developmental processes which direct growth and morphogenesis. Here we examine the evolution of cranial ontogenetic trajectories to shed light on the mechanisms underlying convergent snout evolution. We use geometric morphometrics to quantify skeletogenesis in an evolutionary context and reconstruct ancestral patterns of ontogenetic allometry to understand the developmental drivers of craniofacial diversity within Crocodylia. Our analyses uncovered a conserved embryonic region of morphospace (CER) shared by all non-gavialid crocodylians regardless of their eventual adult ecomorph. This observation suggests the presence of conserved developmental processes during early development (before Ferguson stage 20) across most of Crocodylia. Ancestral state reconstruction of ontogenetic trajectories revealed heterochrony, developmental constraint, and developmental systems drift have all played essential roles in the evolution of ecomorphs. Based on these observations, we conclude that two separate, but interconnected, developmental programmes controlling craniofacial morphogenesis and growth enabled the evolutionary plasticity of skull shape in crocodylians.
Fréquence et distribution des dimères cyclobutyliques de pyrimidines suite à une exposition aux UV et évaluation de l’effet protecteur de l’acide sulfonique 2-phénylbenzymidazole-5

Exposure to the UV component of sunlight is the principal factor leading to skin cancer development. Cyclobutane pyrimidine dimers (CPD) are considered as the most important DNA damage involved in skin carcinogenesis. CPD frequencies and their distribution between the four types of dipyrimidine sites are mostly investigated in vitro or using UVC, even if we are not exposed to these wavelengths. On the other hand, sunscreens are used to protect against CPD formation. The 2-phenylbenzimidazole-5-sulfonic acid (PBSA) is a sunscreen agent used because it absorbs UVB. However, previous studies have shown that PBSA oxidizes guanines in vitro, during UVB exposure. To address these issues, we chose to study the effect of PBSA, the DCP frequencies and their distribution frequency and distribution of CPD, as well as the influence of DNA sequence on CPD formation, in conditions more representative of reality. We irradiated normal human fibroblasts (in cellulo) and purified DNA (in vitro) with UVB and UVC. We compared the CPD distribution in cellulo and in vitro. Our results show that CPD distribution in cellulo is different to CPD distribution in vitro after UVB exposure. Then, we compared the impact of UV type on CPD formation and we found that TT are more frequently damaged after UVC exposure while potentially mutated dipyrimidine sites (dipyrimidine sites containing cytosine) are more frequently damaged after UVB exposure. Concerning the influence of DNA sequence on CPD formation, we observed that some dipyrimidine sites are extremely frequently damaged compared to others and that the position of a dipyrimidine site within a dipyrimidine run is an important factor influencing the frequency of CPD formation. We studied the effect of PBSA, in cellulo and in vitro, during UVA and UVB exposure. We found that PBSA provides good protection against CPD formation during UVB exposure, in cellulo. However, PBSA photosensitized the formation of oxidized guanines during UVA and UVB exposure. This indicates that PBSA can act as a double-edged sword and question its suitability in sunscreens. The works presented in this thesis provide important elements to understand the skin carcinogenesis process and demonstrate the importance to use an effective protection against UV-induced DNA damage.
Disinvasive efficacy of chlorine-based preparations of domestic production for eggs of nematodes of the species Aonchotheca bovis parasitizing in sheep

The paper presents the results of experimental researches on the determination of the disinvasion efficiency of chlorinated chemical preparations of domestic production of “Brovades-plus”, “Bi-dez” and “Dezsans” of NPF “Brovafarma” (Ukraine). The conducted researches on the basis of the parasitology laboratory found that the studied disinfectants possess disinvasive properties in respect of non-invasive test culture of eggs of nematodes of the species Aonchotheca bovis (son Capillaria bovis) López-Neyra, 1947, isolated from gonads of females of worms. The dissimilar stability of eggs of capillaries to the effect of the tested agents in vitro is proved. The most effective disinfectant in the case of eggs of capillaries of the species A. bovis was the preparation “Dezsan”. The high level of its disinvasive efficacy (DE – 91.14–100.0%) was registered at the application of the preparation in 1.0–2.0% of the exposure concentration for 10–60 minutes. The chemicals “Bi-dez” and “Brovadez-plus” proved to be less effective in the relatively non-invasive test culture of A. bovis eggs. The high level of efficiency (DE –92.41–100.00%) of the “Bi-dez” was achieved with its use at concentrations of 1.5% (exposure of 30 and 60 min) and 2.0% (exposure of 10–60 minutes) The “Brovadez plus” preparation in vitro proved to be the least effective means of non-invasive test culture of nematode eggs of the species A. bovis, since a high level of disinvasive efficacy (DE – 100.00%) was achieved only with the use of 2.0% solution per exposure 10–60 min. It was established that the experimentally tested chlorine-based means of domestic production resulted in the death of eggs in the culture in due to the destructive effect of the components of the preparations on the shell, the caps of eggs of the capillaries, as well as on the germ in the middle of the egg. In experimental cultures treated with the means, the destruction of the shell of the egg in the location of the caps, the exit of morulae outside, the cessation of development or shrinkage of the embryo and deformation of the egg shell were recorded.
Deep LSTM-RNN with Word Embedding for Sarcasm Detection on Twitter

In the world full of sarcastic people, it’s becoming challenging for the people of 21st century to detect sarcasm using sentiment analysis efficiently. Sarcasm detection helps us to understand the bitter truth under the sugar coated sentences. It is widely used in various networking sites for understanding the true reviews and taking appropriate actions on the same if needed. Various methods, techniques and algorithms have been applied, although there’s little or much drawback of using the same. For instance, algorithms like logistic regression has been used to detect sarcasm, which has a drawback, can’t be used for continuous datasets. In our paper, we will be discussing about the approach we found appropriate and also provides an increased accuracy. Self designed dataset of sarcastic and non-sarcastic tweets is used for training of proposed model. Use of Recurrent Neural Network, Long Short Term Memory (LSTM) and Word Embeddings can make the sarcasm detection efficient and thereby making the statements from twitter easily classifiable.
Reproductive phenology of Ditassa burchellii (Apocynaceae, Asclepiadoideae), a herbaceous vine, in a semi-deciduous forest from Brazil

Abstract We analyzed the reproductive phenology of Ditassa burchellii and the influence of abiotic factors on the species phenophases. The study was conducted on individuals of a natural population from a semi-deciduous forest (Viçosa municipality, Minas Gerais state, southeastern Brazil). We quantified the activity and intensity indices of the following phenophases: flower bud, flower, immature fruit, and dehiscent fruit. To test for seasonality of phenophases, we analyzed each of them using Rayleigh test. We evaluated whether there was any association between abiotic variables (mean temperature, rainfall, and day length) and phenophases, in the month of occurrence and in the three months prior to the occurrence of each phenophase. The analyzed phenophases occurred mainly at the end of the rainy season and during the dry season, with overlapping periods, but with sequential peaks. The periods of occurrence of reproductive phenophases were similar to the ones in other climbing species and were mainly related to the dispersal mode. All phenophases were seasonal and were associated with at least one abiotic variable, either in the month of their occurrence or in the previous months.
Traffic Modeling & Characterization of Software Defined Networks

Software Defined Networking (SDN) is a trending technology and its popularity can be attributed to its speed and agility in deploying new applications. Realistic modeling of SDN traffic is crucial in designing control algorithms and in provisioning network resources. The purpose of this paper is to model and characterize the SDN traffic. To this end, we have created an SDN environment using the mininet emulator and OpenDayLight (ODL) controller using which we have collected the SDN traffic data traces. The quantiles of inter-arrival times of SDN data traffic have been plotted against the quantiles of theoretical distributions. Then the Kolmogorov Smirnov (KS) test has been applied to model the SDN traffic and to capture its distribution characteristics effectively. From the KS test, it has been inferred that the inter arrival times of SDN traffic follows the Generalized Extreme Value (GEV) distribution. These findings indicate that traditional Poisson models for SDN traffic may not be suitable for evaluating the performance of Software Defined Networks.
Longitudinal retrospective study on the effect of season on milk production and composition in Rio Grande do Sul, Brazil

This longitudinal retrospective study evaluated production and composition of milk from dairy cows according to season on a rural property in Palmeira das Missoes, Rio Grande do Sul, Brazil, between January 2009 and December 2016. Milk yield per hectare per month was the primary variable measured, along with chemical composition (total dry extract, defatted dry extract, fat, protein, and lactose), somatic cell count, and total bacterial count of milk. Production in summer (513.53 kg/ha/month) did not differ (p > 0.05) from that in fall (504.69 kg/ha/month) or spring (564.63 kg/ha/month), but production in winter (639.20 kg/ha/month) was significantly higher than in summer (p 0.05) among seasons. The total dry extract content differed (p 0.05) among seasons. Protein content differed (p 0.05) from fall (3.13%) or spring (3.05%). Winter lactose levels (4.52%) were higher (p 0.05) among seasons, demonstrating that the evaluated herd possesses standard mammary gland health. The total bacterial count did not differ (p > 0.05) among the seasons, demonstrating that the hygiene of the facilities remains constant. As expected, the temperature and humidity index varied (p < 0.0001) with the seasons, and the deleterious effects were more pronounced in summer and spring, as they are the hottest seasons in humid subtropical environments. The results emphasize that the organized management of milk production reduces the variation in milk composition, making it easier to maintain a consistent high milk quality and also generating extra revenue.
Domestic violence and risk of internalizing and externalizing problems in adolescents living with relatives displaying substance use disorders

ABSTRACT Objective To investigate the association between exposure to domestic violence and increased risk of internalizing and externalizing problems and substance use among adolescents living with relatives with substance use disorder (SUD) at a low-income community of São Paulo, Brazil. Methods A cross-sectional study was conducted with 102 adolescents aged 12-17 years (M = 14.2, SD = 1.7) who were living with relatives suffering from SUD. Outcomes were measured using the Youth Self-Report (YSR), psychosocial stress factors questionnaire, Drug Use Screening Inventory (DUSI) and Phrase Inventory of Intrafamily Child Abuse (PIICA). Results The sample presented high prevalence of emotional/behavioral problems with YSR’s scores in the clinical range for Internalizing Problems (24.5%), Externalizing Problems (21.6%), and Total Problems (26.5%). The presence of mental health problems predicted substance use (PR = 2.22; 95% CI = 1.2-4.13), and substance use predicted increased risk of mental health problems. Alcohol use predicted more than double the risk of emotional/behavioral problems (PR = 2.01; 95% CI = 1.08-3.76), while illicit drug use was associated with an almost threefold increase in the prevalence of Internalizing (PR = 2.87; 95% CI = 1.19-6.89) and Externalizing Problems (PR = 3.3; 95% CI = 1.35-8.04). Conclusion Adolescents of relatives with SUD are at risk of developing emotional and behavioral problems. These findings reinforce the need to develop public mental health policies, which include protective interventions to adolescents living in families affected by substance use disorders.
Characterization Of The Coat Protein Of Turnip Mosaic Virus And Its Arabidopsis Interactors In The Virus Infection Process

Viruses are infectious and obligate intracellular parasites. Turnip mosaic virus (TuMV) is a member of the genus Potyvirus which comprises many agriculturally important viral pathogens that threaten crop production. Potyviruses are fully dependent on the host cellular machinery to fulfil their infection cycle in plant hosts. It is well accepted that viral coat protein (CP) is a multifunctional protein that plays key roles in virus propagation and hostvirus interactions. This dissertation project aimed to investigate the role of CP in TuMV cellto-cell movement, to identify the host interactors of TuMV CP, and further to characterize their roles in TuMV infection. To examine the role of CP in viral cell-to-cell movement, a series of CP deletion and point mutations were introduced into a special TuMV infectious clone that allows for distinguishing primarily and secondarily infected cells. It was found that the core domain and C-terminus of CP are critical for TuMV cell-to-cell movement, but the N-terminal domain is dispensable for TuMV movement and virion assembly. Among cell-to-cell movement defective point mutants, R178A and D222A lost the ability to form detectable virions in protoplasts. The CP protein R178A was not as stable as wild-type CP. Overall, the results revealed the CP determinants of TuMV cell-to-cell movement and suggested that there is a correlation between assembly defects and cell-to-cell movement defects in TuMV biology. To identify the host interactors of TuMV CP, a yeast two-hybrid screening against Arabidopsis cDNA library was conducted. The screening resulted in the discovery of two novel host proteins, Patellin 3 (PATL3) and Patellin 6 (PATL6) that bind to CP in yeast. TuMV infection assay on PATLs knockout mutants and stable overexpression lines showed that PATL3 and PATL6 negatively regulate TuMV infection. Subcellular localization studies demonstrated that PATL3, but not PATL6, was partially redistributed to viral replication complexes (VRCs) upon TuMV infection. In addition, PATL3 also interacted with the viral protein cylindrical inclusion protein (CI), an essential component of VRCs, suggesting that PATL3 is recruited to the VRC likely through its interaction with CI. Overall, this study identified two host restriction proteins of TuMV that may be manipulated against TuMV and related viruses.
Predicting the effects of SNPs on transcription factor binding affinity

GWAS have revealed that 88% of disease associated SNPs reside in noncoding regions. However, noncoding SNPs remain understudied, partly because they are challenging to prioritize for experimental validation. To address this deficiency, we developed the SNP effect matrix pipeline (SEMpl). SEMpl estimates transcription factor binding affinity by observing differences in ChIP-seq signal intensity for SNPs within functional transcription factor binding sites genome-wide. By cataloging the effects of every possible mutation within the transcription factor binding site motif, SEMpl can predict the consequences of SNPs to transcription factor binding. This knowledge can be used to identify potential disease-causing regulatory loci.
Taraxacum Genus: Extract Experimental Approaches

This chapter presents factors or considerations to be taken into account when selecting the procedure or method for obtaining extracts and bioactive compounds. The genus Taraxacum has proved to have several interesting properties and there are numerous techniques and bioassays used to test the antimicrobial properties of extracts. However, the extraction process is crucial to optimize the final biological outcomes. Extraction procedures that until now have been used are simple and inexpensive, however, we wanted to report a series of studies that group valuable results, which could be useful for future studies, enhancing the research carried out by authors from all over the world and also allowing the interrelated study of this genus.
The Challenges and Prospects of ICTs in Crime Prevention and Management in Nigeria: A Review of CCTV Cameras in Abuja

Contemporary Nigeria has witnessed monumental rise in crime wave and in the quest to stem the tide, government has adopted various security policies to secure the lives and property of its citizens in the past, but none of these policies have actually yielded positive results. Human abduction, armed robbery, terrorism, bomb attacks and lots more have been the order of the day in the Country. The study seeks to ascertain the impact of closed circuit television (CCTV) cameras in Abuja metropolis. Six research questions and two hypotheses were formulated to guide the study, related literatures were adequately reviewed. A population of size of 900 was selected out of which a sample size of 300 respondents, which cut across all walks of life, participated in the study. Structured questionnaire was designed and used as instrument for data collection. Data collected were analyzed using direct interpretation of results gotten from respondents. Findings of the research revealed significant relationship between closed circuit television cameras and theory of deterrence, criminal justice, fear of crime, legality, policy formation and regulation of closed circuit television (CCTV). The development of software that can be integrated with the CCTV to display a personâ€™s bio-data on the monitor when captured by the CCTV camera is among other recommendations for further research study.
The culture medium volume and the inoculation method should be considered in semi-quantitative screening of calcium phosphate solubilization by bacteria

Agar media with insoluble phosphates are used for semi-quantitative screening of phosphate-solubilizing bacteria based on the solubilization halo formed around the colonies. We show that the volume of the culture medium (15, 20, and 30 mL) and the inoculation method (toothpick vs microdrop) strongly influence the diameter of the solubilization halo, and this should be considered in advance selection of the isolates most efficient in this process.
Multiscale urban air pollution modelling: towards healthier cities

Ambient air pollution is nowadays a serious public health problem worldwide, especially in urban areas due to high population density and intense anthropogenic activity. Among the main urban air pollution sources, the road traffic sector is one of the major concerns and the largest contributor to nitrogen dioxide (NO2) concentrations, though regional background chemical conditions must also be considered. In this context, the use of modelling tools is crucial to understand atmospheric and social dynamics in multiple scales, as well as to support in defining the best air quality improvement strategies. The main objective of this thesis is to develop and apply a multiscale modelling system able to simulate air quality and health impacts in cities. For this purpose, the modair4health multiscale air quality and health risk modelling system was developed and operationalized. It includes the online model WRF-Chem, which provides air quality and meteorological fields from regional to urban scales, and the Computational Fluid Dynamics (CFD) model VADIS, which uses the urban WRF-Chem outputs to calculate flows and dispersion of traffic emissions-related air pollutants in urban built-up areas. A health module, based on linear and nonlinear World Health Organization approaches, was also integrated in modair4health to assess the health impacts resulting from air quality changes, and the overall health damage costs are calculated based on economic studies. The application and assessment of the modair4health system allowed to identify the most appropriate configurations and input data, which were used to apply the system over the case study testing air quality improvement scenarios. One of the busiest road traffic areas of the city of Coimbra (Fernão de Magalhães Avenue) in Portugal was selected as case study. The application considered a 4 domains setup: three nested domains (25, 5 and 1 km2 resolutions) for the WRF-Chem, and the 4th domain (4 m2 resolution) over the target local study area and NO2 for the VADIS. WRF-Chem was applied along the year 2015 and VADIS was simulating two particular periods: one week in winter and another one in summer. Short-term health impacts were estimated and the non-linear approach led to lower health outcomes that seem better adjusted to the local reality. Finally, to assess the modair4health capabilities for decision-making support, two traffic management scenarios were tested over the case study: replacement of 50% of the vehicle fleet below EURO 4 by electric vehicles (ELEC), and introduction of a Low Emission Zone (LEZ). Air quality and health positive impacts were higher for the ELEC scenario. This study represents a scientific advance in multiscale air quality and health modelling. The modair4health system can be easily adapted and applied to other simulation domains, providing urban air pollution levels and subsequent health impacts for different case studies and supporting the assessment of air pollution control policies.