Miracle-dz/UniFAR-FTUs huggingface dataset:
A Novel Class of Intensity-based Metrics for Image Functions which Accommodate a Generalized Weber's Model of Perception

Even though the usual L image fidelity measurements, such as MSE and PSNR, characterize the mean error for each pixel of the images, these traditional measurements are not designed to predict human visual perception of image quality. In other words, the standard L-type optimization in the context of best approximation theory is not in accordance with human visual system. To provide alternative methods of measuring image distortion perceptually, the structural similarity image quality measure (SSIM) was established decades ago. In this thesis, we are concerned with constructing a novel class of metrics via intensitybased measures, which accommodate a well-known psychological model, Weber’s model of perception, by allowing greater deviations at higher intensity values and lower deviations at lower intensity values. The standard Weber model, however, is known to fail at low and high intensities, which has given rise to a generalized class of Weber models. We have derived a set of “Weberized” distance functions which accommodate these generalized models. Mathematically, we prove the existence and uniqueness of the density functions associated with the measures which conform to generalized Weber’s model of perception. Meanwhile, we consider the generalized Weber-based metrics as the optimization criteria and implement them in best approximation problems, where we also prove the existence and uniqueness of best approximations. We compare the results, which are theoretically adapted to the human visual system, with best L-based approximations. Using a functional analysis point of view, we examine the stationary equations associated with the generalized Weber-based metrics to arrive at the Fréchet derivatives of these metrics. Finally, we establish an existence-uniqueness theorem of best generalized Weber-based L approximations in finite-dimensional Hilbert spaces.
A Polygenic Score for Body Mass Index is Associated with Depressive Symptoms via Early Life Stress: Evidence for gene-environment correlation

Background Increasing childhood overweight and obesity rates are associated with not only adverse physical, but also mental health outcomes, including depression. These negative outcomes may be caused and/or exacerbated by the bullying and shaming overweight individuals experience. As body mass index (BMI) can be highly heritable, we hypothesized that a genetic risk toward higher BMI, will predict higher early life stress (ELS), which in turn will predict higher depressive symptoms in adulthood. Such a process will reflect an evocative gene-environment correlation (rGE) wherein an individual’s genetically influenced phenotype evokes a reaction from the environment that subsequently shapes the individual’s health. Methods We modeled genetic risk using a polygenic score of BMI derived from a recent large GWAS meta-analysis. Self-reports were used for the assessment of ELS and depressive symptoms in adulthood. The discovery sample consisted of 524 non-Hispanic Caucasian university students from the Duke Neurogenetics Study (DNS; 278 women, mean age 19.78±1.23 years) and the independent replication sample consisted of 5 930 white British individuals from the UK biobank (UKB; 3 128 women, mean age 62.66±7.38 years). Results A significant mediation effect was found in the DNS (indirect effect=.207, bootstrapped SE=.10, 95% CI: .014 to .421), and then replicated in the UKB (indirect effect=.04, bootstrapped SE=.01, 95% CI: .018 to .066). Higher BMI polygenic scores were associated with higher depressive symptoms through the experience of higher ELS. Conclusions Our findings suggest that evocative rGE may contribute to weight-related mental health problems and stress the need for interventions that aim to reduce weight bias, specifically during childhood.
Identification of extracellular enzyme-producing bacteria (proteolytic, cellulolytic, and amylolytic) in the sediment of extensive ponds in Tanggulrejo, Gresik

The process of aquaculture is an activity that potentially generates organic waste primarily derived from residual feed and the results of excretion (feces). Heterotrophic bacteria have the ability to produce extracellular enzymes (protease enzymes, amylases, and cellulases) that are necessary for the bioremediation of organic waste. The purpose of this study was to investigate the identifiable extracellular enzyme bacteria from extensive pond sediments in Tanggulrejo Village, Gresik. Twenty bacterial isolates were found from pond sediments that had the ability to produce extracellular enzymes and proteolytic, amylolytic and cellulolytic bacteria. The four isolates were identified as genera Bacillus thuringiensis, Bacillus lentus, Bacillus sphaericus and Corynbacterium pilosum. Bacillus thuringiensis bacteria have a hydrolysis zone of protein of 11 mm, a hydrolysis zone of amylum of 10 mm, and a hydrolysis zone of cellulose of 8 mm. Bacillus lentus bacteria have a hydrolysis zone of protein of 14 mm, a hydrolysis zone of amylum of 12 mm and a hydrolysis zone of cellulose of 7 mm.Bacillus sphaericus bacteria have a hydrolysis zone of protein 14 mm, a hydrolysis zone of amylum of 11 mm and a hydrolysis zone of cellulose of 6 mm. Corynebacterium pilosum bacteria have a hydrolysis zone of protein of 10 mm, a hydrolysis zone ofamylum of 14 mm and a hydrolysis zone of cellulose of 16 mm.
Genetic variation within and among four species of Lotus L. (Fabaceae)

Karyotype characters, mitotic metaphase chromosomes, monoploid idiograms, karyograms and pollen abortion of Lotus creticus L. , Lotus glaber Mill. , Lotus halophilus Boiss. and Lotus peregrinus L. were investigated. Analysis of somatic metaphases showed that the chromosome numbers of these taxa were 2n=28 for L. creticus, 2n=12 for L. glaber, 2n= 14 for both L. halophilus and L. peregrinus. Karyotype asymmetry was estimated by many different methods, the total form percent (TF %), the Rec and Syi indices, the intrachromosomal asymmetry index (A1) and interchromosomal asymmetry index (A2). In this study, there is a variation in the frequency of pollen fertility and abortive pollen grains of the Lotus species. The anatomical characteristics of leaf and stemof Lotus species were made. Various genetic markers have been used to estimate the genetic variability within and among the four Lotus species collected from ten different accessions. Protein profile of Lotus species were studied by polyacrylamide gel electrophoresis (SDS-PAGE) technique and generated seventeen bands, six of them monomorphic and eleven polymorphic bands. Five tested primers were used for RAPD technique, a total of 33 well-defined and scorable RAPD bands were obtained as a result of fingerprinting of Lotus species, 12 bands were common for all species and 21 were polymorphic. Perceptual mapping (PERMAP) used for the combination of taxa and attributes PERMAP-Biplot distinguished the taxa into three groups.
Investigating the potential of different dietary fibers to stimulate butyrate production in vitro

The project aimed to evaluate the potential of dietary fiber types to stimulate butyrate production using an in vitro system simulating the gut of pigs. Fecal inoculum from suckling piglets were collected in two different periods and were used as inoculum to ferment s-glucan, inulin and sucrose in two separated in vitro fermentation trials. Gas production profiles, pH, and short chain fatty acids (SCFAs) were measured from samples collected from the in vitro reactors. In addition qPCR were used in an attempt to quantify butyrate producing bacteria. Samples were taken at 6 and 24h for in vitro trial I, and 0, 6, 24, 48h for in vitro trial II. The inoculum were kept overnight in freezer or in refrigerator storage to test the effect of inoculum storage in the first experiment. The results were compared with fresh fecal inoculum sampled 2h prior to the in vitro trial. Gas production from both in vitro trial I and II showed that the replicates had a high similarity for all substrates, s-glucan showed higher gas production than the other substrate types at the beginning of both fermentation trial I and II, while negative controls did not produce any gas. The pH were relatively stable over time in chambers with s-glucan, while pH values for inulin and sucrose were reduced over time in both experiments I and II. All substrates resulted in higher SCFA levels after 24 and 48h. s-glucan substrate induced an increase in SCFAs earlier than the other substrates tested. Propionate, and acetate, were dominant during the whole incubation time. In vitro trial II produced greater amount of SCFAs compared to in vitro trial I. The study did not demonstrate any difference in butyrate production between substrates tested. The results from second in vitro qPCR run showed the decreasing of proportion of Cq values in 10×dilution DNA samples which can justify an absolute increase in butyrate producing bacteria upon s-glucan addition (r2= 0.9982). Results from this study also showed an increase in Cq value, i.e. reduction of butyrate producers at 48h of incubation. In addition, the overall performance of the PCR assay did not have a good efficiency. In conclusion the research did not demonstrate any difference in butyrate production between the substrates tested.
Retina assessment by optical coherence tomography of diabetic dogs

ABSTRACT: Diabetes mellitus is one of the most common endocrine disorders characterized by relative or absolute lack of insulin; this can lead to several ocular manifestations, among them diabetic retinopathy and cataracts. Diabetic retinopathy (DR) is a microangiopathy that involves retinal precapillary arterioles, postcapillary venules, and large vessels, causing them to be functionally and anatomically incompetent. Hyperglycemia seems to be the most probable cause of damage to the retina due to interference in cellular metabolism and transduction processes. The aim of this study was to evaluate retinal thickness in eight diabetic dogs, four females and four males of different breeds and ages ranging from 6 to 15 years, by optical coherence tomography (OCT) and to compare them with non-diabetic dogs. Assessment provided by OCT in diabetic dogs showed retinal layers thinning and loss of stratification when compared to non-diabetic dogs (198μm versus 219μm respectively), with statistical significance (p=0.008). OCT images may suggest that diabetes mellitus causes retinal neuropathy in dogs, as also seen in diabetic humans.
Effect of potassium (K+) on growth, yield components and macronutrient accumulation in Wheat crop

Plant growth, nutrient uptake and yield can be sustained by the application of potassium fertilization. A pot experiment was conducted to study the effect of macronutrients accumulation of wheat about different potassium rates.The results revealed that the effect of different potassium levels on the growth and grain yield of wheat was significant. The application of potassium at 100% increased the most of the growth, yield components and accumulation of nutrients in wheat crop from 20−50% as compared to (control) the plots receiving no potassium application. In comparison to control, potassium application at 75% also significantly increased growth and yield components from 8−40%, however, potassium application of 50 and 25% increased the growth and yield components by 4−20%. As compared to plots receiving no potassium, application of potassium resulted 3−6% higher nitrogen content in grain and 2−11% higher nitrogen content in straw. While, potassium application increased the potassium contents by 50−154% in grain and 70-140% contents of potassium in straw as compared to control plots. However, in comparison to plots without potassium nutrition, application of potassium fertilization improved phosphorus contents by 2−10% in grain and 3-50% in straw of wheat crop. Among potassium levels of 25%, 50%, 75% and 100% were significant indicating that potassium at the rate of 100% was an optimum level for obtaining maximum grain yields in wheat crop. This study concluded that application of potassium nutrition increased the all growth, yield comonents and accumumation of nitrogen, phosphorus and potassium contents in grain and straw of wheat crop.
Investigation of the involvement of mitochondrial DNA variants in cardiometabolic disease : the SABPA study

VIII OPSOMMING . IX LIST OF TABLES . X LIST OF FIGURES . XI CHAPTER 1: PREFACE . 1 1.1 STUDY MOTIVATION AND RATIONALE . 1 1.2 PROBLEM STATEMENT . 3 1.3 AIMS AND OBJECTIVES . 4 1.4 STRUCTURE OF THESIS . 4 1.5 AUTHOR CONTRIBUTIONS . 7 CHAPTER 2: LITERATURE REVIEW . 9 2.1 TITLE. 9 2.2 AUTHORS AND AFFILIATIONS . 9 2.3 ABSTRACT . 9 2.3 INTRODUCTION . 10 2.3.1 Mitochondrial dysfunction and mtDNA damage in vascular health . 11 2.3.2 MtDNA point mutations and cardiac involvement . 14 2.4 CURRENT APPROACHES USED FOR INVESTIGATING MTDNA INVOLVEMENT IN DISEASE . 17 2.4. 1 Mitochondrial DNA copy number . 17 2.4. 2 Common mtDNA population variants . 17 2.4. 3 Rare mtDNA population variants . 19 2.5 ALTERNATIVE APPROACH FOR INVESTIGATING MTDNA INVOLVEMENT IN DISEASE: THE ADJUSTED MUTATIONAL LOAD HYPOTHESIS . 20 2.6 CONCLUSIONS: THE UNIQUE CHALLENGES FACED BY STUDIES IN AFRICAN POPULATIONS . 21 2.7 KEY MESSAGES . 22 2.8 REFERENCES . 22 CHAPTER 3: METHODS . 36 3.1 SABPA COHORT . 36 3.2 HYPERTENSION AND HYPERGLYCAEMIA IN THE SABPA COHORT . 37 3.3 DNA ISOLATION, AMPLIFICATION AND PREPARATION FOR NEXT GENERATION SEQUENCING . 38
Boswellic Acid Synergizes With Low-Level Ionizing Radiation to Modulate Bisphenol Induced-Lung Toxicity in Rats by Inhibiting JNK/ERK/c-Fos Pathway

Bisphenol A (BPA) is a low molecular weight chemical compound that has a deleterious effect on the endocrine system. It was used in plastics manufacturing with injurious effects on different body systems. Occupational exposure to low-level ionizing radiation (<1 Gy) is shown to attenuate an established inflammatory process and therefore enhance cell protection. Therefore, the objective of this study was to investigate the protective effect of boswellic acid (BA) accompanied by whole-body low-dose gamma radiation (γ-R) against BPA-induced lung toxicity in male albino rats. BPA intoxication induced with 500 mg/kg BW. Rats received 50 mg BA/kg BW by gastric gavage concomitant with 0.5 Gy γ-R over 4 weeks. The immunoblotting and biochemical results revealed that BA and/or γ-R inhibited BPA-induced lung toxicity by reducing oxidative damage biomolecules; (MDA and NADPH oxidase gene expression), inflammatory indices (MPO, TNF-α, IL-6, and gene expression of CXCR-4). Moreover, BA and or/γ-R ameliorated the lung inflammation via regulation of the JNK/ERK/c-Fos and Nrf2/ HO-1 signaling pathways. Interestingly, our data demonstrated that BA in synergistic interaction with γ-R is efficacious control against BPA-induced lung injury via anti-oxidant mediated anti-inflammatory activities.
Effects of porphyromonas gingivalis lipopolysaccharide on human gingival fibroblasts

Human gingival fibroblasts (HGF) are major constituent of gingival connective tissue. Various inflammatory cytokines in response to oral bacterial lipopolysaccharide (LPS), such as Porphyromonas gingivalis, are secreted by HGF. This study examined mRNA expression of osteoprotegerin (OPG), receptor activator of NF-kappa B ligand (RANKL), Toll like receptor (TLR) 2, TLR4 and CD14 in fibroblasts after being stimulated with 0.1, 1.0 and 10.0 μg/ml of LPS for 24 h and 48 h by reverse transcription polymerase chain reaction (RT-PCR). It was shown that the primary cultured of HGF from two subjects, (HGF1 and HGF2) expressed OPG, RANKL, TLR2, TLR4, CD14 and RANKL/OPG ratio in both control and experimental groups. OPG mRNA expressed on both HGF cells despite the increased LPS concentrations for 24 h. After 48 h of treatment, OPG mRNA expressions showed a trend for being increased. RANKL mRNA expressions responded to various LPS concentrations of each HGF were different in both 24 h and 48 h of stimulation but the levels of RANKL expression were not showed any significant in each individuals. RANKL/OPG ratio in HGF between control group and experiment groups was not significantly higher in all LPS treated groups and time periods, but there were differences in RANKL/OPG ratio among different individuals. The pattern of TLR2 expression levels diverged between HGF1 and HGF2, but there were no difference in all doses used and time course. LPS from P.gingivalis stimulated TLR4 mRNAs expression, but the expression was dose-and time-independent. The study showed that CD14 expressions were found after treatment with difference LPS doses for 24 h and 48 h but the patterns of expression were different in HGF1 and HGF2. In
Synthesizing Disparate LiDAR and Satellite Datasets through Deep Learning to Generate Wall-to-Wall Regional Forest Inventories

Light detection and ranging (LiDAR) has become a commonly-used tool for generating remotely-sensed forest inventories. However, LiDAR-derived forest inventories have remained uncommon at a regional scale due to varying parameters between LiDAR datasets, such as pulse density. Here we develop a regional model using a three-dimensional convolutional neural network (CNN), a form of deep learning capable of scanning a LiDAR point cloud as well as coincident satellite data, identifying features useful for predicting forest attributes, and then making a series of predictions. We compare this to the standard modeling approach for making forest predictions from LiDAR data, and find that the CNN outperformed the standard approach by a large margin in many cases. We then apply our model to publicly available data over New England, generating maps of fourteen forest attributes at a 10 m resolution over 85 % of the region. Our estimates of attributes that quantified tree size were most successful. In assessing aboveground biomass for example, we achieved a root mean square error of 36 Mg/ha (44 %). Our county-level mapped estimates of biomass were in good agreement with federal estimates. Estimates of attributes quantifying stem density and percent conifer were moderately successful, with a tendency to underestimate of extreme values and banding in low density LiDAR acquisitions. Estimate of attributes quantifying detailed species groupings were less successful. Ultimately we believe these maps will be useful to forest managers, wildlife ecologists, and climate modelers in the region.
Technological and nutritional aspects of gluten-free pasta based on chickpea flour and tiger nut flour

Gluten-free (GF) dry egg pappardelle was prepared with tigernut flour (50%), chickpea flour (50%) and pregelatinized TNF (0, 5, 10%), and compared to plain pasta (100% durum wheat semolina). The GF pasta may have a significant higher content of insoluble fibre, minerals and fat rich in oleic acid and a similar protein content. It was not found any clear relationship between the flour functional properties and its proximate composition. The use of PG did not imply an improvement on the firmness but did provide some continuity to the pasta structure. Keywords: Gluten-free pasta, tigernut flour, chickpea flour, texture, cooking properties.
Parents’ Lived Experiences With the COVID-19 Pandemic

The COVID-19 pandemic has affected people across the globe. We explored 11 parents’ experiences with the pandemic and identified eight themes: (a) educational experience, (b) navigating roles and responsibilities, (c) recognizing privilege, (d) routine, (e) monitoring and communication about COVID, (f) vacillating emotions, (g) connection, and (h) meaningful experiences. We discuss the themes and implications for counseling.
Therapy-related mixed phenotype acute leukemia in a pediatric survivor of Ewing sarcoma with a novel RUNX1-TAF3 fusion: A case report and review of the literature

Increasing treatment intensity for pediatric Ewing sarcoma (ES) has improved survival, but comes with an increased incidence of secondary malignancy. Here, we describe a case of therapy-related mixed phenotype acute leukemia (t-MPAL), T-myeloid type, in a pediatric patient four years after completion of therapy for ES. Genomic evaluation revealed a novel and likely pathogenic RUNX1-TAF3 fusion. This patient did not respond to T-cell leukemia-directed therapy, and while he initially responded to myeloid leukemia-directed therapy, he never achieved complete remission and died of disease 10 months after diagnosis. Here, we present this case and review prior literature regarding t-MPAL.
Update of the risk assessment of nickel in food and drinking water

Abstract The European Commission asked EFSA to update its previous Opinion on nickel in food and drinking water, taking into account new occurrence data, the updated benchmark dose (BMD) Guidance and newly available scientific information. More than 47,000 analytical results on the occurrence of nickel were used for calculating chronic and acute dietary exposure. An increased incidence of post‐implantation loss in rats was identified as the critical effect for the risk characterisation of chronic oral exposure and a BMDL 10 of 1.3 mg Ni/kg body weight (bw) per day was selected as the reference point for the establishment of a tolerable daily intake (TDI) of 13 μg/kg bw. Eczematous flare‐up reactions in the skin elicited in nickel‐sensitised humans, a condition known as systemic contact dermatitis, was identified as the critical effect for the risk characterisation of acute oral exposure. A BMDL could not be derived, and therefore, the lowest‐observed‐adverse‐effect‐level of 4.3 μg Ni/kg bw was selected as the reference point. The margin of exposure (MOE) approach was applied and an MOE of 30 or higher was considered as being indicative of a low health concern. The mean lower bound (LB)/upper bound (UB) chronic dietary exposure was below or at the level of the TDI. The 95th percentile LB/UB chronic dietary exposure was below the TDI in adolescents and in all adult age groups, but generally exceeded the TDI in toddlers and in other children, as well as in infants in some surveys. This may raise a health concern in these young age groups. The MOE values for the mean UB acute dietary exposure and for the 95th percentile UB raises a health concern for nickel‐sensitised individuals. The MOE values for an acute scenario regarding consumption of a glass of water on an empty stomach do not raise a health concern.
Duodenal Perforation: Outcomes after Surgical Management at a Tertiary Care Centre—A Retrospective Cross-Sectional Study

Introduction Duodenal perforation is a common surgical emergency and carries mortality ranging from 4% to 30% reported in Western countries, but there is a paucity of reports from India. We aimed to determine the factors which influence the surgical outcomes in patients with duodenal perforation. Methods We retrospectively analyzed prospectively collected data from January 2010 to December 2018. Results A total of 55 patients were included in the study of which 69% (38) were males and 31% (17) were females (M : F = 4.5 : 2). The mean age was 52.3 years. The cause for duodenal perforation was duodenal ulcer (n = 25, 45.5%), followed by post-ERCP complications (n = 15, 27.3%), surgery (n = 11, 20%), and blunt trauma (n = 4, 7.2%) with perforations localized at D2 (n = 28, 51%) and at D1 (n = 27, 49%). Patients underwent primary repair with an additional diversion procedure (n = 28, 51%) and repair only in 18 (32.8%). There were 21 (38%) deaths. Patients with ERCP-associated duodenal perforation had longer hospital stay (P ≤ 0.001), ICU stay (P=0.049), duration of drainage (P ≤ 0.001), and higher leak rate (P=0.001) and re-exploration rate (P=0.037). A high mortality rate was seen in patients with preoperative organ failure (n = 18, 78% versus 9.4%, P=0.001), postoperative leak (n = 7, 64% versus 32%, P=0.05), and longer duration from onset of symptoms to surgery (≥4 days) (P=0.045). Conclusion Perforation of the duodenum is associated with high morbidity and mortality regardless of its cause and is higher in those who have a longer interval to surgery, preoperative organ failure, and a postoperative leak.