Miracle-dz/UniFAR-FTUs huggingface dataset:
Proximate and Mineral Compositions of Noodles Made from Triticum durum, Digitaria exilis, Vigna unguiculata Flour and Moringa oleifera Powder

The objective of this study was to determine the proximate, mineral and sensory properties of noodles prepared from blends of Triticum durum (wheat), Digitaria exilis(acha), Vigna unguiculata (cowpea) flours and Moringa oleifera leaf powder (MLP). The flour samples were mixed in a four by four factorial, in complete randomized design (CRD) to formulate the composite blends at four different levels (25, 50, 75 and 100) which gave 16 samples. The flour samples were used to produce noodles and subjected to proximate, mineral and sensory analysis. Results of the proximate composition revealed that moisture content of the noodles ranged from 8.04-13.81%, ash 1.84-3.67%, fat 1.95-3.61%, crude protein 10.07-14.44%, carbohydrate 33.15-61.45%, dietary fibre 16.65-36.22% and caloric value 214.53-288.28 kJ/100 g. There was a significant increase (p < 0.05) in the moisture, ash, fat, crude protein and dietary fibre of the noodles on the substitution with cowpea flour, acha flour and MLP. Results of mineral composition also showed that sodium content ranged from 1.58-11.76 mg/100 g, potassium 26.70-40.40 mg/100 g, calcium 18.03-59.02 mg/100 g, iron 6.18-21.53 mg/100 g and phosphorus 0.51-1.54 mg/100 g. Noodle sample produced from 75% wheat and 25% cowpea flours were significantly higher (p < 0.05) in mineral content (except for potassium). Sensory evaluation results showed that cowpea and acha flours can be substituted at 25% levels with 75%, wheat flour and acha flour can as well be substituted at 50% with 50% cowpea flour while MLP at 2% with 50% wheat flour, 23% acha flour and 25% cowpea flour without significantly (p < 0.05) affected the sensory attributes of the noodles. This result therefore indicates that the use of these locally grown crops has the potential to increase the nutritional intake of consumers of this product.
Functional and Antioxidant Properties of Gelatin Hydrolysates Prepared from Skin and Scale of Sole Fish

ABSTRACT Preparation of bioactive hydrolysates is an efficient approach for developing high value industrially important products from fishery waste. In this study, gelatin hydrolysates were prepared from skin and scale of sole fish (Cynoglossus arel) and evaluated for functional and antioxidant properties. Hydrolysis of extracted gelatin solution with alcalase enzyme for 2 h yielded 16.42% (weight yield) skin gelatin hydrolysates (SGH) and 8.44% scale gelatin hydrolysates (SCGH) with 23.6 and 18.57% degree of hydrolysis, respectively. Quantity of proximate components including protein, fat, ash, and moisture of the two hydrolysates did not differ significantly (p > 0.05). SCGH displayed significantly higher (p < 0.05) foaming capacity (54%) and foam stability index (42%) compared to SGH (36 and 34%, respectively). Emulsion activity index was significantly higher with SGH (112.6 m2/g), whereas emulsion stability index was higher for SCGH (15.5 min). 2,2, diphenyl 2 picryl hydrazine (DPPH) free radical scavenging activity, metal reducing power, and metal chelating ability was found to be higher with SCGH than SGH; however, the values were not significantly different with respect to metal chelating activity and reducing power.
Comparative phylogeography as an integrative approach to understand human and other mammal distributions in Europe.

Phylogeography refers to the phylogenetic analysis of organisms in the context of their geographical distribution. The analytical methods build phylogenetic trees and networks from haplotypes in order to investigate the history of the organisms. Phylogeographic studies have revealed the importance of climatic oscillations and the role of the Last Glacial Maximum (27,500 to 16,000 years ago) with the formation of refugia where distinct haplotypes originate in Europe. The population expansions and contractions into these refugial areas have driven the evolution of different lineages but the similarities and differences between species are still poorly understood. This thesis aims to gain a better understanding of the phylogeographical processes of different mammals’ species in Europe. This was done by collecting published mitochondrial DNA control region sequences of 29 different species and analysing them individually and comparatively. This research presents a standardised way of understanding phylogeography from the mitochondrial DNA perspective to improve the comparison of studies in the field. The project investigates the patterns of genetic diversity by examining various diversity indices to test for trends and commonalities. To enhance knowledge in phylogeography and the importance of refugia during the Last Glacial Maximum in Europe through a comparative phylogeographic meta-analysis of mammal species. This thesis developed novel insights into the phylogeographic interactions of different mammal species, including modern humans, in the European geographical context. Modern human phylogeography pattern from the short control region has been contextualised in the patterns observed for other mammal species, showing a homogeneous distribution across the continent. Finally, the commensal species Mus musculus domesticus (western house mouse) was investigated in detail from a current and a past phylogeographic perspective in two islands, Cyprus and Britain, using ancient and modern DNA. This was done using this new knowledge as a bioproxy to understand more recent human movements associated with the transport of this species. This thesis, therefore, provides an integrated study with a new comparative framework and with results on the phylogeographical patterns of humans and other mammals in Europe.
Extended nursing and/or increased starter diet allowances for low weaning weight pigs

Objective To evaluate the use of nurse sows and post-weaning nutrition strategies for low wean weight (WW) pigs on lifetime growth and efficiency. Methods Animals (n = 270) were assigned to one of five treatments at 28 d. Low WW pigs (<6 kg) were either weaned and offered a special dietary regime recommended for low WW pigs (WEAN) or placed on a nurse sow (NURSE) and weaned at 49 d. Normal WW pigs (9 kg) (NORM) were also weaned at 28 d. After weaning, NORM and NURSE pigs were offered either a ‘high’ (4 kg/pig of starter 1 diet followed by 8 kg/pig of starter 2 diet) or ‘low’ (8 kg/pig of starter 2 diet) starter diet allowance in a 2×2 factorial arrangement. A typical grower diet was then offered, followed by a typical finisher diet until 147 d of age. Results NORM pigs where heavier throughout their life compared to NURSE pigs (91.4 kg vs 76.2 kg at 147 d; p<0.001). WEAN pigs were heavier at 70 d compared to NURSE pigs (23.9 kg vs 21.0 kg; p<0.001), but there was no significant difference at 147 d between NURSE and WEAN treatments. NURSE pigs had reduced feed intake throughout the finishing period (1.6 kg/d; p<0.001) compared to WEAN (2.0 kg/d) and NORM (1.9 kg/d) pigs. Feed conversion ratio (FCR) of NURSE (2.20) was lower than NORM and WEAN during the finishing period (2.40 and 2.79, respectively). Conclusion Extended (up to 49 d) nursing for low WW pigs resulted in improved FCR during the finishing period, but no overall improvement in growth rate compared to low WW pigs weaned at 28 d and offered a specialised starter regime. Normal WW pigs where significantly heavier than low WW pigs throughout the study.
Analysing the safe and just operating space of agriculture in the world: past, present and future

Agriculture, along with industry and household sector are three major sectors of human consumption. Agriculture has proved to be a major contributor to exceeding planetary boundaries. Here, we have explored the impact of agriculture in the Earth system processes, through eight dimensions of planetary boundaries or safe operating spaces: climate change (10.73%), freshwater use (91.56%), arable land use (37.27%), nitrogen use (95.77%), phosphorus use (87.28%), ecological footprint (19.42%), atmospheric pollution (2.52% - 38.08%) and novel entities. In this work, we have also shown role of agriculture to the socio-economic development dimensions: gender equality, employment and economic growth. We have shown that the safe operating limits for agriculture are going to decline by almost 55% (climate change), 300% (freshwater use), 50-55% (arable land use), 180% (nitrogen use), 265% (phosphorus use) and 20% (ecological footprint) in 2050, if the most inefficient way of consumption is chosen and continued. To alleviate the role of agriculture in transgressing planetary boundaries, it is indispensable to comprehend how many roles of agriculture is playing and where which target should be set to framework the national agricultural policies in coherence with attaining sustainable development goals of UN by 2030.
Predicting Alzheimer’s disease progression trajectory and clinical subtypes using machine learning

Background Alzheimer’s disease (AD) is a common, age-related, neurodegenerative disease that impairs a person’s ability to perform day-to-day activities. Diagnosing AD is challenging, especially in the early stages. Many patients still go undiagnosed, partly due to the complex heterogeneity in disease progression. This highlights a need for early prediction of the disease course to assist its treatment and tailor therapy options to the disease progression rate. Recent developments in machine learning techniques provide the potential to not only predict disease progression and trajectory of AD but also to classify the disease into different etiological subtypes. Methods and findings The work shown here clusters participants in distinct and multifaceted progression subgroups of AD and discusses an approach to predict the progression rate from baseline diagnosis. We observed that the myriad of clinically reported symptoms summarized in the proposed AD progression space corresponds directly with memory and cognitive measures, which are routinely used to monitor disease onset and progression. Our analysis demonstrated accurate prediction of disease progression after four years from the first 12 months of post-diagnosis clinical data (Area Under the Curve of 0.96 (95% confidence interval (CI), 0.92-1.0), 0.81 (95% CI, 0.74-0.88) and 0.98 (95% CI, 0.96-1.0) for slow, moderate and fast progression rate patients respectively). Further, we explored the long short-term memory (LSTM) neural networks to predict the trajectory of an individual patient’s progression. Conclusion The machine learning techniques presented in this study may assist providers in identifying different progression rates and trajectories in the early stages of the disease, hence allowing for more efficient and personalized healthcare deliveries. With additional information about the progression rate of AD at hand, providers may further individualize the treatment plans. The predictive tests discussed in this study not only allow for early AD diagnosis but also facilitate the characterization of distinct AD subtypes relating to trajectories of disease progression. These findings are a crucial step forward for early disease detection. These models can be used to design improved clinical trials for AD research.
Efficacy of Thermotherapy to Treat Breast Cancer: A Review

This article reviews the use of different types of thermotherapies to treat breast cancer. While hyperthermia, T° 43°C, is usually carried out alone to eradicate small breast tumors. A recently developed thermotherapy, called magnetic hyperthermia, which involves localized heating of nanoparticles under the application of an alternating magnetic field, is also presented. The advantages and drawbacks of these different techniques are highlighted.
Comparative analysis of antioxidant and secondary metabolites contents in eight populations of Medicago ciliaris L.

1 ABSTRACT To identify the suitable genetic resources of forage legumes for animal feeding, the characterization of their chemical and biochemical composition is crucial since forage quality is a limiting factor which affects animal health and performance and consequently human health. In this context, this study carried out for the first time the analyses of the antioxidant compounds and the secondary metabolites (total phenols and tannins and saponins) in whole fresh biomass, flowers and stems of eight populations of Medicago ciliaris L (echinus Medicago) collected in different bioclimatic areas of north Tunisia. The analysis of variance showed significant differences between populations for all parameters (P<0.05) except for anthocyanins (P>0.05). Significant correlations were found between carotenoids and chlorophylls a and b (r= 0.59, n=48; P<0.0001) and between lycopene and β-carotene (r=0.81, n=48; P<0.0001). Multivariate analysis showed that populations 306 and 326 had the highest contents of chlorophyll a and carotenoids while Pop3 had the highest content of lycopene, β-carotenes, saponines and total tannins. These populations will be integrated in a breeding program for quality improvement of forage and will serve for grazing of pods and straw in summer and grazing of green biomass in winter and spring accordingly to their richness in antioxidant compounds.
Differential degradation of RNA species by autophagy related pathways in plants

An important function of the plant vacuole is the recycling of the delivered proteins and RNA by autophagy. We provide the first plant vacuolar small RNome by isolation of intact vacuoles from Barley and Arabidopsis, subsequent RNA purification and Next Generation Sequencing. In these vacuolar sRNomes, all types of cellular RNAs were found including those of chloroplast origin, suggesting a bulk-type of RNA transfer to, and breakdown in vacuoles. ATG5 is a major representative of autophagy genes and the vacuolar RNA composition in corresponding knockout plants differed clearly from controls as most chloroplast derived RNA species were missing. Moreover, the read length distribution of RNAs found in ATG5 mutants differed to control samples, indicating altered RNA processing. In contrast, vacuoloar RNA length and composition of plants lacking the vacuolar RNase2 (rns2-2), involved in cellular RNA homeostasis, showed minor alterations, only. Our data therefore suggests that mainly autophagy components are responsible for selective transport and targeting of different RNA species into the vacuole for degradation. In addition to short RNA fragments of longer RNAs, mature miRNAs were detected in all vacuolar preparations, however in ATG5 mutants at much lower frequency. Read length analysis indicates that vacuolar miRNAs are not degradet suggesting an additional RNA targeting mechanism and a potential new role biological for vacuolar miRNAs.
A Joint Model of RNA Expression and Surface Protein Abundance in Single Cells

Cellular indexing of transcriptomes and epitopes by sequencing (CITE-seq) combines unbiased single-cell transcriptome measurements with surface protein quantification comparable to flow cytometry, the gold standard for cell type identification. However, current analysis pipelines cannot address the two primary challenges of CITE-seq data: combining both modalities in a shared latent space that harnesses the power of the paired measurements, and handling the technical artifacts of the protein measurement, which is obscured by non-negligible background noise. Here we present Total Variational Inference (totalVI), a fully probabilistic end-to-end framework for normalizing and analyzing CITE-seq data, based on a hierarchical Bayesian model. In totalVI, the mRNA and protein measurements for each cell are generated from a low-dimensional latent random variable unique to that cell, representing its cellular state. totalVI uses deep neural networks to specify conditional distributions. By leveraging advances in stochastic variational inference, it scales easily to millions of cells. Explicit modeling of nuisance factors enables totalVI to produce denoised data in both domains, as well as a batch-corrected latent representation of cells for downstream analysis tasks.
Neuroanatomy, Area Postrema

The area postrema is a highly vascular paired structure in the medulla oblongata in the brainstem. It lies in the caudal fourth ventricular floor, overlying the inferior portion of vagal trigone while facing the foramen of Magendie and rostral to the obex, the inferior point of the floor of the fourth ventricle. It is between the funiculus separans and the gracilis tubercle, lying adjacent to the nucleus of tractus solitarius. The description of the structure has been as ‘arched wings’ that are open on the sides of the fourth ventricle, as they separate upward from the central canal.
Investigating the influence of environment on the evolution of Hsp90 using comprehensive fitness maps

Gene-environment interactions have long been theorized to influence molecular evolution. However, the environmental dependence of most mutations remains unknown. Using deep mutational scanning, we engineered budding yeast with all 44,604 single codon changes encoding 14,160 amino acid variants in Hsp90 and quantified growth effects under standard laboratory conditions and under five stress conditions (elevated temperature, nitrogen starvation, elevated salinity, high ethanol concentration, and oxidative stress caused by diamide). To our knowledge these are the largest comprehensive fitness maps of point mutant growth effects that have been determined. The growth effects of many variants differed between each of the conditions, indicating that environmental conditions can have a large impact on the evolution of Hsp90. Multiple variants provided growth advantages relative to wildtype Hsp90 under individual conditions, however these variants tended to exhibit growth defects in other environments. The diversity of Hsp90 sequences observed in extant eukaryotes preferentially contain amino acid variants that supported robust growth under all tested conditions. Thus, rather than favoring substitutions in individual conditions, the long-term selective pressure on Hsp90 may have been that of fluctuating environments, leading to robustness under a variety of conditions.
Karyotype evolution in Helianthemum (Cistaceae): dysploidy, achiasmate meiosis and ecological specialization in H. squamatum, a true gypsophile

Helianthemum squamatum is a specialist gypsophile, the only species of a recently diverged lineage in subgenus Helianthemum characterized by having the lowest chromosome number in the genus (n = 5). With the hypothesis of great genome reorganization in the lineage of H. squamatum, we (1) modelled the evolution of the chromosome number in the genus Helianthemum, (2) analysed the karyotype and the nuclear DNA content of H. squamatum and its sister species H. syriacum (n = 10) and (3) studied in detail the meiotic process of H. squamatum. Our analyses show that: (1) the rate of chromosome losses in the lineage that gave rise to H. squamatum is 100 times higher than in the genus as a whole; (2) compared to its sister species, H. squamatum has a more symmetric karyotype composed of longer metacentric chromosomes and retains c. 80% of its nuclear DNA content and (3) achiasmatic behaviour of chromosomes occurs during microsporogenesis despite full synapsis. Our results are in agreement with previous knowledge showing that reduced chromosome numbers in determinate lineages are found in short-lived species adapted to stressful environments, and we suggest that a combination of fewer chromosomes, a smaller genome, a shorter life cycle and the suppression of meiotic recombination can together contribute to the maintenance of those advantageous allelic combinations that makes H. squamatum a true gypsophile, enabling the individual plants to cope with the harshness imposed by dry gypsum soils.
Common Psychosocial and Spiritual Factors Among Individuals who have healed from Chronic Lyme Disease

This dissertation examined the subjective experience of individuals who have healed from Chronic Lyme Disease (CLD). Despite significant attention paid to the controversy over CLD diagnosis and treatment, scholarly research has neglected the psychosocial and/or spiritual factors that facilitate healing from the perspective of CLD sufferers. This study addressed this research gap by using Interpretive Phenomenological Analysis (IPA) to explore the barriers and facilitators of healing among those who have healed from CLD. Six participants who had suffered from CLD and considered themselves healed from the disease were recruited and interviewed. The qualitative data was reduced to meaning units, which were then grouped into common themes, were clustered into superordinate themes. Quality control procedures, including peer audits and journaling, were implemented to enhance the credibility and trustworthiness of the analysis. Findings revealed that the political controversy over CLD and a lack of understanding from conventional medicine practitioners were barriers to healing. Participants reported that healing in mind, body and spirit was necessary to transcend suffering, and that healing each one of these systems had a reciprocal effect on the others. Participants experienced validation and social support as facilitators to health. Participants explained that changing their ways of life, changing their relationship to thoughts and emotions, engaging in a spiritual practice, looking introspectively, and undergoing a “spiritual awakening” allowed for an increased sense of meaning and agency, which facilitated healing. These spiritual practices included prayer, yoga, meditation, chakra stretching, and a “spiritual retreat. ” Alternative medicine was also cited by participants as helpful in healing from CLD. Some of the implications of these results include a need for (a) improved collaboration between the CLD sufferer and the medical community to minimize perceived stigma; (b) conventional medical COMMON FACTORS IN HEALING FROM CHRONIC LYME DISEASE 2 professionals to refer CLD sufferers to practitioners who recognize, diagnose, and treat CLD in order to shorten the lag time between CLD onset and diagnosis/treatment; and © emotional, introspective, and spiritual help in healing the disease through individual and group therapy. Future research on alternative medicine for CLD, comparative treatment studies, and the effectiveness of individual and group therapy models for CLD is recommended.