Miracle-dz/UniFAR-FTUs huggingface dataset:
An Acoustic Analysis of the Short and Long Vowels in Ekegusii Language

This paper analyzes the vowel lengths of Ekegusii, a Bantu language spoken in southwestern Lake Region of Kenya. Orthographically, the Ekegusii language reveals only five vowels as a, e, i, o, and u. However, pioneering researchers like Guthrie (1948) and Whiteley (1965) have shown that the language has a seven vowel system /a, e, ɛ, i, o, ɔ, u/. These researches and many later researches such as Osinde (1988), Bosire (1993), Cammenga (2002), Nurse and Gerard (2003), and Mecha (2006) among others relied upon impression to identify and describe the vowels. Of recent, however, it has become necessary to use modern scientific acoustic methods of speech analysis to confirm earlier claims about the vowels in the language. In this research, we used Praat Software (Boersma & Weenink 2010) to identify and analyze the vowel system of Ekegusii. Results indicate that vowel length is distinctive in the language. Since vowel duration is phonemic in the language, then the vowels are fourteen as each short vowel has a corresponding long vowel as revealed in the data of this research.
Performance - Based Clustering Enables the Study of Physiological Features Supporting Sustained Attention Capacities

In the present study, we investigated different sustained attention performance profiles in the general adult population and if age is a determinant factor among these profiles. We also reported some specificities in terms of brain oscillations. The sustained attention to response task was applied combined with electrophysiological recordings in 59 adults, aged from 19 to 86 years. We used a hierarchical cluster analysis to group individuals based on similarity of levels and patterns of performance across variables of interest. We focused on the most common attentional–related variables, which allowed us to identify four distinct clusters showing specific sustained attention profiles. Furthermore, our analysis clearly revealed that age was not the determinant factor of these profiles. Finally, we highlighted specificities in terms of brain oscillations. Subjects from cluster 1– the “high-performers” – demonstrated a globally increased theta-gamma coupling maintained over time and an increase of theta activity at the FC6 and F8 electrodes. Subjects from cluster 2, who adopted a more cautious response strategy, presented a higher level of modulation exerted by the electrode FT7 over Oz and a higher theta-gamma coupling at the Oz. This result suggests that cluster-based method to useful in understanding specific mechanisms underlying sustained attention features.
Glucose metabolism in idiopathic pulmonary fibrosis

Idiopathic pulmonary fibrosis (IPF) is a life-threatening interstitial lung disease of unknown aetiology characterized by progressive scarring of the lung parenchyma. Histologically, the hallmark of the disease is the presence of interspersed fibroblastic foci in the lung, composed of contractile myofibroblasts synthesizing a dense collagen-rich matrix. Transforming growth factor-β1 (TGFβ1) has been recognized as a key cytokine in the pathophysiology of IPF and other fibrotic disorders. Highly proliferative cells, such as cancer cells, reprogram their glucose metabolism through the activation of the PI3K-AKT-mTOR axis towards enhanced glycolysis, a process known as aerobic glycolysis. In view of the high biosynthetic nature of myofibroblasts, this thesis aimed to (1) describe the changes in glucose metabolism that occur during the process of TGFβ1-induced fibroblast to myofibroblast differentiation, (2) examine whether these changes are regulated by the PI3K-AKT-mTOR axis, and (3) examine the relationship between glucose uptake and fibrogenesis in an experimental model of lung fibrosis. For the in vitro experiments, the metabolic profile of primary human lung fibroblasts was assessed by examining cellular glucose uptake, glycolytic flux and mitochondrial respiration. Furthermore, using highly selective and potent pharmacological inhibitors, the role of the PI3K-AKT-mTOR pathway in promoting changes in glucose metabolism during fibroblast differentiation was examined. For the in vivo experiments, position emission tomography-computed tomography scanning and autoradiography were performed in the murine bleomycin model of lung injury and fibrosis following administration of radioactive 18F-labeled fluoro-2-deoxyglucose. Taken together, the data presented in this thesis demonstrate that the metabolic phenotype of fibroblasts changes during TGFβ1-induced fibroblast differentiation and is regulated by mTOR, in a PI3K-AKT-independent manner. This metabolic switch may further explain the observation of increased glucose uptake in the fibrotic lesions in the bleomycin model of lung fibrosis. These findings support the notion that pharmacological targeting of glucose metabolism and/or the mTOR kinase may be beneficial in preventing myofibroblast differentiation in IPF.
Radiation Doses to Hanford Workers from Natural Potassium-40

The chemical element potassium is an essential mineral in people and is subject to homeostatic regulation. Natural potassium comprises three isotopes, 39K, 40K, and 41K. Potassium-40 is radioactive, with a half life of 1.248 billion years. In most transitions, it emits a β particle with a maximum energy of 0.560 MeV, and sometimes a gamma photon of 1.461 MeV. Because it is ubiquitous, 40K produces radiation dose to all human beings. This report contains the results of new measurements of 40K in 248 adult females and 2,037 adult males performed at the Department of Energy Hanford Site in 2006 and 2007. Potassium concentrations diminish with age, are generally lower in women than in men, and decrease with body mass index (BMI). The average annual effective dose from 40K in the body is 0.149 mSv y−1 for men and 0.123 mSv y−1 women respectively. Averaged over both men and women, the average effective dose per year is 0.136 mSv y−1. Calculated effective doses range from 0.069 to 0.243 mSv y−1 for adult males, and 0.067 to 0.203 mSv y−1 for adult females, a roughly three-fold variation for each gender. The need for dosimetric phantoms with a greater variety of BMI values should be investigated. From our data, it cannot be determined whether the potassium concentration in muscle in people with large BMI values differs from that in people with small BMI values. Similarly, it would be important to know the potassium concentration in other soft tissues, since much of the radiation dose is due to beta radiation, in which the source and target tissues are the same. These uncertainties should be evaluated to determine their consequences for dosimetry.
Saponins of the extracts of Galium aparine and Galium verum

Aim . To determine the qualitative composition and the quantitative content of saponins in the liquid extracts of the herb of cleavers ( Galium aparine L.) and lady’s bedstraw ( Galium verum L.). Materials and methods . Extracts of the herb of cleavers and lady’s bedstraw were obtained by the triple extraction of the raw material with 96 % ethanol when heating with the subsequent concentration of the combined extracts to the ratio of the raw material : the finished product of 1:1. Saponins were studied by the method of high-performance liquid chromatography (HPLC). Results . As a result of the chromatographic study of extracts of the herb of cleavers and lady’s bedstraw it has been found that they contain 6 and 7 saponins, respectively. The compounds belong to ursane (ursolic, euscaphic, tormentic acids and uvaol), oleanane (oleanolic acid) and lupane (betulin and lupeol) type. In the extract from the herb of cleavers the compounds of ursane derivatives (50 mg/ml) prevail, the dominant compound is euscaphic acid (3.34 mg/ml); in the extract from the herb of lady’s bedstraw there are saponins of lupane derivatives (2.50 mg/ml), lupeol (1.60 mg/ml) is predominant. Conclusions . The results obtained indicate the prospects for further in-depth study of the chemical composition and biological activity of the liquid extracts from the herb of cleavers and lady’s bedstraw.
nsearch: An open source C++ library for processing and similarity searching of next-generation sequencing data

Advancements in DNA sequencing technologies rapidly change the landscape of modern biology. The novel next-generation sequencing (NGS) applications often have special requirements regarding experimental data processing. Software tools developed and used for novel applications are generally designed for specific use cases and as such may be difficult to adapt to new uses. Simultaneously, software tools designed to be general are often difficult to adapt to special use cases. Here, we present nsearch, a modern open source C++11 library and command-line tool for biological sequence data processing. nsearch offers commonly used components for handling of biological sequences including paired-end read merging, quality filtering and sequence similarity searching. nsearch can either be embedded natively into other C++ applications or be packaged as a standalone executable. Functionality and performance of nsearch is shown using benchmark data created using the Rfam 13 database. Benchmarking against common general purpose tools USEARCH and VSEARCH demonstrates that nsearch delivers performance comparable these state-of-the-art tools. nsearch is available on GitHub under the permissive BSD-3-clause license: https://github.com/stevschmid/nsearch
The multi‐feedstock biorefinery – Assessing the compatibility of alternative feedstocks in a 2G wheat straw biorefinery process

For second‐generation (2G) bioethanol refineries, the feedstock supply is one of the important parameters in terms of cost and consistency. Biorefineries are in most cases designed for a specific type of feedstock. For some biorefineries, the use of multiple feedstocks is an option, but how would such feedstocks perform when used in a process designed and optimized for a specific feedstock? There is no “one‐size‐fits‐all” processing package, due to variations in composition and structure of different feedstock types, but due to the size of commercial biorefineries, only minor adjustments of the processing parameters are practically feasible. In this study, 16 alternative feedstocks were characterized and compared to the benchmark feedstock wheat straw under identical processing conditions. The alternative feedstocks studied were as follows: barley straw, rye straw, grass straw, oat straw, Norway spruce sawdust, mixed softwood sawdust, oat wrap, biogas fiber, deep litter, washed deep litter, ryegrass fiber, lucerne fiber, ryegrass chaff, mixed grain chaff, rapeseed press cake, and beer production mash. These biomasses varied in carbohydrate content and accessibility after hydrothermal pretreatment. Applying a hydrothermal pretreatment under identical conditions, the subsequent enzymatic convertibility of these biomasses ranged from 0.5% to complete conversion based on their glucan content. Water retention value was determined and correlated with enzymatic convertibility, which provided a simple method for indirect measurement of biomass recalcitrance. Ethanol potentials were estimated based on carbohydrate release from enzymatic hydrolysis, and yeast toxicity test was performed on liquid fractions from hydrothermal pretreatment. Furthermore, a number of key processing indicators, including market price, logistics and availability, were taken into consideration based on a proposed full‐scale 2G ethanol plant in Denmark. The overall results show that while some feedstocks had inferior performance compared to wheat straw, identical or even superior performance was observed from barley, oat, and ryegrass feedstocks.
Intrathoracic Anastomosis or Cervical Anastomosis for Esophagogastric Junction Cancer Surgery: A Retrospective Cohort Study

This study aimed to determine the degree of reflux esophagitis after either intrathoracic or cervical esophagogastrostomy in patients with esophagogastric junction carcinoma. The study population consisted of 10 and 15 consecutive patients who underwent esophagectomy with gastric conduit reconstruction via intrathoracic (Ivor Lewis) or cervical (McKeown) esophagogastrostomy, respectively. Reflux esophagitis was evaluated annually after surgery and scored on a 0- to 4-point scale corresponding to grades N/M, A, B, C, and D, respectively. The reflux esophagitis score of each patient, defined as the average of scores at 1, 2, and 3 years after surgery, was compared between the groups. Of the 30 planned annual endoscopic follow-ups (3 years in 10 patients) in the Ivor Lewis group and 45 planned follow-ups (3 years in 15 patients) in the McKeown group, 24 and 29 such follow-ups were performed in the Ivor Lewis and McKeown groups, respectively. The reflux esophagitis score was significantly better in the McKeown group than in the Ivor Lewis group (0.51 ± 0.24 versus 1.46 ± 0.29, P = 0.019). Overall survival did not significantly differ between the Ivor Lewis and McKeown groups (respective 5-year survival rates, 64% versus 57%, P = 0.75). The degree of reflux esophagitis may be greater in patients with esophagogastric junction cancer treated by Ivor Lewis esophagectomy than in those treated by McKeown esophagectomy. McKeown esophagectomy might be a more suitable method for the treatment of esophagogastric junction cancer with extended esophageal invasion.
The Influence of Distributed Leadership on Effective School Governance and Improved School Performance

The purpose of this research is to identify the impact of Distributed Leadership (DL) on school governance, leading to an improvement in the overall school performance. This study was conducted in two private schools in the UAE. The review of related literature helped to understand the concept of distributed leadership and its impact on governance, school performance, and organizational hierarchy. The data was collected using a mixed method using surveys and interviews. The data was analyzed using descriptive analysis and moderated regression analysis. The conclusion reached was that DL has a positive impact on the relationship between governance and performance. It was also found that DL was being applied in both schools at varying levels, and each had areas that needed improvement. The most important implication was the connection of DL to governance and performance. The findings offer relevant insights for schools studied, as well as for similar schools.
Assessing the effect of airport physical environment on passenger's satisfaction: a mediating effect of passenger's delight / Nur Aida Amani Baharuddin and Mazlina Mahdzar.

In tourism development, the impact of demand for air transport by travelers is affecting new forms of tourism and new destinations. The airport is a consistent growth segment in the tourism industry and transportation. The objective of the proposed study is to investigate the influence of physical environment of the airport on passengers’ delight and satisfaction. Studies on the physical environment impact on customer delight and satisfaction are still limited, especially in the context of international airports. In order to understand this phenomenon, the study examines the literature, raises issues and develops the framework within the research context. The study will opt a convenience sampling method, with a total of 400 sets of questionnaires will be distributed to local and international passengers at Kota Kinabalu International Airports (KKIA). This study provides theoretical basis for future research on the role of physical environment of international airports and its impact on passengers’ emotions and behavior. It also assists international airport industry practitioners to better understand how airport physical environments affects passengers’ experience and satisfaction.
Developing a computational approach to investigate the impacts of disease-causing mutations on protein function

This project uses bioinformatics protocols to explore the impacts of non-synonymous mutations (nsSNPs) in proteins associated with diseases, including germline, rare diseases and somatic diseases such as cancer. New approaches were explored for determining the impacts of disease-associated mutations on protein structure and function. Whilst this work has mainly concentrated on the analysis of cancer mutations, the methods developed are generic and could be applied to analysing other types of disease mutations. Different types of disease-causing mutations have been studied including germline diseases, somatic cancer mutations in oncogenes and tumour-suppressors, along with known activating and inactivating mutations in kinases. The proximity of disease-associated mutations has been analysed with respect to known functional sites reported by CSA, IBIS, along with predicted functional sites derived from the CATH classification of domain structure superfamilies. The latter are called FunSites, and are highly conserved residues within a CATH functional family (FunFam) – which is a functionally coherent subset of a CATH superfamily. Such sites include key catalytic residues as well as specificity determining residues and interface residues. Clear differences were found between oncogenes, tumour suppressor and germ-line mutations with oncogene mutations more likely to locate close to FunSites. Functional families that are highly enriched in disease mutations were identified and exploited structural data to identify clusters within proteins in these families that are enriched in mutations (using our MutClust program). We examined the tendencies of these clusters to lie close to the functional sites discussed above. For selected genes, the stability effects of disease mutations in cancer have also been investigated with a particular focus on activating mutations in FGFR3. These studies, which were supported by experimental validation, showed that activating mutations implicated in cancer tend to cause stabilisation of the active FGFR3 form, leading to its abnormal activity and oncogenesis. Mutationally enriched CATH FunFams were also used in the identification of cancer driver genes, which were then subjected to pathway and GO biological process analysis.
Ecological succession in a changing world

Ecological succession – how biological communities re‐assemble and change over time following natural or anthropogenic disturbance – has been studied since the birth of ecology, and the resulting theoretical framework underpins many aspects of the discipline. Recently, the mechanistic basis of classic succession theory has been advanced by studies of plant and microbial interactions, functional traits, and retrogressive stages of ecosystem development. This special issue brings together a series of papers that highlight these contemporary novel approaches and how our understanding of ecological succession has advanced. Four key themes emerge from the issue: (a) generalizations about succession, (b) the influence of dispersal and habitat size on successional trajectories, (c) changes in plant functional traits during succession, and (d) belowground community interactions during long term during ecosystem development. Synthesis. The articles in the special issue highlight novel perspectives on succession theory, revealing the importance of historical contingency, disturbance severity, dispersal limitation, functional traits, and belowground community processes in determining patterns of ecosystem development. Together, they reinforce the importance of ecological succession in understanding the response of plant and microbial communities to disturbance in a changing world.
HIV prophylaxis : an essential role for T cells and adjuvants in recombinant mucosal Lactobacillus acidophilus vaccines

ii ACKNOWLEDGEMENTS . iii Chapter 1: Overview of Literature . 1 1.1 Mucosal Immunity . 1 1.1a Cell Junctions and Mucus . 1 1.1b Antimicrobial Peptides . 2 1.1c Innate Lymphoid Cells . 2 1.1d Sampling of Mucosal Lumen . 3 1.1e Pattern Recognition Receptors . 5 1.1f B cells, class switching, and IgA . 6 1.1g T cells . 6 1.2 Human Microbiome . 7 1.3 Microbiome and Disease . 8 1.4 Lactic Acid Bacteria and Probiotics . 9 1.5 Lactobacilli . 10 1.5a Anti-Pathogen Effects . 11 1.5b Anti-Inflammatory Effects . 12 1.5c Adjuvant/Immune Effects . 12 1.6 Lactic Acid Bacteria Vaccines . 13 1.6a Antigen Expression . 14 1.6b Immune Response . 14 1.7 Brief History and Epidemiology of HIV . 15 1.8 HIV Genome Structure and Encoded Proteins . 16 1.8a Gag proteins . 16 1.8b Pol proteins . 17 1.8c Env glycoproteins . 18 1.8d Regulatory and Accessory Proteins . 18 1.8e Other Genome Regions . 19 1.9 HIV Transmission . 20 1.10 HIV Life Cycle . 21 1.10a Attachment and Fusion . 21 1.10b Uncoating, Reverse Transcription and Nuclear Import . 22 1.10c Integration and Latency . 23 1.10d Transcription and Nuclear Export . 24 1.10e Translation, Packaging and Budding . 24 1.11 HIV Vaccine History . 25 1.12 HIV Broadly Neutralizing Antibodies . 26 1.13 HIV Treatment . 27 1.14 Humanized Mice . 28 1.15 Rice Bran . 29
A phosphate starvation response gene (psr1-like) is present and expressed in Micromonas pusilla and other marine algae

Phosphorus (P) limits primary production in regions of the surface ocean, and many plankton species exhibit specific physiological responses to P-deficiency. The metabolic response of Micromonas pusilla, an ecologically relevant marine photoautotroph, to P-deficiency was investigated using environmental metabolomics and comparative genomics. The concentrations of some intracellular metabolites were elevated in the P-deficient cells (e.g., xanthine) and genes involved in the associated metabolic pathways shared a significant motif in the non-coding regions of the gene. The presence of the conserved motif suggests that these genes may be co-regulated, and the motif may constitute a regulatory element for binding a transcription factor (i.e., Psr1). A putative phosphate starvation response gene (psr1-like) was identified in M. pusilla with homology to well characterized psr1/phr1 genes in freshwater algae and plants. This gene appears to be present and expressed in other marine algal taxa, such as the abundant haptophyte Emiliania huxleyi, in chronically phosphorus-limited field sites. Results from the present study have implications for our understanding of taxon-specific roles in mediating P cycling in the ocean.
Molecular characterisation of microbial communities involved in nitrate-driven anaerobic oxidation of methane

Over the last decade, technological advances in whole genome amplification, microfluidics, flow sorting and high-throughput sequencing have led to the development of single cell genomics. Single cell genomic approaches are typically applied to anonymous microbial cells with only morphology providing clues to their identity. However, targeted separation of microorganisms based on phylogenetic markers, such as the 16S rRNA gene, are beginning to emerge in the single cell genomics field. Here, we describe an in-solution fluorescence in situ hybridization (FISH) protocol which can be combined with fluorescence-activated cell sorting (FACS) for separation of single cells or populations of interest from environmental samples. Sequencing of DNA obtained from sorted cells can be used for the recovery of draft quality genomes, and when performed in parallel with deep metagenomics, can be used to validate and further scaffold metagenomic assemblies. We illustrate in this Chapter the feasibility of this FISH-FACS approach by describing the targeted recovery of a novel anaerobic methanotrophic archaeon. 2.