Miracle-dz/UniFAR-FTUs huggingface dataset:
Sensitivity Analysis of the Rainfall–Runoff Modeling Parameters in Data-Scarce Urban Catchment

Rainfall–runoff phenomena are among the main processes within the hydrological cycle. In urban zones, the increases in imperviousness cause increased runoff, originating floods. It is fundamental to know the sensitivity of parameters in the modeling of an urban basin, which makes the calibration process more efficient by allowing one to focus only on the parameters for which the modeling results are sensitive. This research presents a formal sensitivity analysis of hydrological and hydraulic parameters—absolute–relative, relative–absolute, relative–relative sensitivity and R2—applied to an urban basin. The urban basin of Tuxtla Gutiérrez, Chiapas, in Mexico is an area prone to flooding caused by extreme precipitation events. The basin has little information in which the records (with the same time resolution) of precipitation and hydrometry match. The basin model representing an area of 355.07 km2 was characterized in the Stormwater Management Model (SWMM). The sensitivity analysis was performed for eight hydrological parameters and one hydraulic for two precipitation events and their impact on the depths of the Sabinal River. Based on the analysis, the parameters derived from the analysis that stand out as sensitive are the Manning coefficient of impervious surface and the minimum infiltration speed with R2 > 0.60. The results obtained demonstrate the importance of knowing the sensitivity of the parameters and their selection to perform an adequate calibration.
The Evolutionary History and Impact of Bacterial tRNA Modifications

Along with tRNAs, enzymes that modify anticodon bases are a key aspect of translation across the tree of life. tRNA modifications extend wobble pairing, allowing specific (“target”) tRNAs to recognize multiple codons and cover for other (“non-target”) tRNAs, often improving translation efficiency and accuracy. However, the detailed evolutionary history and impact of tRNA modifying enzymes has not been analyzed. Using ancestral reconstruction of five tRNA modifications across 1093 bacteria, we show that most modifications were ancestral to eubacteria, but were repeatedly lost in many lineages. Most modification losses coincided with evolutionary shifts in non-target tRNAs, often driven by increased bias in genomic GC and associated codon use, or by genome reduction. In turn, the loss of tRNA modifications stabilized otherwise highly dynamic tRNA gene repertoires. Our work thus traces the complex history of bacterial tRNA modifications, providing the first clear evidence for their role in the evolution of bacterial translation.
A multi-scale exploration of the drivers and implications of germination strategy in Australian alpine plants

Alpine ecosystems are particularly sensitive to the effects of global warming because they are characterized by species adapted to low temperatures. Although adapted to low temperatures, alpine plants may still be capable of persisting under a changing climate and this will largely be dependent on the ability of their seeds to germinate, establish and reproduce in situ, or after dispersal to new sites. The effects of climate change on regeneration from seeds may be influenced by intrinsic factors such as seed longevity (how long seeds remain viable and able to germinate after dispersal), or germination success (the proportion of a seed population that will germinate following exposure to future climate scenarios), and the seasonal timing of germination. Germination strategy, among the earliest life history traits expressed, reflects germination timing and pattern across the progression of seasons after seed dispersal and I therefore expected germination strategy would be a key trait affecting the responses of species to climate change. To examine seed longevity, which reflects the potential for survival in a soil seed bank or in ex situ conservation, I explored the seed intrinsic lifespan (longevity) and its correlates across 56 species (Chapter 2). I showed that Australian alpine seeds are short-lived, similar to alpine seeds elsewhere and relatively shorter-lived compared to non-alpine Australian seeds. Although relatively short-lived, the seeds do survive long enough to form persistent soil seed banks. However, it is unclear whether the conditions required for germination will still be present in future climate scenarios. Thus, I conducted experimental studies that investigated how germination success in future climate scenarios will differ from germination in ambient climate scenarios, and whether germination strategy moderates the germination responses across 39 species (Chapter 3). This study highlights that when comparing across species, germination strategy moderates the effect of changing climate on germination success such that species with immediate germination strategy that germinate readily after dispersal are less sensitive to changing temperature and winter duration compared to species with dormant seed components (staggered and postponed strategies). Since germination strategy is a significant factor in determining the responses of species to climate change I also examined how within-species variation in germination strategy might affect the adaptability or plasticity of species in response to climate change. I examined the germination strategy variation within-species to specify the climate variables driving variation in germination strategy in wild populations (Chapter 4). I found that within the alpine herb Oreomyrrhis eriopoda, variation in germination strategies is…
Investigating the interplay of intrinsic to extrinsic factors influencing amyotrophic lateral sclerosis disease progression

Amyotrophic lateral sclerosis (ALS) is a relentlessly progressive, neurodegenerative disorder primarily affecting lower motor neurons in the spinal cord and brainstem, and upper motor neurons in the motor cortex. The disorder has a worldwide incidence of 1.7-2.3 per 100,000 population per year, and a prevalence of 4-6 per 100,000 population. The average age of symptom onset is 62 years, the median survival time is 28 months from onset, and the 4-year survival rate is 40%. The disease causes paralysis of the voluntary muscles. ALS is uniformly fatal, and death results from respiratory failure. Riluzole is the only compound approved by the FDA to treat ALS. It extends lifespan by an average of 1-2 months. All of the more than 50 other compounds tested in clinical trials have failed to demonstrate any benefits for patients. The etiology of ALS, especially sporadic ALS (SALS), which comprises approximately 90% of total cases, remains largely unknown. Improved patient outcomes depend on understanding the pathways responsible for disease, and uncovering novel targets for future therapies. The pathogenesis of ALS begins before a diagnosis can be made in the clinic. Significant motor neuron loss occurs prior to the discernable onset of symptoms. Ideally, research would be able to pinpoint the precise temporal and spatial progression of pathophysiological processes underlying ALS, close to their initiating events. However, this is difficult at present. Many experimental models of ALS exist, which should theoretically permit detailed investigation of ALS pathogenesis. However, other than riluzole, no compound with efficacy in pre-clinical models has had measurable clinical benefits, highlighting differences between animal and human biology as well as the importance of translational research. Given the difficulties in analyzing the events precipitating ALS, analysis of the ongoing processes influencing disease progression becomes an important strategy to elucidate disease mechanisms and pinpoint novel drug targets.
Mechanisms of Smaug-mediated Post-transcriptional Regulation in the Early Drosophila Embryo

Post-transcriptional regulation of gene expression can be mediated by cis acting elements within mRNAs that are recognized by RNA binding proteins that control mRNA expression. Smaug is a highly conserved sequence specific RNA-binding protein that is essential for early Drosophila development. Smaug binds to well defined cis elements in target mRNAs and uses protein-protein interactions to recruit additional factors that regulate the bound mRNA. In this thesis I will describe my efforts to identify novel Smaug binding proteins to better understand the mechanisms of Smaug-mediated control. My efforts identified several Smaug binding partners including RNA helicases CG7878 and CG10077; Not1, a component of the CCR4/NOT deadenylase; and the miRISC component Argonaute 1. My work and the work of others suggests that CG7878 along with other RNA helicases could function with Smaug to regulate target transcripts. My identification of the Smaug/Not1 interaction was the basis for the discovery that Smaug induces transcript decay through recruitment of the CCR4/Not deadenylase complex. Finally, I employed both in vitro and in vivo experiments to show that Smaug can directly recruit Argonaute 1 to a target mRNA to repress its translation and that this recruitment does not require a miRNA. Argonaute 1’s interaction with the target mRNA requires the Dop kinase suggesting
The Clinical Applications of Serum and Urinary Biomarkers in Prostate Cancer

At every stage of the prostate cancer journey from screening and diagnosis to management of advanced disease, patients and clinicians face dilemmas and decisions that can impact long-term outcomes. Although traditional risk stratification in prostate cancer is based on serum prostate specific antigen, clinical stage and Gleason score, in recent years, biomarkers have been developed that may be useful in several clinical scenarios. Biomarkers that can accurately predict an individual patient’s risk, prognosis, and response to specific treatments could lead to improvements in decision-making and clinical care. Although there is evidence to support the use of biomarkers to guide management decisions, the optimal scenario in which to use them, how to interpret the results, and how to incorporate those results into clinical decision-making can be confusing. Nevertheless, in the era of personalized and precision medicine, it is important for clinicians to be aware of what tests are available, what clinical questions they seek to answer, and what limitations they have. This review focuses on the serum and urine biomarkers for the management of prostate cancer that have been under intense investigation in recent years.
Probing the ultrafast electron and lattice dynamics of gold using femtosecond mid-infrared pulses

We study the ultrafast electron and lattice dynamics of thin gold films with mid-infrared transmission and reflection pump-probe spectroscopy. We determine the time dependence of the dielectric function, which yields the electron-phonon coupling constant G that determines the energy exchange rate between the electrons and the lattice. From the experimentally obtained dielectric function, we determine the dependence of the electron-electron and the electron-lattice scattering rates on the electron and the lattice temperature.
Reasons for refusing parenteral therapy: a qualitative study of patients with pulmonary arterial hypertension

While parenteral prostacyclin (pPCY) therapy, delivered either subcutaneously or intravenously, is recommended for pulmonary arterial hypertension patients with severe or rapidly developing disease, some patients refuse this treatment. This study aimed to understand, directly from patients with pulmonary arterial hypertension, why pPCY was refused and, in some cases, later accepted. Interviews were conducted with 25 pulmonary arterial hypertension patients who previously refused pPCY therapy (Group A: Refused/Never initiated (n = 9) and Group B: Refused/Initiated (n = 16)). Patients in both groups believed that pPCY could improve their symptoms, slow disease progression, and provide them a greater ability to perform activities. Reasons for refusal included concern over side effects and the perceived limitations of pPCY on daily activities. Group A perceived their decision as a balance between quality of life and prolonging life and most acknowledged they would reconsider pPCY if other treatment options were exhausted. Group B cited they initiated therapy due to a worsening of symptoms, disease progression, to improve quality of life, to be there for their family, or a desire to live. Following initiation, Group B indicated their experience met expectations with reduced symptoms, slowed disease progression, and perception of improved survival; concerns related to pPCY were described as manageable. Given the efficacy of pPCY therapy, clinicians should apply knowledge of these findings in clinical practice. Patients noted improvements to parenteral pump technologies to include smaller size, water resistance, and implantability may increase their acceptance of this modality. Development efforts should focus on technologies that increase the acceptance of pPCY when indicated.
Awareness of Medical Applications of Ozonated Water Therapy Among Dental Students

Ozone (O3) happens to be a triple atomic particle that comprises three oxygen iotas with an atomic load of 47.98 g/mol. Ozone is a thermokinetic coseismal particle which, contingent upon framework conditions like temperature and weight, has a short half-life and breaks down into sub-atomic oxygen (O2). Ozone is utilized asmedication inmany conditions. The study aimed to assess the awareness of medical applications of ozonated water therapy among dental students. A cross sectional study was done with a self-administered questionnaire with 10 questions circulated among 100 dental students. The questionnaire assessed the awareness about ozonewater therapy inmedical applications, their medicinal uses, antiin lammatory activity, mechanism of action and side effects. The responses were recorded and analysed.87% of the respondents were not aware of medical uses of Ozone water therapy . 73% were not aware of antiin lammatory activity of Ozone water therapy.83 % were not aware of themechanism of action of Ozonewater therapy . 85%were not aware of side effects of Ozonewater therapy. The awareness about the use of Ozone water therapy in medical applications is very less among dental students. Increased awareness programs and sensitization and continuing dental education programs along with greater importance to the curricular modi ications should be incorporated to improve the awareness levels.
Simple Sequence Repeat Markers Reveal Genetic Diversity Within and among Landrace Collections of Citron and Dessert Watermelon from South Africa

A BSTRACT . Genetic diversity analysis is fundamental for effective breeding and genetic conservation. The objective of this study was to determine the genetic diversity present among dessert watermelon ( Citrullus lanatus var. lanatus ) and citron watermelon ( C. lanatus var. citroides ) landraces widely grown in South Africa and to select genetically diverse and complimentary genotypes for strategic breeding or conservation. Thirty-one dessert watermelon and 34 citron watermelon landraces were genotyped using 10 polymorphic simple sequence repeat markers. The number of alleles detected per marker ranged from 2 to 23 alleles, with a mean of 13.5 alleles. A total of 135 putative alleles were ampliﬁed from sampled watermelon populations. Number of effective alleles ranged from 1.99 to 10.88 alleles with a mean of 5.83 alleles. The mean observed and expected heterozygosity were 0.50 and 0.79, respectively. The mean polymorphic information content was 0.79. Cluster and principal coordinate analyses grouped the two watermelon populations into two separate clusters. The two populations were genetically differentiated with low gene ﬂow, suggesting the presence of high genetic differences between the two populations. Overall, the study established the existence of considerable genetic diversity among South African grown dessert and citron watermelon landraces. Unique dessert watermelon landraces such as SWM-39, SWM-24, SWM-01, SWM-40, SWM-18, SWM-36, and SWM-26; and citron watermelon genotypes including WWM-24, WWM-37, WWM-28, WWM-34, WWM-02, WWM-22, WWM-50, and WWM-36 were selected based on their high dissimilarity index. These could be useful for breeding and systematic conservation.
Amniote Dental Histology, Development, and Variation: Perspectives From the Fossil Record

Fossil teeth provide a wealth of taxonomic and dietary information for palaeontologists, but the evolution and development of the suite of tissues that attach teeth to the jaws in amniotes remain virtually undocumented. This contrasts strongly with the plethora of studies that have documented the development of the tooth attachment tissues (the periodontium) in modern mammals and crocodilians. The literary consensus is that mammals and crocodilians possess the most complex forms of tooth attachment, because each tooth is housed within a well-defined tooth socket and is suspended by a soft ligament. By comparison, nearly all other amniotes supposedly possess teeth that are fused to the jaws by a single bone tissue. To date, however, the homologues of the dental attachment tissues across Amniota remain unresolved. This thesis represents the first large-scale, comparative study of amniote tooth histology and development. By comparing histological sections of a large sample of modern and extinct amniotes, I establish tooth tissue homology across several major amniote groups and show that even
Changes in the experience of time: The impact of spatial information on the perception and memory of duration

Although it is understood that our experience of time is fluid and subjective, the cognitive mechanisms underlying this phenomenon are not well described. Based on event segmentation theory, we tested the hypothesis that changes in the context, particularly the spatial context, of an experience impact how an individual perceives (encodes) and remembers the length of that event. A group of participants viewed short videos of scenes from movies that either contained shifts in spatial context (e.g., characters moving through doorways) or did not contain any shifts in spatial context. In one task, participants estimated a randomly selected time duration (between 10 and 23 s) when encoding these videos. In a second task, the same participants estimated the duration of the videos after viewing them. We found that even though the presence of spatial shifts impacted how time was perceived, the nature of this effect differed as a function of task. Specifically, when time was estimated at encoding, these estimates were longer for videos that did not contain spatial shifts compared with those with spatial shifts. However, when these estimates were made at retrieval, durations were reported as longer for videos with spatial context shifts than those without. A second experiment replicated these main findings in a new sample. We interpret these results as providing new evidence for theories on how context changes, particularly those in spatial information, distort the experience of time differently during the encoding and retrieval phases of memory.
Single-Fed Broadband CP Bidirectional Antenna with Double-Layer Diagonally Aligned Plates for Universal UHF-RFID Applications

This research proposes a single-fed broadband circularly polarized (CP) bidirectional antenna operable in 840–960 MHz frequency band for readers of universal UHF-RFID applications. The proposed antenna is comprised of upper-layer conductor, lower-layer conductor, and wall patches. The upper-layer conductor consists of two diagonally aligned rectangular copper plates with a feeding gap at the center, and the lower-layer conductor is of two diagonally adjoined rectangular plates. The upper- and lower-layer conductors are adjoined with the wall patches. The diagonal alignment technique of the upper- and lower-layer plates was used to realize circular polarization and improve 3-dB axial ratio (AR) bandwidth. The double layers were deployed to improve impedance bandwidth (|S11| < −10 dB) and achieve bidirectional radiation pattern. The simulated impedance bandwidth and 3-dB AR bandwidth were 772.19–1014.6 MHz (27.13%) and 675–1000 MHz (38.80%), and the corresponding measured results were 759–1011 MHz (28.47%) and 648–1110 MHz (52.55%). The simulated LHCP/RHCP half-power beamwidth (HPBW), 3-dB AR beamwidth, and gain were 56° – 90°/54° – 92°, 60° – 104°, and 4.94 – 5.89 dBic, while the corresponding measured results were 52° – 98°/62° – 97°, 96° – 126°, and 4.28 – 5.72 dBic. As a result, the single-fed broadband CP bidirectional antenna is applicable to universal UHF-RFID readers. Besides, the novelty of this research lies in the use of diagonal alignment of conducting plates to achieve circular polarization and wider AR bandwidth.
Investigation of pathophysiology and therapeutic strategies in PMM2-CDG model zebrafish

Congenital Disorder of Glycosylation PMM2-CDG results from mutations in PMM2, which encodes the phosphomannomutase that converts mannose-6-P to mannose-1P. Patients have wide-spectrum clinical abnormalities associated with impaired protein Nglycosylation. Though widely proposed that PMM2 deficiency depletes mannose-1-P, a precursor of GDP-mannose, and consequently suppresses lipid-linked oligosaccharide (LLO) levels needed for N-glycosylation, these deficiencies have not been demonstrated in patients or any animal model. In order to explore the developmental and biochemical consequences of PMM2 deficiency, we generated and characterized a morpholino-based PMM2-CDG model in zebrafish. Morphant embryos had developmental abnormalities consistent with PMM2-CDG patients, including craniofacial defects and impaired motility associated with altered motor neurogenesis within the spinal cord. Significantly, global Nlinked glycosylation and LLO levels were reduced in pmm2 morphants. Although insufficient to reduce mannose-1-P and GDP-mannose levels, Pmm2 depletion unexpectedly caused accumulation of mannose-6-P, shown earlier to promote LLO cleavage in vitro. In pmm2 morphants, the free glycan by-products of LLO cleavage increased nearly two-fold. Suppression of the mannose-6-P synthesizing enzyme, mannose phosphate isomerase, within the pmm2 background normalized mannose-6-P levels and certain aspects of the craniofacial phenotype, and abrogated pmm2-dependent LLO cleavage. Overexpression of pmm1 mRNA, a homologous enzyme to PMM2, within the pmm2 background not only increased phosphomannomutase activity, but also corrected abnormal phenotypes and deficient glycosylation profiles noted in pmm2 morphants. In summary, we employed the first zebrafish model of PMM2-CDG to uncover novel cellular insights not possible with other systems, including a mannose-6-P accumulation mechanism for under-glycosylation. INDEX WORDS: N-linked glycosylation, lipid-linked oligosaccharide, free oligosaccharide, mannose-6-phosphate, zebrafish, Congenital Disorders of Glycosylation, phosphomannomutase 2, phosphomannomutase1, mannophosphoisomerase, Fluorophore Assisted Carbohydrate Electrophoresis INVESTIGATION OF PATHOPHYSIOLOGY AND THERAPEUTIC STRATEGIES IN PMM2-CDG MODEL ZEBRAFISH