Miracle-dz/UniFAR-FTUs huggingface dataset:
Nonlinear Dynamical Systems Modelling for Environmental Sustainability

Increasing global human population coupled with the climate change pose serious threats on the basic needs of society. The coming decades will witness the challenges associated with the food security, land availability, clean water availability, and energy security. These issues directly or indirectly affect the various components of the Earth’s Critical Zone (ECZ). Our natural resources are finite and hence a policy framework is urgently required to deal with the growing demand in food, clean energy, and water in sustainable ways. This work characterises some key components of the ECZ such as wetlands, through modelling and computational simulation approaches. A data-driven methodology known as the system identification is used to devise a nonlinear dynamic model of the tropical wetlands. The dataset used in the study corresponds to a Global Inundation Extent from Multi-Satellites. The model gives some useful insights about the dynamics of tropical wetlands and the possible effects of climate change on wetlands. The prediction power of this model is shown to be superior than the competing analytical models representing the inundation dynamics. This work also contributes towards the theoretical advancements in the nonlinear system identification method by proposing a new algorithm capable of performing the model structure selection in the NARMAX model class under the Approximate Bayesian Computation (ABC) framework. In addition to the data-driven approach, this thesis also switches to analytical modelling framework for investigating the sustainable ways of food production and climate change mitigation through a Negative Emission Technology (NET) known as enhanced weathering. The recent reports of Intergovernmental Panel on Climate Change have highlighted the need of an NET to meet the ambitious targets of lowering the global temperature. A process-based model representing the enhanced weathering of a mineral is developed and integrated with standard soil, vegetation process models. The integrated model is termed as the Integrated Enhanced Weathering Critical Zone Model, which is used to analyse the potentials of enhanced weathering in the UK conditions. The simulation results indicate that with the implementation of enhanced weathering in the UK farmlands, we can reduce the atmospheric carbon through sequestration as well as increase the crop yield substantially. In another words, food security and climate change mitigation can be addressed simultaneously. In a nutshell, the simulation results and analyses of this thesis can be used to design further experiments for investigating the ECZ processes like inundation dynamics and enhanced weathering. The results can also act as guidelines for framing the relevant policies towards environmental and food sustainability.
Genome sequence of the pink to light reddish-pigmented Rubellimicrobium mesophilum type strain (DSM 19309T), a representative of the Roseobacter group isolated from soil, and emended description of the species

Rubellimicrobium mesophilum Dastager et al. 2008 is a mesophilic and light reddish-pigmented representative of the Roseobacter group within the alphaproteobacterial family Rhodobacteraceae. Representatives of the Roseobacter group play an important role in the marine biogeochemical cycles and were found in a broad variety of marine environments associated with algal blooms, different kinds of sediments, and surfaces of invertebrates and vertebrates. Roseobacters were shown to be widely distributed, especially within the total bacterial community found in coastal waters, as well as in mixed water layers of the open ocean. Here we describe the features of R. mesophilum strain MSL-20T together with its genome sequence and annotation generated from a culture of DSM 19309T. The 4,927,676 bp genome sequence consists of one chromosome and probably one extrachromosomal element. It contains 5,082 protein-coding genes and 56 RNA genes. As previously reported, the G+C content is significantly different from the actual genome sequence-based G+C content and as the type strain tests positively for oxidase, the species description is emended accordingly. The genome was sequenced as part of the activities of the Transregional Collaborative Research Centre 51 (TRR51) funded by the German Research Foundation (DFG).
Financial Intermediary Capital

We propose a dynamic theory of financial intermediaries that are better able to collateralize claims than households, that is, have a collateralization advantage. Intermediaries require capital as they can borrow against their loans only to the extent that households themselves can collateralize the assets backing these loans. The net worth of financial intermediaries and the corporate sector are both state variables affecting the spread between intermediated and direct finance and the dynamics of real economic activity, such as investment, and financing. The accumulation of net worth of intermediaries is slow relative to that of the corporate sector. The model is consistent with key stylized facts about macroeconomic downturns associated with a credit crunch, namely, their severity, their protractedness, and the fact that the severity of the credit crunch itself affects the severity and persistence of downturns. The model captures the tentative and halting nature of recoveries from crises.
Performance analysis on FDE receiver for single carrier transmission

In this paper, single carrier (SC) transmission is considered. We focus on SC frequency domain equalization (FDE) receiver and analyze the signal to noise ratio (SNR) of the time domain output signal estimate and then, derive the achievable bit error rate (BER). For the purpose of comparison, we consider optimal time domain equalization (TDE) receiver as a reference. Our analytical results show the relationship between the FDE and optimal TDE.
Dual-band MEMS Fabry-Pérot filter with two movable reflectors for mid- and long-wave infrared microspectrometers

A tunable dual-band MEMS Fabry-Pérot filter for simultaneous use of the spectral ranges from 8 µm to 10.5 µm and from 4 µm to 5 µm is reported. A peak transmittance of at least 75 % and a FWHM of less than 200 nm were measured. The maximum control voltage is 41 V. Two movable reflector carriers compensate the influence of gravitational force on the central wavelength. The device can withstand mechanical shocks according to Mil-Std-883G, method 2002.4, test condition B. The filter is integrated in a tiny, robust and fast microspectrometer module with the size of a TO-8 housing.
Adaptive Scheduling Framework for Real-Time Video Encoding on Heterogeneous Systems

To challenge real-time encoding of high-definition video sequences on heterogeneous desktop systems, a collaborative central processing units (CPU) + graphics processing unit (GPU) framework for interloop video encoding is proposed herein. The proposed framework considers the overall complexity of the collaborative interloop encoding as a unified optimization problem. Several functional blocks are integrated for simultaneous execution control, automatic data access management, performance characterization, and adaptive scheduling and load balancing. These blocks aim at fully exploiting the performance of heterogeneous devices, asymmetric bandwidth of communication links, and several levels of concurrency between computation and communication. To support a wide range of CPU and GPU architectures, a specific encoding library is developed with highly optimized algorithms for all interloop modules. The experimental results show that the proposed framework allows achieving a real-time encoding of full high-definition sequences in several CPU + GPU systems. It also delivers performance improvements of up to 61.2% over the state-of-the-art solution, while outperforming individual GPU and quad-core CPU executions by more than 2 and 5 times, respectively.
CLIMATE EXTREMES AND PRECIPITATION TRENDS IN KELANI RIVER BASIN, SRI LANKA AND IMPACTS ON STREAMFLOW VARIABILITY UNDER CLIMATE CHANGE

This paper focuses on and analyses the potential hydrological impacts of climate change on the hydrologic regime of Kelani River Basin, Sri Lanka. The basin wide future hydrology is simulated by using downscaled temperature and precipitation outputs from the Canadian Earth System Model Version 2 (CanESM2) and the Hydrologic Engineering Centre’s Hydrologic Modeling System (HEC-HMS). The research further evaluates the long-term behavior and trends of the climate extremes based on the observed historical temperature and precipitation data. The findings suggest that the temperature and precipitation extremes are on the rise while the annual average precipitation in the basin is declining. It is also predicted with the application of statistical downscaling that temperature may rise annually for representative concentration pathways of RCP2.6, RCP4.5 and RCP8.5. A detailed modelling approach is incorporated to Hanwella subwatershed (1799.67 km) of the Kelani River basin to study the subsequent water resource management options required to ensure sustainable development alternatives with the varying streamflow of the Kelani River basin under the effect of the future (2020’s, 2050’s and 2080’s) rainfall and temperature as impending climate change impacts. The paper reviews the current state of the catchment as well as the suitability of applying the GCM’s rather than RCM’s to Sri Lanka to assess this river basin, according to monthly, seasonal and annual variations of the climate data. Further, a quantitative analysis of the change of amount of surface water in the selected river basin with respect to the expected variations in precipitation and temperature is also carried out. The findings of this research and overall outcome will be useful in identifying possible sustainable water management scenarios with best management options and mitigation measures like land use and carbon emission management, etc. in a more meaningful manner in the future. This study will set the baseline for commencing and continuing quantitative studies incorporating the behavior of the basinwide climatology and streamflow variability with the use of GCM’s to achieve sustainable development goals.
The Adaptive Significance of Natural Genetic Variation in the DNA Damage Response of Drosophila melanogaster

Despite decades of work, our understanding of the distribution of fitness effects of segregating genetic variants in natural populations remains largely incomplete. One form of selection that can maintain genetic variation is spatially varying selection, such as that leading to latitudinal clines. While the introduction of population genomic approaches to understanding spatially varying selection has generated much excitement, little successful effort has been devoted to moving beyond genome scans for selection to experimental analysis of the relevant biology and the development of experimentally motivated hypotheses regarding the agents of selection; it remains an interesting question as to whether the vast majority of population genomic work will lead to satisfying biological insights. Here, motivated by population genomic results, we investigate how spatially varying selection in the genetic model system, Drosophila melanogaster, has led to genetic differences between populations in several components of the DNA damage response. UVB incidence, which is negatively correlated with latitude, is an important agent of DNA damage. We show that sensitivity of early embryos to UVB exposure is strongly correlated with latitude such that low latitude populations show much lower sensitivity to UVB. We then show that lines with lower embryo UVB sensitivity also exhibit increased capacity for repair of damaged sperm DNA by the oocyte. A comparison of the early embryo transcriptome in high and low latitude embryos provides evidence that one mechanism of adaptive DNA repair differences between populations is the greater abundance of DNA repair transcripts in the eggs of low latitude females. Finally, we use population genomic comparisons of high and low latitude samples to reveal evidence that multiple components of the DNA damage response and both coding and non-coding variation likely contribute to adaptive differences in DNA repair between populations.
Catheter-related Blood Stream Infection in Patients Receiving Long-term Home Parenteral Nutrition: Tertiary Care Hospital Experience in Saudi Arabia

Background/Aim: Parenteral nutrition (PN) is a lifesaving therapy for patients with many severe conditions, including intestinal failure. Some patients require long-term PN therapy, which makes home parenteral nutrition (HPN) an attractive option to improve the quality of life. Among the most common and serious complications observed in these patients are catheter-related blood stream infections (CRBSIs). The aim of our study is to determine the frequency of CRBSI among patients receiving long-term HPN. Patients and Methods: A retrospective chart review was conducted for patients enrolled in the HPN program between 2006 and 2012. Data on the demographic characteristics, indications and duration of PN therapy, catheter type, number of admissions because of CRBSI, and blood culture results were recorded. Results: Eight pediatric patients were included (mean age of 3.5 years at the start of HPN). Microvillus inclusive disease was noted in 50% of these patients, and 75% of them received HPN under parents' care. CRBSI resulted in 60 admissions with a median of 182 days of hospital stay and 74 changes of central venous catheters. The rate of CRBSI was 2.9 per 1000 catheter days. Staphylococcus species were the most prevalent pathogens (32%), followed by Klebsiella pneumoniae (5%). Conclusion: In this small group of HPN patients, the BSI rate was 2.9 infections per 1000 catheter days, and most common causative organisms were Staphylococcus species. We believe that a well-established training program for caregivers can reduce the rate of infectious complications associated with long-term PN support.
Keratin K18 Increases Cystic Fibrosis Transmembrane Conductance Regulator (CFTR) Surface Expression by Binding to Its C-terminal Hydrophobic Patch*

Background: CFTR function is tightly regulated by many interacting proteins. Results: Intermediate filament protein keratin 18 increases the cell surface expression of CFTR by interacting with the C-terminal hydrophobic patch of CFTR. Conclusion: K18 controls the function of CFTR. Significance: These findings offer novel insights into the regulation of CFTR and suggest that K18 and its dimerization partner, K8, may be modifier genes in cystic fibrosis. Malfunction of the cystic fibrosis transmembrane conductance regulator (CFTR) leads to cystic fibrosis, but the regulation of CFTR is not fully understood. Here, we identified the intermediate filament protein keratin K18 (K18) as a CFTR-binding protein by various approaches. We mapped a highly conserved “hydrophobic patch” (1413FLVI1416) in the CFTR C-terminus, known to determine plasmalemmal CFTR stability, as the K18-binding site. On the other hand, the C-terminal tail of K18 was found to be a critical determinant for binding CFTR. Overexpression of K18 in cells robustly increased the surface expression of wild-type CFTR, whereas depletion of K18 through RNA interference specifically diminished it. K18 binding increased the surface expression of CFTR by accelerating its apical recycling rate without altering CFTR biosynthesis, maturation, or internalization. Importantly, CFTR surface expression was markedly reduced in duodenal and gallbladder epithelia of K18−/− mice. Taken together, our results suggest that K18 increases the cell surface expression of CFTR by interacting with the CFTR C-terminal hydrophobic patch. These findings offer novel insights into the regulation of CFTR and suggest that K18 and its dimerization partner, K8, may be modifier genes in cystic fibrosis.
Limited Carbonate Dissolution by Boring Microflora at Two Volcanically Acidified Temperate Sites: Ischia (Italy, Mediterranean Sea) and Faial (Azores, NE Atlantic Ocean)

In situ effects of ocean acidification on carbonate dissolution by microboring flora, also called biogenic dissolution, have only been studied once in tropical environments. Naturally acidified seawaters due to CO2 vents offer a perfect setting to study these effects in temperate systems. Three sites were selected at Ischia (Italy, Mediterranean Sea) with one experiencing ambient pH and the two others a mean pHT of 7.2 and 7.5. At Faial (Azores, NE Atlantic), one site with ambient pH and one acidified site with a mean pHT of 7.4 were selected. Experiments were carried out during 1.5 months and 6 months in Azores and Ischia, respectively, to determine the effects of OA on microboring communities in various carbonate substrates. Low pH influenced negatively boring microflora development by limiting their depth of penetration and abundance in substrates. Biogenic dissolution was thus reduced by a factor 3 to 7 depending on sites and substrate types. At sites with ambient pH in Faial, biogenic dissolution contributed up to 23% to the total weight loss, while it contributed less than 1% to the total weight loss of substrates at the acidified sites. Most of the dissolution at these sites was due to chemical dissolution (often Ω ≤ 1). Such conditions maintained microboring communities at a pioneer stage with a limited depth of penetration in substrates. Our results, together with previous findings that showed an increase of biogenic dissolution at pH > 7.7, suggest that there is a pH tipping point below which microborer development and thus carbonate biogenic dissolution is strongly limited.
Pathogenic triad in COPD: oxidative stress, protease–antiprotease imbalance, and inflammation

Patients with chronic obstructive pulmonary disease (COPD) exhibit dominant features of chronic bronchitis, emphysema, and/or asthma, with a common phenotype of airflow obstruction. COPD pulmonary physiology reflects the sum of pathological changes in COPD, which can occur in large central airways, small peripheral airways, and the lung parenchyma. Quantitative or high-resolution computed tomography is used as a surrogate measure for assessment of disease progression. Different biological or molecular markers have been reported that reflect the mechanistic or pathogenic triad of inflammation, proteases, and oxidants and correspond to the different aspects of COPD histopathology. Similar to the pathogenic triad markers, genetic variations or polymorphisms have also been linked to COPD-associated inflammation, protease–antiprotease imbalance, and oxidative stress. Furthermore, in recent years, there have been reports identifying aging-associated mechanistic markers as downstream consequences of the pathogenic triad in the lungs from COPD patients. For this review, the authors have limited their discussion to a review of mechanistic markers and genetic variations and their association with COPD histopathology and disease status.
Mefloquine for preventing malaria in non-immune adult travellers.

BACKGROUND Mefloquine is a commonly prescribed antimalarial drug which has now largely replaced earlier malaria chemoprophylaxis, since increasing parasite resistance has meant that these earlier drugs are no longer considered to be effective against all Plasmodium species. However mefloquine may be associated with neuropsychiatric harmful effects. OBJECTIVES The objective of this review was to assess the effects of mefloquine in adult travellers. SEARCH STRATEGY We searched the Cochrane Infectious Diseases Group trials register, MEDLINE, EMBASE, Lilacs, Science Citation Index and reference lists of articles. We contacted researchers in the subject of malaria chemoprophylaxis, and drug companies. SELECTION CRITERIA Randomised trials comparing mefloquine with other standard prophylaxis or placebo in non-immune adult travellers, and in non-travelling volunteers. We compiled and included in the review a database of published case reports of mefloquine adverse effects. DATA COLLECTION AND ANALYSIS We independently assessed trial quality and extracted data. We also contacted study authors. MAIN RESULTS We included 10 trials involving 2750 non-immune adult participants. Five of these were field trials, and of these all were in soldiers. One trial comparing mefloquine with placebo showed mefloquine prevented malaria episodes in an area of drug resistance (odds ratio 0.04, 95% confidence interval 0.02 to 0.08). Withdrawals in the mefloquine group were consistently higher in four placebo controlled trials (odds ratio 3.56, 95% confidence interval 1.67 to 7.60). In five trials comparing mefloquine with other chemoprophylaxis, no difference in tolerability was detected. We found 519 published case reports of mefloquine adverse effects. 71 per cent of these published reports involved tourists and business travellers. REVIEWER'S CONCLUSIONS Mefloquine prevents malaria, but there is not enough evidence to evaluate its tolerability in non-military travellers. There is evidence from non-randomised studies that mefloquine is a potentially harmful drug for tourists and business travellers, needing more careful evaluation. A randomised tolerability study is urgently needed in these groups.
Prevalence and treatment of Alopecia areata in Taif area, KSA

Background: Alopecia areata (AA) is one type of hair loss that typically causes patches of baldness. In some cases, total baldness develops. There are no adequate studies concerning AA on the Taif area residents, KSA. Aim: The present study conducted for the first time prevalence, causes and treatment of AA in Al-Taif area, KSA. Materials and Methods: A questionnaire employed to determine the prevalence of AA in patients attending dermatology clinics in Al-Taif area. The doctors questioned about the number of patients attend dermatology clinics and suffering from AA. Doctors also were asked about types, causes of AA and the treatment/responsiveness. The data collected and analysed statistically. Results: The obtained results showed a noticeable prevalence of AA in Al-Taif area; 6.750% in males and 6.375% in females. Localized AA was the most common (88.75%) as well as the most responsive to the treatment. The emergence of disease was mostly related to the immune system (85%). The Doctors preferred topical corticosteroids or minoxidil plus systemic vitamins and minerals treatment more than others due to its effectiveness (90%, 40% responsiveness in localized and diffused respectively). Conclusion: We concluded that, the incidence of AA disease in Al-Taif area, exceeded expectations and the autoimmune condition is the most predominance reason for its occurrence. The most effective treatment was topical corticosteroids plus systemic vitamins and minerals. Recommendations: We recommend a vitamin-rich diet as well as an increased emphasis on the use of topical rubefacient herbs in addition to the above mentioned treatments of AA.