Miracle-dz/UniFAR-FTUs huggingface dataset:
Design of block transceivers with MMSE decision feedback detection

This paper presents a method for jointly designing the transmitter-receiver pair in a block-by-block transmission system that employs minimum mean square error intra-block decision feedback detection. We provide a recursive closed-form expression for a transceiver which maximizes the Gaussian mutual information and also minimizes the bit error rate at moderate-to-high signal-to-noise ratios (in the absence of error propagation). The proposed design generates uncorrelated inputs to the decision device with equal signal-to-interference-and-noise ratios. These properties suggest that one can approach the capacity of the block transmission system using (independent instances of) the same (Gaussian) code for each element of the block. Our simulation studies indicate that the proposed transceiver performs significantly better than standard transceivers, and that it retains its performance advantages in the presence of error propagation.
In‐Situ Sonication for Enhanced Recovery of Aquifer Microbial Communities

Sampling methods for characterization of microbial communities in aquifers should target both suspended and attached microorganisms (biofilms). We investigated the effectiveness and reproducibility of low‐frequency (200 Hz) sonication pulses on improving extraction efficiency and quality of microorganisms from a petroleum‐contaminated aquifer in Studen (Switzerland). Sonication pulses at different power levels (0.65, 0.9, and 1.1 kW) were applied to three different groundwater monitoring wells. Groundwater samples extracted after each pulse were compared with background groundwater samples for cell and adenosine tri‐phosphate concentration. Turbidity values were obtained to assess the release of sediment fines and associated microorganisms. The bacterial community in extracted groundwater samples was analyzed by terminal‐restriction‐fragment‐length polymorphism and compared with communities obtained from background groundwater samples and from sediment cores. Sonication enhanced the extraction efficiency up to 13‐fold, with most of the biomass being associated with the sediment fines extracted with groundwater. Consecutive pulses at constant power were decreasingly effective, while pulses with higher power yielded the best results both in terms of extraction efficiency and quality. Our results indicate that low‐frequency sonication may be a viable and cost‐effective tool to improve the extraction of microorganisms from aquifers, taking advantage of existing groundwater monitoring wells.
A Background Color Scheme for Piper Plots to Spatially Visualize Hydrochemical Patterns

The combination of ternary diagrams of cations and anions with a central diamond graph make the Piper plot very useful in visualizing groundwater chemistry datasets. One of the major drawbacks is that it is hard to link spatial attributes of the dataset to the plot. In this study, we propose a background color scheme of the Piper plot so that spatial representations of these data can be colored according to their location in the Piper plot. The color scheme is chosen to have maximum resolution while still being perceptually uniform. The linking between Piper plot and maps through this color scheme allows the interpretation of the trends and processes deduced from the Piper plot in terms of the location in the aquifer, the geology, and the groundwater flow dynamics. The colored Piper plot is applied to a groundwater quality dataset of the Condamine Alluvium in Queensland, Australia.
Human Papillomavirus vaccination: Immunological and epidemiological studies

This thesis has evaluated the immunological- and epidemiological aspects of human papillomavirus transmission dynamics and its effect on circumcision. Effective prophylactic vaccines are based on type-specific neutralizing antibodies. A major neutralizing epitope is defined by the monoclonal antibody H16.V5. To investigate the importance of this epitope for overall immunogenicity of HPV16, we engineered HPV16 virus-like particles devoid of the H16.V5 epitope by site-directed mutagenesis of 10 non-conserved, surface exposed residues. Removal of the V5-defined epitope had only marginal effect on antigenic reactivity with antibodies in sera from infected subjects, but affected immunogenicity in experimental immunization of mice, with reduced induction of both antibody responses and CTL responses. A serological survey of HPV16 antibody prevalence by age and sex in Sweden was performed and used it as a basis for modeling the optimal vaccination strategies in this population. By the year 2055, vaccination of females starting at age 12 in 2008 was most efficient, estimated to prevent 5.8 million cumulative HPV16 infections. Catch-up programs had a strong additional preventive effect. Vaccination also targeting males increased protective effect by about 4 percent, but had lower preventive effect per vaccination given. Addition of an HPV serosurvey to existing models and data has enabled us to estimate effect of different vaccination strategies, optimised to the HPV epidemiology in our population. The age-dependent seroprevalence of HPV6, 11, 16, 18, and 52 infection was investigated and further used to asses the transmission dynamics in a representative Swedish population. Analyses of age-specific prevalence revealed different patterns for high- and low-risk HPV infections between females and males. Circumcision has been reported to protect against infection with human papillomavirus in men, but results have been inconsistent. We followed males in a birth cohort born in Dunedin, New Zealand from age 3 to 32 years. Circumcision was not found to be protective, with the adjusted odds ratio (95% confidence interval) for HPV6/11/16/18 seropositivity among the circumcised compared with the uncircumcised being 1.4 (0.89-2.2).
A tutoria acadêmica no contexto histórico da educação: [revisão]

Trata-se de artigo de revisao com o objetivo de orientar a construcao de um modelo tutorial para cursos de graduacao. Dessa forma, busca resgatar a evolucao historica das tutorias na educacao desde a Antiguidade ate a atualidade, inserindo-as em diferentes modelos de universidade. A tutoria, concebida como responsabilidade do mestre pelo aluno ate torna-lo independente e capaz de ensinar outros alunos, surgiu junto com a universidade e, no transcurso dos seculos, foi valorizada como qualificadora do processo pedagogico. Na perspectiva atual, considera-se que a tutoria aglutina a formacao humanistica (cuidativa) e a tecnico-cientifica (educativa) numa dimensao hermeneutico-emancipatoria, compativel com a Pedagogia do Cuidado, orientadora de um modelo tutorial em construcao. It deals with a revision article aiming at guiding the building of a tutorial model for undergraduate courses. Thus, it seeks to ransom the historic evolution of tutoring since ancient times until nowadays, inserting itself into different models of the university. Tutoring, conceived as the responsibility of the teacher for the student until he/she is made independent and able to teach other students, has risen at the university and, along the centuries, has been valued as a qualifier of the pedagogical process. In the present perspective, one considers that tutoring also joins the humanistic (caring) shaping and technical-scientific (educational) shaping in a hermeneutic-emancipating dimension, which is compatible with the Care Pedagogy that guides the tutorial world under construction. Se trata de articulo de revision con el objetivo de orientar la construccion de un modelo tutorial para los cursos de grado. Asi, se busca rescatar la evolucion historica de las tutorias en la educacion desde la Antiguedad hasta la actualidad, insertandolas en diferentes modelos de universidad. La tutoria, concebida como responsabilidad del maestro frente al alumno hasta tornarlo independiente y capaz de ensenar a otros alumnos, surgio con la universidad y en el transcurso de los siglos fue valorada como calificadora del proceso pedagogico. En la actual perspectiva, se considera que la tutoria aglutina la formacion humanistica (cuidativa) y la tecnico-cientifica (educativa) en una dimension hermeneutico-emancipatoria, compatible con la Pedagogia del Cuidado, orientadora de un modelo tutorial en construccion.
Delamanid susceptibility testing of Mycobacterium tuberculosis using the resazurin microtitre assay and the BACTEC™ MGIT™ 960 system.

OBJECTIVES The objective of this study was to develop standardized protocols for rapid delamanid drug susceptibility testing (DST) using the colorimetric resazurin microtitre assay (REMA) and semi-automated BACTEC™ MGIT™ 960 system (MGIT) by establishing breakpoints that accurately discriminate between susceptibility and resistance of Mycobacterium tuberculosis to delamanid. METHODS MICs of delamanid were determined by the MGIT, the REMA and the solid agar method for 19 pre-characterized strains. The MIC distribution of delamanid was then established for a panel of clinical strains never exposed to the drug and characterized by different geographical origins and susceptibility patterns. WGS was used to investigate genetic polymorphisms in five genes (ddn, fgd1, fbiA, fbiB and fbiC) involved in intracellular delamanid activation. RESULTS We demonstrated that the REMA and MGIT can both be used for the rapid and accurate determination of delamanid MIC, showing excellent concordance with the solid agar reference method, as well as high reproducibility and repeatability. We propose the tentative breakpoint of 0.125 mg/L for the REMA and MGIT, allowing reliable discrimination between M. tuberculosis susceptible and resistant to delamanid. Stop codon mutations in ddn (Trp-88 → STOP) and fbiA (Lys-250 → STOP) have only been observed in strains resistant to delamanid. CONCLUSIONS We established protocols for DST of delamanid in the MGIT and REMA, confirming their feasibility in routine TB diagnostics, utilizing the same discriminative concentration for both methods. Moreover, taking advantage of WGS analysis, we identified polymorphisms potentially associated with resistance in two genes involved in delamanid activation.
Chemical Reagents for Investigating the Major Groove of DNA

Chemical modification provides an inexpensive and rapid method for characterizing the structure of DNA and its association with drugs and proteins. Numerous conformation‐specific probes are available, but most investigations rely on only the most common and readily available of these. The major groove of DNA is typically characterized by reaction with dimethyl sulfate, diethyl pyrocarbonate, potassium permanganate, osmium tetroxide, and, quite recently, bromide with monoperoxysulfate. This commentary discusses the specificity of these reagents and their applications in protection, interference, and missing contact experiments.
Recent Advances in RNA Structure Determination by NMR

Despite recent advances in the solution of NMR structures of RNA and RNA‐ligand complexes, the rate limiting step remains the gathering of a large number of NOE and torsion restraints. Additional sources of information for structure determination of larger RNA molecules have recently become available, and it is possible to supplement NOE and J‐coupling data with the measurement of dipolar couplings and cross‐correlated relaxation rates in high‐resolution NMR spectroscopy.
Evidence for Elevated Levels of Arsenic in Public Wells of Bangladesh Due To Improper Installation

One of the mainstays of mitigation to reduce the exposure of the rural population of Bangladesh to arsenic (As) from private, mostly <90‐m deep wells over the past 15 years has been the installation of over 300,000 deeper community wells. A comprehensive testing campaign previously conducted across a 180 km2 of area of Bangladesh identified 9 out of total of 927 wells >90 m deep that contained >50 µg/L arsenic. We show here that for five of these nine wells, conductivity profiles obtained after spiking the well bore with salt indicate a shallow leak that could explain the high As in the well water. In two of the five leaky wells, the presence of additional screens at the depth of the leak was documented with a downhole camera. The downhole camera did not detect anomalies in the construction of the remaining three leaky wells or in the four wells that did not leak. The four wells that did not leak were all >150‐m deep and located in two villages separated by less than 500 m. Excluding these two villages and a handful of leaky wells, the results indicate an aquifer that is consistently low in As over a sizeable area at depths >90 m. Isolated cases of public wells that are elevated in As that have been reported elsewhere in Bangladesh may therefore reflect improper installation rather than actual contamination of the deep aquifer.
Crude Oil Metabolites in Groundwater at Two Spill Sites

Two groundwater plumes in north central Minnesota with residual crude oil sources have 20 to 50 mg/L of nonvolatile dissolved organic carbon (NVDOC). These values are over 10 times higher than benzene and two to three times higher than Diesel Range Organics in the same wells. On the basis of previous work, most of the NVDOC consists of partial transformation products from the crude oil. Monitoring data from 1988 to 2015 at one of the sites located near Bemidji, MN show that the plume of metabolites is expanding toward a lakeshore located 335 m from the source zone. Other mass balance studies of the site have demonstrated that the plume expansion is driven by the combined effect of continued presence of the residual crude oil source and depletion of the electron accepting capacity of solid phase iron oxide and hydroxides on the aquifer sediments. These plumes of metabolites are not covered by regulatory monitoring and reporting requirements in Minnesota and other states. Yet, a review of toxicology studies indicates that polar metabolites of crude oil may pose a risk to aquatic and mammalian species. Together the results suggest that at sites where residual sources are present, monitoring of NVDOC may be warranted to evaluate the fates of plumes of hydrocarbon transformation products.
A Coupled Groundwater–Surface Water Modeling Framework for Simulating Transition Zone Processes

There is an identified need for fully representing groundwater–surface water transition zone (i.e., the sediment zone that connects groundwater and surface water) processes in modeling fate and transport of contaminants to assist with management of contaminated sediments. Most existing groundwater and surface water fate and transport models are not dynamically linked and do not consider transition zone processes such as bioturbation and deposition and erosion of sediments. An interface module is developed herein to holistically simulate the fate and transport by coupling two commonly used models, Environmental Fluid Dynamics Code (EFDC) and SEAWAT, to simulate surface water and groundwater hydrodynamics, while providing an enhanced representation of the processes in the transition zone. Transition zone and surface water contaminant processes were represented through an enhanced version of the EFDC model, AQFATE. AQFATE also includes SEDZLJ, a state‐of‐the‐science surface water sediment transport model. The modeling framework was tested on a published test problem and applied to evaluate field‐scale two‐ and three‐dimensional contaminant transport. The model accurately simulated concentrations of salinity from a published test case. For the field‐scale applications, the model showed excellent mass balance closure for the transition zone and provided accurate simulations of all transition zone processes represented in the modeling framework. The model predictions for the two‐dimensional field case were consistent with site‐specific observations of contaminant migration. This modeling framework represents advancement in the simulation of transition zone processes and can help inform risk assessment at sites where contaminant sources from upland areas have the potential to impact sediments and surface water.
Obesity and its determinants in girls from five ethnic groups

In light of alarming rises in the prevalence of obesity worldwide, tackling the obesity ‘epidemic’ is now a national health priority in many countries. Increasingly, population measures that provide accurate estimates of body fatness in children are required. Body mass index (BMI), or weight standardised for height, remains the most costeffective and practical tool in this regard. However, there is evidence that the association between BMI and body fatness is variable in children from different ethnic backgrounds. The primary aim of this thesis was to investigate the appropriateness of BMI thresholds for defining overweight and obesity in female children and adolescents from five diverse ethnic groups. Secondary objectives were to examine the associations between weight control practices and perceptions, and to compare objectively-measured physical activity levels with participation in active transport (AT). In order to achieve the primary aim stated above, it was necessary to obtain valid and reliable measures of body fat percentage (%BF) in a large sample of children. Bioelectrical impedance analysis (BIA) is well suited for this purpose, providing a portable and cost-effective means to estimate fat-free mass (and subsequently %BF). While equations exist for European, Maori, and Pacific Island children, findings from the preliminary study described in Chapter 2 demonstrate that there are no BIA equations appropriate for Chinese and Indian children. Given that these two groups are two of the fastest growing ethnicities in New Zealand, a new equation was developed that enables Asian girls to be included in future BIA research. The main study of this thesis involved a large-scale investigation of body composition in New Zealand’s five major ethnic groups (European, Maori, Pacific Island, East Asian, and South Asian). A total of 1,081 adolescent girls aged 11-16 years participated in the Girls’ Activity and Body Composition (ABC) Study. To extend the age range, data were combined with another study of 5-11-year-old New Zealand children (595 girls), coined the Body-Size and Steps in Children (BASIC) Study. Both studies measured BMI from height and weight, %BF from bioimpedance measurements, and physical activity using sealed multiday memory pedometers over five consecutive days. A questionnaire was
Prospective Interest of Deep Learning for Hydrological Inference

Introduction Decision making relative to groundwater resources requires the characterization, modeling, and prediction of complex and dynamical systems with many degrees of freedom. Nonetheless, these systems have largescale structure that emerges from hierarchical properties based on conservation principles applied to fundamental physical quantities (e.g., mass, momentum and energy). Difficulties arise as hydrologic systems are inherently heterogeneous and sometimes chaotic. This is not specific to hydrology, but it is generic to natural or manmade complex systems. Two approaches have been proposed to handle these complex systems. Whether they are called model-driven or data-driven, explicit or implicit, they differ widely by methodology. In the explicit model-driven approach, processes are physically modeled at each characteristic scale and progressively scaled up. Patterns, equivalent properties, and effective laws emerge progressively through upscaling. This has been performed extensively in stochastic hydrology to derive equivalent permeability and in percolation theory to identify universal scaling laws (Stauffer and Aharony 1992). Large-scale observations are integrated by adapting the model parameters through the classic, but generally ill-posed, inverse problem (Zimmerman et al. 1998). In the implicit data-driven approach, minimal assumptions are made on the structure of the models developed (Hastie et al. 2003; Montgomery 2006). Rather, this approach relies on generic data-driven analysis based on statistics and artificial intelligence. Among numerous
Demystifying Fisher Information: What Observation Data Reveal about Our Models

Information theory is the basis for understanding how information is transmitted as observations. Observation data can be used to compare uncertainty on parameter estimates and predictions between models. Jacobian Information (JI) is quantified as the determinant of the weighted Jacobian (sensitivity) matrix. Fisher Information (FI) is quantified as the determinant of the weighted FI matrix. FI measures the relative disorder of a model (entropy) in a set of models. One‐dimensional models are used to demonstrate the relationship between JI and FI, and the resulting uncertainty on estimated parameter values and model predictions for increasing model complexity, different model structures, different boundary conditions, and over‐fitted models. Greater model complexity results in increased JI accompanied by an increase in parameter and prediction uncertainty. FI generally increases with increasing model complexity unless model error is large. Models with lower FI have a higher level of disorder (increase in entropy) which results in greater uncertainty of parameter estimates and model predictions. A constant‐head boundary constrains the heads in the area near the boundary, reducing sensitivity of simulated equivalents to estimated parameters. JI and FI are lower for this boundary condition as compared to a constant‐outflow boundary in which the heads in the area of the boundary can adjust freely. Complex, over‐fitted models, in which the structure of the model is not supported by the observation dataset, result in lower JI and FI because there is insufficient information to estimate all parameters in the model.
Insights From a Multi‐Method Recharge Estimation Comparison Study

Although most recharge estimation studies apply multiple methods to identify the possible range in recharge values, many do not distinguish clearly enough between inherent uncertainty of the methods and other factors affecting the results. We investigated the additional value that can be gained from multi‐method recharge studies through insights into hydrogeological understanding, in addition to characterizing uncertainty. Nine separate groundwater recharge estimation methods, with a total of 17 variations, were applied at a shallow aquifer in northwest Ethiopia in the context of the potential for shallow groundwater resource development. These gave a wide range of recharge values from 45 to 814 mm/a. Critical assessment indicated that the results depended on what the recharge represents (actual, potential, minimum recharge or change in aquifer storage), and spatial and temporal scales, as well as uncertainties from application of each method. Important insights into the hydrogeological system were gained from this detailed analysis, which also confirmed that the range of values for actual recharge was reduced to around 280‐430 mm/a. This study demonstrates that even when assumptions behind methods are violated, as they often are to some degree especially when data are limited, valuable insights into the hydrogeological system can be gained from application of multiple methods.