Miracle-dz/UniFAR-FTUs huggingface dataset:
Investigating the Nature of the Interaction between the Inner Membrane Quinol Dehydrogenase CymA and the Periplasmic Fumarate Reductase FccA of Shewanella oneidensis MR-1

Shewanella oneidensis exhibits a diverse respiratory system, able to use over 20 terminal electron acceptors, including solid metal oxides. CymA is located in the inner membrane, facing the periplasmic space, and it is responsible for the re-oxidation of the quinol/quinone pool. A plethora of proteins re-oxidise CymA, such as the periplasmic fumarate reductase FccA. This thesis investigates the nature of the interaction between CymA and FccA with a variety of biochemical and biophysical techniques. Chapter 3 describes a new approach in purifying recombinant form of CymA as a pure monodispersed solution that was developed with the reconstruction of the expression vector. The purity was >90% with a yield of 2 mg L-1 of culture. The biochemical and electrocatalytic properties of the recombinant CymA remained unaltered. Chapter 4 presents for the first time the purification of a soluble version of CymA, CymAsol [CymA-Δ(1-31)], at >95% purity, but with a lower yield of 0.3 mg L-1 of culture due to limitations from the TEV proteolytic cleavage reaction for tag removal. Nonetheless, the first crystallisation attempt was achieved with CymAsol. In total, 2,016 conditions were assayed, from which PEG 3350 seemed to promote atypical protein precipitation, although no crystals were formed. Chapter 5 presents a systematic investigation of the CymA: FccA interaction, where no strong interaction was observed with cyclic voltammetry using a CymA-containing tethered bilayer lipid membrane system, or with QCM-D using a CymA-containing solid supported bilayer lipid membrane system. Dissolved oxygen alone was the only condition that replicated the previously published electrocatalytic data under the same system. This was further validated with isothermal titration calorimetry with CymAsol, while, in a separate experiment, it was shown that CymA is necessary for the FccA-specific fumarate reduction in vitro with an initial rate of 3.3 (±0.3, n=3) µM NADH oxidised min-1. Lastly, QCM-D showed that CymAsol binds to a positively charged lipid bilayer, while the MBP-tag of the whole construct binds to a negatively charged lipid bilayer. Thus, the new evidence presented herein points towards a transient nature of weak interaction between CymA and FccA. The contributions of this work are in advancing the understanding of the anaerobic respiratory system of S. oneidensis.
Secondary attachment discs: a new alternative for restoring populations of Chondracanthus chamissoi (Gigartinales, Rhodophyta)

When facing the growing, international demand for the species Chondracanthus chamissoi as a source of carrageenan and for human food consumption, it is very important to generate new aquaculture techniques that allow for its repopulation, maximizing biomass yield whilst reducing the pressures on existing small, natural populations. This paper describes the use of secondary attachment discs (SAD) as a new vegetative propagation technique. It involves the following two stages: i) Tying the tetrasporophytic and cystocarpic fronds to natural substrates (shells and rocks), the conditions generated in the tanks allowed for quick SAD formation (12 days of experimentation), and ii) The maintenance of SAD under normal conditions (at sea for 83 days). The results indicated a quick formation of SAD, a high capacity of persistence (40%), the growth of new apices (4% d -1 ), quick substrate colonization through colonization discs (SADc), and the formation of reproductive structures. As a result, SAD is therefore proposed as both an innovative way to achieve the recovery of the now reduced natural beds of C. chamissoi and as an alternative to traditional methods of vegetative culturing for a species of high commercial interest.
Estimation of Water Quality Parameters with High-Frequency Sensors Data in a Large and Deep Reservoir

High-frequency sensors can monitor water quality with high temporal resolution and without environmental influence. However, sensors for detecting key water quality parameters, such as total nitrogen(TN), total phosphorus(TP), and other water environmental parameters, are either not yet available or have attracted limited usage. By using a large number of high-frequency sensor and manual monitoring data, this study establishes regression equations that measure high-frequency sensor and key water quality parameters through multiple regression analysis. Results show that a high-frequency sensor can quickly and accurately estimate dynamic key water quality parameters by evaluating seven water quality parameters. An evaluation of the flux of four chemical parameters further proves that the multi-parameter sensor can efficiently estimate the key water quality parameters. However, due to the different optical properties and ecological bases of these parameters, the high-frequency sensor shows a better prediction performance for chemical parameters than for physical and biological parameters. Nevertheless, these results indicate that combining high-frequency sensor monitoring with regression equations can provide real-time and accurate water quality information that can meet the needs in water environment management and realize early warning functions.
Directional passive intermodulation effect by distributed nonlinearities in two‐port network

This work demonstrated the directional passive intermodulation (PIM) product distribution effect in a microwave two‐port network using a distributed nonlinear model. The analysis is demonstrated through the comparison of PIM products at the double ends of a general two‐port network by a microstrip line. The reverse and forward PIM products are compared with the nonlinear source distribution and carrier frequency, the model and experiment demonstrates that the directional PIM effect (the difference by reverse and forward PIM) is caused by the PIM accumulation effect from multiple nonlinear sources, what is more, the frequency dependent phase relation can be one reason for the frequency dependent PIM product on wideband transmission line.
Comparative Analysis of Nutritional Sources on the Morpho-Physiological Characteristics of Mung Bean (Vigna radiata)

1Department of Agronomy, University of Agriculture Faisalabad, 38000, Pakistan. 2Plant Physiology Section, Agronomic Research Institute, Ayub Agricultural Research Institute, Faisalabad, Pakistan. 3Department of Biochemistry, University of Agriculture Faisalabad, 38000, Pakistan. 4Department of Plant Breeding and Genetics, Ghazi University, Dera Ghazi Khan, Pakistan. 5Department of Soil Science and Plant Nutrition, Faculty of Agriculture, Tekirdag Namık Kemal University, Suleymanpasa Tekirdag, Turkey. 6Vegetable and Oil Seed Section, Agronomic Research Institute, Faisalabad, Pakistan. 7Department of Botany, University of Agriculture Faisalabad, 38000-Pakistan. 8Department of Plant Pathology, University of Agriculture Faisalabad, 38000, Pakistan.
“They show how smart you are”: a mixed methods study of primary students’ perceptions of assessment tasks

Across the developed world high stakes assessment is routinely used in primary schools and it is essential educators consider how students perceive assessment. This study used a sequential mixed methods design, incorporating the Student Perceptions of Assessment Questionnaire (SPAQ), to examine the perceptions of 82, year five and six students in three Australian primary schools. Significant negative correlations were obtained between students’ self-efficacy and assessment transparency, congruence with planned learning, and authenticity. Paradoxically, students who had the highest levels of self-efficacy had the least confidence in their knowledge of assessment. Boys obtained significantly higher scores when rating assessment congruency and transparency. Focus group data from 13 students highlighted themes related to intrinsic motivation, affirmation of ability/achievement levels, conformity to expectations, and support/feedback for learning. To improve assessment in the primary years it is recommended that educators use authentic tasks and explicitly discuss the purpose of assessment with their students.
Genetic analysis of wild drone congregations of the stingless bee Scaptotrigona mexicana (Hymenoptera: Apidae) reveals a high number of colonies in a natural protected area in Southern Mexico

In this study, drone congregations of the stingless bee Scaptotrigona mexicana Guerin were genetically analyzed at 5 microsatellite loci to estimate the number of colonies of this species in the La Sepultura Biosphere Reserve, in Chiapas, Mexico. A total of 216 drones from 3 congregations were analyzed. We found that the 3 congregations had enough genetic differences to be considered as coming from different populations. The average number (± SD) of colonies per congregation was 19.8 ± 0.63, 17.6 ± 0.70 and 12. A similar result was reported for areas where stingless beekeeping occurs. We discuss the implications of our findings in a conservation framework in which stingless beekeeping might play a significant role.
From Bright Plots to Blind Spots: Mapping Departures in Case Review Post-Bail Reform in Two New Jersey Courts

This study documents the extent to which prosecutors and judges in New Jersey deviate from new case review protocols post-bail reform. We draw on a random sample of hearings observed in two courts (N = 372) to (a) map prosecutorial requests to depart from risk-based recommendations for pretrial monitoring and (b) explore patterns in judicial review signaling more limited case processing. Findings show that in 16% of cases, prosecutors deviated from guidelines and most of these motions were adopted by judges to increase supervision. Deviations from process by judges were more frequent, with 39% of cases observed linked to one or more markers of reduced review. Multivariate results suggest that case-level factors influenced the patterning of these departures in different ways, with older defendants and most Latinx defendants receiving a more limited assessment of their cases. We discuss findings in connection to literature on corrections reform and smart decarceration initiatives.
Two new Helobdella species (Annelida Hirudinida Glossiphoniidae) from the Intermountain region of the United States, formerly considered as Helobdella stagnalis Linnaeus, 1758

Two Helobdella stagnalis-like leech specimens (Annelida Hirudinida Glossiphoniidae) were histologically examined from Nevada in the Great Basin, and from Utah in the Colorado River Basin (USA) to determine whether or not their crops were similar to those in H. californica Kutschera 1988. The Nevada form was brown and with pigmentation patterns, whereas the Utah form was plain and white. The dorsoventral histological sectioning of these 3 specimens showed the Utah and Nevada forms had compact salivary glands, hitherto noted only in the South American Helobdella and Haementaria species. The pharynx of Nevada individuals was S-shaped, and in the Utah form the ejaculatory ducts formed a Gordian knot in the distal-most posterior region, further distinguishing these 2 intermountain Helobdella-isolates. Comparing these two taxa to other published Helobdella internal morphologies, two new species are proposed: Helobdella humboldtensis n. sp. from Nevada (size and pigmentation similar to H. californica) and Helobdella gordiana n. sp. from Utah, which resembles H. stagnalis from Europe. These findings suggest the Intermountain area may be a prime region to study the evolution of members of the Helobdella species complex.
Performance Evaluation of a Direct Absorption Collector for Solar Thermal Energy Conversion

The solar absorption efficiency of water as a base-fluid can be significantly improved by suspending nanoparticles of various materials in it. This experimental work presents the photo thermal performance of water-based nano-fluids of graphene oxide (GO), zinc oxide (ZnO), copper oxide (CuO), and their hybrids under natural solar flux for the first time. Nanofluid samples were prepared by the two-step method and the photothermal performance of these nanofluid samples was conducted under natural solar flux in a particle concentration range from 0.0004 wt % to 0.0012 wt %. The photothermal efficiency of water-based 0.0012 wt % GO nanofluid was 46.6% greater than that of the other nanofluids used. This increased photothermal performance of GO nanofluid was associated with its good stability, high absorptivity, and high thermal conductivity. Thus, pure graphene oxide (GO) based nanofluid is a potential candidate for direct absorption solar collection to be used in different solar thermal energy conversion applications.
The role of digital presence and investment network signals on the internationalisation of small firms

This article proposes a network signalling theory approach to analyse small firm internationalisation in the digital economy. We use a data set of 4446 small- and medium-sized firms extracted from Funderbeam and logit regression models to test five hypotheses about internationalisation. Exploring a firm’s digital presence indicates that the number of social media followers is a better indicator of internationalisation than website traffic, highlighting the importance of engagement signals in the digital space. Investment signals such as the time and size of funding are also positively related to internationalisation but surprisingly, not the number of investors, suggesting that more focused investment strategies work better in the international context. To complement our international network signalling approach, controlling for firm factors such as age and size and environmental factors such as competition and industry provides a more detailed analysis. Our contribution lies in extending signalling theory in the context of international networks using a novel and extensive data set.
Assessment of the impacts of combustion chamber bowl geometry and injection timing on a reactivity controlled compression ignition engine at low and high load conditions

The present paper aims to assess the impacts of diesel injection timing and two bowl geometries including re-entrant and wide-shallow combustion chambers on the combustion characteristics, emissions formation, and fuel consumption in a reactivity controlled compression ignition diesel engine under low and high load (five and nine bar indicating mean effective pressure) conditions. The results revealed that diesel injection at −60 CA ATDC under low load conditions significantly decreased soot and NOx emissions simultaneously for both piston bowl geometries. The use of the wide-shallow chamber decreased the period of the ignition delay and increased the engine operable load range as a result of more stable combustion under high-load conditions compared to the re-entrant chamber. Moreover, at all diesel injection timings, the indicated specific fuel consumption was decreased by nearly 4.8 and 6.6% under low and high load conditions, respectively when the wide-shallow combustion chamber was used since the heat transfer loss was lower than that of the re-entrant chamber. However, NOx emission under high load conditions at the center of the combustion chamber and more soot emission in the exhaust gas are two disadvantages of the wide-shallow chamber versus the re-entrant combustion chamber.
Fish Bioenergetics 4.0: An R-Based Modeling Application

Bioenergetics modeling is a widely used tool in fisheries management and research. Although popular, currently available software (i.e., Fish Bioenergetics 3.0) has not been updated in over 20 years and is incompatible with newer operating systems (i.e., 64-bit). Moreover, since the release of Fish Bioenergetics 3.0 in 1997, the number of published bioenergetics models has increased appreciably from 56 to 105 models representing 73 species. In this article, we provide an overview of Fish Bioenergetics 4.0 (FB4), a newly developed modeling application that consists of a graphical user interface (Shiny by RStudio) combined with a modeling package used in the R computing environment. While including the same capabilities as previous versions, Fish Bioenergetics 4.0 allows for timely updates and bug fixes and can be continuously improved based on feedback from users. In addition, users can add new or modified parameter sets for additional species and formulate and incorporate modifications such as habitat-dep.
The Impact of In-Scanner Head Motion on Structural Connectivity Derived from Diffusion Tensor Imaging

Multiple studies have shown that data quality is a critical confound in the construction of brain networks derived from functional MRI. This problem is particularly relevant for studies of human brain development where important variables (such as participant age) are correlated with data quality. Nevertheless, the impact of head motion on estimates of structural connectivity derived from diffusion tractography methods remains poorly characterized. Here, we evaluated the impact of in-scanner head motion on structural connectivity using a sample of 949 participants (ages 8-23 years old) who passed a rigorous quality assessment protocol for diffusion tensor imaging (DTI) acquired as part of the Philadelphia Neurodevelopmental Cohort. Structural brain networks were constructed for each participant using both deterministic and probabilistic tractography. We hypothesized that subtle variation in head motion would systematically bias estimates of structural connectivity and confound developmental inference, as observed in previous studies of functional connectivity. Even following quality assurance and retrospective correction for head motion, eddy currents, and field distortions, in-scanner head motion significantly impacted the strength of structural connectivity in a consistency-and length-dependent manner. Specifically, increased head motion was associated with reduced estimates of structural connectivity for high-consistency network edges, which included both short-and long-range connections. In contrast, motion inflated estimates of structural connectivity for low-consistency network edges that were primarily shorter-range. Finally, we demonstrate that age-related differences in head motion can both inflate and obscure developmental inferences on structural connectivity. Taken together, these data delineate the systematic impact of head motion on structural connectivity, and provide a critical context for identifying motion-related confounds in studies of structural brain network development.
Functional determinants of enhanced and depressed inter-areal information flow in NREM sleep between neuronal ensembles in rat cortex and hippocampus

Compared to wakefulness, neuronal activity during non-REM sleep is characterized by a decreased ability to integrate information, but also by the re-emergence of task-related information patterns. To investigate the mechanisms underlying these seemingly opposing phenomena, we measured directed information flow by computing transfer entropy between neuronal spiking activity in three cortical regions and the hippocampus of rats across brain states. State-dependent information flow resulted to be jointly determined by the anatomical distance between neurons and by their functional specialization. We distinguished two regimes, operating at short and long time scales, respectively. From wakefulness to non-REM sleep, transfer entropy at short time scales increased for inter-areal connections between neurons showing behavioral task correlates. Conversely, transfer entropy at long time scales became stronger between non-task modulated neurons and weaker between task- modulated neurons. These results may explain how, during non-REM sleep, a global inter-areal disconnection is compatible with highly specific task-related information transfer. Author Summary The brain remains active during deep sleep, yet we still do not know which rules govern information processing between neurons across wakefulness and sleep. Here we provide a first study of how information flow at the level of spiking activity varies as a function of brain state, temporal scale, brain area and behavioral task correlates of single neurons. We found that inter-areal communication at millisecond time scales is enhanced during sleep compared to wakefulness between neurons that code for task information. Conversely, non-modulated neurons showed more prominent communication at longer time scales. These results indicate that multiple, functionally determined communicative architectures coexist in the brain, and provide a novel framework to understand information processing and its consequences during sleep.
Assessing Significant Factors Affecting Risky Riding Behaviors of Motorcyclists

This study was conducted in Malaysia, where motorcycle traffic accidents represent a high percentage of fatality among overall traffic accidents. Studies have shown that risk perception and positive outcome of risky riding behavior have a significant impact on a rider’s decision making. Therefore, this study is targeted at further understanding of Malaysian motorcyclists within the locality of their home country. A questionnaire survey was conducted to gather motorcycle rider’s information, together with their perception of the three factors mentioned above. A reliability test of the findings was analyzed using Cronbach’s Alpha, while a PCA analysis was conducted to determine the linear combinations that have maximum variance. Subsequently, a statistical model was constructed based on the latent variables’ relations, the relation between the latent variables and observed variables, and also the hypothesis model. The model confirms that the positive affect of the risky behavior has a significant positive relationship with motorcyclists’ risk behavior (estimate coefficient = 1.016). Findings in the model also show that older motorcyclists are less likely to take part in risky riding behavior while riding on the road, with an estimate coefficient of −0.037 and a negative relationship with positive affect (estimate coefficient = −0.032).
Health-related quality of life in children and adolescents with sickle cell disease

To assess the health-related quality of life of children and adolescents with sickle cell disease (SCD). This is a cross-sectional study carried out with 97 male and female patients aged 5 to 18 years with clinical and laboratory diagnosis of SCD, seen at the Hematology and Hemotherapy Hospital of Pernambuco. The Pediatric Quality of Life InventoryTM questionnaires, version 4.0 – child/adolescent report – were applied. Most patients were female (76.3%), had sickle cell anemia (89.7%) and mixed race (59.8%). There was a significant association in the psychosocial domain between age groups 5 to 7 (72.10) and 8 to 12 years (p≤0.05), the latter of which had the worst quality of life score (65.36). There were significant differences between sexes only in patients aged 13 to 18 years for physical functioning and for the overall mean of the domains. The means in both cases were higher in female patients than in male ones (70.89 x 56.88 for physical functioning and 71.72 x 59.77 for the overall mean of the domains). Poor quality of life was observed among children and adolescents with SCD, with negative impacts according to age and sex.