Miracle-dz/UniFAR-FTUs huggingface dataset:
Exploiting Differences in Heme Biosynthesis between Bacterial Species to Screen for Novel Antimicrobials

The final three steps of heme biogenesis exhibit notable differences between di- and mono-derm bacteria. The former employs the protoporphyrin-dependent (PPD) pathway, while the latter utilizes the more recently uncovered coproporphyrin-dependent (CPD) pathway. In order to devise a rapid screen for potential inhibitors that differentiate the two pathways, the genes associated with the protoporphyrin pathway in an Escherichia coli YFP strain were replaced with those for the CPD pathway from Staphylococcus aureus (SA) through a sliding modular gene replacement recombineering strategy to generate the E. coli strain Sa-CPD-YFP. Potential inhibitors that differentially target the pathways were identified by screening compound libraries against the YFP-producing Sa-CPD-YFP strain in comparison to a CFP-producing E. coli strain. Using a mixed strain assay, inhibitors targeting either the CPD or PPD heme pathways were identified through a decrease in one fluorescent signal but not the other. An initial screen identified both azole and prodigiosin-derived compounds that were shown to specifically target the CPD pathway and which led to the accumulation of coproheme, indicating that the main target of inhibition would appear to be the coproheme decarboxylase (ChdC) enzyme. In silico modeling highlighted that these inhibitors are able to bind within the active site of ChdC.
Application of the WEPP model to determine sources of run‐off and sediment in a forested watershed

This study investigates critical run‐off and sediment production sources in a forested Kasilian watershed located in northern Iran. The Water Erosion Prediction Project (WEPP) watershed model was set up to simulate the run‐off and sediment yields. WEPP was calibrated and validated against measured rainfall–run‐off–sediment data. Results showed that simulated run‐off and sediment yields of the watershed were in agreement with the measured data for the calibration and validation periods. While low and medium values of run‐off and sediment yields were adequately simulated by the WEPP model, high run‐off and sediment yield values were underestimated. Performance of the model was evaluated as very good and satisfactory during the calibration and validation stages, respectively. Total soil erosion and sediment load of the study watershed during the study period were determined to be 10 108 t yr−1 and 8735 t yr−1, respectively. The northern areas of the watershed with dry farming were identified as the critical erosion prone zones. To prioritize the subwatersheds based on their contribution to the run‐off and sediment production at the watershed's main outlet, unit response approach (URA) was applied. In this regard, subwatersheds close to the main outlet were found to have the highest contribution to sediment yield of the whole watershed. Results indicated that depending on the objective of land and water conservation practices, particularly, for controlling sediment yield at the main outlet, critical areas for implementing the best management practices may be identified through conjunctive application of WEPP and URA. Copyright © 2014 John Wiley & Sons, Ltd.
Multi-Effects of Acute Salinity Stress on Osmoregulation, Physiological Metabolism, Antioxidant Capacity, Immunity, and Apoptosis in Macrobrachium rosenbergii

Salinity stress can trigger a series of physiological changes. However, the mechanism underlying the response to acute salinity stress in Macrobrachium rosenbergii remains poorly understood. In this study, osmoregulation, physiological metabolism, antioxidant capacity, and apoptosis were examined over 96 h of acute salinity stress. Hemolymph osmolality increased with increasing salinity. After 48 h of salinity exposure, the glucose, triglycerides, total protein, and total cholesterol contents in two salinity stress groups (13 and 26‰ salinity) were significantly lower than those in the 0‰ salinity group. The highest levels of these parameters were detected at 6 h; however, superoxide dismutase (SOD), total antioxidant capacity (T-AOC), and malondialdehyde (MDA) were the lowest at 96 h in the 13‰ salinity group. The activity of immunity-related enzyme alkaline phosphatase (AKP) showed a decreasing trend with increasing salinity and remained at a low level in the 26‰ salinity group throughout the experiment. No significant differences were observed in aspartate aminotransferase (AST), alanine aminotransferase (ALT), or lysozyme (LZM) among the three treatments at 96 h. After 96 h of salinity treatments, the gill filament diameter significantly decreased, and a more pronounced terminal deoxynucleotidyl transferase dUTP nick end labeling (TUNEL)-positive signal was detected in the 13‰ and 26‰ groups compared to that in the 0‰ group. Expression levels of apoptosis-related genes, including Cysteine-aspartic acid protease 3 (Caspase 3), Cysteine-aspartic acid protease 8 (Caspase 8), Cytochrome c (Cyt-c), tumor suppressor gene (P53), Nuclear factor kappa-B (NF-κB), and B cell lymphoma 2 ovarian killer (Bok) were significantly higher in the 26‰ salinity group than in the other groups at 24 h, but lower than those in the 0‰ salinity group at 96 h. Cyt-c and P53 levels exhibited a significantly positive relationship with MDA, AST, and LZM activity during salinity stress. In the 13‰ salinity group, Bok expression was significantly correlated with SOD, T-AOC, AKP, acid phosphatase, and LZM activity, whereas in the 26‰ group, the AST content was positively correlated with Caspase 8, Cyt-c, and P53 expression. A significant negative relationship was observed between Caspase 3 expression and catalase (CAT) activity. These findings provide insight into the mechanisms underlying the response to acute salinity stress and will contribute to improving M. rosenbergii aquaculture and management practices.
Organizational Health Literacy as a Tool for Health Equity: Application in a High-Risk Infant Follow-Up Program

Background: Healthy People 2030 emphasizes personal health literacy (individual skills) and organizational health literacy—the degree to which organizations equitably enable individuals to find, understand, and use information and services to inform health-related decisions and actions for themselves and others. However, research on the latter is in the early stages. Methods: This study describes an organizational health literacy assessment in a U.S. urban academic children’s hospital. A variety of evidence-based health literacy assessments were used to assess patient information materials and the environment, including institutional practices, navigation, culture and language, and communication. Trained interviewers and analysts reached consensus for all assessments. Results: Information Items: SMOG scores (n = 9) ranged from 7th- to 14th-grade reading level (average = 11.3). PEMAT-P scores (n = 9) ranged from 43.8% to 93.8% understandability and 0% to 80% actionability. CDC CCI scores (literacy demand) (n = 6) ranged from 18.2% to 58.8% (≥90% = excellent). SAM scores (suitability) (n = 6) fell in the “adequate” range (43.2–58.3%). The PMOSE/IKIRSCH scores (complexity) (n = 3) noted low-moderate difficulty. Apter’s Hierarchy (n = 4) revealed three numeracy domains (50% = descriptive purposes and decision-making, 100% = interpreting information). Organization-level: Walking interviews highlighted organizational facilitators and barriers related to the pre-visit and visit environments. HLE2 domain scores ranged from 52% to 68%. Conclusions: Organizational health literacy demands far outweigh the average literacy skills of adults in the U.S. (patients and staff). Findings can be used to hone quality improvement and other processes to focus on structural solutions to increase health equity.
Providing architectural support for building context-aware applications

Traditional interactive applications are limited to using only the input that users explicitly provide. As users move away from traditional desktop computing environments and move towards mobile and ubiquitous computing environments, there is a greater need for applications to leverage from implicit information, or context. These types of environments are rich in context, with users and devices moving around and computational services becoming available or disappearing over time. This information is usually not available to applications but can be useful in adapting the way in which it performs its services and in changing the available services. Applications that use context are known as context-aware applications. This research in context-aware computing has focused on the development of a software architecture to support the building of context-aware applications. While developers have been able to build context-aware applications, they have been limited to using a small variety of sensors that provide only simple context such as identity and location. This dissertation presents a set of requirements and component abstractions for a conceptual supporting framework. The framework along with an identified design process makes it easier to acquire and deliver context to applications, and in turn, build more complex context-aware applications. In addition, an implementation of the framework called the Context Toolkit is discussed, along with a number of context-aware applications that have been built with it. The applications illustrate how the toolkit is used in practice and allows an exploration of the design space of context-aware computing. This dissertation also shows how the Context Toolkit has been used as a research testbed, supporting the investigation of difficult problems in context-aware computing such as the building of high-level programming abstractions, dealing with ambiguous or inaccurate context data and controlling access to personal context.
Slip-Partitioned Surface Breaks for the Mw 7.8 2001 Kokoxili Earthquake, China

Slip-partitioned fault breaks have been mapped for a 70-km stretch of the 450-km surface rupture of the 14 November 2001 Kokoxili earthquake. Simultaneous dip-slip and strike-slip motion on parallel faults has been proposed before, but the new observations demonstrate unequivocally that it can occur in a single earthquake and allows the mechanical processes to be scrutinized. Observed normal fault offsets were between 0.5 and 1 m and strike-slip offsets were 3–5 m. The partitioned stretch of faulting has a strike that differs by 2–3° from the pure strike-slip faulting to the east and west. This allows a horizontal opening vector of 0.25 m to be determined for the partitioned region. The distance between the two faults is greatest (∼2 km) at the center of the partitioned portion and diminishes toward the ends. The faulting is modeled to result from strains due to a buried oblique slip-fault dipping at 80° to the south. The depth to the top of the buried fault is shown to vary commensurately with the separation of the surface faults. Clear surface rupture is observed where the predicted model mechanisms are colinear and where substantial faults can develop into a kinematically stable partitioned system. In a few interesting examples fragmentary, oblique surface ruptures occur where the predicted mechanisms are not colinear, but they are not associated with long-term surface faulting. The proposed mechanism for slip partitioning requires that rupture propagates upward from depth. For the Kokoxili surface breaks this is a consequence of coseismic, dynamic rupture traveling faster at depth than near the surface, leaving the surface deformation to catch up. While the mechanism we propose requires slip weakening and localization to create faults or shear zones, it does not require that faults with different mechanisms have different frictional behavior.
Pursuing a proxy for carbon cycling in the temperate North Atlantic: Investigation of the utility of Arctica islandica shell carbonate to millennial-scale dissolved inorganic carbon reconstructions

The marine bivalve species, Arctica islandica, was reared under experimental conditions for 29 weeks in the Gulf of Maine in order to determine the relationship between the carbon isotope composition of shell carbonate (δCS) and ambient seawater dissolved inorganic carbon (δCDIC), as well as to approximate the metabolic contribution (CM) to shell material. Three experimental environments were compared: two flow-through tanks (one at ambient seawater conditions, one with additional food added) and an in-situ cage. Each environment contained 50 juveniles and 30 adults. Both juvenile (2-3 yrs) and adult (19-64 yrs) specimens displayed average percent CM of less than 10% when using three different proxies of respired carbon: digestive gland, adductor muscle and sediment. Hence, the primary control on δCS values is ambient DIC. The relationship between δCDIC and δCS for 114 individuals used in the study was: δCDIC = δCS – 0.96‰ (±0.32‰). No ontogenetic effect on δCS was observed, and growth rates did not generally impact δCS values. Shell material derived from the long-lived ocean quahog (Arctica islandica) constitutes a viable proxy for paleo-DIC from the extratropical Atlantic Ocean.
The Impact of Edema on MRI Radiomics for the Prediction of Lung Metastasis in Soft Tissue Sarcoma

Highlights What are the main findings? Both the model utilizing edema-related features and the model utilizing mass-related features demonstrated promising results in predicting the occurrence of lung metastases, with similar performances. What is the implication of the main finding? The findings suggest that the analysis of radiomic features extracted exclusively from edema can offer valuable insights into the prediction of lung metastases. Abstract Introduction: This study aimed to evaluate whether radiomic features extracted solely from the edema of soft tissue sarcomas (STS) could predict the occurrence of lung metastasis in comparison with features extracted solely from the tumoral mass. Materials and Methods: We retrospectively analyzed magnetic resonance imaging (MRI) scans of 32 STSs, including 14 with lung metastasis and 18 without. A segmentation of the tumor mass and edema was assessed for each MRI examination. A total of 107 radiomic features were extracted for each mass segmentation and 107 radiomic features for each edema segmentation. A two-step feature selection process was applied. Two predictive features for the development of lung metastasis were selected from the mass-related features, as well as two predictive features from the edema-related features. Two Random Forest models were created based on these selected features; 100 random subsampling runs were performed. Key performance metrics, including accuracy and area under the ROC curve (AUC), were calculated, and the resulting accuracies were compared. Results: The model based on mass-related features achieved a median accuracy of 0.83 and a median AUC of 0.88, while the model based on edema-related features achieved a median accuracy of 0.75 and a median AUC of 0.79. A statistical analysis comparing the accuracies of the two models revealed no significant difference. Conclusion: Both models showed promise in predicting the occurrence of lung metastasis in soft tissue sarcomas. These findings suggest that radiomic analysis of edema features can provide valuable insights into the prediction of lung metastasis in soft tissue sarcomas.
Trends in eutrophication research and control

Eutrophication is the natural ageing process of lakes. It is characterized by a geologically slow shift from in-lake biological production driven by allochthonous (external to the water body) loading of nutrients, to production driven by autochthonous (in-lake) processes. This shift typically is accompanied by changes in species and biotic community composition, as an aquatic ecosystem is ultimately transformed into a terrestrial biome. However, this typically slow process can be greatly accelerated by human intervention in the natural biogeochemical cycling of nutrients within a watershed; the resulting cultural eutrophication can create conditions inimical to the continued use of the water body for humandriven economic purposes. Excessive algal and rooted plant growth, degraded water quality, extensive deoxygenation of the bottom water layers and increased fish biomass accompanied by decreased harvest quality, are some features of this process. Following the Second World War, concern with cultural eutrophication achieved an intensity that spurred a significant research effort, culminating in the identification of phosphorus as the single most significant, and controllable, element involved in driving the eutrophication process. During the late 1960s and throughout the 1970s, much effort was devoted to reducing phosphorus in wastewater effluents, primarily in the developed countries of the temperate zone. These efforts generally resulted in the control of eutrophication in these countries, albeit with varying degrees of success. The present effort in the temperate zone, comprising mostly developed nations, has now shifted to the control of diffuse sources of a broader spectrum of contaminants that impact human water use. In the developing countries of the inter-tropical zone, however, rapidly expanding populations, a growing industrial economy and extensive urbanization have only recently reached an intensity at which cultural eutrophication can no longer be ignored. Further, initial attempts at applying temperate zone control measures in this region have been largely unsuccessful. Modification of the temperate zone eutrophication paradigm will be needed, especially to address the differing climatic and hydrological conditions, if cultural eutrophication is to be contained in this region, where eutrophication-related diseases continue to be a primary cause of human distress.
A novel collaborative bearing fault diagnosis method based on multi-scale dynamic fusion network under speed fluctuating condition

Improving bearing fault diagnosis accuracy under speed fluctuation is a challenge in engineering applications. With the development of big data processing technology, a new solution, multi-sensor complementary information, has emerged. However, single-scale dimension compression, which is adopted in most multi-sensor data fusion methods, captures only a small amount of valuable information. To deal with this deficiency, a multi-scale dynamic fusion network (MSDFN) is proposed. First, considering the existence of non-stationary features in the fluctuating speed signal, the FReLU function is adopted to activate the features after considering contextual information. Then, multi-sensor features are fused by multiple scales to obtain richer feature information, and fusion features at different scales are weighted by using the attention mechanism. Finally, batch normalization is employed to standardize the variable speed feature distribution. The validity of the MSDFN is proved by conducting fault diagnosis experiments on two bearings under speed fluctuating conditions. Experimental results indicate that the MSDFN is not only effective in identifying various types of fault samples, but also shows higher stability in multiple trials when compared with other methods.
Combined high-density lidar and multispectral imagery for individual tree crown analysis

Lidar technology has reached a point where ground and forest canopy elevation models can be produced at high spatial resolution. Individual tree crown isolation and classification methods are developing rapidly for multispectral imagery. Analysis of multispectral imagery, however, does not readily provide tree height information and lidar data alone cannot provide species and health attributes. The combination of lidar and multispectral data at the individual tree level may provide a very useful forest inventory tool. A valley following approach to individual tree isolation was applied to both high resolution digital frame camera imagery and a canopy height model (CHM) created from high-density lidar data over a test site of even aged (55 years old) Douglas-fir plots of varying densities (300, 500, and 725 stems/ha) on the west coast of Canada. Tree height was determined from the laser data within the automated crown delineations. Automated tree isolations of the multispectral imagery achieved 80%‐90% good correspondence with the ground reference tree delineations based on ground data. However, for the more open plot there were serious commission errors (false trees isolated) mostly related to sunlit ground vegetation. These were successfully reduced by applying a height filter to the isolations based on the lidar data. Isolations from the lidar data produced good isolations with few commission errors but poorer crown outline delineations especially for the densest plot. There is a complimentarity in the two data sources that will help in tree isolation. Heights of the automated isolations were consistently underestimated versus ground reference trees with an average error of 1.3 m. Further work is needed to test and develop tools and capabilities, but there is an effective synergy of the two high resolution data sources for providing needed forest inventory information.
Ground-motion prediction equations for induced seismicity in the main anticline and main syncline, Upper Silesian Coal Basin, Poland

The purpose of the research was to determine parameters of ground-motion models for two areas characterized by considerable induced seismicity and different geology. Fifty-nine events collected from surface seismological stations of coal mine “Bielszowice” (at the Main Anticline, South Poland) and 144 events from coal mine “Ziemowit” (at the Main Syncline, South Poland) were used for computation. For both areas, simple ground-motion prediction equations (GMPEs) without site effects were derived, but the model was acceptable only for “Bielszowice” area. The GMPE was calculated once again for “Ziemowit”, but this time we took into consideration the amplification coefficient, which significantly improved the model solution. Finally, the theoretical value of amplification was calculated. Knowing that the amplification is associated with subsurface layers, we used three different models of overburden: (i) with Quaternary sediments only, (ii) with a complex of Quaternary-Tertiary sediments, and (iii) with a complex of Quaternary-Tertiary-Triassic sediments and Carboniferous as a basement. Usually, the amplification of vibrations appears in the Quaternary sediments. However, theoretical calculations of amplification were consistent with the results obtained from GMPE when a rigid Carboniferous substratum was applied.