Miracle-dz/UniFAR-FTUs huggingface dataset:
Developing machine learning systems worthy of trust for infection science: a requirement for future implementation into clinical practice

Infection science is a discipline of healthcare which includes clinical microbiology, public health microbiology, mechanisms of microbial disease, and antimicrobial countermeasures. The importance of infection science has become more apparent in recent years during the SARS-CoV-2 (COVID-19) pandemic and subsequent highlighting of critical operational domains within infection science including the hospital, clinical laboratory, and public health environments to prevent, manage, and treat infectious diseases. However, as the global community transitions beyond the pandemic, the importance of infection science remains, with emerging infectious diseases, bloodstream infections, sepsis, and antimicrobial resistance becoming increasingly significant contributions to the burden of global disease. Machine learning (ML) is frequently applied in healthcare and medical domains, with growing interest in the application of ML techniques to problems in infection science. This has the potential to address several key aspects including improving patient outcomes, optimising workflows in the clinical laboratory, and supporting the management of public health. However, despite promising results, the implementation of ML into clinical practice and workflows is limited. Enabling the migration of ML models from the research to real world environment requires the development of trustworthy ML systems that support the requirements of users, stakeholders, and regulatory agencies. This paper will provide readers with a brief introduction to infection science, outline the principles of trustworthy ML systems, provide examples of the application of these principles in infection science, and propose future directions for moving towards the development of trustworthy ML systems in infection science.
Predicting Root Density in Streambanks 1

Abstract: Roots of riparian vegetation increase streambank erosion resistance and structural stability; therefore, knowledge of root density and distribution in streambanks is useful for stream management and restoration. The objective of this study was to compare streambank root distributions for herbaceous and woody vegetation and to develop empirical models to predict root density. Root length density, root volume ratio, soil physical and chemical properties, and above‐ground vegetation densities were measured at 25 sites on six streams in southwestern Virginia. The Mann‐Whitney test was used to determine differences in root density along stream segments dominated by either woody or herbaceous vegetation. Multiple linear regression was used to develop relationships between root density and site characteristics. Study results showed that roots were evenly distributed across the bank face with the majority of roots having diameters less than 2 mm. Soil bulk density and above‐ground vegetation were key factors influencing root density. While significant relationships were developed to predict root density, the predictive capabilities of the equations was low. Because of the highly variable nature of soil and vegetation properties, it is recommended at this time that soil erodibility and root density be measured in the field for design and modeling purposes, rather than estimated based on empirical relationships.
Climate change contributes to more frequent consecutive positive Indian Ocean Dipole events

Are the 2006–2008 three‐consecutive positive Indian Ocean Dipole (pIOD) events linked to climate change? Using 20th century experiments submitted for the Intergovernmental Panel on Climate Change (IPCC) Fourth Assessment Report (AR4), we show that a 19‐model average IOD index over the 1950–1999 period yields an upward trend. The associated circulation trends provide a favourable environment for pIOD development, leading to a 17% increase in pIOD frequency compared with the case in which trends are removed. The majority of the increase manifests as a frequency increase in the two‐ and three‐consecutive events. The circulation trends are in turn consistent with wind changes associated with a weaker Walker circulation in the Pacific and an enhanced land‐sea temperature contrast in the Indian Ocean (IO) sector. Our results suggest that although it is difficult to attribute the trigger of the recent consecutive pIODs, climate change is increasing the occurrences of such events.
No decline in drug overdose deaths in Norway: An ecological approach to understanding at-risk groups and the impact of interventions

Aim: This Norwegian case study examines groups at risk of drug overdose deaths, evidence-based harm reduction interventions, low-threshold services and treatment implemented, as well as trends in drug overdose deaths between 2010 and 2021. We aimed to explore the relevance of interventions for at-risk groups and discuss their potential impact on drug overdose trends. Method/data: Using an ecological approach, we analysed the following: (1) groups identified through latent profile analysis (LPA) among a sample of 413 high-risk drug users collected in 2010–2012, supplemented with other relevant studies up to 2021; (2) published information on harm-reduction interventions, low-threshold services and treatment in Norway; and (3) nationwide drug overdose mortality figures supplemented with published articles on the topic. Results: High-risk drug users in 2010–2012 commonly engaged in frequent illegal drug use, injecting and poly-drug use (including pharmaceutical opioids), which continued into following decade. The interventions implemented between 2010 and 2021 were relevant for at-risk groups identified in the surveys. However, there was no decrease in the trend of drug overdose deaths up to 2021. While relevant interventions may have mitigated a theoretical increase in mortality, new at-risk groups may have contributed to fatal outcomes associated with pharmaceutical opioids. Conclusion: The interventions were relevant to the risk groups identified among high-risk drug users and potentially effective in preventing an increase in drug overdose trends. However, tailored interventions are needed for individuals at risk of death from prescribed opioids. Comprehensive studies encompassing all at-risk populations, including both legal and non-medical users of prescription opioids, are needed.
The Ambivalence of Alexander Berkman’s Anti-Prison Anarchism

Alexander Berkman’s 1912 Prison Memoirs of an Anarchist is a significant book in the development of American anti-prison politics, not despite, but because of its ambivalent approach to prisons. I trace through Berkman’s book and archive an unresolved tension between two approaches to the prison: advocacy for political prisoners, whereby the prison is a state tool for suppressing radical ideas, and advocacy against the politics of prisons, whereby the prison is an “aggravated counterpart” of social structures and a site of struggle. Berkman’s ambivalence between these approaches amid his memoirs and activism exemplifies the complex development of U.S. thinking on prisons and enduring tensions in contemporary prison politics.
Mechanism of Transforming Growth Factor (cid:2) –induced Inhibition of T Helper Type 1 Differentiation

Regulation by transforming growth factor (TGF)- (cid:2) plays an important role in immune homeostasis. TGF- (cid:2) inhibits T cell functions by blocking both proliferation and differentiation. Here we show that TGF- (cid:2) blocks Th1 differentiation by inhibiting the expression of T-bet, the apparent masterregulator of T helper (Th)1 differentiation. Restoration of T-bet expression through retroviral transduction of T-bet into developing Th1 cells abrogated the inhibitory effect of TGF- (cid:2) . In addition, we show that, contrary to prior suggestions, downregulation of interleukin 12 receptor (cid:2) 2 chain is not key to the TGF- (cid:2) –mediated effect. Furthermore, we show that the direct inhibitory effect of TGF- (cid:2) on T cells is responsible, at least in part, for the inability of BALB/c mice to mount a Leishmania -specific Th1 response and to clear Leishmanial infection. were prepared as described previously (3). Subsequently, each sample was subjected to PCR with sense and antisense primers for (cid:2) -actin and T-bet. Primers for (cid:2) -actin were described previously (3) and for T-bet are: 5 (cid:7) TTC CCA TTC CTG TCC TTC ACC G (sense) and 5 (cid:7) GGA AGG TCG GGG TAA AAA C (antisense). To amplify mRNA specifically, and not contaminating genomic DNA, primers for both (cid:2) -actin and T-bet were designed to span an intron. PCR were performed at different numbers of cell cycles to ensure that comparison of PCR products for various samples is performed in the linear part of an amplification curve.
Effects of ozone depletion and increased ultraviolet‐B radiation on northern vegetation

The stratospheric ozone layer has been depleted at high and mid-latitudes as a consequence of man's pollution of the atmosphere, and this results in increasing ultraviolet-B radiation at ground level. We investigate the effects of further radiation increases on plants and ecosystems by irradiating natural sub-Arctic and Arctic vegetation with artificial UV-B radiation in field experiments extending over several years. Our experimental sites are located at Abisko, in northern Sweden (68°N), and Adventdalen, on the island of Spitsbergen (78°N). Additional UV-B induced interspecific differences in plant response in terms of reduced (or, in one case, increased) growth, changed morphology and changed pigment content. In some cases effects seem to be accumulated from one year to another. Plant litter decomposition is retarded. We are also studying how UV-B enhancement may affect the interaction between species. In some experiments we combine UV-B enhancement with changes in other factors: carbon dioxide concentration, water availability, and temperature. In some cases the effect of radiation enhancement is modified, or even reversed, by such changes. Over a four year period we did not find any significant radiation induced change in species composition, but based on the effects on individual plant species, such changes can be expected to take place over a longer time.
High-Resolution Climate Simulations of Oxygen Isotope Stage 3 in Europe 1

Abstract Oxygen isotope stage 3 (OIS 3) climate and its variations are the focus of the Stage 3 Project. The objective of the OIS 3 modeling effort is twofold: (1) to explore the importance of different boundary conditions on the climate of Europe and (2) to develop climate simulations that best reproduce the wealth of OIS 3 observations. Given the complexity of the topography and coastlines, the modeling effort is based on a “nested” General Circulation Model (GCM) and mesoscale model (RegCM2) with climate simulations for Europe on a 60-km grid spacing. The key conclusions are as follows: (1) The mesoscale model, driven by GCM output, does a reasonable job of reproducing the modern European climate. (2) OIS 3 variations in orbit, CO2, and ice-sheet size are of little significance in explaining the observed climate variability. (3) The model results focus attention on North Atlantic sea-surface temperatures (SST) as a major factor in explaining OIS 3 climates. (4) Experiments for different SST values capture a number of systematic changes in sea-level pressure and precipitation. (5) Climate models simulate substantial European cooling and significant changes in precipitation, but they do not explain large differences between OIS 3 warm and cold episodes.
Role of Snow in Runoff Processes in a Subalpine Hillslope: Field Study in the Ward Creek Watershed, Lake Tahoe, California, during 2000 and 2001 Water Years

Field study is an essential component of hydrologic science because all hydrological studies must be conducted by such observation-based knowledge of real watersheds. Hillslope runoff processes have been intensively investigated, but the flow process at the boundary between the snowpack and ground surface has not been well documented. A field site at the northwest sector of the Ward Creek watershed, Lake Tahoe Basin, was built for observations of overland flow, subsurface stormflow, and channel flow, simultaneously with atmospheric measurements to examine the hydrology at a snow-covered hillslope. Also, the groundwater table under the snowpack was monitored by shallow wells at the hillslope. All field-measured atmospheric data were synthesized with an energy-balance snow model, and the snowmelt rate and energy balance were computed. The results of the analyses indicate that most of the snowmelt water infiltrated into the topsoil layers and that saturated subsurface flow was the largest contributor to the .
Land Subsidence as a Result of Sediment Consolidation in the Yellow River Delta

Abstract Land subsidence due to consolidation of sediment was analyzed in the Yellow River delta, using lithological data of deposits, equations of soil mechanics, and empirical relations. Subsidence in an abandoned deltaic lobe largely results from the consolidation of deltaic clay layers accumulated in the prodelta, the bays, and marine clay layers underlying the delta. The prodelta and marine clay layers have a total thickness of approximately 14 m. In the areas where thick bay-clay layers accumulated on the prodelta-clay layers, the total thickness of the clay can reach 20 m. Calculations show that after 15-m-thick deltaic strata were deposited on the seabed, the total consolidation of the 14-m-thick clay layers is approximately 1.44 m and 1.52 m for the 20-m-thick clay layers. After the first 40 years, the rate of land subsidence resulting from consolidation of the 14-m-thick clay layers will decrease gradually to 0.005 m/y. For the 20-m-thick clay layers, it will take 57 years for the rate of subsidence to decrease to 0.005 m/y.
The precipitation climate of Central Asia—intercomparison of observational and numerical data sources in a remote semiarid region

In this study, we systematically compare a wide range of observational and numerical precipitation datasets for Central Asia. Data considered include two re‐analyses, three datasets based on direct observations, and the output of a regional climate model simulation driven by a global re‐analysis. These are validated and intercompared with respect to their ability to represent the Central Asian precipitation climate. In each of the datasets, we consider the mean spatial distribution and the seasonal cycle of precipitation, the amplitude of interannual variability, the representation of individual yearly anomalies, the precipitation sensitivity (i.e. the response to wet and dry conditions), and the temporal homogeneity of precipitation. Additionally, we carried out part of these analyses for datasets available in real time. The mutual agreement between the observations is used as an indication of how far these data can be used for validating precipitation data from other sources. In particular, we show that the observations usually agree qualitatively on anomalies in individual years while it is not always possible to use them for the quantitative validation of the amplitude of interannual variability. The regional climate model is capable of improving the spatial distribution of precipitation. At the same time, it strongly underestimates summer precipitation and its variability, while interannual variations are well represented during the other seasons, in particular in the Central Asian mountains during winter and spring. Copyright © 2007 Royal Meteorological Society
Effect of rainfall errors on accuracy of design flood estimates

A procedure is presented to explicitly evaluate the effect of estimation errors in the temporal and spatial distribution of rainfall on the uncertainty of calibrated rainfall-runoff model parameters. The effect of this uncertainty on the reliability of design flood predictions is considered. A case study of the Hacking catchment, south of Sydney, Australia, is presented to illustrate the procedure. For a major storm event a simple stochastic transformed rainfall model is calibrated and validated using kriging and then used to infer the mean and covariance of subareal rainfall. The RORB model, a distributed nonlinear rainfall-runoff model, is calibrated to this storm event. When allowance is made for uncertainty in the calibration event rainfall, the results indicate that the uncertainty in the calibrated parameters increases, especially in the rainfall excess parameters, and the 90% prediction interval on the 100-year design flood increases by about 100%.
A Dual Spatial-Graph Refinement Network for Building Extraction From Aerial Images

Satisfactory extraction of buildings from aerial images has long been a challenging task. In the recently fully convolutional network (FCN)-based methods, the locality of the convolution operation is detrimental to handling global long-range dependencies for complex buildings, such as those shaded by trees, obscured by the shadow of high-rise ones, and blurred by the high-similarity pixels. Although graph neural networks (GNNs) show clear-cut advantages in modeling semantic correlations between different segments or instances, existing FCN-GNN methods cannot directly perform graph reasoning for spatial features in an end-to-end framework due to two chief limitations: 1) it is costly to construct large fully connected graphs and 2) there is not a standard pixel-based graph reasoning paradigm. We, therefore, developed a hybrid end-to-end FCN-like network to perform better building extraction on complex scenes, termed the dual spatial-graph refinement network (DSRNet). Specifically, we first proposed a spatial-graph reasoning (SR) module, which effectively constructs adjacent relations for dense pixels, to make fast graph reasoning for grid-based features possible. Considering SR as the basis, we further developed a dual spatial-graph refinement (DSR) module, consisting of body and structure SRs (BSR and SSR), to make SR attentively perceive global buildings’ spatial-semantic relationships from two complementary perspectives. BSR was designed to enhance consistency within buildings and SSR models’ correlations of buildings’ structural information to extract buildings with more coherent bodies and tight-fitting edge contours. Finally, we devised a contour alignment (CA) loss function to encourage the segmentation result to align correctly with the contours of the ground truths. DSRNet outperforms state-of-the-art FCN-based methods on Christchurch and Tokyo high-resolution building datasets and consistently shows improvements in building segmentation and contour extraction, especially in the case of complex scenes.
Stability of Waterfront Retaining Wall Subjected to Pseudodynamic Earthquake Forces

This technical note pertains to the study of a waterfront retaining wall, retaining a partially submerged backfill, subjected to seismic forces. The pseudodynamic approach, which considers the effect of primary and shear wave propagation in the backfill soil and wall, is adopted for calculation of the seismic earth pressure considering wall inertia. The point of application of the seismic active earth pressure is also affected by seismicity. Hydrodynamic forces are considered in the analysis. It is observed that when the horizontal seismic acceleration coefficient is increased from 0 to 0.3, there is a 65% decrease in the factor of safety of the retaining wall in sliding mode. To investigate the effects of different parameters on design, a parametric study is done. It is observed that with increase in the value of ϕ from 25 to 35° , there is an increase in the factor of safety in the sliding mode by 50%. Comparison with a previous study suggests that the present pseudodynamic approach gives less conservat.
On the origin of seasonal variation of aerosol optical thickness in UV range over Belsk, Poland

Aerosol optical thickness (AOT) and seasonal variation of AOT over Belsk, Poland, in the UV wavelength range (310–380 nm) have been analysed using results of measurements by Brewer spectrophotometer No. 064 and Cimel sunphotometer data for the 2002–2007 period. The comparison of AOT derived from direct Sun measurements by Brewer spectrophotometer in the 310–320 nm range and retrieved from Cimel measurements at longer wavelengths shows good correlation (R = 0.96), with overestimation of retrieved values compared to the measured ones by about 6%. Basing on aerosol microphysical properties taken from almucantar retrievals and Mie theory, optical properties of aerosol in the UV range has been calculated. Analysis of seasonal variation of AOT at Belsk reveals two maxima: in April and July–August. Analysis of back-trajectories in conjunction with analysis of fire maps from Fire Information For Resource Management System shows that these seasonal maxima are connected with seasonal biomass burning in Eastern and Southern Europe.
Relocating Glyceryl Trinitrate as an Anti-Virulence Agent against Pseudomonas aeruginosa and Serratia marcescens: Insights from Molecular and In Vivo Investigations

The problem of antibiotic resistance is a global critical public health concern. In light of the threat of returning to the pre-antibiotic era, new alternative approaches are required such as quorum-sensing (QS) disruption and virulence inhibition, both of which apply no discernible selective pressure on bacteria, therefore mitigating the potential for the development of resistant strains. Bearing in mind the significant role of QS in orchestrating bacterial virulence, disrupting QS becomes essential for effectively diminishing bacterial virulence. This study aimed to assess the potential use of sub-inhibitory concentration (0.25 mg/mL) of glyceryl trinitrate (GTN) to inhibit virulence in Serratia marcescens and Pseudomonas aeruginosa. GTN could decrease the expression of virulence genes in both tested bacteria in a significant manner. Histopathological study revealed the ability of GTN to alleviate the congestion in hepatic and renal tissues of infected mice and to reduce bacterial and leukocyte infiltration. This study recommends the use of topical GTN to treat topical infection caused by P. aeruginosa and S. marcescens in combination with antibiotics.