Miracle-dz/UniFAR-FTUs huggingface dataset:
Reliability-based seismic performance of masonry arch bridges

Abstract Seismic structural assessment of masonry arch bridges is essential due to their cultural, economic and strategic importance and vulnerability. A realistic and rigorous structural assessment is necessary in order to protect the bridges and use resources carefully. At this time, there are no standardised or widely accepted assessment procedures, and the performance criteria for masonry arch bridges are not available. This study presents an overarching reliability-based seismic assessment methodology based on analytical modelling, laboratory testing and probabilistic assessment. It investigates the performance criteria concept and proposes performance limit states. The methodology is applied to a historical masonry arch bridge in Turkey. To consider rigorously the uncertainties in material properties and seismic input, probabilistic nonlinear analyses are conducted using a detailed 3D finite element model. The results are combined with the proposed limit state definitions to generate the capacity and demand distributions. Both distributions are used in Monte Carlo simulation and First-Order Reliability Method (FORM) to estimate the probability of exceedance and reliability indexes for each limit state. The proposed probabilistic assessment methodology will be a useful approach to obtaining more reliable information about masonry arch bridges' expected seismic performance and for better-informed decision-making, especially when designing intervention actions and post-earthquake scenarios.
Within-Generation and Transgenerational Plasticity of a Temperate Salmonid in Response to Thermal Acclimation and Acute Temperature Stress

The rise in temperature associated with climate change may threaten the persistence of stenothermal organisms with limited capacities for beneficial thermal acclimation. We investigated the capacity for within-generation and transgenerational thermal responses in brook trout (Salvelinus fontinalis), a cold-adapted salmonid. Adult fish were acclimated to temperatures within (10°C) and above (21°C) their thermal optimum for 6 mo before spawning, then mated in a full factorial breeding design to produce offspring from cold- and warm-acclimated parents and bidirectional crosses between parents from both temperature treatments. Offspring from families were subdivided and reared at two acclimation temperatures representing their current (15°C) and anticipated future (19°C) habitat temperatures. Offspring thermal physiology was measured as the rate of oxygen consumption (Mo2) during an acute change in temperature (increase of 2°C h−1) to observe their Mo2-temperature relationship. We recorded resting Mo2, peak (highest achieved, thermally induced) Mo2, and critical thermal maximum (CTM) as performance metrics. Although limited, within-generation plasticity was greater than transgenerational plasticity, with offspring warm acclimation elevating CTM by 0.5°C but slightly lowering peak thermally induced Mo2. Transgenerational plasticity was evident as a slightly elevated resting Mo2 and a shift of the Mo2-temperature relationship to higher rates overall in offspring from warm-acclimated parents. Furthermore, offspring whose parents were warm acclimated were in worse condition than those whose parents were cold acclimated. Both parents contributed to offspring thermal responses; however, the paternal effect was stronger. Despite the existence of within-generation and transgenerational plasticity in brook trout, it is unlikely that these will be sufficient for coping with long-term changes to environmental temperatures.
Bacterial Growth of Uropathogenic Escherichia coli in Pooled Urine Is Much Higher than Predicted from the Average Growth in Individual Urine Samples

Urinary tract infections (UTIs) will affect most women, can recur especially in postmenopausal women, and can become antibiotic recalcitrant. Escherichia coli causes most community-acquired UTIs and recurrent UTIs. Current theories of virulence, based on studies of UTI-associated E. coli, propose multiple virulence mechanisms and complex host-pathogen interactions. ABSTRACT Urinary tract infections (UTIs), mostly caused by uropathogenic E. coli (UPEC), affect most women, and often recur. Genomic and transcriptomic analyses have not identified a common set of virulence genes, which has suggested complex host-pathogen interactions and multiple virulence mechanisms. One aspect of the host-pathogen interaction is rapid UPEC growth in urine in vivo. When bacterial growth in urine is studied in vitro, urine is pooled, which is assumed to diminish individual variation. We grew one nonpathogenic and two pathogenic E. coli strains in urine from individuals who never had a UTI, had a UTI history but no current infection, and had a UTI history with a current infection. Bacterial growth showed large variations in individual urine samples, and pooled urine often supported significantly more growth than the average growth from individual urine samples. Total nutrient content tended to be higher in current group urine samples than the never and history grouped samples urine. We propose that pooling optimizes a nutrient mixture in the never and history group urine samples, which are often studied, whereas urine from current group individuals may have a more optimal nutrient mixture because of additional nutrient sources. We conclude that a pooled urine is not “an average urine sample,” and that the best comparisons of results between labs using pooled urine would also include results with a standardized synthetic urine. IMPORTANCE Urinary tract infections (UTIs) will affect most women, can recur especially in postmenopausal women, and can become antibiotic recalcitrant. Escherichia coli causes most community-acquired UTIs and recurrent UTIs. Current theories of virulence, based on studies of UTI-associated E. coli, propose multiple virulence mechanisms and complex host-pathogen interactions. Studies of bacterial growth in urine samples—one aspect of the host-pathogen interaction—invariably involve pooled urine that are assumed to eliminate variations between individuals. Our results show that a pooled urine is not necessarily an average urine sample, and we suggest that quantitative and qualitative variations in nutrient content are the basis for this discrepancy. Knowledge of growth-promoting urinary components is important for understanding host-pathogen interactions during UTIs and could contribute to developing nonantibiotic-based therapies.
Bacterial Membrane Vesicles as a Novel Strategy for Extrusion of Antimicrobial Bismuth Drug in Helicobacter pylori

Bacterial resistance to antibiotics is a major threat to human health. Treatments combining antibiotics with metals were proposed to circumvent this hurdle. ABSTRACT Bacterial antibiotic resistance is a major threat to human health. A combination of antibiotics with metals is among the proposed alternative treatments. Only one such combination is successfully used in clinics; it associates antibiotics with the metal bismuth to treat infections by Helicobacter pylori. This bacterial pathogen colonizes the human stomach and is associated with gastric cancer, killing 800,000 individuals yearly. The effect of bismuth in H. pylori treatment is not well understood in particular for sublethal doses such as those measured in the plasma of treated patients. We addressed this question and observed that bismuth induces the formation of homogeneously sized membrane vesicles (MVs) with unique protein cargo content enriched in bismuth-binding proteins, as shown by quantitative proteomics. Purified MVs of bismuth-exposed bacteria were strongly enriched in bismuth as measured by inductively coupled plasma optical emission spectrometry (ICP-OES), unlike bacterial cells from which they originate. Thus, our results revealed a novel function of MVs in bismuth detoxification, where secreted MVs act as tool to discard bismuth from the bacteria. Bismuth also induces the formation of intracellular polyphosphate granules that are associated with changes in nucleoid structure. Nucleoid compaction in response to bismuth was established by immunogold electron microscopy and refined by the first chromosome conformation capture (Hi-C) analysis of H. pylori. Our results reveal that even low doses of bismuth induce profound changes in H. pylori physiology and highlight a novel defense mechanism that involves MV-mediated bismuth extrusion from the bacteria and a probable local DNA protective response where polyphosphate granules are associated with nucleoid compaction. IMPORTANCE Bacterial resistance to antibiotics is a major threat to human health. Treatments combining antibiotics with metals were proposed to circumvent this hurdle. Only one such combination is successfully used in clinics associating antibiotics with the metal bismuth to treat infections by the human pathogen Helicobacter pylori. H. pylori causes 800,000 deaths by gastric cancer yearly. How bismuth impacts H. pylori and its response to this toxic metal were ill defined. We discovered that upon bismuth exposure, H. pylori secretes membrane vesicles that are enriched in bismuth. Bismuth also induces the formation of intracellular polyphosphate granules associated with compaction of the chromosome. Upon bismuth exposure, H. pylori displays both defense and protection mechanisms, with bismuth extrusion by vesicles and shielding of the chromosome.
Calibrarion By Simulation for Small Sample Bias Correction

This paper is interested in small sample properties of the indirect inference procedure which has been previously studied only from an asymptotic point of view. First, we highlight the fact that the Andrews(1993) median-bias correction procedure for autoregresssive parameter of an AR(1) process is closely related to indirect inference; we prove that the counterpart of the midian-bias correction for indirect inference estimator is an exact bias correction in the sense of a generalized mean. Next, assuming that the auxiliary estimator admits an Edgeworth expansion, we prove that indirect inference operates automatically a second order bias correction. The latter is a well known property of the Bootstrap estimator; we therefore provide a precise comparison between these two simulation based estimators.
Ethical Future Environments: Engaging refugees in Smart City participation

Aiming to improve quality of life for their citizens, cities and environments regions are becoming increasingly smarter. Smart City research and practice has put emphasis on the importance of citizen-centric processes, collaborating with citizens and other stakeholders, as well as public values in Smart City projects. Nevertheless, cities and governmental organizations continue to adopt technology-push approaches, marginalized citizens such as refugees are often excluded in (urban) digitalization and decision-making processes. Despite their different and valuable perspectives, collaborating with marginalized citizens is not common practice, as it often requires a different approach than traditional citizen participation techniques. During this workshop, we will discuss with Smart City practitioners and refugees how we could broaden participation to include citizens who are still excluded, using a visual card-based game to discuss topics in the Smart City context that are relevant to participants. The expected outcomes of this workshop are an understanding of opportunities for involving marginalized citizens (in this workshop: refugees) in Smart City projects, different perspectives of stakeholders involved, and the setting up of a learning and caring community in which different stakeholders can share their insights and practices.
An Inquiry into the TUI Design Space for Parent-Child Math Engagement at Home

Preschoolers’ early-math development is vital for their later math and academic achievement. Tangible user interfaces (TUI) may support early math as they feature physical objects imperative to math development and multimedia to support engagement. As a potentially meaningful context for TUIs, developmental studies highlight the need to support the home math environment (HME) that covers math-related interactions among parents and children. Therefore, we focus on HME as a design space that has not been investigated in TUI literature. We conducted an observational study involving physical-object based math activities and semi-structured interviews with 13 parent-child dyads. Our findings revealed the multifaceted nature of the HME, where children's agency is valued and providing lasting materials is challenging. Also, we realized that parents juggled their child's demands and the object-based physical activity at once. By reflecting on these findings, we propose design directions for supporting the home-math environment with TUIs.
Computational Aeroacoustic Analysis of a Generic Side View Mirror

Computational fluid dynamics (CFD) simulations of the transient flow-field around a generic side view mirror shape are presented that provide insight into the wind noise generated by the mirror. The generic mirror shape consists of half a cylinder, 0.2 m in diameter and length, topped with a quarter of a sphere of the same diameter. The transient flow past the generic side view mirror is simulated using the commercial CFD code Fluent with the LES turbulence model. A flow velocity of 200 km/hr is considered which correspond to a Reynolds number of 7 x 10 5 . Detailed velocity vectors and contour plots of the time-varying velocity and pressure fields are presented along cut-planes in the flow-field. Mean and transient pressure are also monitored at several points in the flow field and compared to corresponding experimentally data published in literature. The results are also compared with predictions made using the Ffowcs-Williams-Hawkins acoustic analogy.
Electron localizations in double concentric quantum ring

We investigate the electron localization in double concentric quantum rings (DCQRs) when a perpendicular magnetic field is applied. In weakly coupled DCQRs, the situation can occur when the single electron energy levels associated with different rings may be crossed. To avoid degeneracy, the anti-crossing of these levels has a place. We show that in this DCQR the electron spatial transition between the rings occurs due to the electron level anti-crossing. The anti-crossing of the levels with different radial quantum numbers provides the conditions for electron tunneling between rings. To study electronic structure of the semiconductor DCQR, the single sub-band effective mass approach with energy dependence was used. Results of numerical simulation for the electron transition are presented for DCQRs of geometry related to one fabricated in experiment.
Automated Identification and Qualitative Characterization of Safety Concerns Reported in UAV Software Platforms

Unmanned Aerial Vehicles (UAVs) are nowadays used in a variety of applications. Given the cyber-physical nature of UAVs, software defects in these systems can cause issues with safety-critical implications. An important aspect of the lifecycle of UAV software is to minimize the possibility of harming humans or damaging properties through a continuous process of hazard identification and safety risk management. Specifically, safety-related concerns typically emerge during the operation of UAV systems, reported by end-users and developers in the form of issue reports and pull requests. However, popular UAV systems daily receive tens or hundreds of reports of varying types and quality. To help developers timely identify and triage safety-critical UAV issues, we (i) experiment with automated approaches (previously used for issue classification) for detecting the safety-related matters appearing in the titles and descriptions of issues and pull requests reported in UAV platforms and (ii) propose a categorization of the main hazards and accidents discussed in such issues. Our results (i) show that shallow machine learning (ML)-based approaches can identify safety-related sentences with precision, recall, and F-measure values of about 80%; and (ii) provide a categorization and description of the relationships between safety issue hazards and accidents.
Push or Pinch? Exploring Slider Control Gestures for Touchless User Interfaces

Touchless gesture interfaces enable user interaction without the need for direct physical contact. Recently there has been increased interest in deploying such interfaces over concerns about touchscreen sterility. Many touchless displays use gestures that mimic pointer-based interactions, with a ‘cursor’ mapped to finger position, that users activate by ‘pushing’ their finger forwards. Mid-air pushing with a virtual cursor is fine for discrete interactions like button activation; however, users have difficulty exerting control over continuous interactions like sliding and scrolling, because it is challenging to keep the hand at a consistent depth when gesturing. We investigate interaction techniques for slider control that use alternative mode switches between (un)pressed states. Our findings show that pinch gestures are preferred by most users and offer a faster alternative for acquiring control of sliders, as pinching has two clearly defined states and avoids the ambiguous use of depth for delineating input states.
Cloning and expression analysis of SERK1 gene in Diospyros lotus

Abstract Somatic embryogenesis receptor-like kinases (SERKs), a subfamily of receptor-like kinases, play important roles in response to abiotic stresses in addition to apomictic reproductive development in numerous plant species. The purpose of the present work was to determine if an ortholog of the SERK gene is present in the Diospyros lotus genome, isolate it and analyze its expression during embryogeny and abiotic stress. An ortholog of the SERK gene was isolated from the D. lotus genome, and designated as DlSERK1. The physical and chemical properties, protein structure, and evolutionary relationship of the DlSERK1 protein were analyzed by bioinformatics methods, and the expression of DlSERK1 gene during embryonic development and under low-temperature, salt, and drought stresses was examined through real-time quantitative PCR analysis. DlSERK1 contained 1,881 bp open reading frame encoding 626 amino acids, with a molecular mass of 69.18 kDa and pI of 5.34. DlSERK1 had strong hydrophilic property, signal peptide cleavage sites, and two transmembrane regions, indicating that DlSERK1 is a secretory protein. The secondary structure of DlSERK1 was consistent with the tertiary structure, both of which were dominated by random curls and alpha-helices. DlSERK1 had the typical structure of SERK proteins, and harbored multiple phosphorylation and glycosylation sites. Quantitative analysis showed that DlSERK1 was expressed during the embryonic development period, and the highest expression level was at 10 days post-flowering. The DlSERK1 expression level was down-regulated under low-temperature stress and up-regulated under drought and salt stresses. Our study showed that DlSERK1 was expressed in embryo development and could respond to low-temperature, drought, and salt stresses, which lays a foundation for further research on the function of SERK1 in the apomixis growth and development of environmental adaptation in D. lotus.
Finding a Cluster in Incomplete Data

We study two variants of the fundamental problem of finding a cluster in incomplete data. In the problems under consideration, we are given a multiset of incomplete $d$-dimensional vectors over the binary domain and integers $k$ and $r$, and the goal is to complete the missing vector entries so that the multiset of complete vectors either contains (i) a cluster of $k$ vectors of radius at most $r$, or (ii) a cluster of $k$ vectors of diameter at most $r$. We give tight characterizations of the parameterized complexity of the problems under consideration with respect to the parameters $k$, $r$, and a third parameter that captures the missing vector entries.
An Optimized Workflow to Generate and Characterize iPSC-Derived Motor Neuron (MN) Spheroids

Motor neuron diseases (MNDs) are characterized by the progressive degeneration of motor neurons (MNs) from the cortex, brainstem and/or the spinal cord. In an effort to understand the underlying causes of this selective degeneration, a multitude of in vitro models based on induced pluripotent stem cell (iPSC)-derived MNs have been developed. Moreover, different groups have started to use advanced 3D structures, composed of MNs and other cell types to increase the physiological relevance of such in vitro models. For instance, spheroids are simple 3D models that have the potential to be generated in large numbers that can be used across different assays. In this study, we generated MN spheroids and developed a workflow to analyze them. We confirmed the expression of different MN markers as the MN spheroids differentiate, at both the transcript and protein level, as well as their capacity to display functional activity in the form of action potentials (APs) and bursts. We also identified the presence of other cell types, namely interneurons and oligodendrocytes, which share the same neural progenitor pool with MNs. In summary, we successfully developed a MN 3D model, and we optimized a workflow that can be applied to their characterization and analysis. In the future, we will apply this model and workflow to the study of MNDs by generating MN spheroids from patient-derived iPSC lines, aiming to contribute to the development of more advance and physiological in vitro disease models.
Conformational changes linked to ADP release from human cardiac myosin bound to actin-tropomyosin

Following binding to the thin filament, β-cardiac myosin couples ATP-hydrolysis to conformational rearrangements in the myosin motor that drive myofilament sliding and cardiac ventricular contraction. However, key features of the cardiac-specific actin-myosin interaction remain uncertain, including the structural effect of ADP release from myosin, which is ratelimiting during force generation. In fact, ADP release slows under experimental load or in the intact heart due to the afterload, thereby adjusting cardiac muscle power output to meet physiological demands. To further elucidate the structural basis of this fundamental process, we used a combination of cryo-EM reconstruction methodologies to determine structures of the human cardiac actin-myosin-tropomyosin filament complex at better than 3.4 Å-resolution in the presence and in the absence of Mg2+·ADP. Focused refinements of the myosin motor head and its essential light chains in these reconstructions reveal that small changes in the active site are coupled to significant rigid body movements of the myosin converter domain and a 16-degree lever arm swing. Our structures provide a mechanistic framework to understand the effect of ADP binding and release on human cardiac β-myosin and offer insights into the force-sensing mechanism displayed by the cardiac myosin motor. Short Summary Cryo-EM was used to elucidate high-resolution structures of actin-tropomyosin filaments decorated with human cardiac myosin in the rigor and ADP-bound states. Differences in the myosin lever arm orientation detected correlate with the overall actomyosin-linked force-sensitivity.