Miracle-dz/UniFAR-FTUs huggingface dataset:
Fully integrated modeling of surface‐subsurface solute transport and the effect of dispersion in tracer hydrograph separation

Tracer hydrograph separation has been widely applied to identify streamflow components, often indicating that pre‐event water comprises a large proportion of stream water. Previous work using numerical modeling suggests that hydrodynamic mixing in the subsurface inflates the pre‐event water contribution to streamflow when derived from tracer‐based hydrograph separation. This study compares the effects of hydrodynamic dispersion, both within the subsurface and at the surface‐subsurface boundary, on the tracer‐based pre‐event water contribution to streamflow. Using a fully integrated surface‐subsurface code, we simulate two hypothetical 2‐D hillslopes with surface‐subsurface solute exchange represented by different solute transport conceptualizations (i.e., advective and dispersive conditions). Results show that when surface‐subsurface solute transport occurs via advection only, the pre‐event water contribution from the tracer‐based separation agrees well with the hydraulically determined value of pre‐event water from the numerical model, despite dispersion occurring within the subsurface. In this case, subsurface dispersion parameters have little impact on the tracer‐based separation results. However, the pre‐event water contribution from the tracer‐based separation is larger when dispersion at the surface‐subsurface boundary is considered. This work demonstrates that dispersion within the subsurface may not always be a significant factor in apparently large pre‐event water fluxes over a single rainfall event. Instead, dispersion at the surface‐subsurface boundary may increase estimates of pre‐event water contribution. This work also shows that solute transport in numerical models is highly sensitive to the representation of the surface‐subsurface interface. Hence, models of catchment‐scale solute dynamics require careful treatment and sensitivity testing of the surface‐subsurface interface to avoid misinterpretation of real‐world physical processes.
Financial Analysis of Biosimilar Development Candidates: A Case Study on the US Biosimilar Business

This case study investigates the US biosimilar business and the approach that should be implemented when financially analyzing biosimilar development candidates. To challenge the theory that the biosimilar business will be best suited for biologics experiencing the largest sales figures, this case study applied a financial analysis towards two biosimilar development candidates with contrasting sales. Using Soliris (eculizumab) and Remicade (infliximab) biosimilars as a test case, this case study hypothesized that a Soliris biosimilar has the opportunity to create more value over timeÏdespite Soliris® having less sales than Remicade®Ïdue to its favorable market outlook. Over the next few years, the US biosimilar landscape is expected to evolve into a profitable business venture as the first wave of biologics, particularly monoclonal antibodies, begin to lose patent protection. With some biologics experiencing more than $5 billion in annual sales, many analysts believe biosimilars to these biologics will generate more value than a biosimilar to a reference biologic making under $5 billion in sales. However, based on the findings from this case study, the opposite was true. Using a productand market-driven net present value (NPV) evaluation, this case study uncovered that a Soliris biosimilar candidate has the potential to generate more value than a Remicade biosimilar0"Fgoqpuvtcvkpi"vjcv"vjg"tghgtgpeg"dkqnqikeÓu"ucngu"fkf"pqv" translate to a greater valuation for the Remicade biosimilar, this case was able to substantiate the importance in financially analyzing biosimilar development candidates beyond the sales of a reference biologic. In addition, this case study was able to demonstrate the utility in using a productand market-driven valuation approach in the value determination of biosimilar development candidates.
Electromagnetic spectrum survey of the environment in a locality in Kuala Lumpur, Malaysia

The electromagnetic spectrum in the environment is becoming a scarce resource with the emergence of a high number of wireless communications services Cognitive radio (CR) is viewed as a possible solution to the spectrum bottleneck which work in a premise that at an any given time and spatial region there are frequency bands that has no signal occupancy. The CR technique utilizes a temporarily unoccupied licensed band by allowing secondary users to exploit opportunistically the underutilized spectrum licensed to primary users without any harmful interference. Before investigating the technical and political implications of CR, it is necessary to know to what extent the licensed bands are temporally unoccupied. In this paper a spectrum occupancy measurements is conducted to study the utilization of RF spectrum in an environment. The measurements are performed on UHF TV, GSM900 and GSM1800 frequency bands in an urban area in Kuala Lumpur, Malaysia. The evaluation made is based on the power detection principle. From the measurements, the spectrum holes are identified. The obtained results show that the spectral usage is 7.37% for UHF TV band, 12.8% for GSM900 and 5.3% for GSM1800 band leading to the conclusion that a significant amount of spectrum is available for deployment of cognitive radio.
Chirping compact stars: gravitational radiation and detection degeneracy with binaries

Compressible, Riemann S-type ellipsoids can emit gravitational waves (GWs) with a chirp-like behavior (hereafter chirping ellipsoids, CELs). We show that the GW frequency-amplitude evolution of CELs (mass ∼ 1 M⊙, radius ∼ 103 km, polytropic equation of state with index n ≈ 3) is indistinguishable from that emitted by double white dwarfs and by extreme mass-ratio inspirals (EMRIs) composed of an intermediate-mass (e.g. 103 M⊙) black hole and a planet-like (e.g. 10-4 M⊙) companion, in the frequency interval within the detector sensitivity band in which the GW emission of these systems is quasi-monochromatic. For reasonable astrophysical assumptions, the local universe density rate of CELs, double white dwarfs, and EMRIs in the mass range here considered are very similar, posing a detection-degeneracy challenge for space-based GW detectors. We outline the astrophysical implications of this CEL-binary detection degeneracy by space-based GW-detection facilities.
Physics based modeling of LiFePO4 cathodes: effects of electrode parameters on cell performance during fast charging

Lithium-iron phosphate (LFP) has emerged as a potential cathode material due to its lower cost and higher stabilities. This work investigates LFP cell behavior at higher C-rates via a detailed simulation study. To facilitate this investigation, a physics-based electrochemical model is calibrated and validated with in-house experimental data. The validated model is used to study the effect of particle size, lithium diffusivity, and electrode thickness on the charge-discharge capacity of Li-LFP cells for a range of C-rates up to 5 C. A detailed discussion is carried out to explain the results of parametric studies, in terms of transport limitations, irreversible losses (overpotentials) and their dependence on different electrode parameters. The model helps us to depict the effect of these parameters on internal profiles of SOC and overpotentials, allowing for a deeper understanding of the cell behavior. Overall, the simulations show that the LFP cell is able to exhibit good capacity at higher C-rates by tuning the particle size and lithium diffusivity. An optimal combination of material and physical parameters is identified to maximize the possible capacity of LFP electrodes.
Autophagy in normal hematopoiesis and leukemia

Autophagy is a highly regulated catabolic process that involves sequestration and lysosomal degradation of cytosolic components such as damaged organelles and misfolded proteins. While autophagy can be considered to be a general cellular housekeeping process, it has become clear that it may also play cell type-dependent functional roles. In the present study we analyzed the functional importance of autophagy in human hematopoietic stem/progenitor cells (HSPCs), and how this is regulated during differentiation. Western blot-based analysis of LC3-II and p62 levels, as well as flow cytometry-based autophagic vesicle quantification, demonstrated that umbilical cord blood (UCB)-derived CD34 + /CD38 - immature hematopoietic progenitors show a higher autophagic flux than CD34 + /CD38 + progenitors and more differentiated myeloid and erythroid cells. This high autophagic flux was critical for maintaining stem and progenitor function since knockdown of autophagy genes ATG5 or ATG7 resulted in reduced HSPC frequencies in vitro as well as in vivo . This reduction in HSPCs was not due to impaired differentiation, but at least in part due to reduced cell cycle progression and increased apoptosis. This is accompanied by increased expression of p53, pro-apoptotic genes BAX and PUMA, and the cell cycle inhibitor p21, as well as increased levels of cleaved caspase-3 and reactive oxygen species (ROS). Taken together, our data demonstrate that autophagy is an important regulatory mechanism for human HSCs and their progeny, reducing cellular stress and promoting survival.
Prolonged drying trend coincident with the demise of Norse settlement in southern Greenland

Declining temperature has been thought to explain the abandonment of Norse settlements, southern Greenland, in the early 15th century, although limited paleoclimate evidence is available from the inner settlement region itself. Here, we reconstruct the temperature and hydroclimate history from lake sediments at a site adjacent to a former Norse farm. We find no substantial temperature changes during the settlement period but rather that the region experienced a persistent drying trend, which peaked in the 16th century. Drier climate would have notably reduced grass production, which was essential for livestock overwintering, and this drying trend is concurrent with a Norse diet shift. We conclude that increasingly dry conditions played a more important role in undermining the viability of the Eastern Settlement than minor temperature changes.
Implications of the cardiomyocyte stress response on protein homeostasis in atrial fibrillation

cardiomyocytes and in vivo tachypaced Drosophila melanogaster and a canine model for AF. These findings imply that 4PBA comprises a novel therapeutic intervention for treatment of clinical AF. Finally, in chapter 7 we explored mitochondrial function in an experimental AF model, as the ER and mitochondrial function are linked to each other and ER stress often leads to mitochondrial stress. 30 We show tachypacing to induce mitochondrial stress and mitochondrial dysfunction, as exemplified by the increased transcription of the mitochondrial stress chaperones HSP60 and HSP10, fragmentation of the mitochondrial network and reduction of cellular ATP levels, mitochondrial membrane potential, mitochondrial calcium transients and maximal respiratory capacity. Features the Ca 2+ flux from VDAC to the mitochondrial matrix. The connection of Bap31 and Fis1 regulates the activation of the mitochondrial programmed cell death pathway. Mfn2 forms homo- or heterotypic connections with Mfn2 or Mfn1, respectively and Mfn2 is important for mitochondrial fusion and respiration, ER stress and autophagy induction. Furthermore, the ER and the mitochondria are sensitive to each other’s stress through the MAMs. Moreover, the MAMs are implicated to be the site where the formation of the autophagosomes occurs, as ATG14 and ATG5 are present at the MAMs at autophagy initiation.
Cell-autonomous and non-cell autonomous protection of DNAJB6 in Huntington’s disease

Several neurodegenerative diseases like Huntington’s, a polyglutamine (PolyQ) disease, are initiated by protein aggregation in neurons. Furthermore, these diseases are also associated with a multitude of responses in non-neuronal cells in the brain, in particular glial cells, like astrocytes. These non-neuronal responses have repeatedly been suggested to play a disease-modulating role, but how these may be exploited to delay the progression of neurodegeneration has remained unclear. Interestingly, one of the molecular changes that astrocytes undergo includes the upregulation of certain Heat Shock Proteins (HSPs) that are classically considered to maintain protein homeostasis, thus resulting in cell autonomous protection. Previously, we discovered DNAJB6, a member of the human DNAJ family, as potent cell autonomous suppressor of PolyQ aggregation and related neurodegeneration. In the Chapter 4, we confirmed that the cell autonomous protective function of human DNAJB6 against PolyQ aggregation was also maintained in D. melanogaster . In this Chapter, using the same cell type specific expression systems in D. melanogaster , we show that exclusive expression of DNAJB6 in astrocytes (that do not express PolyQ protein) can delay neurodegeneration and expands lifespan when the PolyQ protein is exclusively expressed in neurons (that do not co-express DNAJB6 themselves). This provides direct evidence for a non-cell autonomous protective role of astrocytes in PolyQ diseases.
Passive seismic tomography using induced seismicity at a petroleum field in Oman

A borehole network consisting of five monitoring wells monitored the induced seismicity at a producing petroleum field for about 11 months . Nearly 5400 microseismic events were analyzed and used to image the reservoir based on a new double-difference (DD) seismic tomography. The DD tomography method simultaneously solved for event locations and VP , VS , and VP ∕ VS models using absolute and differential P, S, and S-P arrival times. Microseismicity in the field was caused primarily by compaction of the reservoir in and above the gas-bearing formation and was distributed along the two major northeast-southwest faults in the field. The model resolution analysis based on the checkerboard test and the resolution matrix showed that the central part of the model was resolved relatively well for the depth range of 0.7 to 1.1 km . Clear velocity contrasts were imaged across most parts of the two northeast-southwest faults. The VP ∕ VS ratio estimates from the tomographic inversion were low (<1.75) in the shallow.
Approaches for continuous delivery in regulated environments: the case of passenger-facing software in the aviation industry

of the master’s thesis Author Walter Berggren Title Approaches for continuous delivery in regulated environments: the case of passenger-facing software in the aviation industry Degree programme Computer, Communication and Information Sciences Major Security and Cloud Computing Code of major SCI3084 Supervisor PhD Fabian Fagerholm Advisor MSc Jarkko Kailanto Date 2021-09-24 Number of pages 60 Language English
UvA-DARE (Digital Academic The interface between forensic science and technology how technology could cause a paradigm shift in the role of forensic institutes in the criminal justice system

environment. The benefits of real-time, on-site forensic investigations are manifold and such technology has the potential to strongly increase the speed and efficacy of the criminal justice system. However, such benefits are only realized when quality can be guaranteed at all times and findings can be used as forensic evidence in court. At the Netherlands Forensic Institute, innovationefforts are currently undertaken to develop integrated forensic platform solutions that allow for the forensic investigation of human biological traces, the chemical identification of illicit drugs and the study of large amounts of digital evidence. These platforms enable field investigations, yield robust and validated evidence and allow for forensic intelligence and targeted use of expert capacity at the forensic institutes. This technological revolution in forensic science could ultimately lead to a paradigm shift in which a new role of the forensic expert emerges as developer and custodian of integrated forensic platforms.
Similarity of the wind wave spectrum in finite depth water: 1. Spectral form

A self-similar spectral shape (the TMA spectrum) to describe wind waves in water of finite depth is presented. The parametric spectral form is depth dependent and an extension of the deep water JONSWAP spectrum. The behavior of the spectrum in frequency and wave number space is discussed. About 2800 spectra selected from three data sets (TEXEL storm, MARSEN, ARSLOE) are investigated to show the general validity of the proposal self-similar spectral shape.
Urban Tree Cover Mapping with Relief-corrected Aerial Imagery and Lidar

This article discusses how urban tree canopy cover is often mapped by classifying high-resolution multispectral imagery. However, it can be difficult to differentiate low-lying vegetation from tree cover using optical data alone. Combining a lidar-derived normalized digital surface model (NDSM) improves classification accuracy, but the optical imagery is often imperfectly aligned with the NDSM. Aerial imagery is normally orthorectified using the ground elevation. However, tall objects in the orthorectified imagery still suffer from relief displacement and this can cause classification errors when lidar and the aerial imagery are combined. This article presents an approach for urban tree cover mapping that is composed of two parts. The first part is a method for correcting the relief displacement of trees in previously orthrectified aerial imagery, and the second part is an object-based classification method that combines relief-corrected multispectral aerial imagery with a lidar-derived NDSM. Using these methods, tree cover was mapped for a 1,600 ha region of London, Ontario, Canada with improved positional and classification accuracy.
Explorer Logics for Unranked Trees : An Overview

Labeled unranked trees are used as a model of XML documents, and logical languages for them have been studied actively over the past several years. Such logics have different purposes: some are better suited for extracting data, some for expressing navigational properties, and some make it easy to relate complex properties of trees to the existence of tree automata for those properties. Furthermore, logics differ significantly in their model-checking properties, their automata models, and their behavior on ordered and unordered trees. In this paper we present a survey of logics for unranked trees.
Nauplius-The Journal of The Brazilian Crustacean Society

Many monitoring studies use marking techniques to obtain dispersal data on individuals. Marking procedures may influence the vital activities of the terrestrial isopods, such as feeding behavior. The objective of this study was to identify the efficiency of different materials for external marking of woodlice and the influence on their feeding performance. Cyanoacrylate glue + glitter and nail polish were used as separate marking materials on three species: Balloniscus glaber, Benthana picta and Armadillidium vulgare. The material efficiency was compared using Kaplan-Meier curves and Log-Rank analysis. Individuals were fed with leaf discs of Machaerium stipitatum for feeding performance trials, and consumption rates were compared using ANOVA (α<0.05). There was no difference in durability between the materials used for external markings, except between marked and unmarked Benthana specimens when the observation period exceeded 15 days (Log-Rank=8.446, p=0.015). Nail polish was considered more suitable for feeding experiments. Statistical differences in consumption rates were observed only between the marked individual treatments of Benthana (ANOVA, F=7.5440, p=0.0002). These results indicate that external marking does not affect the feeding habits of the animals and suggest that this technique can be used to monitor dispersal of terrestrial isopods in field conditions for approximately 15 days.
Nanopore sequencing of Giardia reveals widespread intra-isolate structural variation

24 Background: Genomes of the parasite Giardia duodenalis are relatively small for eukaryotic 25 genomes, yet there are only six publicly available. Difficulties in assembling the tetraploid G. 26 duodenalis genome from short read sequencing data likely contribute to this lack of genomic 27 information. We sequenced three isolates of G. duodenalis (AWB, BGS, and beaver) on the 28 Oxford Nanopore Technologies MinION whose long reads have the potential to address genomic 29 areas that are problematic for short reads. 30 Results: Using a hybrid approach that combines MinION long reads and Illumina short reads to 31 take advantage of the continuity of the long reads and the accuracy of the short reads we 32 generated reference quality genomes for each isolate. The genomes for two of the isolates were 33 evaluated against the available reference genomes for comparison. The third genome for which 34 there is no previous data was then assembled. The long reads were used to find structural 35 variants in each isolate to examine heterozygosity. Consistent with previous findings based on 36 SNPs, Giardia BGS was found to be considerably more heterozygous than the other isolates that 37 are from Assemblage A. We also find an enrichment of variant-specific surface proteins in some 38 of the structural variant regions. 39 Conclusions: Our results show that the MinION can be used to generate reference quality 40 genomes in Giardia and further be used to identify structural variant regions that are an 41 important source of genetic variation not previously examined in these parasites.
High-resolution wave-equation AVA imaging: Algorithm and tests with a data set from the Western Canadian Sedimentary Basin

This paper presents a 3D least-squares waveequation migration method that yields regularized common-image gathers (CIGs) for amplitude-versusangle (AVA) analysis. In least-squares migration, we pose seismic imaging as a linear inverse problem; this provides at least two advantages. First, we are able to incorporate model-space weighting operators that improve the amplitude fidelity of CIGs. Second, the influence of improperly sampled data (footprint noise) can be diminished by incorporating data-space weighting operators. To investigate the viability of this class of methods for oil and gas exploration, we test the algorithm with a real-data example from the Western Canadian Sedimentary Basin. To make our problem computationally feasible, we utilize the 3D common-azimuth approximation in the migration algorithm. The inversion algorithm uses the method of conjugate gradients with the addition of a ray-parameter-dependent smoothing constraint that minimizes sampling and aperture artifacts. We show that more robust AVA attributes can be obtained by properly selecting the model and data-space regularization operators. The algorithm is implemented in conjunction with a preconditioning strategy to accelerate convergence. Posing the migration problem as an inverse problem leads to enhanced event continuity in CIGs and, hence, more reliable AVA estimates. The vertical resolution of the inverted image also improves as a consequence of increased coherence in CIGs and, in addition, by implicitly introducing migration deconvolution in the inversion.