Miracle-dz/UniFAR-FTUs huggingface dataset:
Transforming medical imaging with Transformers? A comparative review of key properties, current progresses, and future perspectives

Transformer, one of the latest technological advances of deep learning, has gained prevalence in natural language processing or computer vision. Since medical imaging bear some resemblance to computer vision, it is natural to inquire about the status quo of Transformers in medical imaging and ask the question: can the Transformer models transform medical imaging? In this paper, we attempt to make a response to the inquiry. After a brief introduction of the fundamentals of Transformers, especially in comparison with convolutional neural networks (CNNs), and highlighting key defining properties that characterize the Transformers, we offer a comprehensive review of the state-of-the-art Transformer-based approaches for medical imaging and exhibit current research progresses made in the areas of medical image segmentation, recognition, detection, registration, reconstruction, enhancement, etc. In particular, what distinguishes our review lies in its organization based on the Transformer's key defining properties, which are mostly derived from comparing the Transformer and CNN, and its type of architecture, which specifies the manner in which the Transformer and CNN are combined, all helping the readers to best understand the rationale behind the reviewed approaches. We conclude with discussions of future perspectives.
Linking Innovation to Productivity Growth Using Two Waves of the Community Innovation Survey

Using two waves of the Community Innovation Survey (CIS) for the Netherlands, this paper integrates recent lines of research to estimate the contribution of innovation to manufacturing multifactor productivity (MFP) growth. The model uses CIS data to control for the complementarity between internal and external knowledge bases, and investigates the importance of within-firm time interdependencies for inputs into innovation and innovation output. The results show the benefits of including more information on the technological environment of firms. Furthermore, the model shows that tracking the innovation performance of the same firms over time leads to a lower persistence of innovativeness when measured from the output side than when measured from the input side through use of R&D. Moreover, the contribution of innovation to MFP increases when estimating a static innovation model that uses the data obtained after pooling the two waves of CIS. The latter result reflects the . Liens entre innovation et croissance de la productivite mis en evidence par les deux premieres enquetes communautaires sur l'innovation A partir des deux enquetes communautaires sur l’innovation (ECI) realisees pour les Pays-Bas, le present document reprend les pistes de recherche les plus recentes pour estimer la part de l’innovation dans la croissance de la productivite multi-factorielle. Le modele s’appuie sur les donnees des ECI pour verifier la complementarite entre les bases de connaissances internes et externes, tout en mesurant l’importance des interdependances chronologiques a l’interieur des entreprises, qu’il s’agisse des elements entrant dans l’innovation ou de la production d’innovation. L’interet de prendre en compte davantage d’informations sur le contexte technologique des entreprises est mis en evidence. Le modele montre en outre qu’en suivant dans le temps les caracteristiques de l’innovation pour les memes entreprises, on observe une moindre persistance de la capacite d’innovation si celle-ci est mesuree en termes de resultats que si elle est mesuree en termes de R-D. Qui plus est, la part de .
Spatial variability and temporal stability of throughfall in a eucalyptus plantation in the hilly lowlands of southeastern Brazil

Throughfall has been widely studied in forests but there is a scarcity of studies that focus on the spatial variability and temporal stability of throughfall in eucalyptus plantations. We examined throughfall in a daily basis in a 2·5-year eucalyptus plantation in southeastern Brazil using three sample arrangements: (1) close to tree trunks (CT) and in the central point between trunks (BT), (2) four-radial layout centred in tree trunk and (3) eight-radial layout. Throughfall was spatially non-uniform and varied according to the spatial monitoring arrangement: accumulated throughfall/precipitation ratio of 146% (CT) and 85% (BT) in arrangement 1, mean throughfall of 88% in arrangement 2, 84% (hilltop) and 85% (side slope) in arrangement 3. The highest throughfall values, spatial variability and persistence of dry and wet conditions were found close to eucalyptus trunks. Often accumulated throughfall close to trunks exceeded rainfall, especially for long-duration rainfall > 5 mm. The ‘funnel effect’ was consistently observed in all three arrangements and we speculate that the high throughfall concentration and temporal stability are related to canopy structures of eucalyptus. Copyright © 2011 John Wiley & Sons, Ltd.
A CRISPR-based system to investigate HBV cccDNA biology

ABSTRACT Chronic hepatitis B virus (HBV) infections affect over 250 million people worldwide, and over 800,000 are expected to die yearly from complications including cirrhosis and primary hepatocellular carcinoma. While clinically available nucleoside analog-based antiviral therapies inhibit virus production, they cannot cure infections due to the persistence of covalently closed circular (cccDNA) in the nuclei of infected hepatocytes. Hence, the goals of future curative antiviral therapies for chronic hepatitis B are to either eliminate or permanently silence transcription from cccDNA. Novel antiviral approaches building on a better understanding of the mechanisms underlying transcriptional regulation and the stability of HBV cccDNA will be necessary to accomplish such goals. To advance our understanding of cccDNA biology, we have employed a CRISPR/Cas9-based system to produce extrachromosomal circular (ec) DNA from plasmid DNA integrated into the host genome originally developed by Moller et al. [Nucleic Acid Research 46:(22) e131, 2018]. We modified the enhanced green fluorescent protein (EGFP) reporter system to include portions of the HBV genome encoding wild-type and inactive hepatitis B virus X (HBx) proteins on ecDNA to mimic cccDNA. We demonstrated that expression of EGFP is inhibited by the SMC5/6 complex, as is cccDNA, and that HBx expression can reverse transcriptional silencing of ecDNA. Moreover, we demonstrated that ecDNA is lost during cell division. The system described in this report permits investigations on ecDNA and enables large-scale screening of compound libraries for small molecules targeting host factors involved in ecDNA and, by inference, cccDNA transcription, maintenance, and loss during cell division. IMPORTANCE Hepatitis B virus cccDNA is the key target for the necessary development of antiviral therapies aimed at curing chronic hepatitis B. The CRISPR-based system to produce covalently closed circular (cccDNA)-like extrachromosomal DNAs described in this report enables large-scale screens of chemical libraries to identify drug candidates with the potential to permanently inactivate cccDNA. Moreover, this approach permits investigations on unresolved problems as described in this report concerning cccDNA biology including mechanisms of SMC5/6-dependent transcriptional silencing and the contributions of the SMC5/6 complex to cccDNA stability in resting and dividing hepatocytes. Hepatitis B virus cccDNA is the key target for the necessary development of antiviral therapies aimed at curing chronic hepatitis B. The CRISPR-based system to produce covalently closed circular (cccDNA)-like extrachromosomal DNAs described in this report enables large-scale screens of chemical libraries to identify drug candidates with the potential to permanently inactivate cccDNA. Moreover, this approach permits investigations on unresolved problems as described in this report concerning cccDNA biology including mechanisms of SMC5/6-dependent transcriptional silencing and the contributions of the SMC5/6 complex to cccDNA stability in resting and dividing hepatocytes.
Machine learning methods for tracer kinetic modelling

Abstract Tracer kinetic modelling based on dynamic PET is an important field of Nuclear Medicine for quantitative functional imaging. Yet, its implementation in clinical routine has been constrained by its complexity and computational costs. Machine learning poses an opportunity to improve modelling processes in terms of arterial input function prediction, the prediction of kinetic modelling parameters and model selection in both clinical and preclinical studies while reducing processing time. Moreover, it can help improving kinetic modelling data used in downstream tasks such as tumor detection. In this review, we introduce the basics of tracer kinetic modelling and present a literature review of original works and conference papers using machine learning methods in this field.
Petrology of the highlands massifs at Taurus-Littrow - An analysis of the 2-4 mm soil fraction

The petrography, phase chemistry, and Ar-40/Ar-39 ages of 2-4 mm fragments from the soils of both mare and highlands stations sampled by Apollo 17 are studied. It is found that the massifs consist of a complex stratigraphy of interlayered noritic breccias of varying metamorphic grades, melt rocks, and anorthositic rocks. A stratigraphic correlation of the lithologies within the North Massif and the South Massif is carried out. The petrogenesis of rock types with respect to thermal and impact history is discussed. The observed spinel cataclasites may represent relatively deep material sampled by the Serenitatis event.
Photographic evidence from a recreational angler of the northernmost record of the bull shark Carcharhinus leucas (Elasmobranchii: Carcharhinidae) in the western Pacific Ocean

Abstract Photographs of a single shark specimen (1040 mm in total length) caught in the Oyodo River estuary, Miyazaki Prefecture, Kyushu, Japan, by a recreational angler and uploaded to the social networking service Facebook, were identified as a juvenile specimen of the bull shark Carcharhinus leucas. The photographic record, now deposited in the Kanagawa Prefectural Museum of Natural History collection, represents the northernmost record of this species in the western Pacific Ocean. Although C. leucas is known to utilize primarily tropical estuarine habitats as nursery grounds, a few reports exist regarding the utilization of subtropical and warm-temperate latitude estuaries, as in this case. From the perspectives of species conservation and shark-bite mitigation in warm-temperate latitudes, further information on C. leucas occurrence around its northern distribution limit is required.
Mercury distribution in water, sediment and soil in the Idrijca and SoĉAhca river systems

Although the production of mercury (Hg) at the Idrija mercury mine, Slovenia, stopped in 1994, the tailings and contaminated soils in the mining region are continuously eroded and serve as a permanent source of Hg to the downstream rivers, flood plains and the Gulf of Trieste. The present article describes measurements of total Hg and monomethylmercury (MeHg) in various environmental compartments in the rivers Idrijca and So|$$|Ahca and the Gulf of Trieste during the period 1998–2000. Total Hg in the Idrijca river water upstream of the mercury mine varied between 2.8 and 6.9 ng l−1 and increased to 197 ng l−1 downstream of the mercury mine and remained elevated further downstream along the rivers Idrijca and So|$$|Ahca (from c. 10 to 59 ng l−1), with lowest concentrations found in marine waters (from 0.2 to 2.0 ng l−1). The concentrations of total Hg were higher after the rain, which caused erosion and transport of particles enriched with Hg. Concentrations of MeHg were quite variable and did not follow the same trend as total Hg. The concentrations of MeHg in August 1999 were significantly higher than in June 1998, indicating the importance of seasonal effects, as well as hydrological conditions, on the production of MeHg. Above the mercury mine, MeHg was 0.1–0.2 ng l−1 and doubled below the mercury mine. Downstream, in the rivers Idrijca and So|$$|Ahca, MeHg varied from 0.05 to 0.53 ng l−1 and in marine waters from 0.06 to 0.08 ng l−1. Concentrations of Hg in sediments also increased downstream several fold with a value of 5.39 μg g−1 above the mercury mine to a maximum of 727 μg g−1 below the mine in the silt and clay fraction. The coarser-grained fraction (0.063 < d < 1.4 mm) frequently exceeded the value of total Hg in the silt and clay fraction due to the presence of particles of cinnabar. The concentrations of MeHg in sediments did not follow the same trend as total mercury. Highest concentrations of 14.1 and 10.0 ng g−1 were found downstream of the peak total Hg concentration in sediments. In general, higher MeHg concentrations were associated with the silt and clay fraction, and accounted for 0.001–0.144% of total Hg. Total Hg in flood plain surficial soils varied from 60 to 150 μg g−1 with less than 0.01% of mercury as MeHg. The results confirmed the fact that beside soils that are naturally elevated in Hg due to the high levels of Hg in geological materials in the Idrija district, there are also Hg-laden materials and tailings that are continuously eroded and deposited in flood plains downstream and serve as an important additional source of Hg to the rivers and the Gulf of Trieste. Important transformation mechanisms take place during fluvial transport, evidenced by the presence of MeHg in the various samples analyzed.
The behavioural response of juvenile Atlantic salmon (Salmo salar) and brook trout (Salvelinus fontinalis) to experimental hydropeaking on a Newfoundland (Canada) river

Deregulation of the electric power market globally will lead to increased requirement for electricity on demand resulting in more emphasis on ‘hydropeaking’ generation. A research study was conducted on the regulated West Salmon River, Newfoundland, Canada, to examine habitat selection and movement of juvenile Atlantic salmon (Salmo salar) and brook trout (Salvelinus fontinalis) in response to flow changes related to ‘experimental’ peaking flow power generation. Fish were surgically implanted with microscale radio transmitters, released into an experimental study, and discharge was experimentally manipulated simulating two scenarios: (i) water storage during the day and generation at night, with a 2 hour transition; and (ii) night‐time storage with generation during the day. Experiments were repeated in the summer and fall. Fish were tracked throughout the diurnal cycle of each manipulation and precisely positioned in two‐dimensional space. Atlantic salmon exhibited two distinct patterns to movement: fish that showed high site fidelity and those that moved considerably during trials. Both salmon and trout were more active during fall hydropeaking experiments. Fish generally did not move long distances and moved more in a longitudinal fashion than laterally. Salmon moved greater distances, on average, than trout under all experimental conditions and during both seasons but these differences were not statistically significant. Brook trout moved more in relation to dynamic events (up‐ and down‐ramping) than at steady state flows. Trout also moved more at night during these dynamic changes and under low flow conditions. These results will assist producers of hydroelectricity to reduce the impacts of hydropeaking operations on fish and fish habitat. Copyright © 2003 John Wiley & Sons, Ltd.
AIRBORNE VIDEOGRAPHY: PRINCIPLES AND PRACTICE

On a utilise les cameras-video de facon intermittente depuis les annees 1960 pour recueillir des images de la surface terrestre. D'importantes ameliorations introduites recemment dans la technologie des cameras-video et dans celle des bandes d'enregistrement, notamment par l'utilisation de capteurs a transfert de charges (CCD/DTC) et d'obturateurs a stroboscopie dans les cameras et par le remplacement les bandes VHS par le Super- VHS, se sont traduites par de grandes ameliorations dans la geometrie, la stabilite et la qualite de l'image. Une etude comparative de la resolution spatiale d'une video S-VHS et de photographies a petit ou moyen format, a montre que, pour une meme hauteur de vol, la bande video S-VHS donnait des resultats tout a fait similaires a ceux d'une photographie 35 mm faite avec un objectif de focale 40 mm.
A multiproxy analysis of sedimentary organic carbon in the Changjiang Estuary and adjacent shelf

Surface sediments from the Changjiang Estuary and adjacent shelf were analyzed using a variety of bulk and molecular techniques, including grain size composition, sediment surface area (SSA), elemental composition (C, N), stable carbon isotopic composition (δ13C), n‐alkanes, lignin phenols, and glycerol dialkyl glycerol tetraether lipids to obtain a more comprehensive understanding of the sources and fate of sedimentary organic carbon (SOC) in this dynamic region. Bulk N/C ratios of 0.09 to 0.15, δ13C of −24.4‰ to −21.1‰, branched/isoprenoid tetraether index of 0 to 0.74, n‐alkane content of 0.02 to 0.37 mg g−1 organic carbon (OC), and lignin content (Λ8) of 0.10 to 1.46 mg/100 mg OC and other related molecular indices in these samples indicate a mixed source of marine, soil, and terrestrial plant‐derived OC in the study area. A three‐end‐member mixing model using principal component analysis (PCA) factors as source markers and based on Monte Carlo (MC) simulation was constructed to estimate the relative contributions of OC from different sources. Compared with traditional mixing models, commonly based on a few variables, this newly developed PCA‐MC model supported bulk and biomarker data and yielded a higher‐resolution OC inputs to different subregions of this system. In particular, the results showed that the average contributions of marine, soil, and terrestrial OC in the study area were 35.3%, 47.0%, and 17.6%, and the highest contribution from each OC source was mainly observed in the shelf, inner estuary, and coastal region, respectively.
A paired‐watershed budget study to quantify interbasin groundwater flow in a lowland rain forest, Costa Rica

A paired‐watershed budget study was used to quantify the annual water and major ion (sodium, potassium, magnesium, calcium, chloride, and sulfate) budgets of two adjacent lowland rain forest watersheds in Costa Rica. Interbasin groundwater flow (IGF) accounted for about two thirds of the water input and about 97% of the solute input (an average over the six major ions) to one watershed but little or none of the inputs to the adjacent watershed in which IGF was at most marginally distinguishable from zero. Results underscore the significance of IGF as a potential control on the hydrology and water quality of lowland watersheds, the spatial complexity of its occurrence in lowlands (where its influence may range from dominating to negligible on adjacent watersheds), and the importance of accounting for IGF in the design and execution of watershed studies and in water management.
Genitourinary Conditions in Young Dancers: Relationship between Urinary Incontinence and Foot Flexibility

Research into dance pathology usually focuses on musculoskeletal and endo-crine-nutritional conditions. However, when practiced full time other systems can also be affected. The aim of this work was to determine the prevalence of genitourinary conditions in dance and to establish whether any correlation exists between stress urinary incontinence (SUI) and the cushioning capacity of the foot. A total of 32 pre-professional dancers (27 females and 5 males; 19 ± 2.2 years old) who practiced several types of dance in the Madrid Professional Conservatoire of Dance were studied. The data were obtained using a questionnaire, personal interviews, and physical examination. The height of the internal plantar arch of both feet was measured before and after training, estimating the flexibility of the plantar arch (percentage change in height of arch between both situations). Multiple regression analysis was used to analyze the existence of a possible relationship between SUI and plantar flexibility. A total of 68.7% of dancers had suf-fered a genitourinary condition at some time during their lives, and 48.1% of the female dancers and 20% of the males had suffered SUI. SUI was triggered by dance in 69.2% of the females with urinary incontinence, and was considered as problematic by 30.7%. SUI occurs during the classes in 55% of cases, mainly during ballet activities, followed by flamenco tap dancing. SUI associated with dance is more closely related to the flexibility of the plantar arch in basal conditions (r2 = 0.64, p < 0.05, t-stat = 3.57) and after training (r2 = 0.76, p < 0.05, t-stat = 3.52), than that presenting in diverse situations (r2 = 2.07, p < 0.05, t-stat = 3.1), for which other causal factors must be sought. Lower genitourinary tract disorders are more prevalent in pre-professional dancers than in the general population; and dance itself is the main triggering factor of SUI. We, therefore, recommend that more attention be paid to the genitourinary system in dance medicine and propose a series of preventive measures.
WiFi Sensing with Single-Antenna Devices for Ambient Assisted Living

The absolute coverage WiFi networks is higher than it has ever been and WiFi sensing offers a device-free, contactless alternative to intrusive wearable devices for a variety of applications, in particular for ambient assisted living (AAL). However, a majority of sensing systems proposed in literature use multiple antennas for sensing, resulting in high cost that hinders development of such solutions in real life. This work surveys existing single-antenna systems as a low-cost solution in an AAL scenario. The capabilities of these systems are examined regarding their practical applicability based on testing in AAL environments, leveraging multiple links (i.e. transmitter-receiver pairs) and considering mobile and repositioned receivers. It is found that while the AAL use-cases of respiration monitoring, fall detection and activity recognition are realised by existing systems, further testing in realistic AAL environments with the inclusion of activities of daily living is needed. Additionally the full use of multiple links and consideration of a mobile receiver is still rare, but shows promising improvements. A multi-task system enabling all three applications is discussed using the Model for Ethical Evaluation of Socio-Technical Arrangements (MEESTAR). We suggest an ethically sensitive use, but identify a need for mitigation strategies to address privacy-related concerns of potentially unwilling users.
Construction of All Multilayer Monolithic RSMTs and Its Application to Monolithic 3D IC Routing

Monolithic three-dimensional (M3D) integration allows ultra-thin silicon tier stacking in a single package. The high-density stacking is acquiring interest and is becoming more popular for smaller footprint areas, shorter wirelength, higher performance, and lower power consumption than the conventional planar fabrication technologies. The physical design of M3D integrated circuits requires several design steps, such as three-dimensional (3D) placement, 3D clock-tree synthesis, 3D routing, and 3D optimization. Among these, 3D routing is significantly time consuming due to countless routing blockages. Therefore, 3D routers proposed in the literature insert monolithic interlayer vias (MIVs) and perform tier-by-tier routing in two substeps. In this article, we propose an algorithm to build a routing topology database (DB) used to construct all multilayer monolithic rectilinear Steiner minimum trees on the 3D Hanan grid. To demonstrate the effectiveness of the DB in various applications, we use the DB to construct timing-driven 3D routing topologies and perform congestion-aware global routing on 3D designs. We anticipate that the algorithm and the DB will help 3D routers reduce the runtime of the MIV insertion step and improve the quality of the 3D routing.