Miracle-dz/UniFAR-FTUs huggingface dataset:
A question of uncertainty

Hydrology, like other environmental sciences, entails sample collection as well as numerous and diverse physical and chemical measurements. Eventually, all these data are used to describe or infer processes, or to calculate various parameters such as annual fluxes of suspended sediment, rates of erosion, various yields, and so forth. In many cases, these measurements also are used to address regulatory requirements, to determine if there has been some sort of environmental impact, or to determine if remediation efforts have achieved stated goals. Despite our best efforts, every step through all these sampling and measurement processes entails some level of uncertainty (error). Some of this uncertainty results from the instrument(s) used to generate the data whereas others are associated with the operator. Regardless of the source, all the measurements and calculated values that we generate and report, whilst typically represented by a single tabulated number, actually represent a range of values. In turn, all the interpretations that we make from these measurements and calculated values are subject to the cumulative effects of all this uncertainty. In other words, defensible data reporting and interpretations require an adequate estimate of the uncertainty associated with their generation and should be an integral part of any technical report or scientific publication. As a relatively simple example, consider the determination of a suspended sediment flux. The flux calculation requires two measurements — discharge and the concentration of suspended sediment — in conjunction with a constant to obtain an appropriate reporting unit. Evaluations of a substantial number of discharge records indicate that even at a good site, the uncertainty (measurement error) for any single discharge measurement is on the order of ±5 to 8% (Sauer and Meyer, 1992). Additionally, near simultaneous replicate collections of suspended sediment using depth‐and‐width‐integrated isokinetic sampling typically fall within the range of ±10% at concentrations greater than 20 mg/l (e.g., Edwards and Glysson, 1999; Horowitz, 2013). Cumulatively that indicates a potential range in the flux estimate on the order of ±15 to 18%. Hence, any subsequent flux calculations falling within that ±15 to 18% range should not be viewed as being significantly different. Chemical analyses of different environmental samples provide another example and tend to display typical uncertainty on the order
Virtual twins for model‐informed precision dosing of clozapine in patients with treatment‐resistant schizophrenia

Abstract Model‐informed precision dosing using virtual twins (MIPD‐VTs) is an emerging strategy to predict target drug concentrations in clinical practice. Using a high virtualization MIPD‐VT approach (Simcyp version 21), we predicted the steady‐state clozapine concentration and clozapine dosage range to achieve a target concentration of 350 to 600 ng/mL in hospitalized patients with treatment‐resistant schizophrenia (N = 11). We confirmed that high virtualization MIPD‐VT can reasonably predict clozapine concentrations in individual patients with a coefficient of determination (R 2) ranging between 0.29 and 0.60. Importantly, our approach predicted the final dosage range to achieve the desired target clozapine concentrations in 73% of patients. In two thirds of patients treated with fluvoxamine augmentation, steady‐state clozapine concentrations were overpredicted two to four‐fold. This work supports the application of a high virtualization MIPD‐VT approach to inform the titration of clozapine doses in clinical practice. However, refinement is required to improve the prediction of pharmacokinetic drug–drug interactions, particularly with fluvoxamine augmentation.
Deep learning model for extensive smartphone-based diagnosis and triage of cataracts and multiple corneal diseases.

AIM To develop an artificial intelligence (AI) algorithm that diagnoses cataracts/corneal diseases from multiple conditions using smartphone images. METHODS This study included 6442 images that were captured using a slit-lamp microscope (6106 images) and smartphone (336 images). An AI algorithm was developed based on slit-lamp images to differentiate 36 major diseases (cataracts and corneal diseases) into 9 categories. To validate the AI model, smartphone images were used for the testing dataset. We evaluated AI performance that included sensitivity, specificity and receiver operating characteristic (ROC) curve for the diagnosis and triage of the diseases. RESULTS The AI algorithm achieved an area under the ROC curve of 0.998 (95% CI, 0.992 to 0.999) for normal eyes, 0.986 (95% CI, 0.978 to 0.997) for infectious keratitis, 0.960 (95% CI, 0.925 to 0.994) for immunological keratitis, 0.987 (95% CI, 0.978 to 0.996) for cornea scars, 0.997 (95% CI, 0.992 to 1.000) for ocular surface tumours, 0.993 (95% CI, 0.984 to 1.000) for corneal deposits, 1.000 (95% CI, 1.000 to 1.000) for acute angle-closure glaucoma, 0.992 (95% CI, 0.985 to 0.999) for cataracts and 0.993 (95% CI, 0.985 to 1.000) for bullous keratopathy. The triage of referral suggestion using the smartphone images exhibited high performance, in which the sensitivity and specificity were 1.00 (95% CI, 0.478 to 1.00) and 1.00 (95% CI, 0.976 to 1.000) for 'urgent', 0.867 (95% CI, 0.683 to 0.962) and 1.00 (95% CI, 0.971 to 1.000) for 'semi-urgent', 0.853 (95% CI, 0.689 to 0.950) and 0.983 (95% CI, 0.942 to 0.998) for 'routine' and 1.00 (95% CI, 0.958 to 1.00) and 0.896 (95% CI, 0.797 to 0.957) for 'observation', respectively. CONCLUSIONS The AI system achieved promising performance in the diagnosis of cataracts and corneal diseases.
Unmutated but T cell dependent IgM antibodies targeting Streptococcus suis play an essential role in bacterial clearance

Streptococcus suis serotype 2 is an important encapsulated bacterial swine pathogen and zoonotic agent for which no effective vaccine exists. The interaction with B cells and the humoral response against S. suis are poorly understood despite their likely relevance for a potential vaccine. We evaluated germinal center (GC) B cell kinetics, as well as the production and role of S. suis-specific antibodies following infections in a mouse model. We found that mice infected with S. suis developed GC that peaked 13–21 days post-infection. GC further increased and persisted upon periodic reinfection that mimics real life conditions in swine farms. Anti-S. suis IgM and several IgG subclasses were produced, but antibodies against the S. suis capsular polysaccharide (CPS) were largely IgM. Interestingly, depletion of total IgG from the wild-type mice sera had no effect on bacterial killing by opsonophagocytosis in vitro. Somatic hypermutation and isotype switching were dispensable for controlling the infection or anti-CPS IgM production. However, T cell-deficient (Tcrb-/-) mice were unable to control bacteremia, produce optimal anti-CPS IgM titers, or elicit antibodies with opsonophagocytic activity. SAP deficiency, which prevents GC formation but not extrafollicular B cell responses, ablated anti S. suis-IgG production but maintained IgM production and eliminated the infection. In contrast, B cell deficient mice were unable to control bacteremia. Collectively, our results indicate that the antibody response plays a large role in immunity against S. suis, with GC-independent but T cell-dependent germline IgM being the major effective antibody specificities. Our results further highlight the importance IgM, and potentially anti-CPS antibodies, in clearing S. suis infections and provide insight for future development of S. suis vaccines.
Many-core algorithms for high-dimensional gradients on phylogenetic trees

Abstract Motivation Advancements in high-throughput genomic sequencing are delivering genomic pathogen data at an unprecedented rate, positioning statistical phylogenetics as a critical tool to monitor infectious diseases globally. This rapid growth spurs the need for efficient inference techniques, such as Hamiltonian Monte Carlo (HMC) in a Bayesian framework, to estimate parameters of these phylogenetic models where the dimensions of the parameters increase with the number of sequences N. HMC requires repeated calculation of the gradient of the data log-likelihood with respect to (wrt) all branch-length-specific (BLS) parameters that traditionally takes O(N2) operations using the standard pruning algorithm. A recent study proposes an approach to calculate this gradient in O(N), enabling researchers to take advantage of gradient-based samplers such as HMC. The CPU implementation of this approach makes the calculation of the gradient computationally tractable for nucleotide-based models but falls short in performance for larger state-space size models, such as Markov-modulated and codon models. Here, we describe novel massively parallel algorithms to calculate the gradient of the log-likelihood wrt all BLS parameters that take advantage of graphics processing units (GPUs) and result in many fold higher speedups over previous CPU implementations. Results We benchmark these GPU algorithms on three computing systems using three evolutionary inference examples exploring complete genomes from 997 dengue viruses, 62 carnivore mitochondria and 49 yeasts, and observe a >128-fold speedup over the CPU implementation for codon-based models and >8-fold speedup for nucleotide-based models. As a practical demonstration, we also estimate the timing of the first introduction of West Nile virus into the continental Unites States under a codon model with a relaxed molecular clock from 104 full viral genomes, an inference task previously intractable. Availability and implementation We provide an implementation of our GPU algorithms in BEAGLE v4.0. 0 (https://github.com/beagle-dev/beagle-lib), an open-source library for statistical phylogenetics that enables parallel calculations on multi-core CPUs and GPUs. We employ a BEAGLE-implementation using the Bayesian phylogenetics framework BEAST (https://github.com/beast-dev/beast-mcmc).
Cidades médias: Do crescimento demográfico à consolidação territorial

Este artigo analisa a evolucao demografica de quatro cidades alentejanas ao longo do seculo XX. Pretende-se caracterizar os diversos tipos de crescimento populacional a partir da relacao desenvolvida entre areas urbanas e rurais. Deste modo, verificaremos ate que ponto se estabelece uma interdependencia entre o aumento do volume populacional destas cidades medias e a consolidacao de dinâmicas territoriais expressas na reanimacao de espacos envolventes, que caminhavam para uma continua regressao.
Twentieth century warming of the tropical Atlantic captured by Sr‐U paleothermometry

Coral skeletons are valuable archives of past ocean conditions. However, interpretation of coral paleotemperature records is confounded by uncertainties associated with single element-ratio thermometers, including Sr/Ca. A new approach, Sr-U, uses U/Ca to constrain the influence of Rayleigh fractionation on Sr/Ca [DeCarlo et al., 2016]. Here, we build on the initial Pacific Porites Sr-U calibration to include multiple Atlantic and Pacific coral genera from multiple coral reef locations spanning a temperature range of 23.15-30.12 °C. Accounting for the wintertime growth cessation of one Bermuda coral, we show that Sr-U is strongly correlated with the average water temperature at each location (r2 = 0.91, P < 0.001, n = 19). We applied the multi-species spatial calibration between Sr-U and temperature to reconstruct a 96-year long temperature record at Mona Island, Puerto Rico using a coral not included in the calibration. Average Sr-U derived temperature for the period 1900-1996 is within 0.12 °C of the average instrumental temperature at this site and captures the 20th century warming trend of 0.06 °C per decade. Sr-U also captures the timing of multi-year variability but with higher amplitude than implied by the instrumental data. Mean Sr-U temperatures and patterns of multi-year variability were replicated in a second coral in the same grid box. Conversely, Sr/Ca records from the same two corals were inconsistent with each other and failed to capture absolute sea temperatures, timing of multi-year variability or the 20th century warming trend. Our results suggest that coral Sr-U paleothermometry is a promising new tool for reconstruction of past ocean temperatures.
Exploring expectations and readiness for healthy lifestyle promotion in Swedish primary health care: a qualitative analysis of managers, facilitators, and professionals

Abstract Objective Prior to a multifaceted implementation strategy for a healthy lifestyle-promoting practice the expectations of primary health care managers, appointed internal facilitators and health care professionals on supporting change was explored. Design This study had an explorative qualitative design using data gathered from individual interviews and focus groups. Qualitative content analysis with a deductive category development was applied using the Consolidated Framework for Implementation Research. Setting and participants The study was conducted in a primary care setting in central Sweden as a part of the Act in Time research project. Prior to a multifaceted implementation strategy, we held 16 individual interviews with managers and appointed facilitators and five focus groups with 26 health care professionals. Results Managers, facilitators, and professionals held similar expectations, where their expressed need for support corresponded to three constructs: Readiness for implementation, Implementation climate, and Engaging. Our findings indicate the need for strong leadership engagement to focus on how the healthy lifestyle-promoting practice can be anchored among the professionals. Managers at all levels should communicate the vision and goals, enable facilitators and professionals to improve their competencies, build inter-professional teams, and jointly plan the new practice. Conclusion To change to a healthy lifestyle promoting practice professionals request support from their managers, who in turn need support from the middle and top managers. The requested support includes helping to prioritise health promotion and enabling the primary care centres to build competence and take ownership of the implementation. Trial registration ClinicalTrials.gov NCT04799860
Studies on construction and performance of the Qiantang River water diversion de-nitrification demonstration project

In this experiment,a biological-ecological process in which modified water mat pond coupling with integrated vertical-flow constructed wetland(IVCW)was proposed considering the low carbon high nitrogen characteristics of West Lake water diversion from the Qiantang River,meanwhile,the construction of nitrogen reducing demonstration project and the performance of coupled system was studied.The experimental results revealed that the average removal rate of COD,TN,NO-3-N and TP during the stable running period of coupling system was 52.27%,52.49%,53.69% and 52.79%,respectively,the effluent COD,NO-3-N and TP could meet grade Ⅳ of surface water environmental quality standards(GB 3838-2002). The modified water mat pond and IVCW as the two important components of the coupling system had complementary advantages in the removal of nitrogen and phosphorus,and ensuring the stability of effluent water quality indexes.In IVCW unit,temperature and influent C/N was in positive correlated with COD and TN removal,and their effect on COD removal was greater than on TN removal.
Characterization of channel oil reservoirs with an aquifer using EnKF, DCT, and PFR

Reservoir characterization is necessary for making reliable models to have future reservoir performances. Since an aquifer typically has positive influences on oil production, its characterization has rarely been regarded as a critical issue. However, in channel oil reservoirs, an aquifer amplifies uncertainty of permeability estimations and has its own uncertainty due to limited information without any direct measurement. Although there have been some researches on channel oil reservoirs using discrete cosine transformation, we cannot characterize reliably an aquifer using discrete cosine transformation alone. Thus, we need additional schemes to manage increased uncertainty by an aquifer and to estimate the aquifer itself. In this study, ensemble Kalman filter with the combination of preservation of facies ratio and discrete cosine transformation is proposed for channel reservoirs with an aquifer. By the proposed method, we confirm that discrete cosine transformation and preservation of facies ratio contribute to preservation of overall channel properties and fine-tuning of the channel in the ensemble Kalman filter algorithm, respectively. Consequently, the proposed method gives us stable characterization performances on oil and water productions, permeability distribution, and aquifer strengths for a reasonable decision.
Lumbar infusion test in normal pressure hydrocephalus

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Substorm occurrence rates, substorm recurrence times, and solar wind structure

Two collections of substorms are created: 28,464 substorms identified with jumps in the SuperMAG AL index in the years 1979–2015 and 16,025 substorms identified with electron injections into geosynchronous orbit in the years 1989–2007. Substorm occurrence rates and substorm recurrence‐time distributions are examined as functions of the phase of the solar cycle, the season of the year, the Russell‐McPherron favorability, the type of solar wind plasma at Earth, the geomagnetic‐activity level, and as functions of various solar and solar wind properties. Three populations of substorm occurrences are seen: (1) quasiperiodically occurring substorms with recurrence times (waiting times) of 2–4 h, (2) randomly occurring substorms with recurrence times of about 6–15 h, and (3) long intervals wherein no substorms occur. A working model is suggested wherein (1) the period of periodic substorms is set by the magnetosphere with variations in the actual recurrence times caused by the need for a solar wind driving interval to occur, (2) the mesoscale structure of the solar wind magnetic field triggers the occurrence of the random substorms, and (3) the large‐scale structure of the solar wind plasma is responsible for the long intervals wherein no substorms occur. Statistically, the recurrence period of periodically occurring substorms is slightly shorter when the ram pressure of the solar wind is high, when the magnetic field strength of the solar wind is strong, when the Mach number of the solar wind is low, and when the polar‐cap potential saturation parameter is high.
On the Wave Energy Assessment in the South China Sea

This paper presents a thirty year (1976-2005) assessment of wave energy resource within the South China Sea (SCS) by simulation. Significant wave height (SWH) between simulation and observation shows good agreement. This shows the reliability of an along-side simulated wave period in estimating wave energy in the SCS. Results show that estimates of wave power density are more reliable in the north-central SCS and most sufficient during winter. The annual mean wave power density peaked at 12.7kW/m and 12.9kW/m during years 1986 and 1999 respectively while the highest seasonal mean of 29kW/m occurred in year 1999 during winter. The wave power density is most stable in winter and is generally more stable in offshore regions of SCS. Wave power density is most stable in years 1976, 1997 and 2004 with stability values of 1.96, 1.98 and 1.9 respectively. The stability value of 0.9 in year 1980 is the greatest in the winter of all years. Relative-rich energy regions occupy the largest area during winter. The relatively richest energy is generally concentrated in the central and north-central SCS. No area is identified as a relative-rich energy region during spring. Winter 1999 has the highest relative-rich energy with value of 37kW/m.
Matters: Neural Processing of Food-Flavored E-Cigarettes and the Influence of Smoking

E-cigarettes are harmful, addictive, and popular. In e-cigarettes, nicotine is often paired with food-flavors. How this pairing of nicotine and food cues influences neural processing warrants investigation, as in smokers, both types of cues activate similar brain regions. Additionally, while most e-cigarettes are sweet, savory e-cigarettes are seemingly absent, although savory flavors are commonly liked in food. To understand how smoking status and type of flavor modulate reactions to food-flavored e-cigarettes, in comparison to actual food, neural and subjective responses to food odors were measured in a 2 (sweet vs. savory odor) x2 (food vs. e-cigarette context) x2 (smokers vs. non-smokers) design in 22 occasional/light smokers and 25 non-smokers. During fMRI scanning, participants were exposed to sweet and savory odors and pictures creating the two contexts. Liking and wanting were repeatedly measured on a 100-unit visual-analogue-scale. Results show that sweet e-cigarettes were liked (Δ = 14.2 ± 1.7) and wanted (Δ = 39.5 ± 3.1) more than savory e-cigarettes, and their cues activated the anterior cingulate more (cluster-level qFDR = 0.003). Further, we observed context-dependent variations in insula response to odors (cluster-level qFDR = 0.023, and = 0.030). Savory odors in an e-cigarette context were wanted less than the same odors in a food-context (Δ = 32.8 ± 3.1). Smokers and non-smokers reacted similarly to flavored product cues. Our results indicate that the principles of flavor preference in food cannot directly be applied to e-cigarettes and that it is challenging to design sweet and savory e-cigarettes to appeal to smokers only.
Comparing submarine and fluvial channel kinematics: Implications for stratigraphic architecture

Submarine and fluvial channels exhibit qualitatively similar geomorphic patterns, yet produce very different stratigraphic records. We reconcile these seemingly contradictory observations by focusing on the channel belt scale and quantifying the time-integrated stratigraphic record of the belt as a function of the scale and trajectory of the geomorphic channel, applying the concept of stratigraphic mobility. By comparing 297 submarine and fluvial channel belts from a range of tectonic settings and time intervals, we identify channel kinematics (trajectory) rather than channel morphology (scale) as the primary control on stratigraphic architecture and show that seemingly similar channel forms (in terms of scaling) have the potential to produce markedly different stratigraphy. Submarine channel belt architecture is dominated by vertical accretion (aggradational channel fill deposits), in contrast to fluvial systems that are dominated by lateral accretion (point bar deposits). This difference is best described with the channel belt aspect ratio, which is 9 for submarine systems and 72 for fluvial systems. Differences in channel kinematics and thus stratigraphic architecture between the two environments appear to result from markedly different coupling between channel aggradation and overbank deposition. The methodology and results presented here are also applicable to interpreting channelized stratigraphy on other planets and moons.