Miracle-dz/UniFAR-FTUs huggingface dataset:
Preliminary Hydrogeologic Characterization Results from the Wallula Basalt Pilot Study

The DOE's Big Sky Regional Carbon Sequestration Partnership has completed drilling the first continental flood basalt sequestration pilot borehole to a total depth (TD) of 4,110 feet on the Boise White Paper Mill property at Wallula, Washington. Site suitability was assessed prior to drilling by the 2007-2008 acquisition, processing and analysis of a four-mile, five-line three component seismic swath, which was processed as a single data-dense line. Analysis of the seismic survey data indicated a composite basalt formation thickness of {approx}8,000 feet and absence of major geologic structures (i.e., faults) along the line imaged by the seismic swath. Drilling of Wallula pilot borehole was initiated on January 13, 2009 and reached TD on April 6, 2009. Based on characterization results obtained during drilling, three basalt breccia zones were identified between the depth interval of 2,716 and 2,910 feet, as being suitable injection reservoir for a subsequent CO2 injection pilot study. The targeted injection reservoir lies stratigraphically below the massive Umtanum Member of the Grande Ronde Basalt, whose flow-interior section possesses regionally recognized low-permeability characteristics. The identified composite injection zone reservoir provides a unique and attractive opportunity to scientifically study the reservoir behavior of three inter-connected reservoir intervals below primary and secondary caprock confining zones. Drill cuttings, wireline geophysical logs, and 31one-inch diameter rotary sidewall cores provided geologic data for characterization of rock properties. XRF analyses of selected rock samples provided geochemical characterizations of the rocks and stratigraphic control for the basalt flows encountered by the Wallula pilot borehole. Based on the geochemical results, the pilot borehole was terminated in the Wapshilla Ridge 1 flow of the Grande Ronde Basalt Formation. Detailed hydrologic test characterizations of 12 basalt interflow reservoir zones and 3 flow-interior/caprock intervals were performed during drilling and immediately following reaching the final borehole drilling depth (i.e., 4,110 ft). In addition, six of the 12 basalt interflow zones were selected for detailed hydrochemical characterization. Results from the detailed hydrologic test characterization program provided the primary information on basalt interflow zone transmissivity/injectivity, and caprock permeability characteristics.
Association between SARS‐CoV‐2 viral kinetics and clinical score evolution in hospitalized patients

The role of antiviral treatment in coronavirus disease 2019 hospitalized patients is controversial. To address this question, we analyzed simultaneously nasopharyngeal viral load and the National Early Warning Score 2 (NEWS‐2) using an effect compartment model to relate viral dynamics and the evolution of clinical severity. The model is applied to 664 hospitalized patients included in the DisCoVeRy trial (NCT04315948; EudraCT 2020‐000936‐23) randomly assigned to either standard of care (SoC) or SoC + remdesivir. Then we use the model to simulate the impact of antiviral treatments on the time to clinical improvement, defined by a NEWS‐2 score lower than 3 (in patients with NEWS‐2 <7 at hospitalization) or 5 (in patients with NEWS‐2 ≥7 at hospitalization), distinguishing between patients with low or high viral load at hospitalization. The model can fit well the different observed patients trajectories, showing that clinical evolution is associated with viral dynamics, albeit with large interindividual variability. Remdesivir antiviral activity was 22% and 78% in patients with low or high viral loads, respectively, which is not sufficient to generate a meaningful effect on NEWS‐2. However, simulations predicted that antiviral activity greater than 99% could reduce by 2 days the time to clinical improvement in patients with high viral load, irrespective of the NEWS‐2 score at hospitalization, whereas no meaningful effect was predicted in patients with low viral loads. Our results demonstrate that time to clinical improvement is associated with time to viral clearance and that highly effective antiviral drugs could hasten clinical improvement in hospitalized patients with high viral loads.
Vegetation survey of Namibia

Plant communities form the basic units in all ecological processes, and are thus also to be regarded as basic units of natural resources management (like pasture management). Unfortunately, no concise description of the vegetation is available. The preliminary vegetation map (Giess 1971), although being reprinted for the 3 time during 1998, is providing a general overview with virtually no baseline information on the vegetation types of the country. In contrast with the Acocks map of 1956 of the RSA, also no reference relevé data exist. The Relative Homogenous Farming Areas Map of 1979 has been published by the then Department of Agriculture Technical Services, describing the basic suitability of the commercial farming areas for various farming options. In terms of vegetation, however, it gives only an estimate of the grazing capacity a concept which has been found to be inaccurate and misleading. For planning purposes, more than just a vegetation map is needed. Baseline information on species composition can reveal problems with poisonous plants and/or encroacher species early. A general need for long-term monitoring is also being realised. A project has been initiated to update the Vegetation Map of Namibia at a scale of 1:1 000 000, as part of the Agro-Ecological Zoning Project. This paper gives an overview of the project. Some preliminary results regarding the vegetation of south-eastern Namibia are also presented.
Multi-site performance evaluation of the Alinity m Molecular assay for quantifying Epstein-Barr virus DNA in plasma samples

ABSTRACT Detection and monitoring of acute infection or reactivation of Epstein-Barr virus (EBV) are critical for treatment decision-making and to reduce the risk of EBV-related malignancies and other associated diseases in immunocompromised individuals. The analytical and clinical performance of the Alinity m EBV assay was evaluated at two independent study sites; analytical performance was assessed by evaluating precision with a commercially available 5-member EBV verification panel, while the clinical performance of the Alinity m EBV assay was compared to the RealTime EBV assay and a laboratory-developed test (LDT) as the routine test of record (TOR). Analytical analysis demonstrated standard deviation (SD) between 0.08 and 0.13 Log IU/mL. A total of 300 remnant plasma specimens were retested with the Alinity m EBV assay, and results were compared to those of the TOR at the respective study sites (n = 148 with the RealTime EBV assay and n = 152 with the LDT EBV assay). Agreement between Alinity m EBV and RealTime EBV or LDT EBV assays had kappa values of 0.88 and 0.84, respectively, with correlation coefficients r of 0.956 and 0.912, while the corresponding observed mean bias was −0.02 and −0.19 Log IU/mL. The Alinity m EBV assay had a short median onboard turnaround time of 2:40 h. Thus, the Alinity m system can shorten the time to results and, therefore, to therapy.
Elevated temperature fatally disrupts nuclear divisions in the early Drosophila embryo

Temperature fluctuations can challenge animal survival, especially in embryos of animals that can’t actively regulate their body temperature. Previous work in insects suggests that spatial gradients and temporal variations in temperature can affect embryonic development in a region-specific manner. Yet, it is unclear if elevated temperature produces developmental defects, and if so, how the disruption may manifest. Here we use early embryonic development of the fruit fly Drosophila melanogaster as a model to address consequences of elevated temperature on fly embryonic development. We identified the syncytial blastoderm stage as a critical time window, being particularly sensitive to elevated temperature. The syncytial blastoderm stage involves 4 rounds of meta-synchronous nuclear divisions at the embryo cortex, followed by cellularization to form the cellular blastoderm. Live imaging these processes at elevated temperature revealed an increase in mitotic failures and a loss of cortical nuclei, both, during syncytial- and cellular-blastoderm stage. Additionally, embryos developing at elevated temperature show a local crowding of nuclei and an increase in asynchrony between the nuclear cycles in the middle vs. anterior/posterior poles. Interestingly, nuclear crowding and nuclear cycle asynchrony cooperatively amplify the frequency of mitotic failures, leading to holes in the blastoderm epithelium. Strikingly, the same treatment also increased embryonic lethality. We propose that the loss of nuclei results in a loss of patterning information and the abrogation of proper embryonic development. We identified genes that regulate mitosis, especially the ones mediating the interaction between microtubules and F-actin, and functionally tested their capacity to rescue the embryonic lethality. Our results expose a vulnerability at elevated temperatures in the interaction between cortical actin and microtubules, which leads to mitotic failures, and can be potentially rescued by modulating the expression of just a few factors. We propose that the expression levels of the corresponding genes could be used as indicators to predict fitness effects on insect populations that are exposed to increasing temperature variations.
A fish-based estuarine health index for the Swan Estuary, WA

We describe the development of a fish-based, multimetric estuarine health index (EHI) for the Swan Estuary, Western Australia. A suite of fish community characteristics (metrics), including measures of species composition, diversity and abundance, trophic structure and life history function, were selected via a weight of evidence approach, on the basis of their sensitivity to detect interannual change. Reference conditions for each selected metric were established for each region of the Swan Estuary using historical fish assemblage data, and represent a best available standard of biotic integrity against which the current and future health of the estuary may be assessed and compared. Scores for each metric were assigned according to the extent of the metric’s deviation from its reference condition. Values for the EHI were calculated from summed metric scores for each main region of the Swan Estuary for each season and year, to identify trends in the recent health of the estuary, and to validate the sensitivity and reliability of the index. The index, which is the first such tool to be developed for Western Australia, will provide managers with a reliable and cost-effective, quantitative method for assessing and communicating the health of the Swan Estuary.
Towards Data-centric Graph Machine Learning: Review and Outlook

Data-centric AI, with its primary focus on the collection, management, and utilization of data to drive AI models and applications, has attracted increasing attention in recent years. In this article, we conduct an in-depth and comprehensive review, offering a forward-looking outlook on the current efforts in data-centric AI pertaining to graph data-the fundamental data structure for representing and capturing intricate dependencies among massive and diverse real-life entities. We introduce a systematic framework, Data-centric Graph Machine Learning (DC-GML), that encompasses all stages of the graph data lifecycle, including graph data collection, exploration, improvement, exploitation, and maintenance. A thorough taxonomy of each stage is presented to answer three critical graph-centric questions: (1) how to enhance graph data availability and quality; (2) how to learn from graph data with limited-availability and low-quality; (3) how to build graph MLOps systems from the graph data-centric view. Lastly, we pinpoint the future prospects of the DC-GML domain, providing insights to navigate its advancements and applications.
Prevalence and public health relevance of enteric parasites in domestic dogs and cats in the region of Madrid (Spain) with an emphasis on Giardia duodenalis and Cryptosporidium sp.

Abstract Background Pet dogs and cats exert an unquestionable beneficial effect in the well‐being of their owners, but can also act as a source of zoonotic infections if improperly cared. Objectives We investigated the occurrence, risk factors, genetic variability and zoonotic potential of intestinal parasites in dogs and cats attended in a clinical veterinary setting in Spain. Methods Canine (n = 252) and feline (n = 35) faecal samples were collected during 2017–2019 and analysed by coproparasitological methods. A rapid lateral immunochromatographic test (ICT) was used for detecting Giardia duodenalis and Cryptosporidium sp. Samples positive at microscopy examination and/or ICT were reassessed by molecular methods. Results Overall, 48.8% (123/252) of dogs and 48.6% (17/35) of cats were infected by enteric parasites. In dogs, G. duodenalis was the most prevalent species (40.9%), followed by Cystoisospora sp. (7.1%), and Toxocara canis (5.2%). In cats, Joyeuxiella sp. and Toxocara cati were the dominant species (20.0% each), followed by G. duodenalis (14.3%), D. caninum (5.7%) and Cystoisospora felis and Toxascaris leonina (2.9% each). Pups and kittens were more likely to harbour intestinal parasites and develop clinical signs. Sequence analyses of dog isolates revealed the presence of assemblages A (n = 1), C (n = 4), D (n = 4) and C+D (n = 1) within G. duodenalis; C. parvum (n = 1) and C. canis (n = 4) within Cryptosporidium and PtEb IX (n = 1) in Enterocytozoon bieneusi. A novel C. canis subtype family, named XXi, is reported. Conclusions Our results highlight that (i) well‐cared dogs carry zoonotic enteric protozoan parasites of public health relevance, (ii) proper hygiene practices and routine veterinary treatment are essential to prevent zoonotic infections, (iii) vulnerable populations should avoid contact with pups/kittens with diarrhoea and (iv) infected dogs might be major contributors to the environmental contamination with soil‐transmitted helminths (STHs) eggs.
Is it true that negative emotions cause more utilitarian judgements? from the influence of emotion and cognition

ABSTRACT The affect-as-information (AAI) model proposes that emotions influence the accessibility and value of information (Avramova & Inbar, 2013). Furthermore, according to the dual-process model of moral judgement, emotions and cognition influence moral judgement (Greene, 2007; Greene et al., 2001, 2008); however, there is no direct evidence of a causal chain to support this model’s proposition. By using a 3 (emotions: positive vs. neutral vs. negative) × 2 (primed rule: save lives vs. do not kill) between-participants design, we examined two hypotheses in two experiments: supraliminal (Experiment 1) and subliminal (Experiment 2) priming. Our results partially supported the AAI model and confirmed that emotions and cognition independently influence moral judgement. Specifically, the positive emotions group made more utilitarian decisions after being primed with the “save lives” rule and more deontological decisions after being primed with the do not kill rule. However, priming did not affect moral judgement in the negative emotion condition. Further, irrespective of whether priming was done, the negative emotion group mostly made utilitarian decisions. Accordingly, we propose a dynamic dual-process model of moral judgement, that can help clarify how emotion and cognition influence moral judgement.
Cities and transport energy: lessons from a global survey

We have shown in this paper how there is almost a 200 times difference in gasoline use across a sample of 32 of the world's major cities. In a regional context the ten US cities consume on average some 10 times more than the Asian cities, 4.5 times more than the European cities and 2 times more than the Australian cities. These large differences in gasoline use are only partially explained by a combination of larger vehicle sizes, greater wealth and cheaper gasoline characteristic of US cities. Much of the remaining differences in gasoline use between cities can be understood by reference to the land use and transport characteristics of the cities. We have shown for example, that cities with the highest automobile dependence and gasoline use also have very much lower densities and less use of non-automobile modes, as well as much higher road provision and parking. Metropolitan population density increases some ten times as you move from US and Australian cities with the highest automobile dependence and gasoline use to European and Asian cities with the lowest. The urban and transport planning policy directions needed to guide cities towards lower gasoline use are outlined in terms of re-urbanisation and re-orientation of transport priorities. These policies seek to make cities more compact and mixed in their land use development patterns and strongly based around centres as well as more orientated to public transport, walking and cycling. The policies of re-urbanisation and re-orientation of transport priorities work best when they are fashioned in concert with one another. The policies must be characterised by strong planning and economic incentives for less automobile dependent land use patterns and greater use of non-automobile modes as well as significant disincentives to automobile use.
Biological insights from RIL-seq in bacteria

Bacteria reside in constantly changing environments and require rapid and precise adjustments of gene expression to ensure survival. Small regulatory RNAs (sRNAs) are a crucial element that bacteria utilize to achieve this. sRNAs are short RNA molecules that modulate gene expression usually through base-pairing interactions with target RNAs, primarily mRNAs. These interactions can lead to either negative outcomes such as mRNA degradation or translational repression or positive outcomes such as mRNA stabilization or translation enhancement. In recent years, high-throughput approaches such as RIL-seq (RNA interaction by ligation and sequencing) revolutionized the sRNA field by enabling the identification of sRNA targets on a global scale, unveiling intricate sRNA-RNA networks. In this review, we discuss the insights gained from investigating sRNA-RNA networks in well-studied bacterial species as well as in under-studied bacterial species. Having a complete understanding of sRNA-mediated regulation is critical for the development of new strategies for controlling bacterial growth and combating bacterial infections.
Standardized circuit class group training versus individualized goal-directed group training to improve upper limb function in stroke survivors during in-patient rehabilitation: a pragmatic trial.

PURPOSE To investigate the usability and effectiveness of standardized circuit class group training (CCT) compared to individualized goal-directed group training (GDT) in subacute stroke survivors. MATERIALS AND METHODS This study consists of three parts. Part 1 involved a pragmatic, non-randomized controlled trial with subacute participants and their therapists, who participated in four weeks either CCT or GDT. Superiority of the intervention was defined as significantly larger improvement on the Motor Activity Log for patients and lower workload for therapists. In Part 2, six additional workstations were developed for CCT. Part 3 replicated the study of Part 1 with the expanded CCT. RESULTS Part 1 showed no difference in effectiveness between training methods. CCT did not match the rehabilitation goals of the patient sufficiently, however mental workload seemed lower for therapists. An expansion of CCT could improve the match between the patient's goals and the training (Part 2). Results of Part 3 showed again no difference in effectiveness between methods. CCT was however perceived as less engaging compared to GDT, but mental load for therapists remained lower. CONCLUSIONS A standardized training could reduce the mental workload for therapists, but patients seemed less engaged. A combination of both might be most beneficial.Trial registration: Dutch Trial Register: NL8844 and NL9471IMPLICATIONS FOR REHABILITATIONProviding a standardized training program after stroke reduces therapists' mental workload.Individualized goal-directed group training results in the best achievement of rehabilitation goals.A combination of standardized and individual training would use best of both intervention modalities.Patients should be involved in the co-creation developing process of training programs.
Mental representation and processing of reduced words in casual speech

representation, the size of the priming effect should be independent of the detailed acoustic similarity between the prime and target. Most experiments demonstrated that priming effects are larger if primes and targets are identical, suggesting that acoustic details are stored in the form of exemplars. Interestingly, some of these priming experiments suggested that exemplar-based priming effects only arise under certain conditions, but not consistently. For example, McLennan et al. (2003) found exemplar effects but only if processing was relatively fast, whereas McLennan & Luce (2005) and Mattys & Liss (2008) found effects only if processing was relatively slow. Similarly, Goldinger (1996) reported that if the participants had to indicate for each target whether it had also occurred before, exemplar effects were present after a day if they had heard stimuli produced by two or ten voices but not by six voices. This raises the question about how robust exemplar effects are. In Chapter 4, we investigate this question further. It focuses on schwa in Dutch word-initial syllables, which is often reduced in casual speech (see Chapter 2). Chapter 4 presents four long-term priming experiments, in which we study the robustness of exemplars in three ways. First, we examine whether exemplar effects arise for different speakers, by using two very different speakers. Second, we investigate whether listeners also use exemplars if, in contrast to the priming studies mentioned above, it is less clear for them that words are repeated. Finally, we examine whether exemplar effects can also be found if listeners hear not one but two types of variation (i.e., pronunciation variation and speaker voice).
Tumor-derived biomarkers predict efficacy of B7H3 antibody-drug conjugate treatment in metastatic prostate cancer models

Antibody-drug conjugates (ADCs) are a promising targeted cancer therapy; however, patient selection based solely on target antigen expression without consideration for cytotoxic payload vulnerabilities has plateaued clinical benefits. Biomarkers to capture patients who might benefit from specific ADCs have not been systematically determined for any cancer. We present a comprehensive therapeutic and biomarker analysis of a B7H3-ADC with pyrrolobenzodiazepine(PBD) payload in 26 treatment-resistant, metastatic prostate cancer (mPC) models. B7H3 is a tumor-specific surface protein widely expressed in mPC, and PBD is a DNA cross–linking agent. B7H3 expression was necessary but not sufficient for B7H3-PBD-ADC responsiveness. RB1 deficiency and/or replication stress, characteristics of poor prognosis, and conferred sensitivity were associated with complete tumor regression in both neuroendocrine (NEPC) and androgen receptor positive (ARPC) prostate cancer models, even with low B7H3 levels. Non-ARPC models, which are currently lacking efficacious treatment, demonstrated the highest replication stress and were most sensitive to treatment. In RB1 WT ARPC tumors, SLFN11 expression or select DNA repair mutations in SLFN11 nonexpressors governed response. Importantly, WT TP53 predicted nonresponsiveness (7 of 8 models). Overall, biomarker-focused selection of models led to high efficacy of in vivo treatment. These data enable a paradigm shift to biomarker-driven trial designs for maximizing clinical benefit of ADC therapies.