Miracle-dz/UniFAR-FTUs huggingface dataset:
Practical Applications of Engineering Geophysics to Help Solve Tough Problems and Lead to Improved Technologies

Professor Richard D. Woods has been a pioneer in the development and application of engineering geophysical methods in geotechnical engineering over the past four decades. First, the paper reviews several case studies of the application of geophysical methods in geotechnical engineering. The case studies are from projects in which the author has directly collaborated with Professor Woods, and they demonstrate the wide breadth of application of these technologies . Second, the paper reviews significant technical advances in geophysical test methodologies over the two decades in which the author has collaborated with Professor Woods.
Trajectory of emotion dysregulation in positive and negative affect across childhood predicts adolescent emotion dysregulation and overall functioning

Abstract Emotion dysregulation is cross-diagnostic and impairing. Most research has focused on dysregulated expressions of negative affect, often measured as irritability, which is associated with multiple forms of psychopathology and predicts negative outcomes. However, the Research Domain Criteria (RDoC) include both negative and positive valence systems. Emerging evidence suggests that dysregulated expressions of positive affect, or excitability, in early childhood predict later psychopathology and impairment above and beyond irritability. Typically, irritability declines from early through middle childhood; however, the developmental trajectory of excitability is unknown. The impact of excitability across childhood on later emotion dysregulation is also yet unknown. In a well-characterized, longitudinal sample of 129 children studied from ages 3 to 5.11 years through 14 to 19 years, enriched for early depression and disruptive symptoms, we assessed the trajectory of irritability and excitability using multilevel modeling and how components of these trajectories impact later emotion dysregulation. While irritability declines across childhood, excitability remains remarkably stable both within and across the group. Overall levels of excitability (excitability intercept) predict later emotion dysregulation as measured by parent and self-report and predict decreased functional magnetic resonance imaging activity in cognitive emotion regulation regions during an emotion regulation task. Irritability was not related to any dysregulation outcome above and beyond excitability.
EVALUATING AN ECOLOGICALLY-BASED SYSTEM FOR SUSTAINABLE MANAGEMENT OF NITROGEN FERTILISER

SUSTAINABLY managing N fertiliser is an increasing challenge for sugarcane production, as losses of N impact the health of ecosystems and contribute to climate change (through emissions of the greenhouse gas nitrous oxide). The N Replacement (NR) system is a new, ecologically-based concept for N management in sugarcane designed to meet this challenge. The NR system aligns N applications with actual cane production, rather than potential production, by relying on soil N reserves to buffer differences in crop N needs and N fertiliser supply in individual crops. We evaluated the NR system in 11 on-farm experiments in Australia, conducted over a wide range of environments for up to five years. Average yields in the NR treatment were similar to those achieved with the farmers’ conventional N management that had average N applications 66 kg/ha greater than in the NR treatments. Yields increased relative to the farmers’ conventional N management through time, from ~5 t/ha lower in the first crops of the experiments to 2.6 (standard error = 1.2) t/ha higher in the fourth, suggesting a physiological response in the crops to the variable N applications in the NR system. The crop N surplus, an estimate of N potentially lost to the environment, was 55% lower in the NR treatment compared with conventional N management. This reduction in N surplus was not as great as had been anticipated, as N concentrations and N uptake in cane for most crops in all treatments were lower than those previously reported. The results show that the ecologically-based N Replacement system may deliver superior environmental outcomes without significantly reducing production. The results also show that predicting yield of the coming crop, a common basis for N management, is not necessary in sugarcane N management, provided N applications and production are matched in the longer term.
Propagation characteristics of superconducting microstrip lines

The modified spectral-domain approach is applied to study the propagation characteristics of high temperature superconducting microstrip lines whose signal strip and ground plane are of arbitrary thickness. In this study, numerical results for effective dielectric constant, attenuation constant, and strip current distribution are presented to discuss the effects due to frequency, temperature, strip thickness, and substrate loss tangent. In particular, the conductor and dielectric attenuation constants of superconducting microstrip line are depicted separately to discuss the mechanism of the line losses. A comparison with published theoretical and experimental results is also included to check the accuracy of the new approach's results.
Canine Meningoencephalitis of Unknown Origin—The Search for Infectious Agents in the Cerebrospinal Fluid via Deep Sequencing

Meningoencephalitis of unknown origin (MUO) describes a group of meningoencephalitides in dogs with a hitherto unknown trigger. An infectious agent has been suggested as one possible trigger of MUO but has not been proven so far. A relatively new method to screen for viral RNA or DNA is next-generation sequencing (NGS) or deep sequencing. In this study, a metagenomics analysis of the virome in a sample is analyzed and scanned for known or unknown viruses. We examined fresh-frozen CSF of 6 dogs with MUO via NGS using a modified sequence-independent, single-primer amplification protocol to detect a possible infectious trigger. Analysis of sequencing reads obtained from the six CSF samples showed no evidence of a virus infection. The inability to detect a viral trigger which could be implicated in the development of MUO in the examined population of European dogs, suggests that the current techniques are not sufficiently sensitive to identify a possible virus infection, that the virus is already eliminated at the time-point of disease outbreak, the trigger might be non-infectious or that there is no external trigger responsible for initiating MUO in dogs.
Photodynamic and Photothermal Therapy of Hepatocellular Carcinoma

Hepatocellular carcinoma (HCC) is the most common primary liver tumor. It is ranked the sixth most common neoplasm and the third most common cause of cancer mortality. At present, the most common treatment for HCC is surgery, but the 5-year recurrence rates are still high. Patients with early stage HCC with few nodules can be treated with resection or radiofrequency ablation (RFA); while for multinodular HCC, transarterial chemoembolization (TACE) has been the first-line treatment. In recent years, based on medical engineering cooperation, nanotechnology has been increasingly applied to the treatment of cancer. Photodynamic therapy and photothermal therapy are effective for cancer. This paper summarizes the latest progress of photodynamic therapy and photothermal therapy for HCC, with the aim of providing new ideas for the treatment of HCC.
Predictive Performance of Serum S100B Versus LDH in Melanoma Patients: A Systematic Review and Meta-Analysis

Background Currently, no consensus on the use of blood tests for monitoring disease recurrence in patients with resected melanoma exists. The only meta-analysis conducted in 2008 found that elevated serum S100B levels were associated with significantly worse survival in melanoma patients. Serum LDH is an established prognostic factor in patients with advanced melanoma. Objective To compare the discriminative and prognostic ability of serum S100B with that of serum LDH in patients with melanoma. Methods This systematic review and meta-analysis were reported in accordance with the PRISMA Statement. The study protocol was registered in the International Prospective Register of Systematic Reviews (PROSPERO; CRD42019137138). Results A quantitative analysis of data from 6 eligible studies included 1,033 patients with cutaneous melanoma. The discriminative ability of serum S100B at identifying disease relapse [pooled Area Under the ROC (AUROC) 78.64 (95% CI 70.28; 87.01)] was significantly greater than the discriminative ability of serum LDH [AUROC 64.41 (95% CI 56.05; 7278)] (p=0.013). Ten eligible studies with 1,987 patients were included in the risk of death analysis. The prognostic performance of serum S100B [pooled estimate of adjusted hazard ratio (HR) 1.78 (95% CI 1.38; 2.29)] was independent but not superior to that of serum LDH [HR 1.60 (95% CI 1.36; 2.29)]. Limitations A relatively small number of articles were eligible and there was considerable heterogeneity across the included studies. Conclusions Serum biomarkers may provide relevant information on melanoma patient status and should be further researched. Serum S100B is a valid marker for diagnosis of melanoma recurrence. Systematic Review Registration The study protocol was registered in the International Prospective Register of Systematic Reviews (PROSPERO; CRD42019137138).
Combined Stereotactic Body Radiotherapy and Immunotherapy Versus Transarterial Chemoembolization in Locally Advanced Hepatocellular Carcinoma: A Propensity Score Matching Analysis

Immunotherapy has achieved modest clinical activity in HCC patients. Propensity score matching analysis was conducted to compare the efficacy and safety of combined stereotactic SBRT-IO versus TACE in patients with locally advanced HCC in a tertiary center of Hong Kong. Patients with locally advanced HCC who were medically inoperable for, refractory to, or refused to curative surgical interventions were eligible. The primary outcome was PFS; the secondary outcomes were OS, ORR as per mRECIST version 1.1, and TRAEs. Matching pair analysis was performed to compare the clinical outcomes. A total of 226 patients were eligible. Approximately 16 patients in the SBRT-IO group were matched with 48 patients treated with TACE. The median tumor size was 10 cm (range: 2.9–19.6 cm) and 20.3% of the patients had portal vein invasion. The 12- and 24-month PFS were significantly better in the SBRT-IO group (93.3% vs 16.7% and 77.8% vs 2.1%, respectively, p <0.001); the 12- and 24-month OS were also better in the SBRT-IO arm (93.8% vs 31.3% and 80.4% vs 8.3%, respectively, p <0.001). The ORR was 87.5% (CR: 50%, PR: 37.5%) in SBRT-IO arm compared to 16.7% (CR: 2.4%, PR: 14.3%) in those receiving TACE alone (p <0.001). There were fewer ≥grade 3 TRAE (60.4% vs 18.8%, p = 0.004) and treatment discontinuations (25% vs 12.5%, p = 0.295) due to adverse events in the SBRT-IO arm. SBRT-IO had significant superior survival and less treatment toxicity than TACE in patients with locally advanced HCC. Our results provide rationale for studying this combination therapy in prospective randomized trials.
Gene-Based Therapeutics for Acquired Retinal Disease: Opportunities and Progress

Acquired retinal diseases such as age-related macular degeneration and diabetic retinopathy rank among the leading causes of blindness and visual loss worldwide. Effective treatments for these conditions are available, but often have a high treatment burden, and poor compliance can lead to disappointing real-world outcomes. Development of new treatment strategies that provide more durable treatment effects could help to address some of these unmet needs. Gene-based therapeutics, pioneered for the treatment of monogenic inherited retinal disease, are being actively investigated as new treatments for acquired retinal disease. There are significant advantages to the application of gene-based therapeutics in acquired retinal disease, including the presence of established therapeutic targets and common pathophysiologic pathways between diseases, the lack of genotype-specificity required, and the larger potential treatment population per therapy. Different gene-based therapeutic strategies have been attempted, including gene augmentation therapy to induce in vivo expression of therapeutic molecules, and gene editing to knock down genes encoding specific mediators in disease pathways. We highlight the opportunities and unmet clinical needs in acquired retinal disease, review the progress made thus far with current therapeutic strategies and surgical delivery techniques, and discuss limitations and future directions in the field.
Experimental study of the flows in a non-axisymmetric ellipsoid under precession

Abstract Precession driven flows are of great interest for both, industrial and geophysical applications. While cylindrical, spherical and spheroidal geometries have been investigated in great detail, the numerically and theoretically more challenging case of a non-axisymmetric cavity has received less attention. We report experimental results on the flows in a precessing triaxial ellipsoid, with a focus on the base flow of uniform vorticity, which we show to be in good agreement with existing theoretical models. As predicted, the uniform vorticity component exhibits two branches of solutions leading to a hysteresis cycle as a function of the Poincaré number. The first branch is observed at low forcing and characterized by large amplitude of the total fluid rotation and a moderate tilt angle of the fluid rotation axis. In contrast, the second branch displays only a moderate fluid rotation and a large tilt angle of the fluid rotation axis, which tends to align with the precession axis. In addition, we observe the occurrence of parametric instabilities early in the first branch, which saturate in the second branch, where we observe the same order of the kinetic energy in the base flow and instabilities.
Application of Parallel Reaction Monitoring in 15N Labeled Samples for Quantification

Accurate relative quantification is critical in proteomic studies. The incorporation of stable isotope 15N to plant-expressed proteins in vivo is a powerful tool for accurate quantification with a major advantage of reducing preparative and analytical variabilities. However, 15N labeling quantification has several challenges. Less identifications are often observed in the heavy labeled samples because of incomplete labeling, resulting in missing values in reciprocal labeling experiments. Inaccurate quantification can happen when there is contamination from co-eluting peptides or chemical noise in the MS1 survey scan. These drawbacks in quantification can be more pronounced in less abundant but biologically interesting proteins, which often have very few identified peptides. Here we demonstrate the application of parallel reaction monitoring (PRM) to 15N labeled samples on a high resolution, high mass accuracy Orbitrap mass spectrometer to achieve reliable quantification even of low abundance proteins in samples.
Attracting pollinators vs escaping herbivores: eco-evolutionary dynamics of plants confronted with an ecological trade-off

Many plant traits are subject to an ecological trade-off between attracting pollinators and escaping herbivores. The interplay of both plant-animal interaction types determines their evolution. As most studies focus on either pollination or herbivory, how they jointly affect the eco-evolutionary dynamics of plant-animal communities is often left unknown. Within a plant-pollinator-herbivore community where interaction strengths depend on trait matching, we consider the evolution of a plant trait involved in both plant-animal interactions. Using adaptive dynamics, we uncover when stabilizing, runaway (i.e. directional) or disruptive selection emerges and its consequences for multispecies coexistence. We find that strong pollination relative to herbivory favors stabilizing selection and coexistence. Strong herbivory relative to pollination fosters runaway selection and threatens coexistence. Importantly, given balanced interactions, joint effects may lead to disruptive selection, allowing the emergence of plant dimorphism. The strength of the ecological trade-off largely explains the occurrence of these contrasting eco-evolutionary dynamics. In particular, plant diversification requires strong trade-offs, with the strongest trade-offs allowing long-term polymorphism. We discuss how our results relate to various empirical cases where the interplay of pollination and herbivory maintains plant polymorphism. Beyond maintenance, our work suggests that it might also have fueled the diversification process itself. Graphical Abstract Eco-evolutionary dynamics resulting from the evolution of plant phenotype under ecological trade-off A. Typical eco-evolutionary landscape. The type of selection and the ecological outcome depend on the dissimilarity between animal phenotypes (i.e. preferences for plant phenotype), which is a proxy for the strength of the ecological trade-off. B. The long-term community composition depends on the type of selection. (1) Runaway selection leads to the extinction of a first animal species as the plant phenotype is diverging. (a) Pollinators are lost first so that runway selection continues until herbivores are also lost. (b) Herbivores are lost first so that selection turns stabilizing over time, leading to a perfect plant-pollinator matching. (2) Stabilizing selection can enable the maintenance of coexistence. (3) Disruptive selection leads to the emergence of plant dimorphism.
An Empirical Study of Graph Neural Networks Based Semantic Parsing

Existing neural semantic parsers either only consider the word sequence for encoding or decoding, and ignore important syntactic information useful to parsing purposes. In this paper, we present a novel Graph Neural Networks (GNN) based neural semantic parser, namely Graph2Tree consisting of a graph encoder and a hierarchical tree decoder, that embraces the advantages of both worlds. In addition, we conduct a first study on the impacts of different syntactic graph constructions on the performance of GNNs for semantic parsing. We find that both noisy information and structural complexity introduced by a graph construction, due to imperfection of dependency tree parser or complex constituency tree, could lead to significantly detrimental effect on the performance of GNN-based semantic parsers.
The Role of Cingulate Cortex Dysfunction in Obsessive– Compulsive Disorder

Chapter contents Goals of This Chapter 588 Structural Brain Imaging 588 Structural MRI studies 589 Magnetic Resonance Spectroscopy 591 Functional Imaging Techniques for OCD 592 Functional Imaging Comparing OCD Patients with Normal Controls at Baseline 592 Neural Correlates of OCD Symptom Factors at Baseline 592 Neurotransmitter and Receptor System Imaging 593 Functional Neuroimaging of OCD before and after Treatment 594 Pre-treatment Functional Neuroimaging: Predictors of Treatment Response in OCD 596 Neuroimaging During OCD Symptom Provocation 596 Neuroimaging During Cognitive Tasks 599 Neuroimaging During Emotion 601 Electrical and Magnetic Evoked Responses 602 Cingulate Abnormalities in OCD 604 Dysfunction of Anterior Midcingulate Cortex in OCD 604 A Cingulate Circuit Model of the Pathophysiology of OCD 605 Future Directions 606 References 606
The Central Bank, the Treasury, or the Market: Which One Determines the Price Level?∗

This paper studies a model in which the price level is the outcome of dynamic strategic interactions between a fiscal authority, a monetary authority, and investors in government bonds and reserves. The“unpleasant monetarist arithmetic”whereby aggressive fiscal expansion forces the monetary authority to chicken out and inflate away public liabilities may be contained by market forces: Monetary dominance prevails if such fiscal expansion is met with a higher real interest rate on public liabilities, due for example to the crowding out of private investment opportunities. We derive policy implications regarding central bank balance sheet management and the need of fiscal requirements. ∗Barthélemy: Banque de France, 31 rue Croix des Petits Champs, 75001 Paris, France. Email: jean.barthelemy@banque-france.fr. Mengus: HEC Paris and CEPR, 1 rue de la Liberation, 78350 Jouyen-Josas, France. Email: mengus@hec.fr. Plantin: Sciences Po and CEPR, 28 rue des Saints-Peres, 75007 Paris, France. Email: guillaume.plantin@sciencespo.fr. This paper supersedes Barthélemy and Plantin (2018) and Barthélemy et al. (2020), revisiting the issues addressed in these papers in a new and unified framework. We thank participants in many seminars and conferences for helpful comments. The views expressed in this paper do not necessarily reflect the opinion of the Banque de France or the Eurosystem.
Self-Supervised Learning of Image Scale and Orientation

We study the problem of learning to assign a characteristic pose, i.e., scale and orientation, for an image region of interest. Despite its apparent simplicity, the problem is non-trivial; it is hard to obtain a large-scale set of image regions with explicit pose annotations that a model directly learns from. To tackle the issue, we propose a self-supervised learning framework with a histogram alignment technique. It generates pairs of image patches by random rescaling/rotating and then train an estimator to predict their scale/orientation values so that their relative difference is consistent with the rescaling/rotating used. The estimator learns to predict a non-parametric histogram distribution of scale/orientation without any supervision. Experiments show that it significantly outperforms previous methods in scale/orientation estimation and also improves image matching and 6 DoF camera pose estimation by incorporating our patch poses into a matching process.
SPATIAL PERCEPTION OF WHOLE-BODY ORIENTATION DEPENDS ON GYMNASTS’ EXPERTISE

The perception of spatial orientation of the body is a fundamental process in the precise performance of complex motor tasks, such as those found in acrobatic sports. While visual information is thought to be an important informational source when performing gymnastics skills, it is still questionable, which role visual information plays in the perception of spatial orientation in matters of gymnastics expertise and task specificity. Thus, this study targets the question, which role visual information plays in the perception of spatial orientation as a function of specific task demands and gymnastics expertise. High-skilled and low-skilled gymnasts were compared in their estimation of body tilt while being rotated about the transverse axis and the anterior-posterior axis in a human gyroscope with either full visual information available or occluded visual information. Results revealed that high-skilled gymnasts exhibited a better estimation of body tilt as compared to low-skilled gymnasts. Estimated tilt angles varied as a function of rotation axis and expertise, but not as a function of visual information. It was concluded that an increased spatial orientation ability may result from an increased sensitivity in individual sensory systems, and/or from an optimized processing of interacting sensory information that is specific to gymnasts’ experience with particular motor tasks and the corresponding task demands.