Miracle-dz/UniFAR-FTUs huggingface dataset:
Influence of turbulence variability on osmotrophic plankton dynamics in a coastal area

Turbulence affects plankton at very different levels and scales. The study of this topic has been mainly based on the assessment of effects of constant levels of turbulence, particularly through experimental studies, and little is known about the influence of intermittent patterns. The aim of the present thesis is to address how the variability in forcing factors, especially turbulence, affects the dynamics of coastal plankton communities. To do so the distribution of wind events as a proxy of the variability of turbulent energy input in a coastal zone, has been first studied. Turbulent forcing derived from wind in the Catalan coast is shown to have a large spatial and temporal variability. An empirical model has been developed which allows predicting the distribution of wind events with an ecologically relevant intensity. An assessment of the statistical distribution of turbulence in the Catalan coast is given. In chapter 2 the actual turbulence levels achieved in the laboratory set-ups used for experimental research are measured. These analyses have been extended to a range of different set-ups frequently used in experimental studies of plankton and turbulence, including different oscillating-grid systems and orbital shakers with common laboratory containers. In the case of oscillating grid systems, measurements have shown that turbulence is isotropic, and homogeneously distributed within cylindrical containers as long as the stroke length is comparable to the water column height. Away from the grid oscillation dissipations decay nonlinearly. Turbulence can be trustfully estimated using theoretical considerations about the energy entered into the system by the oscillating grid. A list of drag coefficients for different grids inferred from turbulence measurements is provided. In order to identify the variability in the responses of the planktonic community to realistic episodes of turbulence, two complementary approaches have been developed: a time series analysi
Colonization Rate and Risk Factors of Vancomycin-Resistant Enterococci among Patients Received Hematopoietic Stem Cell Transplantation in Shiraz, Southern Iran

Background: Infections caused by antimicrobial-resistant bacteria are associated with increased mortality and health care costs. Enterococci have been recognized as a clinically important pathogen in hospitalized patients. Vancomycin-resistant enterococci (VRE) infections cause significant morbidity and mortality among patients undergoing transplantation. Objective: To identify epidemiology of VRE colonization and related risk factors among patients with hematological malignancies after hematopoietic stem cell transplantation (HSCT). Methods: This cross-sectional study was performed on 42 patients who underwent bone-marrow transplantation between July 2013 and March 2014. A stool sample was taken from each patient 3–5 days after transplantation and cultured on appropriate media. Suspected colonies of enterococci were detected to species level by their culture characteristics, biochemical reactions and molecular features. VRE were confirmed via phenotypic and genotypic methods. Results: VRE were detected in 14 (33%) of studied samples. 10 (71%) of the detected VRE isolates were identified as high level vancomycin-resistant E. faecium with minimum inhibitory concentration (MIC) of ≥256 μg/mL of vancomycin; 3 isolates were E. galinarum and 1 was E. casseliflavus with an MIC of 8–16 μg/mL. VanA was dominant phenotype and all VRE isolates with high-level of vancomycin resistance had vanA gene. VRE isolation was mostly observed in patients with acute lymphoblastic leukemia (ALL) than other diseases. Moreover, antibiotic prophylaxis and hospitalization were independent risk factors for acquisition of VRE after transplantation. Conclusion: We found high level of vancomycin-resistance in E. faecium isolates obtained from HSCT patients. The vancomycin-resistant isolates of E. faecium had vanA and/or simultaneously vanB genes.
Time-dependent heterogeneity leads to transient suppression of the COVID-19 epidemic, not herd immunity

Significance Epidemics generally spread through a succession of waves that reflect factors on multiple timescales. Here, we develop a general approach bridging across these timescales and demonstrate how to incorporate population heterogeneity into a wide class of epidemiological models. We demonstrate that a fragile state of transient collective immunity emerges during early, high-paced stages of the epidemic, leading to suppression of individual epidemic waves. However, this state is not an indication of lasting herd immunity: Subsequent waves may emerge due to stochastic changes in individual social activity. Parameters of transient collective immunity are estimated using empirical data from the COVID-19 epidemic in several US locations. Epidemics generally spread through a succession of waves that reflect factors on multiple timescales. On short timescales, superspreading events lead to burstiness and overdispersion, whereas long-term persistent heterogeneity in susceptibility is expected to lead to a reduction in both the infection peak and the herd immunity threshold (HIT). Here, we develop a general approach to encompass both timescales, including time variations in individual social activity, and demonstrate how to incorporate them phenomenologically into a wide class of epidemiological models through reparameterization. We derive a nonlinear dependence of the effective reproduction number Re on the susceptible population fraction S. We show that a state of transient collective immunity (TCI) emerges well below the HIT during early, high-paced stages of the epidemic. However, this is a fragile state that wanes over time due to changing levels of social activity, and so the infection peak is not an indication of long-lasting herd immunity: Subsequent waves may emerge due to behavioral changes in the population, driven by, for example, seasonal factors. Transient and long-term levels of heterogeneity are estimated using empirical data from the COVID-19 epidemic and from real-life face-to-face contact networks. These results suggest that the hardest hit areas, such as New York City, have achieved TCI following the first wave of the epidemic, but likely remain below the long-term HIT. Thus, in contrast to some previous claims, these regions can still experience subsequent waves.
Pinwheel valence bond crystal ground state of the spin-12 Heisenberg antiferromagnet on the shuriken lattice

: We investigate the nature of the ground state of the spin-12 Heisenberg antiferromagnet on the shuriken lattice by complementary state-of-the-art numerical techniques, such as variational Monte Carlo (VMC) with versatile Gutzwiller-projected Jastrow wave functions, unconstrained multivariable variational Monte Carlo (mVMC), and pseudofermion/pseudo-Majorana functional renormalization group (PFFRG/PMFRG) methods. We establish the presence of a quantum paramagnetic ground state and investigate its nature, by classifying symmetric and chiral quantum spin liquids, and inspecting their instabilities towards competing valence bond crystal (VBC) orders. Our VMC analysis reveals that a VBC with a pinwheel structure emerges as the lowest-energy variational ground state, and it is obtained as an instability of the U(1) Dirac spin liquid. Analogous conclusions are drawn from mVMC calculations employing accurate BCS pairing states supplemented by symmetry projectors, which confirm the presence of pinwheel VBC order by a thorough analysis of dimer-dimer correlation functions. Our work highlights the nontrivial role of quantum fluctuations via the Gutzwiller projector in resolving the subtle interplay between competing orders. We investigate the nature of the ground state of the spin- 12 Heisenberg antiferromagnet on the shuriken lattice by complementary state-of-the-art numerical techniques, such as variational Monte Carlo (VMC) with versatile Gutzwiller-projected Jastrow wave functions, unconstrained multivariable variational Monte Carlo (mVMC), and pseudofermion / pseudo-Majorana functional renormalization group (PFFRG/PMFRG) methods. We establish the presence of a quantum paramagnetic ground state and investigate its nature, by classifying symmetric and chiral quantum spin liquids, and inspecting their instabilities towards competing valence bond crystal (VBC) orders. Our VMC analysis reveals that a VBC with a pinwheel structure emerges as the lowest-energy variational ground state, and it is obtained as an instability of the U(1) Dirac spin liquid. Analogous conclusions are drawn from mVMC calculations employing accurate BCS pairing states supplemented by symmetry projectors, which conﬁrm the presence of pinwheel VBC order by a thorough analysis of dimer-dimer correlation functions. Our work highlights the nontrivial role of quantum ﬂuctuations via the Gutzwiller projector in resolving the subtle interplay between competing orders.
Generation and stability of inertia–gravity waves

In the ocean, stratification and rotation allow for the existence of inertia–gravity waves. Instabilities of these waves, such as triadic resonant instability (TRI), may play a key role in the mixing process of the deep ocean. In an experimental set-up, we generate inertia–gravity waves which may become unstable depending on the background rotation and wave frequency. The instability produces secondary waves that match the spatial and temporal resonance conditions of TRI. The effect of rotation is introduced in a pre-existing theory and results in a prediction of the growth rate of TRI in the case of an infinite plane wave. The issue of finite size of the beam is then addressed using a simple model in which we show that the instability is enhanced in a given range of Coriolis parameter. Finally, we compare the experimental threshold of the instability with the model, and find good agreement except at higher rotation rate. At constant primary wave frequency, we analyse the evolution of the secondary wave characteristics with rotation. The appearance of unexpected sub-inertial secondary waves may be related to the discrepancy observed between predicted and experimental thresholds at higher rotation.
Numerical Models of AGN Jet Feedback

Active Galactic Nuclei (AGNs) power the most luminous sources in the Universe, and generate very energetic large-scale radio jets. These processes are important in galaxy formation models and numerical simulations, which require energy from AGNs to prevent central gas from overcooling. In this thesis we use hydrodynamical simulations to explore the impact of jets on the intra-galactic medium of individual halos, with particular focus on massive galaxies. The simulations are performed with the FLASH code, and we took advantage of the Adaptive Mesh Refinement scheme to deal with the complex, multiscale physics of AGNs on scales ranging from Megaparsec down to a few tens of parsecs. In the first part of this thesis we describe in detail the first few millions years of AGN jets, identifying precise evolutionary stages and testing our findings against theoretical models. We discuss gas circulation within the “cocoon” carved by the jet as a possible self-regulation mechanism for jet activities. In the second part, we extend the analysis to cosmologically relevant timescales, and carry on a detailed thermodynamyc analysis of the jet-gas system, including mechanical work, global energy transfer and volume fraction of the heated gas. Finally, we present a few extensions of our model such as multiple jet events, and take a few steps towards direct comparison with X-ray observations.
Project 2 : An Isoperimetric Sloshing Problem in a Shallow Container with Pinned Contact Line

I am an applied mathematician who is interested in using methods from the calculus of variations, applied analysis, and asymptotic analysis to answer questions about ordinary and partial differential equations (ODEs and PDEs) that arises in physical and life sciences, particularly fluid dynamics. The primary focus of my dissertation investigates how the presence of surface tension on the fluid free surface influences the (natural) sloshing frequencies of an incompressible, inviscid fluid with irrotational flow in rigid containers.
Targeted Photodynamic Therapy: A Novel Approach to Abolition of Human Cancer Stem Cells

Cancer is a global burden that has prompted extensive research into prevention and treatment, over many decades. Scientific studies have shown that subset of cells within a tumour, known as cancer stem cells (CSCs), are responsible for tumourigenesis, metastasis, drug resistance, and recurrences. CSCs have characteristic features of enhanced self-renewal, proliferation, and limited but multidirectional differentiation capacity. The discovery of CSCs has initiated extensive research into novel cancer treatment regimes. Evidence indicates that CSCs are resistant to conventional chemo- and radiation therapy leading to treatment failures, cancer metastasis, secondary cancer formation, and relapse. Because of the observed phenomena in the course of cancer prognosis, a need for treatment modalities targeting CSCs is important. Photodynamic therapy (PDT) is a clinically approved, minimally invasive, therapeutic procedure that can exert a selective cytotoxic activity toward cancerous cells while reducing toxicity to normal cells. It uses a photosensitizer (PS) that becomes excited when subjected to light at a specific wavelength, and the PS forms reactive oxygen species (ROS) killing malignant cells. Currently, PDT is being investigated as a target specific treatment for CSCs by the addition of carrier molecules and antibody conjugates bound to the PS. Targeted PDT (TPDT) may be able to not only eradicate the tumour mass but kill CSCs as well.
M3P: Learning Universal Representations via Multitask Multilingual Multimodal Pre-training

This paper presents a Multitask Multilingual Multimodal Pre-trained model (M3P) that combines multilingual-monomodal pre-training and monolingual-multimodal pre-training into a unified framework via multitask learning and weight sharing. The model learns universal representations that can map objects that occurred in different modalities or expressed in different languages to vectors in a common semantic space. To verify the generalization capability of M3P, we fine-tune the pre-trained model for different types of downstream tasks: multilingual image-text retrieval, multilingual image captioning, multimodal machine translation, multilingual natural language inference and multilingual text generation. Evaluation shows that M3P can (i) achieve comparable results on multilingual tasks and English multimodal tasks, compared to the state-of-the-art models pre-trained for these two types of tasks separately, and (ii) obtain new state-of-the-art results on non-English multimodal tasks in the zero-shot or few-shot setting. We also build a new Multilingual Image-Language Dataset (MILD) by collecting large amounts of (text-query, image, context) triplets in 8 languages from the logs of a commercial search engine
On the link between the North Atlantic storm track and precipitation deuterium excess in Reykjavik

This study establishes a robust process‐based dynamical link between the variability of the deuterium excess (d) in monthly winter precipitation in Reykjavik and the frequency of strong large‐scale ocean evaporation (SLOE) events in the subpolar North Atlantic. SLOE events are induced by cold advection in the rear of extratropical cyclones. The link between SLOE and d emerges from the fact that a substantial fraction of moisture that precipitates in Reykjavik in winter originates from SLOE events. It is shown that positive anomalies of monthly d co‐occur with positive anomalies in the frequency of SLOE events at the moisture source of Reykjavik precipitation. An intensification and a northeastwards shift of the North Atlantic storm track acts as a driver for the enhanced SLOE frequency in months with positive anomalies in d. This link also implies that in the subpolar North Atlantic, variations of d in monthly (or seasonal) precipitation reveal information about the storm track dynamics in the vicinity of Iceland. Potential implications of this finding for the interpretation of d as a proxy for the location and intensity of storm tracks are discussed.
Valproate‐associated Coagulopathies Are Frequent and Variable in Children

Summary: Purpose: Valproic acid (VPA) is an antiepileptic drug (AED) commonly used for generalized and focal epilepsies. The clinical relevance of coagulopathies, known as side effects of VPA therapy, especially thrombocytopenia, von Willebrand disease, and a decrease of factor XIII, is still unclear.
Epilepsy in Resource Poor Countries—Suggestion of an Adjusted Classification

According to the WHO 50 million people suffer from epilepsy; 80% of them live in resource poor countries (WHO, 2001). In these settings, classification of seizures in view of adequate treatment has been difficult due to lack of diagnostic tools such as electroencephalograms (EEG) and imaging. Drawing from a vast working experience of many years in neurology in developing countries, the authors developed a classification system for seizures suitable for local circumstances. Considering clinical, diagnostic, prognostic and therapeutic needs, we adjusted the International Classification of Epileptic Seizures (ICES) and opted for a simple-structured, easy-to-understand classification of epileptic seizures which is still in accordance with the ICES and in fact shares many similarities with the ILAE version of guidelines for epidemiologic studies on epilepsy (ILAE 1981, ILAE 1993). EEG and neuroimaging are normally not available in developing countries, thus the diagnosis is based on clinical symptomatology alone. We suggest the following classification:
Deep Visuo-Tactile Learning: Estimation of Tactile Properties from Images (Extended Abstract)

Estimation of tactile properties from vision, such as slipperiness or roughness, is important to effectively interact with the environment. These tactile properties help humans, as well as robots, decide which actions they should choose and how to perform them. We, therefore, propose a model to estimate the degree of tactile properties from visual perception alone (e.g., the level of slipperiness or roughness). Our method extends an encoder-decoder network, in which the latent variables are visual and tactile features. In contrast to previous works, our method does not require manual labeling, but only RGB images and the corresponding tactile sensor data. All our data is collected with a webcam and tactile sensor mounted on the end-effector of a robot, which strokes the material surfaces. We show that our model generalizes to materials not included in the training data.
Geometry of Prym varieties for special bielliptic curves of genus three and five

We derive explicit normal forms for two pencils of bielliptic curves of genus three and genus five. The first pencil is associated with an abelian surface with a polarization of type $(1,2)$. The second pencil is related to the first by an unramified double cover, the Prym variety of which is canonically isomorphic to the Jacobian of a general curve of genus two. Our results are obtained by analyzing suitable elliptic fibrations on associated Kummer surfaces and rational double covers among them.
Minimal Realizations of Input–Output Behaviors by LPV State-Space Representations With Affine Dependence

This letter makes the first steps towards a behavioral theory of LPV state-space representations with only affine dependence on the scheduling signal, by characterizing minimality of such state-space representations. We show that minimality is equivalent to observability, and that minimal realizations of the same behavior are isomorphic. Finally, we establish a formal relationship between minimality of LPV state-space representations with an affine dependence on the scheduling signal and minimality of LPV state-space representations with a dynamic and meromorphic dependence on the scheduling signal.
Small, balanced, efficient, optimal, and near rotatable response surface designs for factorial experiments asymmetrical in some quantitative, qualitative factors

ABSTRACT We present a structured method of constructing cost-efficient response surface designs (RSDs) as compared to the replicated central composite designs (RCCDs), that are useful for modelling and optimization of the experiments asymmetric in some qualitative, quantitative factors with at least two unrestricted quantitative factors while the remaining take two or three levels. We demonstrate the method by designing various experimental situations in 3 to 6 factors, and the analysis competency of the RSDs by analysing a published data set from an optimization experiment. The structural and prediction properties make our RSDs a good alternative to the known RSDs.
Environmental Conditions Associated with Observed Snowband Structures within Northeast U.S. Winter Storms

Northeast U.S. winter storms commonly exhibit multiple meso-β-scale (L < 200 km) bands of enhanced radar reflectivity and precipitation. We use radar observations, upper-air soundings, and reanalyses from 108 cases of cool season (October–April) storms from 1996 to 2016 that occurred within the coastal corridor from Delaware to Maine to identify and assess various banding structures and environments. Banding can occur in several configurations among storms, and banding characteristics can differ at different times within the same storm. We classified 6-h storm periods as containing long (>200 km) single bands, single bands co-occurring with sets of mesoscale multibands, multibands only, and radar echoes without any bands using a combination of automated and manual methods. Use of radar reflectivity data at 0.5-dB precision and a variable rather than a fixed threshold showed that the occurrence of long single bands without any mesoscale multibands was rare, occurring in only 5 of 113 6-h periods. The most frequently occurring band configuration (55%) was concurrent single bands and multibands, which usually were present in the northwest quadrant of mature cyclones. Sets of multibands without a nearby single band usually occurred in the northeast quadrant of a cyclone poleward of weak midlevel forcing along a warm front. Overall, mesoscale single and multibands more commonly occurred after the cyclone occluded than in the developing stages. Multibands occurred in a wide range of frontogenesis and moist potential vorticity environments.
Whole-Body Positron Emission Tomography and Fluorodeoxyglucose

Background. The clinical staging and management of both primary and metastatic lung lesions depends on accurate imaging techniques. Biochemical imaging with positron emission tomography, (PET], and the glucose analog 2-['8F]-fluoro-2-deoxy-D-glucose, (FDG), complements anatomic imaging with conventional radiologic methods. A new "whole-body" PET FDG technique that produces two-dimensional, nontomographic and tomographic longitudinal images of the entire body has been developed at UCLA. Sixteen patients with known pulmonary nodules who had undergone thoracic computed tomography (CT] were studied with whole-body PET FDG imaging at the UCLA Medical Center. This PET FDG imaging method identified metabolically active tumor foci in all eight patients with bronchogenic carcinomas, four patients with metastatic lesions to the thorax, and two patients with Hodgkin disease. All diagnoses were confirmed histologically. Additionally, the PET FDG technique detected extrathoracic metastases in 4 of 16 patients, Thoracic CT was not diagnostic of neoplasm in two of the eight patients with bronchogenic carcinomas. In one patient with an ACTH-producing bronchial carcinoid, the lesion ultimately was deMethods.