Miracle-dz/UniFAR-FTUs huggingface dataset:
On the integrated density of states for the Schrödinger operators with certain random electromagnetic potentials

$-(1/2)d^{2}/dx^{2}+V^{\omega}$ , for which fairly satisfactory theory has been developed. Therefore we throughout assume that $d\geqq 2$ . As usual we call $V^{\omega}$ the (electric) scalar potential. Such Schr\"odinger operators arise in quantum models of disordered systems (see, $e.g.$ , [5], [9], [11], [13], [17] and references therein) and the spectral properties are one of the main targets of the study. Among them we are interested in the integrated density of states (IDS for short). The IDS is defined as follows. Let $\Lambda_{r},$ $r=0,1,2,$ $\cdots$ be a sequence of hypercubes increasing to $R^{d}$ and $H_{\Lambda_{r}}^{D}(\omega)$ be the restriction of $H(\omega)$ given by (1.1) to $L^{2}(\Lambda_{r})$ with the Dirichlet boundary condition. We denote by $\rho_{\Lambda_{r}}^{D}(\lambda, \omega)$ the number of the eigenvalues less than $\lambda$ of $H_{\Lambda_{r}}^{D}(\omega)$ . Then the IDS $\rho^{D}$ is defined by
Infinite planar arrays of arbitrarily bent thin wire radiators

A plane wave expansion moment method is presented for computing active impedances and current distributions of infinite planar arrays of thin wire radiating elements. The array lattices can be rectangular or triangular. The excitations can be plane waves or progressively phased voltage sources. Each radiating element, including feedline, can be any collection of bent thin wires. Results are given for arrays of straight dipoles with straight feedlines, straight dipoles with bent feedlines, and swept back dipoles (arms inclined with respect to the array planes) with straight feedlines. The experimentally observed phenomenon of array blindness as a consequence of feedline scattering is verified theoretically. The absence of this effect when the dipole arms are inclined with respect to the array plane also is verified.
Performance of an electronic nose for quality estimation of ground meat

An electronic nose is described, which consists of a gas sensor array combined with a pattern recognition routine. The sensor array used consists of ten metal-oxide-semiconductor field effect transistors with gates of catalytically active metals. It also contains four commercially available chemical sensors based on tin dioxide, so-called Taguchi sensors. In some studies, a carbon dioxide monitor based on infrared absorption is also used. Samples of ground beef and pork, stored in a refrigerator, have been studied. Gas samples from the meat were then led to the sensor array, and the resulting patterns of sensor signals were treated with pattern recognition software based on an artificial neural network as well as with an algorithm based on an abductory induction mechanism. When using all sensors for learning, the two nets could predict both type of meat and storage time quite well. Omitting the carbon dioxide monitor, both nets could predict type of meat, but storage time not so well. Finally, it is also shown how a net based on unsupervised training could be used to predict storage time for ground beef.
Vortical Structures in Homogeneously Sheared Turbulence Subjected to Background Rotation

The homogeneously sheared turbulence subjected to a background rotation that cancels the shear vorticity is investigated numerically. The vortex structures that appear in the rotating flow are only longitudinal vortex tubes which are highly elongated in the streamwise direction. The vertical components of fluid velocity and particle diffusion are activated compared with spanwise components, reflecting the arrangement of the vortical structures, which leads to a large particle diffusion in the streamwise direction as well.
Exploring Mothers' and Fathers' Reported Use of Discipline Practices With Their Preschoolers: Associations With Parental Well-Being

Abstract:Supporting parents in use of effective, evidence-based discipline remains an important goal for research, practice, and policy. This study explored parental well-being and reported discipline practices with preschoolers (2–5 years). Parents (N = 205; 97 fathers) completed a Qualtrics-based survey assessing discipline practices, feelings of judgment in the parental role, anxiety and depression symptoms, and fear of happiness. Parents higher on anxiety used greater structure/limit setting. Higher parental anxiety and depression symptoms related to greater fear of happiness, and fathers higher on anxiety reported greater judgment in the parental role. For mothers, fear of happiness was modestly and positively associated with use of directive/punitive discipline and negatively associated with use of structure/limit setting. Results suggest parental well-being may be linked to discipline use in unique ways for mothers and fathers. Findings can support researchers and community professionals in understanding an array of parental characteristics that may relate to discipline practices.
The ionic conductivity of electrified clouds

Calculations have been made, on the basis of the ionic balance equations derived by Phillips (1967), of the electrical conductivity of clouds in the presence, and in the absence, of secondary ion production resulting from corona. In weakly electrified clouds - no corona - the immobilization of ions on cloud droplets resulting from diffusional capture results in a reduced ionic concentration and conductivity. The normalized conductivity λ the ratio of the in-cloud value to the clear-air value at the same altitude Z was calculated for three different cloud types (cumulus congestus, strato-cumulus and fog) as a function of Z, liquid water content L, droplet charge Q and field strength E. λ was found to be very sensitive to variations in L and E, but only slightly affected by changes in Z, Q and the manner in which the charge is distributed over the size-spectrum. For example, when E = O λ possessed the values 0.034 and 0.17 in a cumulus congestus cloud for L = 0.5 gm/m3 and 0.1 gm/m3 respectively, whereas when E = 90 kV/m λ was 1.5 times; 10−3 and 7.6 times; 10−3 respectively for the same two values of L. The experimental measurements of corona onset fields and currents from ice hydrometeors, Ec and ic respectively, made by Griffiths and Latham (1974) were used to calculate the normalized conductivity within strongly electrified clouds. Corona from ice provides a copious supply of positive and negative ions which causes λ to increase from between 10−3 and 10−4 to greater than 1 when Ec is achieved. The value of λ once corona is initiated depends on L and the concentration of corona sites, J. In this situation altitude Z plays an important role because Ec decreases quite rapidly with decreasing pressure. For example, with a typical distribution of temperature and pressure within a thundercloud, corona will be initiated from hailstones at Ec = 720 kV/m if Z = 2.5 km (0° C) and 540 kV/m at 5.5 km (-18° C); the corresponding values of Ec for snowflakes are 540 and 390 kV/m respectively. At 2.5 km is slightly higher than and lower than 10 respectively, as L is increased from 1 to 5 gm/m3 with J = 1 m−3. It is concluded that the introduction of an ionic leakage current into calculations of field growth within thunderclouds is unnecessary, and that the distribution of electric field is crucial in determining whether corona, once initiated, will trigger lightning or merely increase the ionic conductivity.
Estimation When a Parameter is on a Boundary

This paper establishes the asymptotic distribution of extremum estimators when the true parameter lies on the boundary of the parameter space. The boundary may be linear, curved, and/or kinked. Typically the asymptotic distribution is a function of a multivariate normal distribution in models without stochastic trends and a function of a multivariate Brownian motion in models with stochastic trends. The results apply to a wide variety of estimators and models. Examples treated in the paper are: (1) quasi-ML estimation of a random coefficients regression model with some coefficient variances equal to zero and (2) LS estimation of an augmented Dickey-Fuller regression with unit root and time trend parameters on the boundary of the parameter space.
The landscape of alternative polyadenylation during EMT and its regulation by the RNA-binding protein Quaking

Epithelial-mesenchymal transition (EMT) plays important roles in tumour progression and is orchestrated by dynamic changes in gene expression. While it is well established that post-transcriptional regulation plays a significant role in EMT, the extent of alternative polyadenylation (APA) during EMT has not yet been explored. Using 3’ end anchored RNA sequencing, we mapped the alternative polyadenylation landscape (APA) following TGF-β-mediated induction of EMT in human mammary epithelial cells and found APA generally causes 3’UTR lengthening during this cell state transition. Analysis of the RNA-binding protein Quaking (QKI), a splicing factor induced during EMT, revealed enrichment of its binding adjacent to cleavage and polyadenylation sites within 3’UTRs. Following QKI knockdown, APA of many transcripts are altered to produce predominantly shorter 3’UTRs associated with reduced gene expression. Among these, QKI binds to its own cleavage site to produce a transcript with a longer 3’UTR. These findings reveal extensive changes in APA occur during EMT and identify a novel function for QKI in this process.
Arabidopsis hydathodes are sites of intense auxin metabolism and nutrient scavenging

Hydathodes are small organs located on the leaf margins of all vascular plants. They release excess xylem sap through guttation when stomata are closed or when the humidity level is high. Many promoter analyses have suggested other hydathode functions in metabolite transport and auxin metabolism, but experimental demonstration is still lacking. Here, we compared the transcriptomic and metabolomic features of mature Arabidopsis hydathodes to the leaf blade. 1460 differentially-expressed genes were identified revealing that genes related to auxin metabolism, transport, stress, DNA, plant cell wall, RNA or wax were on average more expressed in hydathodes. On the other hand, genes involved in glucosinolate metabolism, sulfation pathway, metal handling or photosynthesis were downregulated in hydathodes. In hydathodes, there are an increased expression of auxin transcriptional regulators and biosynthetic genes, a lower expression of auxin transport genes and a differential expression of genes related to its vacuolar storage that is consistent with increased contents of free and conjugated auxin. We also found that ca. 78% of the total content of 52 xylem sap metabolites were removed from guttation fluid at the hydathode level. Using reverse genetics, we showed that the capture of nitrate and phosphate in the guttation fluid relies on the NRT2.1 and PHT1;4 transporters, respectively. Thus, hydathodes absorb a significant part of xylem sap nutrients, limiting the loss of valuable chemicals during guttation. Our transcriptomic and metabolomic analyses reveal an organ with its own transcriptomic and physiological identity and highlight hydathode biological processes that may impact the whole plant. One sentence summary Transcriptome and physiological analysis of mature and healthy hydathodes of Arabidopsis demonstrates that those organs are sites of intense auxin metabolism and nutrient scavenging
Two structural switches in HIV-1 capsid regulate capsid curvature and host factor binding

The mature HIV-1 capsid protects the viral genome and interacts with host proteins to travel from the cell periphery into the nucleus. To achieve this, the capsid protein, CA, constructs conical capsids from a lattice of hexamers and pentamers, and engages in and then relinquishes multiple interactions with cellular proteins in an orchestrated fashion. Cellular host factors including Nup153, CPSF6 and Sec24C engage the same pocket within CA hexamers. How CA assembles pentamers and hexamers of different curvatures, how CA oligomerization states or curvature might modulate host-protein interactions, and how binding of multiple co-factors to a single site is coordinated, all remain to be elucidated. Here, we have resolved the structure of the mature HIV-1 CA pentamer and hexamer from conical CA-IP6 polyhedra to high resolution. We have determined structures of hexamers in the context of multiple lattice curvatures and number of pentamer contacts. Comparison of these structures, bound or not to host protein peptides, revealed two structural switches within HIV-1 CA that modulate peptide binding according to CA lattice curvature and whether CA is hexameric or pentameric. These observations suggest that the conical HIV-1 capsid has different host-protein binding properties at different positions on its surface, which may facilitate cell entry and represent an evolutionary advantage of conical morphology. Significance statement HIV-1 particles contain a characteristic, conical capsid that shields the genome from the cellular immune system and recruits cellular proteins to direct the capsid to the nucleus. The cone forms from hexamers of CA protein, and twelve pentamers that accommodate curvature. We obtained detailed 3D models of pentamers and hexamers at positions on capsid surfaces with different curvatures. We find two places in CA that switch conformation according to the local capsid curvature and whether CA is in a pentamer or hexamer. We also obtained models of CA bound to peptides from cellular proteins. The data show how switches in CA help it form a cone shape, and interact differently with cellular proteins at different positions on the cone surface.
Tests of the post-punching behavior of the reinforced concrete flat slabs

Keywords: effondrement progressif ; modele analytique ; modele mathematique ; plancher-dalle ; poinconnement ; progressive collapse ; analytic model ; mathematical model ; flat slab ; punching Reference EPFL-REPORT-163118 Record created on 2011-02-07, modified on 2017-08-01
Viral burdens are associated with age and viral variant in a population-representative study of SARS-CoV-2 that accounts for time-since-infection related sampling bias

In this study, we evaluated the impact of viral variant, in addition to other variables, on within-host viral burdens, by analysing cycle threshold (Ct) values derived from nose and throat swabs, collected as part of the UK COVID-19 Infection Survey. Because viral burden distributions determined from community survey data can be biased due to the impact of variant epidemiology on the time-since-infection of samples, we developed a method to explicitly adjust observed Ct value distributions to account for the expected bias. Analysing the adjusted Ct values using partial least squares regression, we found that among unvaccinated individuals with no known prior infection, the average Ct value was 0.94 lower among Alpha variant infections, compared those with the predecessor strain, B.1. 177. However, among vaccinated individuals, it was 0.34 lower among Delta variant infections, compared to those with the Alpha variant. In addition, the average Ct value decreased by 0.20 for every 10 year age increment of the infected individual. In summary, within-host viral burdens are associated with age, in addition to the interplay of vaccination status and viral variant.
Shifting effects of host physiological condition following pathogen establishment

Understanding host persistence with emerging pathogens is essential for conserving populations. Hosts may initially survive pathogen invasions through pre-adaptive mechanisms. However, whether pre-adaptive traits are directionally selected to increase in frequency depends on the heritability and environmental dependence of the trait and the costs of trait maintenance. Body condition is likely an important pre-adaptive mechanism aiding in host survival, although can be seasonally variable in wildlife hosts. We used data collected over seven years on bat body mass, infection, and survival to determine the role of host body condition during the invasion and establishment of the emerging disease, white-nose syndrome. We found that when the pathogen first invaded, bats with higher body mass were more likely to survive, but this effect dissipated following the initial epizootic. We also found that heavier bats lost more weight overwinter, but fat budgeting depended on infection severity. Lastly, we found little support that bat mass increased in the population after pathogen arrival, and there was high annual plasticity in individual bat masses. Overall, our results suggest that factors that contribute to host survival during pathogen invasion may diminish over time, and are potentially replaced by other host adaptations.
Development of non-alcoholic steatohepatitis is associated with gut microbiota but not oxysterol synthesis

Liver steatosis is the most frequent liver disorder and its advanced stage, non-alcoholic steatohepatitis (NASH), will soon become the main reason for liver fibrosis and cirrhosis. The “multiple hits hypothesis” suggests that progression from simple steatosis to NASH is triggered by multiple factors including the gut microbiota composition. The Epstein Barr virus induced gene 2 (EBI2) is a receptor for the oxysterol 7a, 25-dihydroxycholesterol synthesized by the enzymes CH25H and CYP7B1. EBI2 and its ligand control activation of immune cells in secondary lymphoid organs and the gut. Here we show a concurrent study of the microbial dysregulation and perturbation of the EBI2 axis in a mice model of NASH. We used mice with wildtype, or littermates with CH25H-/-, EBI2-/-, or CYP7B1-/- genotypes fed with a high-fat diet (HFD) containing high amounts of fat, cholesterol, and fructose for 20 weeks to induce liver steatosis and NASH. Fecal and small intestinal microbiota samples were collected, and microbiota signatures were compared according to genotype and NASH disease state. We found pronounced differences in microbiota composition of mice with HFD developing NASH compared to mice did not developing NASH. In mice with NASH, we identified significantly increased 33 taxa mainly belonging to the Clostridiales order and/ or the family, and significantly decreased 17 taxa. Using an Elastic Net algorithm, we suggest a microbiota signature that predicts NASH in animals with a HFD from the microbiota composition with moderate accuracy (area under the receiver operator characteristics curve=0.64). In contrast, no microbiota differences regarding the studied genotypes (wildtype vs knock-out CH25H-/-, EBI2-/-, or CYP7B1-/-) were observed. In conclusion, our data confirm previous studies identifying the intestinal microbiota composition as a relevant marker for NASH pathogenesis. Further, no link of the EBI2 – oxysterol axis to the intestinal microbiota was detectable in the current study.
Plasmonic Stimulation of Gold Nanorods for the Photothermal Control of Engineered Living Materials

Engineered living materials (ELMs) use encapsulated microorganisms within polymeric matrices for biosensing, drug delivery, capturing viruses, and bioremediation. It is often desirable to control their function remotely and in real time. Suitable, genetically engineered microorganisms respond to changes of their environment. Here, we combine this local sensitivity with a nanostructured encapsulation material to sensitize the ELM for infrared light. Previously, blue light has been used to stimulate microorganisms that contain optogenetic modules responsive to those wavelengths without the need for exogenous cofactors. Here, we use plasmonic gold nanorods (AuNR) that have a strong absorption maximum at 808 nm, a wavelength where human tissue is relatively transparent. Biocompatible composites of a Pluronic-based hydrogel and AuNR are prepared without agglomeration; they react to illumination by local heating. We measure a photothermal conversion efficiency of 47 % in transient temperature measurements. Steady-state temperature profiles from local photothermal heating are quantified using infrared photothermal imaging, correlated with measurements inside the gel, and applied to stimulate thermoresponsive bacteria. Using a bilayer ELM construct with the thermoresponsive bacteria and the thermoplasmonic composite gel in two separate but connected hydrogel layers, it is shown that the bacteria can be stimulated to produce a fluorescent protein using infrared light in a spatially controlled manner.
Time of Day Analysis over a Field Grown Developmental Time Course in Rice

Plants integrate time of day (TOD) information over an entire season to ensure optimal growth, flowering time, and grain fill. However, most TOD expression studies have focused on a limited number of combinations of daylength and temperature under laboratory conditions. Here we re-analyze an Oryza sativa (rice) expression study that followed TOD expression in the field over an entire growing season. We find that like Arabidopsis thaliana, almost all rice genes have a TOD specific expression over the developmental time course. As has been suggested in other grasses, thermocycles were a stronger cue for TOD expression than the photocycles over the growing season. All the core circadian clock genes display consistent TOD expression over the season with the interesting exception that the two grass paralogs of EARLY FLOWERING 3 (ELF3) display a distinct phasing based on the interaction between thermo- and photo-cycles. The dataset also revealed how specific pathways are modulated to distinct TOD over the season consistent with the changing biology. The data presented here provides a resource for researchers to study how TOD expression changes under natural conditions over a developmental time course, which will guide approaches to engineer more resilient and prolific crops.
Multisite Thalamic Recordings to Characterize Seizure Propagation in the Human Brain

Neuromodulation of the anterior nuclei of the thalamus (ANT) has shown to be efficacious in patients with refractory focal epilepsy, but it is not uniformly effective. One important uncertainty is to what extent thalamic subregions other than the ANT are recruited earlier and more prominently in the propagation of seizures in patients with presumed temporal lobe epilepsy (TLE). To address this unknown, we studied 11 patients with clinical manifestations of TLE planned to undergo invasive stereo-encephalography (sEEG) monitoring. We extended cortical electrodes to reach thalamic nuclear subdivisions in the anterior (ANT), middle (mediodorsal) and or posterior (pulvinar) sites. This multisite thalamic sampling was without any adverse events. Intracranial EEG (iEEG) recordings confirmed seizure-onset in medial temporal lobe, insula, orbitofrontal and temporal neocortical sites – highlighting the importance of iEEG for more accurate localization of seizure foci. Visual review of EEGs documented early and prominent involvement of specific thalamic sites. Seizures originating from the same brain origin produced a stereotyped thalamic EEG signature. Visual review of EEGs, validated with singlepulse corticothalamic evoked potentials, documented early and prominent involvement of thalamic sites that would have not been predicted given the anatomy of seizure onset zones. Pulvinar was involved earlier and more prominently than other sampled nuclear subgroups in 60% of patients, even though all patients had a presumed diagnosis of TLE prior to invasive monitoring. Our findings document the feasibility and safety of multisite sampling from the human thalamus and suggest that the anatomy of thalamic involvement may not be entirely predictable on the basis of clinical information or lobar localization of seizures. Future clinical trials can establish whether offering more personalized targets for thalamic neuromodulation will lead to greater meaningful improvements in outcome.