Miracle-dz/UniFAR-FTUs huggingface dataset:
Quantifying the Relationship between SARS-CoV-2 Wastewater Concentrations and Building-Level COVID-19 Prevalence at an Isolation Residence: A Passive Sampling Approach

Abstract SARS-CoV-2 RNA loads can be detected in the excreta of individuals with COVID-19 and have demonstrated positive correlations with clinical infection trends. Consequently, wastewater-based epidemiology (WBE) approaches have been implemented globally as a public health surveillance tool to monitor community-level prevalence of infections. The majority of wastewater specimens are gathered as either composite samples via automatic samplers (autosamplers) or grab samples. However, autosamplers are expensive and can be challenging to maintain in cold weather, while grab samples are particularly susceptible to temporal variation when sampling sewage directly from complex matrices outside residential buildings. Passive sampling can provide an affordable, practical, and scalable sampling system while maintaining a reproducible SARS-CoV-2 signal. In this regard, we deployed tampons as passive samplers outside of a COVID-19 isolation unit (a segregated residence hall) at a university campus from 1 February 2021–21 May 2021. Samples (n = 64) were collected 3–5 times weekly and remained within the sewer for a median duration of 24 h. SARS-CoV-2 RNA was quantified using reverse-transcription quantitative polymerase chain reaction (RT-qPCR) targeting the N1 and N2 gene fragments. We quantified the mean viral load captured per individual and the association between the daily viral load and total persons, adjusting for covariates using multivariable models to provide a baseline estimate of viral shedding. Samples were processed through two distinct laboratory pipelines on campus, yielding highly correlated N2 concentrations. Data obtained here highlight the success of passive sampling utilizing tampons to capture SARS-CoV-2 in wastewater coming from a COVID-19 isolation residence, indicating that this method can help inform building-level public health responses.
Noise in physical systems and 1/f fluctuations

These proceedings represent research done on fluctuations andnoise in physical and biological systems. Both stochastic andchaotic fluctuations are considered. For physical systems, electric current and voltage fluctuations in semiconductor devices, films,metals, and superconductors are considered. The quantum 1/ffluctuation theory is based on quantum electrodynamics and isincreasingly relevant to high-technology device development. Therewere one hundred and fifty nine papers presented at the conferenceand four have been abstracted for the database. (AIP)
Virial masses of galactic haloes from galaxy–galaxy lensing: theoretical modelling and application to Sloan Digital Sky Survey data

We present a theoretical analysis of galaxy–galaxy lensing in the context of halo models with cold dark matter motivated dark matter profiles. The model enables us to distinguish between the central galactic and non-central group/cluster contributions. We apply the model to the recent Sloan Digital Sky Survey (SDSS) measurements with known redshifts and luminosities of the lenses. This allows one to model accurately the mass distribution of a local galaxy population around and above L*. We find that the virial mass of an L* galaxy is M200= (5 − 10) × 1011h−1 M⊙ depending on the colour of the galaxy. This value varies significantly with galaxy morphology, with M* for late types being lower by a factor of 10 in u′, a factor of 7 in g′ and a factor of 2.5–3 in r′, i′ and z′ relative to early types. The fraction of non-central galaxies in groups and clusters is estimated to be below 10 per cent for late types and around 30 per cent for early types. Using the luminosity dependence of the signal, we find that for early types the virial halo mass M scales with luminosity as M∝L1.4±0.2 in red bands above L*. This shows that the virial mass-to-light ratio (M/L) is increasing with luminosity for galaxies above L*, as predicted by theoretical models. The virial mass-to-light ratio in the i′ band is 17 (45) h M⊙/L⊙ at L* for late (early) types. Combining this result with cosmological baryon fraction, one finds that 70 (25) per cent h−1ΥiΩm/12Ωb of baryons within r200 are converted to stars at L*, where Υi is the stellar mass-to-light ratio in the i′ band. This indicates that for both early- and late-type galaxies around L* a significant fraction of all the baryons in the halo is transformed into stars.
Extreme Star Formation in the Interacting Galaxy Arp 299 (IC 694 + NGC 3690)

We present a comprehensive study of the star formation properties of the infrared luminous galaxy Arp 299 (IC 694 + NGC 3690). The observations include Hubble Space Telescope (HST) NICMOS imaging and Multiple Mirror Telescope optical and near-infrared spectroscopy together with HST archival data. We correct the galaxy parameters for extinction and use the results as boundary conditions for evolutionary starburst models. These models and other arguments show that Arp 299 has been going through a broad variety of interaction-induced star formation for the last ~15 Myr. In addition to nuclear starbursts in the two colliding galaxies, there are nearby luminous star-forming regions that may be the result of molecular clouds breaking up and starting to form massive stars as they approach the nuclear potential. Two regions near the interaction region have very recently formed massive stars (~4 Myr old). One of these regions in particular appears to have undergone a starburst of very short duration, in contrast with the 5-10 Myr durations that are typical of nuclear events. These regions will probably form gravitationally bound new dwarf galaxies, although they are close enough to the more massive original galaxies that they will probably eventually be subsumed into them. In addition, we find 19 H II regions at least as energetic as 30 Doradus, and 21 older star clusters that likely are the products of similar H II regions formed in the past. This population of supergiant H II regions is unprecedented in normal galaxies and emphasizes that the effects of the interaction propagate through the entire pair of galaxies.
Spatial and spectral characteristics of information flux between turbulent boundary layers and porous media

Abstract The interaction between boundary layer turbulence and a porous layer is the cornerstone of interface engineering. In this study, the spatial and spectral-resolved transfer entropy is used to assess the asymmetry of the causal interaction next to the permeable wall. The analysis is based on pore-resolved direct numerical simulation of turbulent channel flow over cylinder arrays. The spatial map of transfer entropy reveals the information flux between the porous medium and arbitrary nearby positions, and paths connecting locations with maximum information transfer are identified. The paths in the ‘top-down’ and ‘bottom-up’ directions, respectively, lean upstream and downstream, demonstrating that the coupling process is directionally dependent. The scale dependence of transfer entropy is inspected with a surrogate data strategy. As wall permeability increases, the active scale range in causal interaction shifts from near-wall vortices to Kelvin–Helmholtz type eddies. In addition, linear stochastic estimation is used to determine the statistical velocity field for a local informative event. In an average sense, the interaction between a convecting sweep or ejection event and the up/down-welling motions at the pore unit is the core mechanism that contributes to the causal coupling. The statistical findings derived from the transfer entropy are then validated using a neural network-based remote sensing model.
Endovascular treatment of main trunk aneurysms in the residual anterior circulation in moyamoya disease

Background Main trunk aneurysms in the residual anterior circulation in moyamoya disease (MMD) are uncommon, and in such cases, endovascular treatment (EVT) is a good choice. Materials and methods A retrospective study was performed on 35 consecutive patients admitted to our hospital who were diagnosed with MMD and main trunk aneurysms in the residual anterior circulation and were treated with EVT. Result The 35 patients were aged 38–77 years (mean, 56.1 ± 8.8 years) and included 17 females (48.6%, 17/35). There were 29 cases (82.9%, 29/35) of hemorrhagic onset. In 35 patients, there were 38 main trunk aneurysms in the residual anterior circulation. Thirty-eight aneurysms underwent coiling; among them, coiling with stent assistance was used in the treatment of 6 (15.8%, 6/38) aneurysms. The immediate modified Raymond-Roy classification (MRRC) was grade I for all aneurysms. Among 35 patients, intraoperative bleeding occurred in 2 (5.7%, 2/35) patients. After EVT, immediate hemiplegia occurred in 4 (11.4%, 4/35) patients, and immediate coma occurred in 1 (2.9%, 1/35) patient. At discharge, in 35 patients, the Glasgow Outcome Scale (GOS) was five in 88.6% of them. Of 35 patients, 68.6% had follow-up data, GOS was five in 87.5% patients, and the MRRC was grade I for all aneurysms in the follow-up angiography. Conclusion For main trunk aneurysms in the residual anterior circulation in MMD, although EVT was accompanied by potential ischemic and hemorrhagic complications, which should be considered, EVT can still offer an acceptable prognosis in more than 85% of patients.
Do thrifty genes exist? Revisiting uricase

Sixty years ago, the geneticist James Neel proposed that the epidemics of obesity and diabetes today may have evolutionary roots. Specifically, he suggested that our ancestors may have accumulated mutations during periods of famine that provided a survival advantage at that time. However, the presence of this “thrifty genotype” in today's world, where food is plentiful, would predispose us to obesity and diabetes. The “thrifty gene” hypothesis, attractive to some, has been challenged over the years. The authors have previously postulated that the loss of the uricase gene, resulting in a rise in serum and intracellular uric acid levels, satisfies the criteria of a thrifty genotype mutation. This paper reviews and brings up‐to‐date the evidence supporting the hypothesis and discusses the current arguments that challenge this hypothesis. Although further studies are needed to test the hypothesis, the evidence supporting a loss of uricase as a thrifty gene is substantial and supports a role for evolutionary biology in the pathogenesis of the current obesity and diabetes epidemics.
Numerical Experiments to Analyze Cloud Microphysical Processes Depicted in Vertical Profiles of Radar Reflectivity of Warm Clouds

AbstractInformation about microphysical processes in warm clouds embedded in satellite measurements must be untangled to be used to improve the parameterization in global models. In this paper, the relationship between vertical profiles of horizontally averaged radar reflectivity Zm and cloud optical depth from cloud top τd was investigated using a hybrid cloud microphysical model and a forward simulator of satellite measurements. The particle size distributions were explicitly simulated using a bin method in a kinematic framework. In contrast to previous interpretations of satellite-observed data, three patterns of the Zm–τd relationship related to microphysical processes were identified. The first is related to the autoconversion process, which causes Zm to increase upward with decreasing τd. Before the initiation of surface precipitation, Zm increases downward with τd in the upper part of the cloud, which is considered to be a second characteristic pattern and is caused by the accretion process. The ap.
In vivo expression vector derived from anhydrobiotic tardigrade genome enables live imaging in Eutardigrada

Water is essential for life, but anhydrobiotic tardigrades can survive almost complete dehydration. Anhydrobiosis has been a biological enigma for more than a century with respect to how organisms sustain life without water, but the few choices of genetic toolkits available in tardigrade research have been a challenging circumstance. Here, we report the development of an in vivo expression system for tardigrades (the TardiVec system). TardiVec is based on a plasmid vector with promoters that originated from an anhydrobiotic tardigrade Ramazzottius varieornatus. It enables the introduction of GFP-fused proteins and genetically encoded indicators such as the Ca2+ indicator GCaMP into tardigrade cells; consequently, the dynamics of proteins and cells in tardigrades may be observed by fluorescence live imaging. This system is applicable for several tardigrades in the class Eutardigrada: the promoters of anhydrobiosis-related genes showed tissue-specific expression in this work. Surprisingly, promoters functioned similarly between multiple species, even for species with different modes of expression of anhydrobiosis-related genes, such as Hypsibius exemplaris, in which these genes are highly induced upon facing desiccation, and Thulinius ruffoi, which lacks anhydrobiotic capability. These results suggest that the highly dynamic expression changes in desiccation-induced species are regulated in trans. Tissue-specific expression of tardigrade-unique unstructured proteins also suggests differing anhydrobiosis machinery depending on the cell types. We believe that TardiVec opens up various experimental possibilities in tardigrade research, especially to explore anhydrobiosis mechanisms.
Computer generation of fruit shapes from DNA sequence

The generation of realistic plant and animal images from marker information could be a main contribution of artificial intelligence to genetics and breeding. Since morphological traits are highly variable and highly heritable, this must be possible. However, a suitable algorithm has not been proposed yet. This paper is a proof of concept demonstrating the feasibility of this proposal using ‘decoders’, a class of deep learning architecture. We apply it to Cucurbitaceae, perhaps the family harboring the largest variability in fruit shape in the plant kingdom, and to tomato, a species with high morphological diversity also. We generate Cucurbitaceae shapes assuming a hypothetical, but plausible, evolutive path along observed fruit shapes of C. melo. In tomato, we used 353 images from 129 crosses between 25 maternal and 7 paternal lines for which genotype data were available. In both instances, a simple decoder was able to recover expected shapes with large accuracy. For the tomato pedigree, we also show that the algorithm can be trained to generate offspring images from their parents’ shapes, bypassing genotype information. Data and code are available at https://github.com/miguelperezenciso/dna2image.
Specific codons control cellular resources and fitness

As cellular engineering progresses from simply overexpressing proteins to imparting complex metabolic and regulatory phenotypes through multigene expression, judicious appropriation of cellular resources is essential. Since there is degeneracy in codons and their use is biased, codons may control cellular resources at a translational level. We investigate how partitioning tRNA resources by incorporating dissimilar codon usage can drastically alter interdependence of expression level and burden on the host. By isolating the effect of individual codons’ use during elongation, while eliminating confounding factors like mRNA structure, GC content, transcript level, and translation initiation rates, we show that codon choice can trans-regulate fitness of the host and expression of other heterologous genes. We correlate specific codon usage patterns with host fitness, and derive a coding scheme for multi-gene expression called the Codon Health Index (CHI, χ). This empirically derived coding scheme (χ) enables the design of multi-gene expression systems that avoid catastrophic cellular burden and is robust across multiple growth conditions.
FGF21 protects against hepatic lipotoxicity and macrophage activation to attenuate fibrogenesis in nonalcoholic steatohepatitis

Analogues of the hepatokine FGF21 are in clinical development for type 2 diabetes and nonalcoholic steatohepatitis (NASH) treatment. Although their glucose-lowering and insulin-sensitizing effects have been largely unraveled, the mechanisms by which they alleviate liver injury have only been scarcely addressed. Here, we aimed to unveil the mechanisms underlying the protective effects of FGF21 on NASH using APOE*3-Leiden.CETP mice, a well-established model for human-like metabolic diseases. Liver-specific FGF21 overexpression was achieved in mice, followed by administration of a high-fat high-cholesterol diet for 23 weeks. FGF21 prevented hepatic lipotoxicity, accompanied by activation of thermogenic tissues and attenuation of adipose tissue inflammation, improvement of hyperglycemia and hypertriglyceridemia, and upregulation of hepatic programs involved in fatty acid oxidation and cholesterol removal. Furthermore, FGF21 inhibited hepatic inflammation, as evidenced by reduced Kupffer cell (KC) activation, diminished monocyte infiltration and lowered accumulation of monocyte-derived macrophages. Moreover, FGF21 decreased lipid- and scar-associated macrophages, which correlated with less hepatic fibrosis as demonstrated by reduced collagen accumulation. Collectively, hepatic FGF21 overexpression limits hepatic lipotoxicity, inflammation and fibrogenesis. Mechanistically, FGF21 blocks hepatic lipid influx and accumulation through combined endocrine and autocrine signaling, respectively, which prevents KC activation and lowers the presence of lipid- and scar-associated macrophages to inhibit fibrogenesis.
Chemokines form complex signals during inflammation and disease that can be decoded by extracellular matrix proteoglycans

Chemokine driven leukocyte recruitment is a key component of the immune response and is central to a wide range of diseases. However, there has yet to be a clinically successful therapeutic approach that targets the chemokine system during inflammatory disease; possibly due to the supposed redundancy of the chemokine system. A range of recent studies have demonstrated that the chemokine system is in fact based on specificity of function. Here we have generated a resource to analyse chemokine gene (ligand and receptor) expression across different species, tissues and diseases; revealing complex expression patterns whereby multiple chemokine ligands that mediate recruitment of the same leukocyte type are expressed in the same context, e.g. the CXCR3 ligands CXCL9, 10 and 11. We use biophysical approaches to show that CXCL9, 10 and 11 have very different interactions with extracellular matrix glycosaminoglycans (GAGs) which is exacerbated by specific GAG sulphation. Finally, in vivo approaches demonstrate that GAG-binding is critical for CXCL9 driven recruitment of specific T cell subsets (e.g. CD4+) but not others (e.g. CD8+), independent of CXCR3 expression. Our data demonstrate that chemokine expression is complex and that multiple ligands are likely needed for robust leukocyte recruitment across tissues and diseases. We also demonstrate that ECM GAGs facilitate decoding of these complex chemokine signals so that they are either primarily presented on GAG-coated cell surfaces or remain more soluble. Our findings represent a new mechanistic understanding of chemokine mediated immune cell recruitment and identify novel avenues to target specific chemokines during inflammatory disease.
Liquid-liquid phase separation of intrinsically disordered FG-Nups is driven by highly-dynamic hydrophobic FG-motifs

The intrinsically disordered FG-Nups in the NPC central channel can undergo liquid-liquid phase sepration (LLPS) into liquid condensates that display NPC-like permeability barrier properties. Here we present LLPS characteristics of each of the disordered FG-Nups of the yeast NPC. Using molecular dynamics simulations at amino acid resolution, FG-Nup condensates are studied and the main physicochemical driving forces for FG-Nup LLPS are identified. We show that FG-motifs that are predominantly present in the disordered domain of FG-Nups act as highly-dynamic hydrophobic stickers that are essential for the formation of stable liquid-like condensates. Next to that, we study LLPS of an FG-Nup mixture that resembles the NPC stoichiometry and observe that an NPC condensate is formed containing multiple types of FG-Nups. We find that the LLPS of this NPC condensate is also driven by FG–FG interactions, similar to the homotypic FG-Nup condensates. Based on the observed LLPS behavior, we categorize the different FG-Nups of the yeast NPC into two classes: The GLFG-Nups located in the central channel of the NPC phase separate into liquid-like condensates, forming a high-density cohesive barrier that can exclude inert particles. The FG-Nups at the entry and exit of the NPC channel, containing no GLFG-motifs, do not phase separate and possibly form a repulsive barrier by entropically excluding inert particles.
Research progress on the relationship between the TOR signaling pathway regulator, epigenetics, and tumor development

Almost all cellular activities depend on protein folding, signaling complex assembly/disassembly, and epigenetic regulation. One of the most important regulatory mechanisms responsible for controlling these cellular processes is dynamic protein phosphorylation/dephosphorylation. Alterations in phosphorylation networks have major consequences in the form of disorders, including cancer. Many signaling cascades, including the target of rapamycin (TOR) signaling, are important participants in the cell cycle, and dysregulation in their phosphorylation/dephosphorylation status has been linked to malignancies. As a TOR signaling regulator, protein phosphatase 2A (PP2A) is responsible for most of the phosphatase activities inside the cells. On the other hand, TOR signaling pathway regulator (TIPRL) is an essential PP2A inhibitory protein. Many other physiological roles have also been suggested for TIPRL, such as modulation of TOR pathways, apoptosis, and cell proliferation. It is also reported that TIPRL was increased in various carcinomas, including non-small-cell lung carcinoma (NSCLC) and hepatocellular carcinomas (HCC). Considering the function of PP2A as a tumor suppressor and also the effect of the TIPRL/PP2A axis on apoptosis and proliferation of cancer cells, this review aims to provide a complete view of the role of TIPRL in cancer development in addition to describing TIPRL/PP2A axis and its epigenetic regulation.