Miracle-dz/UniFAR-FTUs huggingface dataset:
C. elegans RIG-I-like receptor DRH-1 signals via CARDs to activate anti-viral immunity in intestinal cells

Upon sensing viral RNA, mammalian RIG-I-like receptors activate downstream signals using caspase activation and recruitment domains (CARDs), which ultimately promote transcriptional immune responses that have been well-studied. In contrast, the downstream signaling mechanisms for invertebrate RIG-I-like receptors are much less clear. For example, the Caenorhabditis elegans RIG-I-like receptor DRH-1 lacks annotated CARDs and upregulates the distinct output of RNA interference (RNAi). Here we found that, similar to mammal RIG-I-like receptors, DRH-1 signals through two tandem caspase activation and recruitment domains (2CARD) to induce a transcriptional immune response. Expression of DRH-1(2CARD) alone in the intestine was sufficient to induce immune gene expression, increase viral resistance, and promote thermotolerance, a phenotype previously associated with immune activation. We also found that DRH-1 is required in the intestine to induce immune gene expression, and we demonstrate subcellular colocalization of DRH-1 puncta with double-stranded RNA inside the cytoplasm of intestinal cells upon viral infection. Altogether, our results reveal mechanistic and spatial insights into anti-viral signaling in C. elegans, highlighting unexpected parallels in RIG-I-like receptor signaling between C. elegans and mammals. Significance Viruses are ubiquitous pathogens that challenge diverse organisms, from bacteria to killer whales. While anti-viral defense has been well-studied in mammals, less is known about defense in invertebrates, including the roundworm Caenorhabditis elegans. Here we show that the C. elegans viral sensor DRH-1 shares similarities to a viral sensor in mammals called RIG-I. We find that DRH-1 has a signaling motif resembling the 2CARD motif, which is found in RIG-I and activates anti-viral immunity. We demonstrate that overexpression of DRH-1(2CARD) in C. elegans promotes resistance to viral infection, and that DRH-1 forms clusters inside intestinal cells during viral infection, similar to RIG-I in humans. Overall, these findings provide insights into C. elegans anti-viral immunity, highlighting similarities with mammalian anti-viral immunity.
Fine-grained neural coding of bodies and body parts in human visual cortex

The visual image of a human body provides a valuable source of socially relevant information. However, our understanding of the neuronal mechanisms underlying body perception in humans remains limited given the spatiotemporal constraints of functional imaging. Here we recorded multi-unit spiking activity in two neurosurgical patients in or near the extrastriate body area (EBA), a critical region for body perception. Our recordings revealed a strong preference for human bodies over a large range of control stimuli. Notably, this preference was driven by a distinct selectivity for body parts. Moreover, the observed body selectivity generalized to non-photographic depictions of bodies such as silhouettes and stick figures. Overall, our study provides an unprecedented access into the representation of bodies in the human visual cortex to bridge the gap between human neuroimaging and macaque electrophysiology studies, and form a solid basis for computational models of human body processing.
Loss of function in RBBP5 results in a syndromic neurodevelopmental disorder associated with microcephaly

Purpose Epigenetic dysregulation has been associated with many inherited disorders. RBBP5 encodes a core member of the protein complex that methylates histone 3 lysine-4 (H3K4) and has not been implicated in human disease. Methods We identify five unrelated individuals with de novo heterozygous pathogenic variants in RBBP5. Three truncating and two missense variants were identified in probands with neurodevelopmental symptoms including global developmental delay, intellectual disability, microcephaly, and short stature. Here, we investigate the pathogenicity of the variants through protein structural analysis and transgenic Drosophila models. Results Both missense p.T232I and p.E296D variants affect evolutionarily conserved amino acids and are expected to interfere with the interface between RBBP5 and the histones. In Drosophila, ubiquitous overexpression of human RBBP5 is lethal in the larval developmental stage. Loss of Rbbp5 leads to a reduction in brain size, and the human reference, p.T232I, or p.E296D variant transgenes fail to rescue loss of Rbbp5. Expression of either missense variant in an Rbbp5 null background results in a less severe microcephaly phenotype than the human reference, indicating both p.T232I and p.E296D variants are loss-of-function alleles. Conclusion De novo heterozygous variants in RBBP5 are associated with a syndromic neurodevelopmental disorder. Graphical abstract
EffLiFe: Efficient Light Field Generation via Hierarchical Sparse Gradient Descent

—With the rise of Extended Reality (XR) technology, there is a growing need for real-time light ﬁeld generation from sparse view inputs. Existing methods can be classiﬁed into ofﬂine techniques, which can generate high-quality novel views but at the cost of long inference/training time, and online methods, which either lack generalizability or produce unsatisfactory results. However, we have observed that the intrinsic sparse manifold of Multi-plane Images (MPI) enables a signiﬁcant acceleration of light ﬁeld generation while maintaining rendering quality. Based on this insight, we introduce EffLiFe, a novel light ﬁeld optimization method, which leverages the proposed Hierarchical Sparse Gradient Descent (HSGD) to produce high-quality light ﬁelds from sparse view images in real time. Technically, the coarse MPI of a scene is ﬁrst generated using a 3D CNN, and it is further sparsely optimized by focusing only on important MPI gradients in a few iterations. Nevertheless, relying solely on optimization can lead to artifacts at occlusion boundaries. Therefore, we propose an occlusion-aware iterative reﬁnement module that removes visual artifacts in occluded regions by iteratively ﬁltering the input. Extensive experiments demonstrate that our method achieves comparable visual quality while being 100x faster on average than state-of-the-art ofﬂine methods and delivering better performance (about 2 dB higher in PSNR) compared to other online approaches.
Exploring the effects of a nonhydrostatic dynamical core in high‐resolution aquaplanet simulations

This study explores the impact of a nonhydrostatic dynamical core in high‐resolution regional climate simulations using an aquaplanet framework. The Weather Research and Forecasting (WRF) model is used to conduct simulations with both hydrostatic (H) and nonhydrostatic (NH) solvers at horizontal grid spacings (Δx) of 36, 12, and 4 km. The differences between the H and NH simulated precipitation (ΔP) are notable even at Δx = 12 km in the intertropical convergence zone and the transition region to the drier subtropics. At gray zone grid spacing (12 km and 4 km) over the tropics, ΔP is sensitive to whether a cumulus parameterization scheme is used or not. With an idealized Witch of Agnesi land mountain, differences in the precipitation and circulation (vertical velocity) between the H and NH simulations are significant even at Δx = 36 km in the tropics due largely to the strong feedbacks related to moist processes. The differences increase as the model grid spacing and mountain half width (a) are reduced, accompanied by a shift toward a more nonhydrostatic flow regime at a = 24 km. Latent heat release drastically enhances the differences between the NH and H simulations and extends the effect of nonhydrostatic dynamics to a broader region over the mountain and downstream over the tropics. Overall, differences exist between H and NH simulations even at resolutions between 12 and 36 km, but the differences are sensitive to the representations of moist physics and other features such as horizontal diffusion used in the WRF model.
Nová radiofarmaka a aplikace pozitronové emisní tomografie naMasarykově onkologickém ústavu v Brně

Výstavba a zahajeni provozu cyklotronu a PET centra na Masarykově onkologickem ustavu provozovaneho ve spolupraci s Ustavem pro jaderný výzkum Řež umožňuje Masarykovu onkologickemu ustavu zapojit se do výzkumu a aplikaci nových radi ofarmak vcetně latek znacených pozitronovými zařici s kratkým polocasem rozpadu (zejmena 11C). V budo ucnu jso u tak projektovany napřiklad studi e za po užiti radi ofarmak 18F fluoro L thymidin (FLT), markeru proliferace, ne uro onkologicke studi e s po užitim markeru aminokyselinoveho transportu a proteosyntezy 11C methioninu, připadně i dalsich latek aplikovatelných i mimo onkologii. Existence PET centra na Masarykově onkologickem ustavu tak nabizi siroko u skalu nových možnosti paci entům i lekařům nejen v brněnskem regi onu.
Growth and yield studies in the Tapajós region

SUMMARY Growth and yield plots have been monitored in the Tapajos region, Para State, Brazil, since 1981 in four research sites: unlogged primary forest, two areas logged 7 and 13 years before the last assessment, and a secondary forest ca. 50 years old. Diameter increment, mortality and volume increment in these sites are reported. Growth responses were investigated in relation to crown illumination and ecological guild of species. Irrespective of ecological guild, the amount of light received by crowns appeared to produce significant differences in tree growth. A hierarchy of growth rates was observed: rates of diameter increment of intolerant species > tolerant canopy species > understorey tolerant species. Mortality rates were higher for weed species in all study areas except in secondary forest. At this site understorey tolerant species showed higher mortality rates, followed by weed species. Average annual volume increment ranged from 1.6 m3 ha1 yr1 in primary unlogged forest to 4.8 m3 ha"1 yr1 in primary logged forest. Commercial species produced just over 1 m3 ha1 yr1 in the logged stands. Establishing cutting cycles in the Tapajos region and other similar sites must have regard to these low increment rates.
Impact of Workplace Spirituality on Frontline Medical Staff's Sense of Happiness in The Workplace: Empirical Evidence From The Public Health Sector in Duhok City, Kurdistan Region-Iraq

Medical staff in general and front-line medical staff in particular work in difficult working conditions, and it is expected that this will affect their sense of happiness in the work environment. Therefore, in these difficult circumstances, they need the availability of workplace of spirituality that motivates them to perform their tasks efficiently. This descriptive study contributes to reducing the gap in the experimental studies conducted in this field by examining the impact of workplace spirituality including meaningful work, sense of community, and alignment with organizational values on the frontline medical staff's sense of happiness in the workplace. This study adopts a quantitative approach using a survey questionnaire to collect data from 237 frontline medical staff in four public hospitals in Duhok city, Kurdistan region of Iraq. The results showed that all dimensions of workplace spirituality have a significant positive impact on sense of happiness in the workplace among frontline medical staff. The results also support the acceptability of the proposed model. The study recommended that the hospital administrations surveyed should work to enhance the medical staff on the front lines’ sense of happiness in the workplace.
Peopling of Western Japan, Focusing on Kyushu, Shikoku, and Ryukyu Archipelago

The discovery of the Iwajuku site in Japan is the beginning of the study of the first Paleolithic cultures in the region. In this paper we examine the timing of the earliest colonization of southern Japan, especially focusing on the areas of Kyushu, Shikoku, and the Ryukyu archipelago. Osteological studies have proposed the ultimate origin of these western Japanese Paleolithic populations in Southeast Asia. If this hypothesis is correct, Native Americans may be remotely related to the populations of this region. Greater attention to data from areas such as Japan is necessary to understand the timing and nature of New World colonization.
Invasions by non-indigenous species

10.1 Marine invaders: background Invasions by marine non-indigenous species (NIS, see Box 10.1 for definitions) have long been recognised. For example, Carl Emil Hansen Ostenfeld described the invasion of the planktonic diatom Biddulphia (Odontella) sinensis Grev. into the North Sea in 1903, probably transported by ships (Ostenfeld, 1908), and over 50 years ago Charles Elton provided the first overview with narrative accounts of impacts associated with high profile marine invasions by oysters and cordgrass (Elton, 1958). However, marine invasions were first approached with a systematic research effort following J. Carlton’s seminal work in San Francisco Bay (Carlton, 1979). Today it is recognised that marine NIS comprise a diverse group of organisms found in most marine systems. In a recent review, Hewitt and Campbell (2010) tallied almost 1800 marine NIS and cryptogenic species (Box 10.1) worldwide, dominated by arthropods (444), molluscs (350), fish (166), red algae (153), annelids (104, mainly polychaetes), cnidarians (100), heterokonts (73), bryozoans (73) and green algae (51). Although marine NIS have been introduced around the world, some bioregions are more invaded than others; the most heavily invaded regions are the Mediterranean Sea (467 NIS), Australia and New Zealand (429), the South Pacific (289), the north-east Pacific (284) and the north-east Atlantic (216) (Hewitt and Campbell, 2010). More locally, estuaries centred around metropolitan areas and with extensive shipping traffic are typically the most invaded systems. For example, c. 230, 200 and 100 marine NIS are found in San Francisco Bay, Chesapeake Bay and Port Phillip Bay, respectively (Hewitt et al., 2004; Ruiz et al., 2011). The most
Role of Endoscopic Ultrasound in Staging and Vascular Assessment of Pancreatic Cancer

Introduction Computed tomography (CT) of the abdomen with contrast stands as the gold standard for assessing pancreatic cancer, encompassing both staging and vascular analysis. However, not all patients are suitable candidates for contrast-enhanced CT (CECT) scans due to factors such as contrast agent allergies, pregnancy, renal impairment, radiation risks, and limited tissue sampling capability in CECT scans of the abdomen. In light of these challenges, this study evaluated the diagnostic capabilities of endoscopic ultrasound (EUS) compared to CECT for staging and vascular assessment of pancreatic cancer. Methods Fifty patients diagnosed with pancreatic cancer underwent evaluations using both CECT scans and EUS, focusing on staging and vascular invasion assessment. Vascular evaluation was carried out using a categorization system based on EUS findings, classifying them into three types based on the tumor-vessel relationship: Type 1 indicating clear invasion or encasement of a vessel by a tumor or contact with a vessel wall exceeding 180 degrees, Type 2 representing abutment, wherein a tumor contacts a vessel wall but at an angle less than 180 degrees, and Type 3 implying clear non-invasion, where a discernible distance exists between a tumor and a vessel. In this categorization, Type 1 and Type 2 indicated signs of vascular invasion, while Type 3 indicated vascular non-invasion. These findings were subsequently compared to the results from CECT scans. The endoscopist performing EUS was blinded to the CT outcomes prior to the examination. Results Regarding pancreatic cancer staging, EUS exhibited remarkable sensitivity, specificity, and accuracy rates of 100% according to the T criterion.As for vascular invasion assessment, EUS demonstrated sensitivity, specificity, and accuracy of 100%, 95.93%, and 96%, respectively, for venous invasion. For arterial invasion, the figures were 95.65% sensitivity, 100% specificity, and an overall accuracy of 99.5%. Conclusion EUS is an effective modality for evaluating both staging and vascular invasion in pancreatic cancer, boasting exceptional sensitivity, specificity, and accuracy rates. The findings are robust enough to consider EUS a viable alternative to CT scans in evaluation, with the added advantage of EUS offering tissue sampling capability.
Can Precipitation and Temperature from Meteorological Reanalyses Be Used for Hydrological Modeling

AbstractThis paper investigates the potential of reanalyses as proxies of observed surface precipitation and temperature to force hydrological models. Three global atmospheric reanalyses (ERA-Interim, CFSR, and MERRA), one regional reanalysis (NARR), and one global meteorological forcing dataset obtained by bias-correcting ERA-Interim [Water and Global Change (WATCH) Forcing Data ERA-Interim (WFDEI)] were compared to one gridded observation database over the contiguous United States. Results showed that all temperature datasets were similar to the gridded observation over most of the United States. On the other hand, precipitation from all three global reanalyses was biased, especially in summer and winter in the southeastern United States. The regional reanalysis precipitation was closer to observations since it indirectly assimilates surface precipitation. The WFDEI dataset was generally less biased than the reanalysis datasets. All datasets were then used to force a global conceptual hydrological model.
The effect of Kuroshio Current on nitrate dynamics in the southern East China Sea revealed by nitrate isotopic composition

In spring 2014 (May‒June), in the southern East China Sea (ECS) and east of Taiwan, nutrient and isotope samples were collected and analyzed. Also, dissolved oxygen (DO), chlorophyll-a, and physical parameters were determined. The Kuroshio subsurface water intruded into the ECS and separated into two branches on the continental shelf: the nearshore Kuroshio branch current (NKBC) and the offshore Kuroshio branch current (OKBC). Nitrate concentration in the Kuroshio subsurface water slightly decreased east of Taiwan by assimilation, and was supplied by upwelling currents northeast of Taiwan. The variations of DO, nitrate and nitrogen isotopes in the bottom water showed that continuous nitrification occurred in the NKBC after intrusion into the ECS. This process might contribute to the hypoxia zone near the coast of Zhejiang Province, China. Our results also indicated that internal nitrogen cycles appeared in NKBC since the isotope fractionation ratio of oxygen and nitrogen (18ɛ:15ɛ) in NO3- was 1.40. The NO3- flux and budget were calculated in the NKBC via numerical simulations. It demonstrated that at least ∼0.52 kmol NO3-·s−1 was produced by nitrification from DH9 to DH5 transect, and ∼0.11 kmol NO3-·s−1 was consumed in the DH4 transect. Moreover, according to the Rayleigh model, primary production in most of southern ECS was supported by the intrusion of the Kuroshio subsurface water, causing 5‰ isotope fractionation. In some of nearshore stations which located in the northern investigated area, the assimilated nitrate was contributed from both the NKBC and coastal currents originated from the Changjiang diluted water. This article is protected by copyright. All rights reserved.
The Urban Wage Premium: Sorting, agglomeration economies or statistical artifact? The problem of sampling from lognormals

Economic explanations for the urban wage premium (UWP) fall in two categories: sorting of more productive individuals into larger cities, or agglomeration externalities. We present a third hitherto neglected mechanism: a statistical artifact arising from sampling lognormally distributed wages. We show how this artificial UWP emerges, systematically and predictably, when the variance of log-wages is larger than twice the log-size of workers sampled in the smallest city. We present an analytic derivation of this connection between lognormals and increasing returns to scale using extreme value theory. We validate our results analyzing simulated data and real data on more than six million real Colombian wages across more than five hundred municipalities. We find that when taking random samples of $1\%$, or less, of all Colombian workers the estimated real and artificial UWP are both $7\%$, and become statistically indistinguishable, yet both significantly larger than zero. This highlights the importance of working with large samples of workers. We propose a method to tell whether an estimate of UWP is real or an artifact.
Modeling wind waves from deep to shallow waters in Lake Michigan using unstructured SWAN

Accurate wind-wave simulations are vital for evaluating the impact of waves on coastal dynamics, especially when wave observations are sparse. It has been demonstrated that structured-grid models have the ability to capture the wave dynamics of large-scale offshore domains, and the recent emergence of unstructured meshes provides an opportunity to better simulate shallow-water waves by resolving the complex geometry along islands and coastlines. For this study, wind waves in Lake Michigan were simulated using the unstructured-grid version of Simulating Waves Nearshore (un-SWAN) model with various types of wind forcing, and the model was calibrated using in situ wave observations. Sensitivity experiments were conducted to investigate the key factors that impact wave growth and dissipation processes. In particular, we considered (1) three wind ﬁeld sources, (2) three formulations for wind input and whitecapping, (3) alternative formulations and coefﬁcients for depth-induced breaking, and (4) various mesh types. We ﬁnd that un-SWAN driven by Global Environmental Multiscale (GEM) wind data reproduces signiﬁcant wave heights reasonably well using previously proposed formulations for wind input, recalibrated whitecapping parameters, and alternative formulations for depth-induced breaking. The results indicate that using GEM wind ﬁeld data as input captures large waves in the midlake most accurately, while using the Natural Neighbor Method wind ﬁeld reproduces shallow-water waves more accurately. Wind input affects the simulated wave evolution across the whole lake, whereas whitecapping primarily affects wave dynamics in deep water. In shallow water, the process of depth-induced breaking is dominant and highly dependent upon breaker indices and mesh types.
A City's Schools: From equality of input to inequality of outcome

This paper analyses the educational attainment of the total primary school population (13,984 children) of a city based on a series of tests between the ages of 6 and 12. The children were surveyed in Aberdeen in the 1960s. The attainment of each age-group in each school is analysed against the background of their parental class, the social status of their neighbourhood and the life style of their family. A steep gradation of attainment across all class levels, already apparent in early school years, persisted unchanged up to the age of 12. Class influence on physical development was similarly marked at school entry. School intakes reflected the social character of their neighbourhood which in turn dominated the schools' educational potential. The paper looks at attainments atypical of nominal class and asks why a system based on equality of input produces gross inequality of outcome.