Miracle-dz/UniFAR-FTUs huggingface dataset:
Strongest Correlation Between Contrast Sensitivity and Morphological Characteristics in Bilateral nAMD

In patients with neovascular age-related macular degeneration (nAMD) there is often an inconsistency between their subjective visual impairment and a still relatively preserved standard Early Treatment of Diabetic Retinopathy Study (ETDRS) best corrected visual acuity. Therefore, in order to better capture the specific functional defects in nAMD, other tests need to be evaluated. In a previous study, we reported contrast sensitivity of the better eye to best correlate with near distance and distance vision related quality of life in patients with bilateral nAMD. Here, we evaluated Pelli-Robson contrast sensitivity, ETDRS visual acuity, low luminance visual acuity and Radner maximum reading speed and correlated them with several morphologic parameters as measured on fundus autofluorescence imaging, optical coherence tomography and optical tomography angiography in 54 patients. A multiple regression analysis was performed which correlated each visual function parameter with the anatomic features. The results showed the strongest correlations between the total area of macular geographic atrophy as well as the percentage of geographic atrophy in the central 1 mm and contrast sensitivity. Further, the regression model selected the total area of macular geographic atrophy, the photoreceptor inner and outer segments interface disruption score, the presence of subretinal fibrosis in the central 1 mm and the central retinal thickness as the variables that explained 71% of the variation in contrast sensitivity when including all eyes. Hence, our results suggest that among the evaluated measures of vision, contrast sensitivity is best correlated with the morphologic impairment in bilateral nAMD. Thus, contrast sensitivity may complement ETDRS visual acuity in clinical trials and serve as a standard diagnostic tool in clinical practice.
Patterns in Benthic Microbial Community Structure Across Environmental Gradients in the Beaufort Sea Shelf and Slope

The paradigm of tight pelagic-benthic coupling in the Arctic suggests that current and future fluctuations in sea ice, primary production, and riverine input resulting from global climate change will have major impacts on benthic ecosystems. To understand how these changes will affect benthic ecosystem function, we must characterize diversity, spatial distribution, and community composition for all faunal components. Bacteria and archaea link the biotic and abiotic realms, playing important roles in organic matter (OM) decomposition, biogeochemical cycling, and contaminant degradation, yet sediment microbial communities have rarely been examined in the North American Arctic. Shifts in microbial community structure and composition occur with shifts in OM inputs and contaminant exposure, with implications for shifts in ecological function. Furthermore, the characterization of benthic microbial communities provides a foundation from which to build focused experimental research. We assessed diversity and community structure of benthic prokaryotes in the upper 1 cm of sediments in the southern Beaufort Sea (United States and Canada), and investigated environmental correlates of prokaryotic community structure over a broad spatial scale (spanning 1,229 km) at depths ranging from 17 to 1,200 m. Based on hierarchical clustering, we identified four prokaryotic assemblages from the 85 samples analyzed. Two were largely delineated by the markedly different environmental conditions in shallow shelf vs. upper continental slope sediments. A third assemblage was mainly comprised of operational taxonomic units (OTUs) shared between the shallow shelf and upper slope assemblages. The fourth assemblage corresponded to sediments receiving heavier OM loading, likely resulting in a shallower anoxic layer. These sites may also harbor microbial mats and/or methane seeps. Substructure within these assemblages generally reflected turnover along a longitudinal gradient, which may be related to the quantity and composition of OM deposited to the seafloor; bathymetry and the Mackenzie River were the two major factors influencing prokaryote distribution on this scale. In a broader geographical context, differences in prokaryotic community structure between the Beaufort Sea and Norwegian Arctic suggest that benthic microbes may reflect regional differences in the hydrography, biogeochemistry, and bathymetry of Arctic shelf systems.
TFH Cells Induced by Vaccination and Following SIV Challenge Support Env-Specific Humoral Immunity in the Rectal-Genital Tract and Circulation of Female Rhesus Macaques

T follicular helper (TFH) cells are pivotal in lymph node (LN) germinal center (GC) B cell affinity maturation. Circulating CXCR5+ CD4+ T (cTFH) cells have supported memory B cell activation and broadly neutralizing antibodies in HIV controllers. We investigated the contribution of LN SIV-specific TFH and cTFH cells to Env-specific humoral immunity in female rhesus macaques following a mucosal Ad5hr-SIV recombinant priming and SIV gp120 intramuscular boosting vaccine regimen and following SIV vaginal challenge. TFH and B cells were characterized by flow cytometry. B cell help was evaluated in TFH-B cell co-cultures and by real-time PCR. Vaccination induced Env-specific TFH and Env-specific memory (ESM) B cells in LNs. LN Env-specific TFH cells post-priming and GC ESM B cells post-boosting correlated with rectal Env-specific IgA titers, and GC B cells at the same timepoints correlated with vaginal Env-specific IgG titers. Vaccination expanded cTFH cell responses, including CD25+ Env-specific cTFH cells that correlated negatively with vaginal Env-specific IgG titers but positively with rectal Env-specific IgA titers. Although cTFH cells post-2nd boost positively correlated with viral-loads following SIV challenge, cTFH cells of SIV-infected and protected macaques supported maturation of circulating B cells into plasma cells and IgA release in co-culture. Additionally, cTFH cells of naïve macaques promoted upregulation of genes associated with B cell proliferation, BCR engagement, plasma cell maturation, and antibody production, highlighting the role of cTFH cells in blood B cell maturation. Vaccine-induced LN TFH and GC B cells supported anti-viral mucosal immunity while cTFH cells provided B cell help in the periphery during immunization and after SIV challenge. Induction of TFH responses in blood and secondary lymphoid organs is likely desirable for protective efficacy of HIV vaccines.
Protein Farnesylation Takes Part in Arabidopsis Seed Development

Protein farnesylation is a post-translational modification regulated by the ERA1 (Enhanced Response to ABA 1) gene encoding the β-subunit of the protein farnesyltransferase in Arabidopsis. The era1 mutants have been described for over two decades and exhibit severe pleiotropic phenotypes, affecting vegetative and flower development. We further investigated the development and quality of era1 seeds. While the era1 ovary contains numerous ovules, the plant produces fewer seeds but larger and heavier, with higher protein contents and a modified fatty acid distribution. Furthermore, era1 pollen grains show lower germination rates and, at flower opening, the pistils are immature and the ovules require one additional day to complete the embryo sac. Hand pollinated flowers confirmed that pollination is a major obstacle to era1 seed phenotypes, and a near wild-type seed morphology was thus restored. Still, era1 seeds conserved peculiar storage protein contents and altered fatty acid distributions. The multiplicity of era1 phenotypes reflects the diversity of proteins targeted by the farnesyltransferase. Our work highlights the involvement of protein farnesylation in seed development and in the control of traits of agronomic interest.
STIM2 Mediates Excessive Store-Operated Calcium Entry in Patient-Specific iPSC-Derived Neurons Modeling a Juvenile Form of Huntington's Disease

Huntington's disease (HD) is a severe autosomal-dominant neurodegenerative disorder caused by a mutation within a gene, encoding huntingtin protein. Here we have used the induced pluripotent stem cell technology to produce patient-specific terminally differentiated GABA-ergic medium spiny neurons modeling a juvenile form of HD (HD76). We have shown that calcium signaling is dramatically disturbed in HD76 neurons, specifically demonstrating higher levels of store-operated and voltage-gated calcium uptakes. However, comparing the HD76 neurons with the previously described low-repeat HD models, we have demonstrated that the severity of calcium signaling alterations does not depend on the length of the polyglutamine tract of the mutant huntingtin. Here we have also observed greater expression of huntingtin and an activator of store-operated calcium channels STIM2 in HD76 neurons. Since shRNA-mediated suppression of STIM2 decreased store-operated calcium uptake, we have speculated that high expression of STIM2 underlies the excessive entry through store-operated calcium channels in HD pathology. Moreover, a previously described potential anti-HD drug EVP4593 has been found to attenuate high levels of both huntingtin and STIM2 that may contribute to its neuroprotective effect. Our results are fully supportive in favor of the crucial role of calcium signaling deregulation in the HD pathogenesis and indicate that the cornerstone of excessive calcium uptake in HD-specific neurons is a calcium sensor and store-operated calcium channels activator STIM2, which should become a molecular target for medical treatment and novel neuroprotective drug development.
Electrochemical Sensing Performances for Uric Acid Detection on Various Amine Adlayers Used in Immobilizing Reduced Graphene Oxide

We investigated an influence of amine adlayer on electrochemical sensing performances for uric acid detection on reduced graphene oxide (RGO)-decorated indium-tin oxide electrode surfaces. Various amine-terminated molecules including aminoethyl aryldiazonium cation, 2,2′-(ethylenedioxy)bis(ethylamine), 3-aminopropyltriethoxysilane, polyethyleneimine were introduced as adlayers to electrostatically immobilize RGO on the electrode surfaces. The anodic oxidation current of uric acid was observed on the various surfaces with differential pulse voltammetry. The current was highly enhanced by electrocatalytic activity of RGO. The sensing performances including linearity, sensitivity, limit of detection, and correlation coefficient were measured and compared. The adlayer with 3-aminopropyltriethoxysilane showed the best performances on the RGO-modified surface.
Regulatory Mechanisms of Vitellogenesis in Insects

Vitellogenesis is pre-requisite to insect egg production and embryonic development after oviposition. During insect vitellogenesis, the yolk protein precursor vitellogenin (Vg) is mainly synthesized in the fat body, transported by the hemolymph through the intercellular spaces (known as patency) in the follicular epithelium to reach the membrane of maturing oocytes, and sequestered into the maturing oocytes via receptor-mediated endocytosis. Insect vitellogenesis is governed by two critical hormones, the sesquiterpenoid juvenile hormone (JH) and the ecdysteriod 20-hydroxyecdysone (20E). JH acts as the principal gonadotropic hormone to stimulate vitellogenesis in basal hemimetabolous and most holometabolous insects. 20E is critical for vitellogenesis in some hymenopterans, lepidopterans and dipterans. Furthermore, microRNA (miRNA) and nutritional (amino acid/Target of Rapamycin and insulin) pathways interplay with JH and 20E signaling cascades to control insect vitellogenesis. Revealing the regulatory mechanisms underlying insect vitellogenesis is critical for understanding insect reproduction and helpful for developing new strategies of insect pest control. Here, we outline the recent research progress in the molecular action of gonadotropic JH and 20E along with the role of miRNA and nutritional sensor in regulating insect vitellogenesis. We highlight the advancements in the regulatory mechanisms of insect vitellogenesis by the coordination of hormone, miRNA and nutritional signaling pathways.
Extracellular Vesicles as Inflammatory Drivers in NAFLD

Non-alcoholic fatty liver disease (NAFLD) is a highly prevalent chronic liver disease in most parts of the world affecting one-third of the western population and a growing cause for end-stage liver diseases such as hepatocellular carcinoma (HCC). Majorly driven by obesity and diabetes mellitus, NAFLD is more of a multifactorial disease affected by extra-hepatic organ crosstalk. Non-alcoholic fatty liver (NAFL) progressed to non-alcoholic steatohepatitis (NASH) predisposes multiple complications such as fibrosis, cirrhosis, and HCC. Although the complete pathogenic mechanisms of this disease are not understood, inflammation is considered as a key driver to the onset of NASH. Lipotoxicity, inflammatory cytokines, chemokines, and intestinal dysbiosis trigger both hepatic and systemic inflammatory cascades simultaneously activating immune responses. Over a few years, extracellular vesicles studied extensively concerning the pathobiology of NAFLD indicated it as a key modulator in the setting of immune-mediated inflammation. Exosomes and microvesicles, the two main types of extracellular vesicles are secreted by an array of most mammalian cells, which are involved mainly in cell-cell communication that are unique to cell type. Various bioactive cargoes containing extracellular vesicles derived from both hepatic and extrahepatic milieu showed critical implications in driving steatosis to NASH reaffirming inflammation as the primary contributor to the whole process. In this mini-review, we provide brief insights into the inflammatory mediators of NASH with special emphasis on extracellular vesicles that acts as drivers of inflammation in NAFLD.
Vegetation Restoration Alters Fungal Community Composition and Functional Groups in a Desert Ecosystem

Revegetation is regarded as an effective means to improve the ecological environment in deserts and profoundly influences the potential ecological functions of the soil fungal community. Therefore, Illumina high-throughput sequencing was performed to characterize the soil fungal diversity and community composition at two soil depths (0–10 cm and 10–20 cm) with four revegetation durations (natural grassland, half-mature, nearly mature, and mature Pinus. sylvestris var. mongolica plantations) in the Mu Us Sandy Land, China. The effects of soil properties on soil fungal communities were also examined to reveal the connection between fungal function and soil environment. The results indicated that 1) soil nutrient content and enzyme activity showed significant differences through the restoration durations, 2) there was no significant effect of soil depth on soil fungal diversity, while the Shannon diversity index of all fungal communities was significantly different among different revegetation durations, 3) compared with grassland, ectomycorrhizal fungi (notably, Inocybe, Tuber, and Calostoma) were abundant in plantations. The endophyte fungus Mortierella was among the top 10 genera in all soil samples and arbuscular mycorrhizal fungus Diversispora was the indicator genus of the grassland, and 4) catalase and total nitrogen were the main factors affecting fungal community composition and were closely related to saprotrophs and pathotrophs, respectively. This new information indicates the variation of soil fungal communities along revegetation durations and highlights the interaction between fungal functions and desert ecosystems.
Comparison of Human Social Brain Activity During Eye-Contact With Another Human and a Humanoid Robot

Robot design to simulate interpersonal social interaction is an active area of research with applications in therapy and companionship. Neural responses to eye-to-eye contact in humans have recently been employed to determine the neural systems that are active during social interactions. Whether eye-contact with a social robot engages the same neural system remains to be seen. Here, we employ a similar approach to compare human-human and human-robot social interactions. We assume that if human-human and human-robot eye-contact elicit similar neural activity in the human, then the perceptual and cognitive processing is also the same for human and robot. That is, the robot is processed similar to the human. However, if neural effects are different, then perceptual and cognitive processing is assumed to be different. In this study neural activity was compared for human-to-human and human-to-robot conditions using near infrared spectroscopy for neural imaging, and a robot (Maki) with eyes that blink and move right and left. Eye-contact was confirmed by eye-tracking for both conditions. Increased neural activity was observed in human social systems including the right temporal parietal junction and the dorsolateral prefrontal cortex during human-human eye contact but not human-robot eye-contact. This suggests that the type of human-robot eye-contact used here is not sufficient to engage the right temporoparietal junction in the human. This study establishes a foundation for future research into human-robot eye-contact to determine how elements of robot design and behavior impact human social processing within this type of interaction and may offer a method for capturing difficult to quantify components of human-robot interaction, such as social engagement.
Haspin Modulates the G2/M Transition Delay in Response to Polarization Failures in Budding Yeast

Symmetry breaking by cellular polarization is an exquisite requirement for the cell-cycle of Saccharomyces cerevisiae cells, as it allows bud emergence and growth. This process is based on the formation of polarity clusters at the incipient bud site, first, and the bud tip later in the cell-cycle, that overall promote bud emission and growth. Given the extreme relevance of this process, a surveillance mechanism, known as the morphogenesis checkpoint, has evolved to coordinate the formation of the bud and cell cycle progression, delaying mitosis in the presence of morphogenetic problems. The atypical protein kinase haspin is responsible for histone H3-T3 phosphorylation and, in yeast, for resolution of polarity clusters in mitosis. Here, we report a novel role for haspin in the regulation of the morphogenesis checkpoint in response to polarity insults. Particularly, we show that cells lacking the haspin ortholog Alk1 fail to achieve sustained checkpoint activation and enter mitosis even in the absence of a bud. In alk1Δ cells, we report a reduced phosphorylation of Cdc28-Y19, which stems from a premature activation of the Mih1 phosphatase. Overall, the data presented in this work define yeast haspin as a novel regulator of the morphogenesis checkpoint in Saccharomyces cerevisiae, where it monitors polarity establishment and it couples bud emergence to the G2/M cell cycle transition.
Only Extreme Fluctuations in Light Levels Reduce Lettuce Growth Under Sole Source Lighting

The cost of providing lighting in greenhouses and plant factories can be high. In the case of variable electricity prices, providing most of the light when electricity prices are low can reduce costs. However, it is not clear how plants respond to the resulting fluctuating light levels. We hypothesized that plants that receive a constant photosynthetic photon flux density (PPFD) will produce more biomass than those grown under fluctuating light levels. To understand potential growth reductions caused by fluctuating light levels, we quantified the effects of fluctuating PPFD on the photosynthetic physiology, morphology, and growth of ‘Little Gem’ and ‘Green Salad Bowl’ lettuce. Plants were grown in a growth chamber with dimmable white LED bars, alternating between high and low PPFDs every 15 min. The PPFDs were ∼400/0, 360/40, 320/80, 280/120, 240/160, and 200/200 μmol⋅m−2⋅s–1, with a photoperiod of 16 h and a DLI of ∼11.5 mol⋅m−2⋅day–1 in all treatments. CO2 was ∼800 μmol⋅mol–1. Plants in the 400/0 μmol⋅m−2⋅s–1 treatment had ∼69% lower An,30 (net assimilation averaged over 15 min at high and 15 min at low PPFD) than plants grown at a PPFD of 320/80 μmol⋅m−2⋅s–1 (or treatments with smaller PPFD fluctuations). The low An,30 in the 400/0, and to a lesser extent the 360/40 μmol⋅m−2⋅s–1 treatment was caused by low net assimilation at 360 and 400 μmol⋅m−2⋅s–1. Plants grown at 400/0 μmol⋅m−2⋅s–1 also had fewer leaves and lower chlorophyll content compared to those in other treatments. The four treatments with the smallest PPFD fluctuations produced plants with similar numbers of leaves, chlorophyll content, specific leaf area (SLA), dry mass, and leaf area. Chlorophyll content, An,30, and dry mass were positively correlated with each other. Our results show that lettuce tolerates a wide range of fluctuating PPFD without negative effects on growth and development. However, when fluctuations in PPFD are extreme (400/0 or 360/40 μmol⋅m−2⋅s–1), chlorophyll levels and An,30 are low, which can explain the low poor growth in these treatments. The ability of lettuce to tolerate a wide range of fluctuating light levels suggests that PPFD can be adjusted in response to variable electricity pricing.
Casting a Wider Net on Ocean NETs

Societal issues involving policies and publics are generally understudied in research on ocean-based Negative Emission Technologies (NETs), yet will be crucial if novel techniques are ever to function at scale. Public attitudes are vital for emerging technologies: publics influence political mandates, help determine the degree of uptake by market actors, and are key to realizing broader ambitions for robust decision-making and responsible incentivization. Discourses surrounding ocean NETs will also have fundamental effects on how governance for the techniques emerges, shaping how they are defined as an object of governance, who is assigned the authority to govern, and what instruments are deemed appropriate. This Perspective brings together key insights on the societal dimensions of ocean NETs, drawing on existing work on public acceptability, policy assessment, governance, and discourse. Ocean iron fertilization is the only ocean NET on which there exists considerable social science research thus far, and we show that much evidence points against its social desirability. Taken in conjunction with considerable natural science uncertainties, this leads us to question whether further research is actually necessary in order to rule out ocean iron fertilization as an option. For other ocean NETs, there is a need for further research into social dimensions, yet research on analogous technologies shows that ocean interventions will likely evoke strong risk perceptions, and evidence suggests that the majority of ocean NETs may face a greater public acceptability challenge than terrestrial NETs. Ocean NETs also raise complex challenges around governance, which pose questions well-beyond the remit of the natural sciences and engineering. Using a conceptual exploration of the ways in which different types of discourse may shape emerging ocean NETs governance, we show that the very idea of ocean NETs is likely to set the stage for a whole new range of contested futures.