Miracle-dz/UniFAR-FTUs huggingface dataset:
Induced Arp2/3 Complex Depletion Increases FMNL2/3 Formin Expression and Filopodia Formation

The Arp2/3 complex generates branched actin filament networks operating in cell edge protrusion and vesicle trafficking. Here we employ a novel, conditional knockout mouse model permitting tissue- or cell-type specific deletion of the murine Actr3 gene (encoding Arp3). A functional Actr3 gene appeared essential for fibroblast viability and growth. Thus, we developed cell lines for exploring the consequences of acute, tamoxifen-induced Actr3 deletion causing near-complete loss of Arp/3 complex function as well as abolished lamellipodia formation and membrane ruffling, as expected. However, Arp3-depleted cells displayed enhanced rather than reduced cell spreading, employing numerous filopodia, and showed little defects in individual cell migration. Reduction of collective cell migration as observed for instance in wound healing assays likely derived from defects in maintaining directionality during migration, while the principal ability to chemotax was only moderately affected. Analyses of actin turnover at the cell periphery revealed reduced actin turnover rates in Arp2/3-deficient cells, clearly deviating from previous sequestration approaches. Most surprisingly, induced removal of Arp2/3 complexes reproducibly increased FMNL formin expression, which correlated with the explosive induction of filopodia formation. Our results thus highlight both direct and indirect effects of acute Arp2/3 complex removal on actin cytoskeleton regulation.
Absorção de nutrientes e crescimento do arroz com suprimento combinado de amônio e nitrato

Rice is classified as an ammonium (NH4+)- tolerant plant due the predominance of this ion in flooded soils. However, in the oxygenated zones of flooded soil and in the rice rhizosphere, nitrate (NO3-) can be formed and become an important nitrogen (N) source for the crop. This experiment was carried out to evaluate the effect of different ammonium:nitrate proportions on rice development in nutrient solution. The experiment was carried out in a greenhouse, from January until February 2008 in a nutrient solution with the following NH4+: NO3- proportions: 100:0, 75:25; 50:50; 25:75 and 0:100, at 5.0 mmol L-1 N. The genotype IRGA 417 was used and the biomass production, the nitrogen, calcium, magnesium and potassium contents in tissue and xylem sap were evaluated. The presence of ammonium at the proportions 100:0 and 75:25 resulted in plant toxicity, as well as for nitrate at the proportions 25:75 and 0:100. The combined supply of ammonium and nitrate increased biomass production in relation to solely NH4+ or NO3- supply. Ammonium in solution affected negatively Ca and Mg, whereas no effect was observed on N or K tissue contents. However, in the xylem sap, both K, Ca and Mg contents were affected by ammonium. The higher total absorbed quantities of N, K, Ca, and Mg and better rice development indicated that the combined supply results in higher nutrient absorption efficiency than solely ammonium or nitrate supply.
Enhancing Biodegradation of Dibenzothiophene by Bacillus sphaericus HN1 Using Factorial Design and Response Surface Optimization of Medium Components

Abstract Based on four levels of full factorial design, a statistical design of experiments is used to investigate two cases of dibenzothiophene biodegradation in batch processes using Bacillus sphaericus HN1, involving as factors, yeast extract and dimethylsulfoxide or magnesium sulfate for first and second cases, respectively. Predictive models have been correlated finding out how significant the effects of these variables (factors) and their interactions are in practice. Also, response surface methodology has been applied to visualize the effect of the studied factors and LINGO software was used to find out the optimum values of the variables for enhancing the process.
Characterization of emeralds by micro-Raman spectroscopy

In recent years, the use of Raman spectroscopy as a gemological tool has largely increased, in particular in the conservation science field where a non-destructive and contactless identification is required. In this work, we show the large amount of information which is possible to obtain with Raman analysis on one of the most important gems, emerald, the green variety of beryl. In particular, 14 not certified faceted emeralds have been studied by means of a standard micro-Raman spectrometer, allowing also the identification of some fakes (garnet, glass, and quartz). All the emerald gems have been fully characterized from the vibrational point of view. In particular, the high frequency spectrum, in the OH region, has been exploited to estimate the amount of alkali ions present in the channels of the crystalline structure. In addition, solid and fluid inclusions have been identified and were useful to hypothesize the provenance of the mineral. The shape and position of the characteristic laser-induced luminescence of chromium ions have helped to better define the origin of the gems. Copyright © 2014 John Wiley & Sons, Ltd.
Synergy between a shallow root system with a DRO1 homologue and localized P application improves rice P uptake

The development of genotypes and fertilizer management practices that facilitate high phosphorus (P) use efficiency is needed given the depleting phosphorus ore deposits and increasing ecological concerns about its excessive use. Root system architecture (RSA) is important in efficiently capturing immobile P in soils, while agronomically, localized P application near the roots is a potential approach to address this issue. However, the interaction between genetic traits of RSA and localized P application has not been examined. Near-isogenic lines (NILs) and their parent of rice (qsor1-NIL, Dro1-NIL, and IR64, with shallow, deep, and intermediate root growth angles (RGA), respectively) were grown in flooded pots in a uniform and P-sufficient condition (Pinco), and with localized P application by dipping seedling roots into P-enriched slurry at transplanting (P-dipping). The P-dipping created an available P hotspot at the soil surface and substantially improved applied P-use efficiency (equivalent biomass at one fifth of application rate of the Pinco). Further, the qsor1-NIL had significantly greater biomass and P uptake than the other genotypes in the P-dipping. The qsor1-NIL consistently had a greater root biomass and surface area in the 0–3 cm soil layer, despite that there were no genotype differences in total values and that the other genotypes also reduced their RGAs responding to the P hotspot in the P-dipping. The shallow root system of qsor1-NIL facilitated P uptake from the P hotspot. P-use efficiency in crop production can be further increased by combining genetic traits of RSA and localized P application.
What Is the Standard First-Line Treatment for Advanced Non–Small Cell Lung Cancer?

Abstract The initial treatment regimens for advanced non–small cell lung cancer (NSCLC) have drastically evolved over the last 15 years with the rapid development of improved genomic sequencing technologies and the emergence of immune checkpoint inhibitors. Highly active oral kinase inhibitors are now approved for several molecularly defined subsets of NSCLC, including those harboring alterations in the EGFR, ALK, ROS1, BRAF, MET, RET, and NTRK genes, although acquired resistance to these targeted therapies remains a significant clinical challenge. In lung cancers lacking targetable mutations, programmed death 1/programmed death ligand 1 immune checkpoint inhibitors, used alone or in combination with cytotoxic T-lymphocyte-associated protein 4 inhibitors and/or cytotoxic chemotherapy, have led to meaningful improvements in overall survival. With many therapeutic options available to patients, here we review the recommended frontline treatment regimens for advanced NSCLC with and without targetable genomic drivers.
A meta-analysis on uncertainty monitoring in four non-primate animal species: Pigeons, rats, large-billed crows, and bees

Humans have the metacognitive capacity to be aware of what they do and do not know. While uncertainty monitoring has long been regarded as uniquely human, researchers in search of the polygenetic root of this ability have gathered evidence that primate species possess functional features parallel to humans. However, there were no systematic studies that quantitively take into account of extant data for these non-primate animals. Through a meta-analysis, we collected published data reported in 11 articles from 55 individual non-primate animals spanning over four species on the “opt-out” paradigm, the most prevailing paradigms used to test nonhuman animals’ uncertainty monitoring. We used chosen-forced advantage and opt-out rate to quantify animals’ performance results for computing the aggregated effect size for this literature. We found that these four NPA species process a significantly positive effect size for both scores and identified the moderators that have contributed to the inconsistencies across these studies. Implications for theories on metacognition are discussed.
Freely Behaving Mice Can Brake and Turn During Optogenetic Stimulation of the Mesencephalic Locomotor Region

Background Stimulation of the Mesencephalic Locomotor Region (MLR) is increasingly considered as a target to improve locomotor function in Parkinson’s disease, spinal cord injury and stroke. A key function of the MLR is to control the speed of forward symmetrical locomotor movements. However, the ability of freely moving mammals to integrate environmental cues to brake and turn during MLR stimulation is poorly documented. Objective/hypothesis We investigated whether freely behaving mice could brake or turn based on environmental cues during MLR stimulation. Methods We stimulated the cuneiform nucleus in mice expressing channelrhodopsin in Vglut2-positive neurons in a Cre-dependent manner (Vglut2-ChR2-EYFP) using optogenetics. We detected locomotor movements using deep learning. We used patch-clamp recordings to validate the functional expression of channelrhodopsin and neuroanatomy to visualize the stimulation sites. Results Optogenetic stimulation of the MLR evoked locomotion and increasing laser power increased locomotor speed. Gait diagram and limb kinematics were similar during spontaneous and optogenetic-evoked locomotion. Mice could brake and make sharp turns (∼90⁰) when approaching a corner during MLR stimulation in an open-field arena. The speed during the turn was scaled with the speed before the turn, and with the turn angle. In a reporter mouse, many Vglut2-ZsGreen neurons were immunopositive for glutamate in the MLR. Patch-clamp recordings in Vglut2-ChR2-EYFP mice show that blue light evoked short latency spiking in MLR neurons. Conclusion MLR glutamatergic neurons are a relevant target to improve locomotor activity without impeding the ability to brake and turn when approaching an obstacle, thus ensuring smooth and adaptable navigation. Highlights - Mice brake and turn when approaching the arena’s corner during MLR-evoked locomotion - Speed decrease is scaled to speed before the turn during MLR-evoked locomotion - Turn angle is scaled to turn speed during MLR-evoked locomotion - Gait and limb kinematics are similar during spontaneous and MLR-evoked locomotion
A Computational Expedition into the Undiscovered Country - Evaluating Neural Networks for the Identification of Hamlet Text Reuse

In this article, we describe a two-step processing pipeline for identifying text reuse of Shakespeare’s Hamlet in a corpus of postmodern fiction by comparing n-grams from both sources. A key feature of our approach lies in a pre-filtering step, in which we select target sentences in the fiction corpus that are potential candidates for Hamlet text reuse. Without pre-filtering, the amount of text reuse pairs (that are no actual quotes) would be extremely high. In a second filtering step, we compare potential text reuse pairs by their vector representation using a neural network trained in an unsupervised manner. We found that using the vector similarity produces a problematic amount of false positives. The created vector representations are created using an unsupervised training approach, resulting in similarity aspects that are unfavorable for our use case.
Ambient and high‐pressure synthesis, composition, and crystal structure of B‐mullites

The chemical compositions of several B‐doped mullite samples were analyzed using prompt gamma activation analyses (PGAA) indicating that 15% of the Si in the crystal structure of mullite can be replaced by B during sol‐gel synthesis at ambient pressure and 1200°C without the formation of impurities. Furthermore the PGAA results agree very well with the chemical compositions derived from Rietveld refinements based on neutron diffraction data. High‐pressure and high‐temperature synthesis yielded a B‐mullite with significantly higher B‐content than observed before (close to composition Al8Si2B2O19). The results of PGAA, XRD, and neutron diffraction experiments show linear behavior of lattice parameters b and c as well as of the inclination angle ω of the AlO6 octahedra in the ab‐plane with increasing B‐content. The Rietveld refinements support the substitution mechanism known for B‐mullites, involving the formation of oxygen vacancies and the replacement of 40% of the tetrahedral Si by BO3 units during the synthesis at 875°C and 10 kbar. However, the refined chemical composition as well as a very low lattice parameter a suggest a second mechanism for the incorporation of B into mullite. This is clearly supported by the 11B MAS NMR experiment indicating the presence of B in BO4 configuration but BO3 being dominant. Here for the first time a B‐mullite crystal structure is presented yielding BO3 and BO4 units in space group Pbam.
Equation of state of a hard‐disk fluid. I. The virial expansion

The existing values of the sixth and seventh virial coefficients of hard disks have been improved upon. The subsequent three coefficients (B8,B9,B10) have been estimated using various extrapolation techniques. Furthermore, the equation of state of the fluid has been evaluated by means of various theories. The results obtained by these methods are very consistent with each other.
Deep immune profiling reveals targetable mechanisms of immune evasion in checkpoint blockade-refractory glioblastoma

Background Glioblastoma (GBM) is refractory to checkpoint blockade immunotherapy (CPI). We sought to determine to what extent this immune evasion is due to intrinsic properties of the tumor cells versus the specialized immune context of the brain, and if it can be reversed. Methods We used CyTOF mass cytometry to compare the tumor immune microenvironments (TIME) of human tumors that are generally CPI-refractory (GBM and sarcoma) or CPI-responsive (renal cell carcinoma), as well as mouse models of GBM that are CPI-responsive (GL261) or CPI-refractory (SB28). We further compared SB28 tumors grown intracerebrally versus subcutaneously to determine how tumor site affects TIME and responsiveness to dual CTLA-4/PD-1 blockade. Informed by these data, we explored rational immunotherapeutic combinations. Results CPI-sensitivity in human and mouse tumors was associated with increased T cells and dendritic cells, and fewer myeloid cells, in particular PD-L1+ tumor associated macrophages. The SB28 mouse model of GBM responded to CPI when grown subcutaneously but not intracerebrally, providing a system to explore mechanisms underlying CPI resistance in GBM. The response to CPI in the subcutaneous SB28 model required CD4 T cells and NK cells, but not CD8 T cells. Recombinant FLT3L expanded dendritic cells, improved antigen-specific T cell priming, and prolonged survival of mice with intracerebral SB28 tumors, but at the cost of increased Tregs. Targeting PD-L1 also prolonged survival, especially when combined with stereotactic radiation. Conclusions Our data suggest that a major obstacle for effective immunotherapy of GBM is the low antigenicity of the tumor cells coupled with poor antigen presentation in the brain, rather than intrinsic immunosuppressive properties of GBM tumor cells. Deep immune profiling identified dendritic cells and PD-L1+ tumor-associated macrophages as promising targetable cell populations, which was confirmed using therapeutic interventions in vivo. Graphical Abstract In Brief In mice and humans, tumors that were sensitive to checkpoint blockade had consistent immunological features. A mouse model of glioma that is refractory to checkpoint blockade was sensitized by increasing antigen presentation through a variety of approaches.
Scale-Free Dynamics in Animal Groups and Brain Networks

Collective phenomena fascinate by the emergence of order in systems composed of a myriad of small entities. They are ubiquitous in nature and can be found over a vast range of scales in physical and biological systems. Their key feature is the seemingly effortless emergence of adaptive collective behavior that cannot be trivially explained by the properties of the system’s individual components. This perspective focuses on recent insights into the similarities of correlations for two apparently disparate phenomena: flocking in animal groups and neuronal ensemble activity in the brain. We first will summarize findings on the spontaneous organization in bird flocks and macro-scale human brain activity utilizing correlation functions and insights from critical dynamics. We then will discuss recent experimental findings that apply these approaches to the collective response of neurons to visual and motor processing, i.e. to local perturbations of neuronal networks at the meso- and microscale. We show how scale-free correlation functions capture the collective organization of neuronal avalanches in evoked neuronal populations in nonhuman primates and between neurons during visual processing in rodents. These experimental findings suggest that the coherent collective neural activity observed at scales much larger than the length of the direct neuronal interactions is demonstrative of a phase transition. We discuss the experimental support for either discontinuous or continuous phase transitions. We conclude that at or near a phase-transition neuronal information can propagate in the brain with the same efficiency as proposed to occur in the collective adaptive response observed in some animal groups.
Water retention properties of a sandy soil with superabsorbent polymers as affected by aging and water quality

Hydraulic properties, specifically the water holding capacity of soils, play a key role in the ability of soils to sustain plant growth. Additions of hydrophilic polymers (superabsorbents) can improve the water holding capacity of sandy soils. This has led to practical applications of these materials particularly in arid regions and countries, where water is the limiting factor for plant production. The objectives of this study are to investigate how effective hydraulic properties of polymer-soil mixtures are affected by addition of absorbents in different concentrations. Novel aspects are the investigation of aging under repeated wetting–drying-cycles over an appreciable time in the field and a systematic investigation of the salt influence on the water uptake of polymers. We added the polymer Super AB, A-200 (Iran Polymer Institute), to dune sand in ratios of 0.3%, 0.6%, and 1% w/w. We found that the effective water retention characteristics of the soil–absorbent mixtures were improved with respect to plant-available water compared to the pure sand, and the improvement was related to the respective amount of absorbent in the mixture. The plant available water content (PAW) increased from 0.005 for the untreated sand to 0.06, 0.20, and 0.28 g g−1, respectively, for the sand with the three polymer additions. Due to aging of the polymers, PAW decreased after 6 months of cyclic drying and wetting to about half of the value immediately after the initial treatment. We attribute this to the effect of salts. This is corroborated by the results from water uptake experiments by the pure polymers. Repeated cycles of water uptake showed that salts in the water greatly reduced the uptake capacity of the polymers after few cycles. The effect was strong for bivalent cations and less pronounced for monovalent cations.
Temperature but not ocean acidification affects energy metabolism and enzyme activities in the blue mussel, Mytilus edulis

In mosaic marine habitats such as intertidal zones ocean acidification (OA) is exacerbated by high variability of pH, temperature, and biological CO2 production. The non-linear interactions among these drivers can be context-specific and their effect on organisms in these habitats remains largely unknown, warranting further investigation. We were particularly interested in Mytilus edulis (the blue mussel) from intertidal zones of Gulf of Maine (GOM), USA for this study. GOM is a hot spot of global climate change (average SST increasing by > 0.2 °C y-1) with > 60% decline in mussel population over the past 40 years. Here, we utilize bioenergetic underpinnings to identify limits of stress tolerance in M. edulis from GOM exposed to warming and OA. We have measured whole-organism oxygen consumption rates and metabolic biomarkers in mussels exposed to control and elevated temperatures (10 vs. 15 °C) and moderate PCO2 levels (~ 400 vs. 800 μatm). Our study demonstrates that adult M. edulis from GOM are metabolically resilient to the moderate OA scenario but responsive to warming as seen in changes in metabolic rate, energy reserves, metabolite profiles and enzyme activities. Our results are in agreement with recent literature that OA scenarios for the next 100-300 years do not affect this species, possibly as a consequence of maintaining its in vivo acid-base balance.
Three-dimensional hierarchical nitrogen-doped arch and hollow nanocarbons: morphological influences on supercapacitor applications

We report nitrogen (N) doped nanocarbons with two different morphologies, arch and hollow structure, for supercapacitor (SC) application. A simple co-axial electrospinning approach and subsequent leaching and carbonization processes are employed to fabricate N-doped carbon nanostructures. The fabricated N-doped arch and hollow nanocarbons exhibit high N-contents of 9.02 and 8.73 wt%, high surface areas of 619 and 557 m2 g−1, and total pore volumes of 0.6589 and 0.5681 cm3 g−1, respectively. The N-doped arch and hollow nanocarbons exhibit the maximum specific capacitances (Csp) of 417 and 371 F g−1 at 2 mV s−1 in a three-electrode system and Csp values of 230 and 212 F g−1 at 2 mV s−1 for a two-electrode system, respectively, in 1 M H2SO4 solution. The maximum energy densities of 8.4 and 7.5 W h kg−1 are obtained for N-doped arch and hollow nanocarbons, respectively. Further, these novel carbon nanostructures also deliver good cycle stabilities of 98% for 5000 cycles at a current density of 1 A g−1. Such outstanding SC electro-sorption ability is due to the high micro-texture and high N-content characteristics of carbon nanostructures.
Desulfurization reactions on Ni2P(001) and α-Mo2C(001) surfaces : Complex role of P and C sites

X-ray photoelectron spectroscopy and first-principles density-functional calculations were used to study the interaction of thiophene, H2S, and S2 with Ni2P(001), α-Mo2C(001), and polycrystalline MoC. In general, the reactivity of the surfaces increases following the sequence MoC < Ni2P(001) < α-Mo2C(001). At 300 K, thiophene does not adsorb on MoC. In contrast, Ni2P(001) and α-Mo2C(001) can dissociate the molecule easily. The key to establish a catalytic cycle for desulfurization is in the removal of the decomposition products of thiophene (CxHy fragments and S) from these surfaces. Our experimental and theoretical studies indicate that the rate-determining step in a hydrodesulfurization (HDS) process is the transformation of adsorbed sulfur into gaseous H2S. Ni2P is a better catalyst for HDS than Mo2C or MoC. The P sites in the phosphide play a complex and important role. First, the formation of Ni−P bonds produces a weak “ligand effect” (minor stabilization of the Ni 3d levels and a small Ni → P charge.