Miracle-dz/UniFAR-FTUs huggingface dataset:
Topological vortex formation in a Bose-Einstein condensate under gravitational field

Topological phase imprinting is a unique technique for vortex formation in a Bose-Einstein condensate (BEC) of an alkali-metal gas, in that it does not involve rotation: the BEC is trapped in a quadrupole field with a uniform bias field which is reversed adiabatically leading to vortex formation at the center of the magnetic trap. The scenario has been experimentally verified by Leanhardt et al. employing {sup 23}Na atoms. Recently similar experiments have been conducted by Hirotani et al. in which a BEC of {sup 87}Rb atoms was used. In the latter experiments the authors found that fine-tuning of the field reverse time T{sub rev} is required to achieve stable vortex formation. Otherwise, they often observed vortex fragmentation or a condensate without a vortex. It is shown in this paper that this behavior can be attributed to the heavy mass of the Rb atom. The confining potential, which depends on the eigenvalue m{sub B} of the hyperfine spin F along the magnetic field, is now shifted by the gravitational field perpendicular to the vortex line. Then the positions of two weak-field-seeking states with m{sub B}=1 and 2 deviate from each other. This effect is more prominent for BECs with a heavymore » atomic mass, for which the deviation is greater and, moreover, the Thomas-Fermi radius is smaller. We found, by solving the Gross-Pitaevskii equation numerically, that two condensates interact in a very complicated way leading to fragmentation of vortices, unless T{sub rev} is properly tuned. « less
A Real-Time Eulerian Photochemical Model Forecast System: Overview and Initial Ozone Forecast Performance in the Northeast U.S. Corridor

This article reports on the first implementation of a real-time Eulerian photochemical model f o recast system in the United States. The forecast system consists of a tripartite set of one-way coupled models that run routinely on a parallel micro process or supercomputer. The component models are the fifth-generation Pennsylvania State University (PSU)–NCAR Mesoscale Model (MM5), the Sparse-Matrix Operator Kernel for Emissions (SMOKE) model, and the Multiscale Air Quality Simulation Platform—Real Time (MAQSIPRT) photochemical model. Though the system has been run in real time since the summer of 1998, forecast results obtained during August of 2001 at 15-km grid spacing over New England and the northern mid-Atlantic—conducted as part of an “early start” NOAA air quality forecasting initiative—are described in this article. The development and deployment of a real-time numerical air quality prediction (NAQP) system is technically challenging. MAQSIP-RT contains a full photochemical oxidant gas-phase chemic.
Smoothened-dependent and -independent pathways in mammalian noncanonical Hedgehog signaling

Hedgehog proteins are pivotal morphogens acting through a canonical pathway involving first activation of ligand binding to Patched followed by alleviation of Smoothened receptor inhibition, leading to activation of Gli transcription factors. Noncanonical Hedgehog signaling remains poorly characterized but is thought to be mainly dependent on Smoothened. However, Smoothened inhibitors have yielded only partial success in combating Hedgehog signal transduction–dependent cancer, suggesting that noncanonical Smoothened-independent pathways also are clinically relevant. Moreover, several Smoothened-dependent effects (e.g. neurite projection) do not require transcriptional activation, further suggesting biological importance of noncanonical Smoothened-dependent pathways. We comprehensively characterized the cellular kinome in Hedgehog-challenged murine WT and Smoothened−/− fibroblasts as well as Smoothened agonist–stimulated cells. A peptide assay–based kinome analysis (in which cell lysates are used to phosphorylate specific kinase substrates), along with endocytosis, Lucifer Yellow–based, and immunoblotting assays, identified an elaborate signaling network of both Smoothened-dependent and -independent pathways that mediates actin reorganization through Src-like kinases, activates various proinflammatory signaling cascades, and concomitantly stimulates Wnt and Notch signaling while suppressing bone morphogenetic protein (BMP) signaling. The contribution of noncanonical Smoothened-independent signaling to the overall effects of Hedgehog on cellular physiology appears to be much larger than previously envisioned and may explain the transcriptionally independent effects of Hedgehog signaling on cytoskeleton. The observation that Patched-dependent, Smoothened-independent, noncanonical Hedgehog signaling increases Wnt/Notch signaling provides a possible explanation for the failure of Smoothened antagonists in combating Hedgehog-dependent but Smoothened inhibitor–resistant cancer. Our findings suggest that inhibiting Hedgehog–Patched interaction could result in more effective therapies as compared with conventional Smoothened-directed therapies.
Polystyrene-colonizing bacteria are enriched for long-chain alkane degradation pathways

One of the most promising strategies for the management of plastic waste is microbial biodegradation, but efficient degraders for many types of plastics are still lacking, including for polystyrene (PS). Genomics has emerged as a powerful tool for mining environmental microbes that may have the ability to degrade different types of plastics. In this study, we use 16S sequencing to analyze the microbiomes for multiple PS samples collected from sites with different vegetation in Taiwan to reveal potential common properties between species that have exhibit growth advantages on PS surfaces. Phylum enrichment analysis identified Cyanobacteria and Deinococcus-Thermus as being the most over-represented groups on PS, and both phyla include species known to reside in extreme environments and could encode unique enzymes that grant them properties suitable for colonization on PS surfaces. Investigation of functional enrichment in PS-enriched species highlighted carbon metabolic pathways, especially those related to hydrocarbon degradation. This is corroborated by the finding that genes encoding long-chain alkane hydroxylases such as AlmA are more prevalent in the genomes of PS-associated bacteria. Our analyses illustrate how plastic in the environment support the colonization of different microbes compared to surrounding soil. In addition, our results point to the possibility that alkane hydroxylases could confer growth advantages of microbes on PS.
Sex-specific transcriptomic profiling of reward and sensory brain areas in perinatal fentanyl exposed juvenile mice.

BACKGROUND: Use of the synthetic opioid fentanyl increased ~300% in the last decade, including among women of reproductive ages. Adverse neonatal outcomes and long-term behavioral disruptions are associated with perinatal opioid exposure. Our previous work demonstrated that perinatal fentanyl exposed (PFE) mice displayed enhanced negative affect and somatosensory circuit and behavioral disruptions during adolescence. However, little is known about molecular adaptations across brain regions that underlie these outcomes. We performed RNA-sequencing across three reward and two sensory brain areas to study transcriptional programs in PFE juvenile mice. METHODS: C57BL/6 pregnant dams received 10 µ g/ml fentanyl in the drinking water from embryonic day 0 (E0) through gestational periods until weaning at postnatal day 21 (P21). RNA was extracted from nucleus accumbens (NAc), prelimbic cortex (PrL), ventral tegmental area (VTA), somatosensory cortex (S1) and ventrobasal thalamus (VBT) from PFE mice of both sexes at P35. RNA-sequencing was performed, followed by analysis of differentially expressed genes (DEGs) and gene co-expression networks. RESULTS: Transcriptome analysis revealed sex-specific DEGs and gene modules significantly associated with PFE. The VTA had the most DEGs, while pronounced gene enrichment occurred in NAc. Genes enriched in mitochondrial respiration were pronounced in NAc and VTA of PFE males, extracellular matrix (ECM) and neuronal migration enrichment were pronounced in NAc and VTA of PFE males, while genes associated with vesicular cycling and synaptic signaling were markedly altered in NAc of PFE female mice. In sensory areas from PFE females, we found alterations in mitochondrial respiration, synaptic and ciliary organization processes. CONCLUSION: Our findings demonstrate sex-specific neuroadaptations in PFE mice. Our studies identify distinct transcriptomes across reward and sensory brain regions that may underlie disrupted behavioral and circuit states in PFE mice. In conclusion, our findings elucidate that PFE induces sex-specific transcriptional alterations in reward and sensory brain areas with marked changes in the NAc, VTA and S1 areas. PFE male juvenile mice showed the most transcriptional perturbations specifically in processes relating to mitochondrial respiration, ECM and neuronal guidance. PFE female mice showed transcriptional alterations in genes enriched for vesicular and synaptic signaling processes. The altered functional enrichment we observe are consistent with opioid induced gene enrichment described in the literature. We highlight that these altered processes have a developmental root and as such early intervention beginning precisely at the early stages of abstinence may prevent or reduce some of these neuro-molecular changes and possibly behavioral adaptations.
The Mangrove Microbiome of the Malay Peninsula

Microbes have fundamental roles underpinning the functioning of our planet, they are involved in global carbon and nutrient cycling, and support the existence of multicellular life. The mangrove ecosystem is nutrient limited and without microbial cycling, life in this harsh environment would likely not exist. The mangroves of Southeast Asia are the oldest and most biodiverse of all the planets. They have vital roles helping to prevent shoreline erosion, act as nursery grounds for many marine species and contain significant stocks of sequestered carbon. Despite these recognised benefits and the importance of microbes in these ecosystems, studies examining the mangrove microbiome are scarce, especially in the Southeast Asian biodiversity hotspot. Here we examine the microbiome of Avicenia alba and Sonneratia alba and identify a core microbiome of 81 taxa, a further eight taxa (Pleurocapsa, Tunicatimonas, Halomonas, Marinomonas, Rubrivirga, Altererythrobacte, Lewinella, and Erythrobacter) were found to be differentially abundant suggesting key roles in this microbiome, with the identified dimethylsulfoniopropionate (DMSP) metabolisers having important functions in these habitats. The majority of those identified are involved in nutrient cycling or involved in the production of compounds that promote host survival. Increasingly, blue carbon and nature-based solutions to climate change are heralded as viable mitigation steps to limit climate change, however, this is done with little to no consideration of the microbial communities that cycle sequestered carbon in these environments. Here, we examine the microbial communities present in sediment samples taken in close proximity to each tree, sediment samples represent a major sink of atmospheric carbon and understanding how the associated communities will change as climate change advances will become an increasingly important part of carbon stock assessments. Knowing what microbes are presently there is an important first step in this process.
DNA bridging explains sub-diffusive movement of chromosomal loci in bacteria

Chromosomal loci in bacterial cells show a robust sub-diffusive scaling of the mean square displacement, MSD(τ) ∼ τα, with α < 0.5. On the other hand, recent experiments have also shown that DNA-bridging Nucleoid Associated Proteins (NAPs) play an important role in chromosome organisation and compaction. Here, using polymer simulations we investigate the role of DNA bridging in determining the dynamics of chromosomal loci. We find that bridging compacts the polymer and reproduces the sub-diffusive elastic dynamics of monomers at timescales shorter than the bridge lifetime. Consistent with this prediction, we measure a higher exponent in a NAP mutant (ΔH-NS) compared to wild-type E. coli. Furthermore, bridging can reproduce the rare but ubiquitous rapid movements of chromosomal loci that have been observed in experiments. In our model the scaling exponent defines a relationship between the abundance of bridges and their lifetime. Using this and the observed mobility of chromosomal loci, we predict a lower bound on the average bridge lifetime of around 5 seconds. Significance Statement The bacterial chromosome exhibits dynamics that cannot be explained by simple polymer models. In particular, the mean square displacement of individual chromosomal loci exhibits a power law scaling with an exponent less than that predicted by polymer theory. Here, we use polymer simulations and experiments to show that DNA bridging by Nucleoid Associated Proteins can explain these anomalous dynamics. Consistent with this, we show that in the absence of the bridging protein H-NS, the scaling exponent increases. Chromosomal loci also display rare rapid movements not explainable by polymer theory, even accounting for the viscoelasticity of the cytoplasm. Our simulations show that bridging can additionally explain this behaviour. Finally, we predict a lower bound on the average bridge lifetime within cells.
Characterizing adjuvants’ effects at the murine immunoglobulin repertoire level

High-throughput immunoglobulin sequencing (IgSeq) has been developed and applied to study the adaptive immune response extensively for more than a decade. However, generating large-scale, high-fidelity sequencing data is still challenging, and furthermore, not much has been done to characterize adjuvants’ effects at the repertoire level. Thus, we developed an improved library prep protocol and standardized the data analysis pipeline for accurate repertoire profiling. In addition, two metrics were implemented to assess repertoire clone properties. We then studied systemically the effects of two adjuvants, CpG and Alum, on the Ig heavy chain repertoire using the ovalbumin (OVA) challenged mouse model. Ig repertoires of different tissues (spleen and bone marrow) and isotypes (IgG and IgM) were examined and compared in terms of sequence mutation frequency, IGHV gene usage, CDR3 length, rescaled Hill numbers for clonal diversity, and clone selection strength. As a result, Ig repertoires of different tissues or isotypes exhibited distinguishable profiles at the non-immunized steady state. Adjuvanted immunizations further resulted in statistically significant alterations in Ig repertoire compared with PBS or OVA alone immunized groups. Lastly, we applied unsupervised machine learning techniques – multiple factor analysis and clustering – to identify Ig repertoire signatures in different compartments and under varying immunizations. We found that the IGH repertoires of distinct tissue-isotype compartments or under varying immunizations differed in unique sets of properties. Notably, Alum and CpG effects on the Ig repertoire exhibited different tissue and isotype preferences. The former led to increased diversity of abundant clones of both isotypes in BM only, and the latter promoted the selection of IgG clones only but in both tissues. The patterns of Ig repertoire changes likely reflected possible action mechanisms of these two adjuvants.
Germline variation contributes to false negatives in CRISPR-based experiments with varying burden across ancestries

Reducing disparities is critical to promote equity of access to precision treatments for all patients with cancer. While socioenvironmental factors are a major driver behind such disparities, biological differences also are likely to contribute. The prioritization of cancer drug targets is foundational for drug discovery, yet whether ancestry-related signals in target discovery pipelines exist has not been systematically explored due to the absence of data at the appropriate scale. Here, we analyzed data from 611 genome-scale CRISPR/Cas9 viability experiments in human cell line models as part of the Cancer Dependency Map to identify ancestry-associated genetic dependencies. Surprisingly, we found that most putative associations between ancestry and dependency arose from artifacts related to germline variants that are present at different frequencies across ancestry groups. In 2-5% of genes profiled in each cellular model, germline variants in sgRNA targeting sequences likely reduced cutting by the CRISPR/Cas9 nuclease. Unfortunately, this bias disproportionately affected cell models derived from individuals of recent African descent because their genomes tended to diverge more from the consensus genome typically used for CRISPR/Cas9 guide design. To help the scientific community begin to resolve this source of bias, we report three complementary methods for ancestry-agnostic CRISPR experiments. This report adds to a growing body of literature describing ways in which ancestry bias impacts cancer research in underappreciated ways.
Precueing Sequential Rotation Tasks in Augmented Reality

Augmented reality has been used to improve sequential-task performance by cueing information about a current task step and precueing information about future steps. Existing work has shown the benefits of precueing movement (translation) information. However, rotation is also a major component in many real-life tasks, such as turning knobs to adjust parameters on a console. We developed an AR testbed to investigate whether and how much precued rotation information can improve user performance. We consider two unimanual tasks: one requires a user to make sequential rotations of a single object, and the other requires the user to move their hand between multiple objects to rotate them in sequence. We conducted a user study to explore these two tasks using circular arrows to communicate rotation. In the single-object task, we examined the impact of number of precues and visualization style on user performance. Results show that precues improved performance and that arrows with highlighted heads and tails, with each destination aligned with the next origin, yielded the shortest completion time on average. In the multiple-object task, we explored whether rotation precues can be helpful in conjunction with movement precues. Here, using a rotation cue without rotation precues in conjunction with a movement cue and movement precues performed the best, implying that rotation precues were not helpful when movement was also required.
Angle-dependence and auxin asymmetry: towards the formulation of a universal theory of root gravitropism

Gravitropism has been conceptualized through three main theories: the starch-statolith model for sensing, the Cholodny-Went model of growth control via auxin asymmetry, and the law of angle-dependence for behavior, in which the magnitude of gravitropic response increases with displacement from the vertical. While experimental data show that the generation of both Cholodny-Went-type auxin gradients and angle-dependent behavior requires statolith sedimentation, a link between auxin asymmetry and angle-dependence has not been demonstrated. Here, we use large scale reorientation assays of Arabidopsis roots, epidermal length measurements, and confocal microscopy to quantify auxin distribution and PIN localization during graviresponse. We show angle-dependence in auxin asymmetry and growth response, even at low stimulation angles. As such, our work integrates the three theories sensing, signal transduction and behavior into a single unified model of gravitropism and provides an important framework for exploring major outstanding questions in the field.
Accurate Computational Design of 3D Protein Crystals

Protein crystallization plays a central role in structural biology1, with broad impact2 in pharmaceutical formulation3, drug delivery4, biosensing5, and biocatalysis6,7. Despite this importance, the process of protein crystallization remains poorly understood and highly empirical8–10, with largely unpredictable crystal contacts, lattice packing arrangements, and space group preferences, and the programming of protein crystallization through precisely engineered sidechain-sidechain interactions across multiple protein-protein interfaces is an outstanding challenge. Here we develop a general computational approach to designing three-dimensional (3D) protein crystals with pre-specified lattice architectures at atomic accuracy that hierarchically constrains the overall degree of freedoms (DOFs) of the system. We use the approach to design three pairs of oligomers that can be individually purified, and upon mixing, spontaneously self-assemble into large 3D crystals (>100 μm). Small-angle X-ray scattering and X-ray crystallography show these crystals are nearly identical to the computational design models, with the design target F4132 and I432 space groups and closely corresponding overall architectures and protein-protein interfaces. The crystal unit cell dimensions can be systematically redesigned while retaining space group symmetry and overall architecture, and the crystals are both extremely porous and highly stable, enabling the robust scaffolding of inorganic nanoparticle arrays. Our approach thus enables the computational design of protein crystals with high accuracy, and since both structure and assembly are encoded in the primary sequence, provides a powerful new platform for biological material engineering.
Nebula: An Affordable Open-Source and Autonomous Olfactory Display for VR Headsets

The impact of olfactory cues on user experience in virtual reality is increasingly studied. However, results are still heterogeneous and existing studies difficult to replicate, mainly due to a lack of standardized olfactory displays. In that context, we present Nebula, a low-cost, open-source, olfactory display capable of diffusing scents at different diffusion rates using a nebulization process. Nebula can be used with PC VR or autonomous head-mounted displays, making it easily transportable without the need for an external computer. The device was calibrated to diffuse at three diffusion rates: no diffusion, low and high. For each level, the quantity of delivered odor was precisely characterized using a repeated weighting method. The corresponding perceived olfactory intensities were evaluated by a psychophysical experiment on sixteen participants. Results demonstrated the device capability to successfully create three significantly different perceived odor intensities (Friedman test p < 10− 6, Wilcoxon tests padj < 10− 3), without noticeable smell persistence and with limited noise and discomfort. For reproducibility and to stimulate further research in the area, 3D printing files, electronic hardware schemes, and firmware/software source-code are made publicly available.
Overexpression of PSR1 in Chlamydomonas reinhardtii induces luxury phosphorus uptake

Remediation using micro-algae offers an attractive solution to environmental phosphate (Pi) pollution. However, for maximum efficiency, pre-conditioning of algae to induce ‘luxury phosphorus (P) uptake’ is needed. Here we show that natural pre-conditioning can be mimicked through over-expression of a single gene, the global regulator PSR1 (Myb transcription factor: Phosphate Starvation Response 1), raising P levels to 8% dry cell weight from 2% in control. Complete removal of Pi occurred in log phase, unlike the control. This was associated with increases in PolyP granule size and uptake of Mg2+, the principal counterion. Hyper-accumulation of P depended on a feed-forward mechanism, where a small set of ‘Class I’ genes were activated despite abundant external Pi levels. This drove a reduction in external Pi levels, permitting more genes to be expressed (Class II), leading to more Pi-uptake. These discoveries enable a bio-circular approach of recycling nutrients from wastewater back to agriculture. Teaser Manipulating a single gene drove uptake of P and a Mg2+ counter-ion for increased PolyP accumulation.