Miracle-dz/UniFAR-FTUs huggingface dataset:
Spatial Structure Formation by RsmE-Regulated Extracellular Secretions in Pseudomonas fluorescens Pf0-1

In densely populated colonies of the bacterium Pseudomonas fluorescens Pf0-1, diverse mutations in the rsmE gene are naturally selected by solving the problem of overcrowding. Here, we show that RsmE-regulated secretions function together to create and protect space of low cell density. ABSTRACT Cells in microbial communities on surfaces live and divide in close proximity, which greatly enhances the potential for social interactions. Spatiogenetic structures are manifested through competitive and cooperative interactions among the same and different genotypes within a shared space, and extracellular secretions appear to function dynamically at the forefront. A previous experimental evolution study utilizing Pseudomonas fluorescens Pf0-1 colonies demonstrated that diverse mutations in the rsmE gene were repeatedly and exclusively selected through the formation of a dominant spatial structure. RsmE’s primary molecular function is translation repression, and its homologs regulate various social and virulence phenotypes. Pseudomonas spp. possess multiple paralogs of Rsm proteins, and RsmA, RsmE, and RsmI are the most prevalent. Here, we demonstrate that the production of a mucoid polymer and a biosurfactant are exclusively regulated through RsmE, contradicting the generalized notion of functional redundancy among the Rsm paralogs. Furthermore, we identified the biosurfactant as the cyclic lipopeptide gacamide A. Competition and microscopy analyses showed that the mucoid polymer is solely responsible for creating a space of low cellular density, which is shared exclusively by the same genotype. Gacamide A and other RsmE-regulated products appear to establish a physical boundary that prevents the encroachment of the competing genotype into the newly created space. Although cyclic lipopeptides and other biosurfactants are best known for their antimicrobial properties and reducing surface tension to promote the spreading of cells on various surfaces, they also appear to help define spatial structure formation within a dense community. IMPORTANCE In densely populated colonies of the bacterium Pseudomonas fluorescens Pf0-1, diverse mutations in the rsmE gene are naturally selected by solving the problem of overcrowding. Here, we show that RsmE-regulated secretions function together to create and protect space of low cell density. A biosurfactant generally promotes the spreading of bacterial cells on abiotic surfaces; however, it appears to function atypically within a crowded population by physically defining genotypic boundaries. Another significant finding is that these secretions are not regulated by RsmE’s paralogs that share high sequence similarity. The experimental pipeline described in this study is highly tractable and should facilitate future studies to explore additional RsmE-regulated products and address why RsmE is functionally unique from its paralogs.
Prior parental experience attenuates hormonal stress responses and alters hippocampal glucocorticoid receptors in both sexes of the biparental rock dove

In the face of challenges, animals must balance investments in reproductive effort versus their own survival. Physiologically, this tradeoff may be mediated by glucocorticoid release by the hypothalamic-pituitary-adrenal (HPA) axis and prolactin release from the pituitary to maintain parental care. The degree to which animals react to, and recover from, stressors likely affects their ability to maintain parental behavior and ultimately, fitness. However, less is known about how the stress response changes when animals gain parental experience, and what mechanisms may underlie any effect of experience on hormonal stress responses. To address these questions, we measured the corticosterone (CORT) and prolactin (PRL) stress response in both sexes of the biparental rock dove (Columba livia) that had never raised chicks versus birds that had fledged at least one chick. We measured both CORT and PRL at baseline and after an acute stressor (30 minutes restraint). We also measured negative feedback ability by administering dexamethasone, a synthetic glucocorticoid that suppresses CORT release, and measuring CORT and PRL after 60 minutes. All hormones we measured when birds were not actively nesting, allowing us to assess any lasting effects of parental experience beyond the parental care period. Birds with parental experience had lower stress-induced and negative-feedback CORT, and higher stress-induced PRL than inexperienced birds. In a separate experiment, we measured glucocorticoid receptor subtype expression in the hippocampus, a key site of negative feedback regulation. We found that experienced birds expressed higher glucocorticoid receptors than inexperienced controls, which may mediate their ability to attenuate the hormonal stress response. Together, these results shed light on potential mechanisms by which gaining experience may improve parental performance and fitness. Summary statement Experienced rock dove parents show lower corticosterone and higher prolactin levels after an acute stressor than birds without parental experience and increased glucocorticoid receptor expression in the hippocampus may mediate this effect.
MINFLUX dissects the unimpeded walking of kinesin-1

We report on an interferometric MINFLUX microscope that records protein movements with down to 1.7 nm precision within less than 1 ms. While such spatio-temporal resolution has so far required linking a strongly scattering 30-500 nm diameter bead to the much smaller protein, MINFLUX localization requires the detection of only down to 20 photons from an ~1-nm sized fluorophore. Harnessing this resolution, we dissect the unhindered stepping of the motor protein kinesin-1 on microtubules at up to physiological ATP concentrations. By attaching the fluorophore to different kinesin-1 sites and resolving steps and substeps of these protein constructs, we uncover a three-dimensional orientation change of the unbound kinesin head. We also find that kinesin-1 takes up ATP while only one head is bound, whereas hydrolysis of ATP occurs with both heads bound to the microtubule, resolving a long-standing conundrum of its mechanochemical cycle. Our results establish MINFLUX as a non-invasive tool for tracking protein movements and probing submillisecond structural rearrangements with nanometer resolution.
Single neurons in thalamus and subthalamic nucleus process cardiac and respiratory signals in humans

Visceral signals are constantly processed by our central nervous system, enable homeostatic regulation, and influence perception, emotion, and cognition. While visceral processes at cortical level have been extensively studied using non-invasive imaging techniques, very few studies have investigated how this information is processed at the single neuron level, both in humans and animals. Subcortical regions, relaying signals from peripheral interoceptors to cortical structures, are particularly understudied and how visceral information is processed in thalamic and subthalamic structures remains largely unknown. Here, we took advantage of intraoperative microelectrode recordings in patients undergoing surgery for deep brain stimulation (DBS) to investigate the activity of single neurons related to cardiac and respiratory functions in three subcortical regions: Ventral Intermedius nucleus (Vim) and Ventral caudalis nucleus (Vc) of the thalamus, and subthalamic nucleus (STN). We report that the activity of a large portion of the recorded neurons (about 70%) was modulated by either the heartbeat, the cardiac inter-beat interval, or the respiration. These cardiac and respiratory response patterns varied largely across neurons both in terms of timing and their kind of modulation. We observed neurons with increases or decreases in firing rate in response to either the heartbeat or the inter-beat interval. Peaks of neural activity were found at different phases of the cardiac and respiratory cycles. Whereas most neurons only responded to one of the tested signals, a substantial proportion of these visceral neurons (30%) was responsive to more than one of the tested signals, underlining specialization and integration of cardiac and respiratory signals in STN and thalamic neurons. By extensively describing for the first time single unit activity related to cardiorespiratory function in thalamic and subthalamic neurons, our results highlight the major role of these subcortical regions in the processing of visceral signals.
Gene expression profiles of chemosensory genes of termite soldier and worker antennae

Termite caste differentiation and social behavior are appropriately regulated by the chemical signals among individuals in each colony. Signal transduction is well known to be triggered by the reception of odorant molecules by some binding proteins in the antennae, after which, a signal is transmitted to chemosensory receptors. However, there is insufficient information on the role of chemosensory genes involved in signal transduction in termites. Here, we identified the genes involved in chemosensory reception in the rhinotermitid termite Reticulitermes speratus, and performed a genome-wide comparative transcriptome analysis of worker and soldier antennae. First, we identified 31 odorant-binding proteins (OBPs), and three chemosensory protein A (CheA) from the available genome sequence data. Thereafter, we performed RNA sequencing to compare the expression levels of OBPs, CheAs, and previously identified chemosensory receptor genes between workers and soldiers antennae. Of note, there were no receptor genes with significant differences in expression between castes. However, the expression levels of three non-receptor genes (OBP, CheA, and Sensory neuron membrane protein) were significantly different between castes. Quantiative polymerase chain reaction (qPCR) analysis using antennae and other head parts confirmed that these genes were highly expressed in soldier antennae. Finally, independent qPCR analysis showed that the expression patterns of these genes were altered in soldiers from different social contexts. The present results suggest that some non-receptor protein genes are involved in the social behaviors of termites.
Rational Point Counts for del Pezzo Surfaces over Finite Fields and Coding Theory

The goal of this thesis is to apply an approach due to Elkies to study the distribution of rational point counts for certain families of curves and surfaces over finite fields. A vector space of polynomials over a fixed finite field Fq gives rise to a linear code, and the weight enumerator of this code gives information about point count distributions. The MacWilliams theorem gives a relation between the weight enumerator of a linear code and the weight enumerator of its dual code. For certain codes C coming from families of varieties where it is not known how to determine the distribution of point counts directly, we analyze low-weight codewords of the dual code and apply the MacWilliams theorem and its generalizations to gain information about the weight enumerator of C. These low-weight dual codes can be described in terms of point sets that fail to impose independent conditions on this family of varieties. Our main results concern rational point count distributions for del Pezzo surfaces of degree 2, and for certain families of genus 1 curves. These weight enumerators have interesting geometric and coding theoretic applications for small q.
Attenuation of Radar Signal by a Boreal Forest Canopy in Winter

An investigation of boreal forest attenuation of a radar signal in winter is presented, applying a multifrequency (1–10 GHz) ground-based synthetic aperture radar (GB-SAR). As stable targets, corner reflectors (CRs) with known radar cross section (RCS) were used under the forest canopy. This enabled to relate changes in observed wideband backscattering from the reflectors to attenuation of the radar signal in forest vegetation, eliminating the influence of the background, such as snow and soil. We found that ambient temperature affected the observed attenuation of the radar signal in the entire 1–10-GHz frequency range. For temperatures <inline-formula> <tex-math notation="LaTeX">$T < 0 ~^{\circ }\text{C}$ </tex-math></inline-formula>, attenuation was found to decrease by up to 4.3 dB at the lowest observed temperatures of −36 °C, with peak attenuation occurring at <inline-formula> <tex-math notation="LaTeX">$T \approx 0 ~^{\circ }\text{C}$ </tex-math></inline-formula>. The overall apparent two-way attenuation increased by up to 18 dB from L- to X-band. The presence of snow on the canopy was found to increase attenuation by 1–4 dB, the effect increasing with frequency while having only negligible effects on vegetation backscatter.
A Method for Exploring Systematics Due to Galactic Interstellar Emission Modeling: Application to the Fermi LAT SNR Catalog

Galactic interstellar emission contributes substantially to Fermi LAT observations in the Galactic plane, where the majority of Supernova Remnants (SNRs) are located. We have developed a method to explore some systematic effects on SNRs' properties caused by interstellar emission modeling. We created eight alternative Galactic interstellar models by varying a few input parameters to GALPROP, namely the height of the cosmic ray propagation halo, cosmic ray source distribution in the Galaxy, and atomic hydrogen spin temperature. We have analyzed eight representative candidate SNRs chosen to encompass a range of Galactic locations, extensions, and spectral properties using the eight different interstellar emission models. The models were fitted to the LAT data with free independent normalization coefficients for the various components of the model along the line of sight in each region of interest. We will discuss the results and compare them with those obtained with the official LAT interstellar emission model.
Tissue-resident memory T cells mediate mucosal immunity to recurrent urinary tract infection

Urinary tract infection (UTI) is one of the most prevalent human bacterial infections. New therapeutic approaches, including vaccination and immunotherapy, are urgently needed to combat the rapid global dissemination of multidrug-resistant uropathogens. Development of therapies is impeded by an incomplete understanding of memory development during UTI. Here, we found that reducing bacterial load early in infection, by reducing the inoculum or with antibiotics after infection, completely abrogated the protective memory response. We observed a mixed T helper cell polarization, comprised of Th1, Th2, and Th17 T cells, among T cells infiltrating the bladder during primary infection. Thus, we hypothesized that reducing antigen load altered T helper cell polarization leading to poor memory. Surprisingly, however, T helper cell polarization was unchanged in these scenarios. Instead, we uncovered a population of tissue resident memory (TRM) T cells that was significantly reduced in the absence of sufficient antigen. Demonstrating that TRM cells are necessary for immune memory, transfer of lymph node or spleen-derived infection-experienced T cells to naïve animals did not confer protection against infection. Supporting that TRM cells are sufficient to protect against recurrent UTI, animals depleted of systemic T cells, or treated with FTY720 to block memory lymphocyte migration from lymph nodes to infected tissue, were equally protected compared to unmanipulated mice against a second UTI. Thus, we uncovered an unappreciated key role for TRM cells in the memory response to bacterial infection in this mucosa, providing a target for non-antibiotic-based immunotherapy and/or new vaccine strategies to prevent recurrent UTI. One Sentence Summary TRM are necessary and sufficient for memory to recurrent UTI
Ray splitting with ghost orbits: explicit, analytical and exact solution for spectra of scaling step potentials with tunnelling

In the familiar concept of ray splitting, a ray incident on an interface splits into reflected and transmitted rays. Tunnelling adds something new to ray splitting: an incident Newtonian ray splits into a reflected Newtonian ray and a transmitted ray with complex classical action—a ghost orbit. Using novel periodic-orbit expansion techniques, we are able to compute explicitly and analytically energy eigenvalues of an energy-scaling one-dimensional step potential. Inclusion of all periodic orbits in our series expansions, in particular a class of orbits called pure ghosts with imaginary classical action, makes our formulae exact. We suggest an experiment that may be used to verify the importance of pure ghosts.
Measuring concentration with Voronoï diagrams: the study of possible biases

In the context of turbulent flows laden with inertial particles, the accurate estimation of preferential concentration is particularly relevant. We have recently proposed to use Voronoï diagrams to estimate concentration fields from two-dimensional imaging techniques implemented around wind tunnel experiments. Due to various experimental biases, the relevance of such an analysis becomes questionable. In this paper, we show the robustness of the Voronoï analysis with respect to the three more important identified biases possibly present in such experiments.
Malignant oligoastrocytoma in the spinal cord of a cat

A 12-year and 3-month spayed female mixed cat was presented with severe lumbar pain. Magnetic resonance imaging and postmortem examination revealed a swollen lesion in the spinal cord at L3 level. Histologic examination identified extensive neoplastic cell proliferation with massive necrosis in the tumor tissue. Two types of neoplastic cells were recognized. One type of neoplastic cells were large cells characterized by round to polygonal shape and abundant eosinophilic cytoplasm (referred to as “large cells”). The other neoplastic cells were small, densely proliferated, and had round to irregular shape and scant eosinophilic cytoplasm (referred to as “small cells”). Both types of cells were positive for oligodendrocyte transcription factor 2 and SRY-box transcription factor 10. Glial fibrillary acidic protein was positive in large cells but negative in most small cells. Digital analysis for Ki-67-stained tumor tissues found that total 21.1% ± 6.5% of tumor cells were positive for Ki-67. Based on these findings, we diagnosed malignant oligoastrocytoma in the spinal cord.
High Frequencies of Phenotypically and Functionally Senescent and Exhausted CD56CD57PD-1

8 Laboratory of Cellular and Molecular Immunology, Gavin Herbert Eye Institute, University of 9 California Irvine, School of Medicine, Irvine, CA 92697; Department of Molecular Biology & 10 Biochemistry; and Department of Vaccines and Immunotherapies, TechImmune, LLC, University Lab 11 Partners, Irvine, CA 92660-7913;Institute for Immunology; University of California Irvine, School of 12 Medicine, Irvine, CA 92697. 13 14
Physical properties of the seasonal snow cover in Dronning Maud Land, East Antarctica

Snow stratigraphy was analyzed in the Maudheimvidda area of western Dronning Maud Land, East Antarctica, during austral summer 1999/2000 as a part of the Finnish Antarctic Research Programme (FINNARP). Measurements were made in shallow (1^2m) snowpits alonga 350kmtransect fromthecoasttothepolarplateau, coveringatleast one annual cycle and an elevation range from sea level to about 2500m.The aim of the study is to document spatial andtemporal variations in snow-cover properties, withthe further aim of relating these variations to environmental factors and to patterns observable by remote sensing.The measurements suggest five principal snowzones: (i) sea ice, (ii) the seawardedge zone of the ice shelf, (iii) the inner parts of the ice shelf, (iv) the snowcover abovethe ground- ing line and (v) the local topographic highs. Local topographic highs such as ice domes and ice rises differ from other snow environments: the snow is less densely packed, possibly an indication of locally reduced speed of the katabatic outflow. Fewer and thinner crusts on the topographichighs are consistent with RADARSAT backscatter variations.
Characterizing the spatial properties of high harmonic generation

This thesis is concerned with describing a novel technique for characterizing the (spectrally resolved) spatial properties of light. The new approach, known as Scanning Interference Method for Integrated Transverse Analysis of Radiation (SCIMITAR), is a specific implementation of a variable-separation two-pinhole interferometer. Evaluation of the series of interference patterns produced by a SCIMITAR measurement allows the transverse profiles of intensity and spatial phase to be retrieved, while at the same time characterizing the spatial coherence of light. Including a diffraction grating in the simple experimental arrangement permits the spectral dependence of the aforementioned quantities to be measured. The SCIMITAR technique was demonstrated by characterizing the spatial properties of high harmonic generation (HHG). Excellent agreement with an alternate characterization technique known as SWORD was observed. The spectral dependence of the harmonic spatial properties was also investigated. Evidence suggesting absorption may play a role in shaping the harmonic intensity and spatial coherence was presented. Treating the harmonic radiation as either a fully coherent or partially coherent beam allowed the intensity width, spatial phase curvature and coherence width of the harmonic radiation source to be deduced. Measurement of the fine variation of the harmonic complex coherence factor (CCF) with pinhole separation revealed distinctive modulations. The Van Cittert-Zernike theorem was modified by including a Gerchberg-Saxton inspired improvement, allowing data missing from the SCIMITAR measurement to be inferred. The harmonic equivalent incoherent source intensity profile was found to be asymmetric with low intensity features isolated away from the optical axis. Calculations of the diffraction pattern produced by illumination of a non-redundant array of pinholes showed that the modulated harmonic properties could adversely influence lensless imaging-type experiments.
CD10 and CA19.9 Immunohistochemical Expression in Transitional Cell Carcinoma of the Urinary Bladder

Objectives: To determine the frequency of immunohistochemical expression of CD10 and CA19.9 in patients with papillary urothelial carcinoma of the bladder in accordance with the WHO 2004 grading of the tumor. Methodology: This descriptive cross-sectional study was conducted at the Foundation University Medical College Islamabad, from October 2017 to October 2018. Seventy-five patients from both genders, aged 40 to 80 years, undergoing trans urethral resection of bladder tumors to diagnose papillary urothelial bladder were included in our study. The data were analyzed with SPSS version 17. Immunohistochemical processing was performed and the results were interpreted by the consultant pathologist for the expression of CD10 and CA19.9 on transitional cell carcinoma with respect to the 2004 grading of the tumor. Results: age range in this study was from 40 to 80 years with a mean age of 52.60 ± 7.60 years. Out of these 75 patients, 39 (52.0%) were male and 36 (48.0%) were female, with a male-to-female ratio of 1.1:1. The frequency of positive expression of CD10 and CA19.9 on immunohistochemistry in patients with papillary urothelial carcinoma of the bladder was found in 41 (54.67%) and 39 (52.0%) cases, respectively. It was seen that positive CD10 expression was found in 12 (31.58%) low grade tumors and in 24 (63.16%) high grade tumors. Positive CA19.9 expression was found in 29 (78.38%) low grade tumors and 15 (40.54%) high grade tumors. Conclusion: The study concluded that there was a slightly increased expression of CD10 in transitional cell carcinoma of the urinary bladder compared with CA19.9. However, high-grade urothelial carcinomas showed increased expression of CD10 in contrast to low-grade urothelial carcinomas, which revealed increased positive expression of CA19.9.