Miracle-dz/UniFAR-FTUs huggingface dataset:
Photoreceptor organization and rhythmic phagocytosis in the nile rat Arvicanthis ansorgei: a novel diurnal rodent model for the study of cone pathophysiology.

PURPOSE To characterize rod and cone distribution, organization, and phagocytosis in the diurnal mouse-like rodent Arvicanthis ansorgei. METHODS Retinas of adult A. ansorgei were processed for histology, electron microscopy and immunohistochemistry using rod- and mouse cone-specific antibodies. For phagocytosis studies, retinas were sampled every 3 hours under a 12-hour light-dark cycle and processed for double-label immunohistochemistry. The number of phagosomes in the retinal pigmented epithelium were quantified with a morphometric system. RESULTS A. ansorgei retinas were composed of 33% cones and 67% rods, approximately 10 times more cones than mice and rats. Cones were arranged in two cell layers at the scleral surface, distributed uniformly across the entire retina. Cone arrestin was distributed throughout the dark-adapted cones, from outer segments to synapses, whereas short- and mid-wavelength cone opsins were restricted to outer segments. Short-wavelength cone density was mapped in wholemounted retinas, in a significantly higher number in the central region. Rhodopsin immunopositive (rod) phagosomes showed a small peak late in the dark phase, then a large burst 1 to 2 hours after light onset, after decreasing to low baseline levels by 12 AM. Mid-wavelength cone opsin immunopositive (cone) phagosomes were 10 times less numerous than rods, and demonstrated a broad peak 1 to 2 hours after light onset. CONCLUSIONS The diurnal rodent A. ansorgei possesses a large number of cones, organized in a strict anatomic array. Rod and cone outer segment phagocytosis and shedding can be monitored simultaneously and show similar profiles but different amplitudes. This species may constitute a valuable novel animal model for investigating cone pathophysiology.
Proving security protocols with model checkers by data independence techniques

Model checkers such as FDR have been extremely effective in checking for, and finding, attacks on cryptographic protocols. Their use in proving protocols has, on the other hand, generally been limited to showing that a given small instance, usually restricted by the finiteness of some set of resources such as keys and nonces, is free of attacks. While for specific protocols there are frequently good reasons for supposing that this will find any attack, it leaves a substantial gap in the method. The purpose of this paper is to show how techniques borrowed from data independence and related fields can be used to achieve the illusion, that nodes can call upon an infinite supply of different nonces, keys, etc., even though the actual types used for these things remain finite. It is thus possible to create models of protocols in which nodes do not have to stop after a small number of runs and to claim that, within certain limits, a finite-state run on a model checker has proved that a given protocol is secure from attack. The author uses a single protocol as a case study, but believe our techniques are much more widely applicable.
Evolution of Female Preference for Younger Males

Previous theoretical work has suggested that females should prefer to mate with older males, as older males should have higher fitness than the average fitness of the cohort into which they were born. However, studies in humans and model organisms have shown that as males age, they accumulate deleterious mutations in their germ-line at an ever-increasing rate, thereby reducing the quality of genes passed on to the next generation. Thus, older males may produce relatively poor-quality offspring. To better understand how male age influences female mate preference and offspring quality, we used a genetic algorithm model to study the effect of age-related increases in male genetic load on female mate preference. When we incorporate age-related increases in mutation load in males into our model, we find that females evolve a preference for younger males. Females in this model could determine a male's age, but not his inherited genotype nor his mutation load. Nevertheless, females evolved age-preferences that led them to mate with males that had low mutation loads, but showed no preference for males with respect to their somatic quality. These results suggest that germ-line quality, rather than somatic quality, should be the focus of female preference in good genes models.
Simulations of Magnetorotational Instability in a Magnetized Couette Flow

In preparation for an experimental study of magnetorotational instability (MRI) in liquid metal, we present nonideal two-dimensional magnetohydrodynamic simulations of the nonlinear evolution of MRI in the experimental geometry. The simulations adopt initially uniform vertical magnetic fields, conducting radial boundaries, and periodic vertical boundary conditions. No-slip conditions are imposed at the cylinders. Our linear growth rates compare well with existing local and global linear analyses. The MRI saturates nonlinearly with horizontal magnetic fields comparable to the initial axial field. The rate of angular momentum transport increases modestly but significantly over the initial state. For modest fluid and magnetic Reynolds numbers Re,Rem ~ 102-103, the final state is laminar reduced mean shear except near the radial boundaries, and with poloidal circulation scaling as the square root of resistivity, in partial agreement with the analysis of Knobloch and Julien. A sequence of simulations at Rem = 20 and 102 ≲ Re ≲ 104.4 enables extrapolation to the experimental regime (Rem ≈ 20, Re ~ 107), albeit with unrealistic boundary conditions. MRI should increase the experimentally measured torque substantially over its initial purely hydrodynamic value.
Automatic Alignment of Local Representations

We present an automatic alignment procedure which maps the disparate internal representations learned by several local dimensionality reduction experts into a single, coherent global coordinate system for the original data space. Our algorithm can be applied to any set of experts, each of which produces a low-dimensional local representation of a high-dimensional input. Unlike recent efforts to coordinate such models by modifying their objective functions [1, 2], our algorithm is invoked after training and applies an efficient eigensolver to post-process the trained models. The post-processing has no local optima and the size of the system it must solve scales with the number of local models rather than the number of original data points, making it more efficient than model-free algorithms such as Isomap [3] or LLE [4].
Evidence of a general 2/3-power law of scaling leaf nitrogen to phosphorus among major plant groups and biomes

Scaling relations among plant traits are both cause and consequence of processes at organ-to-ecosystem scales. The relationship between leaf nitrogen and phosphorus is of particular interest, as both elements are essential for plant metabolism; their limited availabilities often constrain plant growth, and general relations between the two have been documented. Herein, we use a comprehensive dataset of more than 9300 observations of approximately 2500 species from 70 countries to examine the scaling of leaf nitrogen to phosphorus within and across taxonomical groups and biomes. Power law exponents derived from log–log scaling relations were near 2/3 for all observations pooled, for angiosperms and gymnosperms globally, and for angiosperms grouped by biomes, major functional groups, orders or families. The uniform 2/3 scaling of leaf nitrogen to leaf phosphorus exists along a parallel continuum of rising nitrogen, phosphorus, specific leaf area, photosynthesis and growth, as predicted by stoichiometric theory which posits that plants with high growth rates require both high allocation of phosphorus-rich RNA and a high metabolic rate to support the energy demands of macromolecular synthesis. The generality of this finding supports the view that this stoichiometric scaling relationship and the mechanisms that underpin it are foundational components of the living world. Additionally, although abundant variance exists within broad constraints, these results also support the idea that surprisingly simple rules regulate leaf form and function in terrestrial ecosystems.
The Closest Relatives of Icosahedral Viruses of Thermophilic Bacteria Are among Viruses and Plasmids of the Halophilic Archaea

ABSTRACT We have sequenced the genome and identified the structural proteins and lipids of the novel membrane-containing, icosahedral virus P23-77 of Thermus thermophilus. P23-77 has an ∼17-kb circular double-stranded DNA genome, which was annotated to contain 37 putative genes. Virions were subjected to dissociation analysis, and five protein species were shown to associate with the internal viral membrane, while three were constituents of the protein capsid. Analysis of the bacteriophage genome revealed it to be evolutionarily related to another Thermus phage (IN93), archaeal Halobacterium plasmid (pHH205), a genetic element integrated into Haloarcula genome (designated here as IHP for integrated Haloarcula provirus), and the Haloarcula virus SH1. These genetic elements share two major capsid proteins and a putative packaging ATPase. The ATPase is similar with the ATPases found in the PRD1-type viruses, thus providing an evolutionary link to these viruses and furthering our knowledge on the origin of viruses.
Biologically Inspired Feature Manifold for Scene Classification

Biologically inspired feature (BIF) and its variations have been demonstrated to be effective and efficient for scene classification. It is unreasonable to measure the dissimilarity between two BIFs based on their Euclidean distance. This is because BIFs are extrinsically very high dimensional and intrinsically low dimensional, i.e., BIFs are sampled from a low-dimensional manifold and embedded in a high-dimensional space. Therefore, it is essential to find the intrinsic structure of a set of BIFs, obtain a suitable mapping to implement the dimensionality reduction, and measure the dissimilarity between two BIFs in the low-dimensional space based on their Euclidean distance. In this paper, we study the manifold constructed by a set of BIFs utilized for scene classification, form a new dimensionality reduction algorithm by preserving both the geometry of intra BIFs and the discriminative information inter BIFs termed Discriminative and Geometry Preserving Projections (DGPP), and construct a new framework for scene classification. In this framework, we represent an image based on a new BIF, which combines the intensity channel, the color channel, and the C1 unit of a color image; then we project the high-dimensional BIF to a low-dimensional space based on DGPP; and, finally, we conduct the classification based on the multiclass support vector machine (SVM). Thorough empirical studies based on the USC scene dataset demonstrate that the proposed framework improves the classification rates around 100% relatively and the training speed 60 times for different sites in comparing with previous gist proposed by Siagian and Itti in 2007.
Antagonism of the Met5‐enkephalin‐opioid growth factor receptor‐signaling axis promotes MSC to differentiate into osteoblasts

Chronic opioid therapy is associated with bone loss. This led us to hypothesize that the opioid antagonists, that include naloxone, would stimulate bone formation by regulating MSC differentiation. The opioid growth factor receptor (OGFR) is a non‐canonical opioid receptor that binds naloxone with high affinity whereas the native opioid growth factor, met5‐enkephalin (met5), binds both the OGFR and the canonical delta opioid receptor (OPRD). Naloxone and an shRNA OGFR lentivirus were employed to disrupt the OGFR‐signaling axis in cultured MSC. In parallel, naloxone was administered to bone marrow using a mouse unicortical defect model. OPRD, OGFR, and the met5‐ligand were highly expressed in MSC and osteoblasts. A pulse‐dose of naloxone increased mineral formation in MSC cultures in contrast to MSC treated with continuous naloxone or OGFR deficient MSC. Importantly, SMAD1 and SMAD8/9 expression increased after a pulse dose of naloxone whereas SMAD1, SMAD7, and ID1 were increased in the OGFR deficient MSC. Inhibited OGFR signaling decreased proliferation and increased p21 expression. The addition of naloxone to the unicortical defect resulted in increased bone formation within the defect. Our data suggest that novel mechanism through which signaling through the OGFR regulates osteogenesis via negative regulation of SMAD1 and p21. © 2015 Orthopaedic Research Society. Published by Wiley Periodicals, Inc. J Orthop Res 34:1195–1205, 2016.
Large eddy simulation using high-resolution and high-order methods

Restrictions on computing power make direct numerical simulation too expensive for complex flows; thus, the development of accurate large eddy simulation (LES) methods, which are industrially applicable and efficient, is required. This paper reviews recent findings about the leading order dissipation rate associated with high-resolution methods and improvements to the standard schemes for use in highly turbulent flows. Results from implicit LES are presented for a broad range of flows and numerical schemes, ranging from the second-order monotone upstream-centered schemes for conservation laws to very high-order (up to ninth-order) weighted essentially non-oscillatory schemes.
B-cell activation by lipopolysaccharide. Distinct pathways for induction of mitosis and antibody production

The role played by macrophages in two effects of lipopolysaccharide (LPS) on the immune system of the mouse-substitution for helper T cells and induction of B-cell mitosis-has been investigated. C3H/HeJ mice are unresponsive and do not produce (as other strains do) antibody to 2,4,6- trinitrophenol (TNP) conjugated with autologous mouse erythrocytes (MRBC-TNP) in the presence of LPS. We found that C3H/HeJ spleen cells produce antibody to MRBC-TNP when (a) LPS and macrophages from LPS- responsive C3HeB/FeJ mice or (b) tumor necrosis serum ([TNS] induced by LPS in responsive mice) are added. The mitotic response was not restored. The findings suggest that adjuvanticity and mitogenicity represent distinct pathways of B-cell activation by LPS, subject to different regulatory mechanisms.
Detecting user engagement in everyday conversations

This paper presents a novel application of speech emotion recognition: estimation of the level of conversational engagement between users of a voice communication system. We begin by using machine learning techniques, such as the support vector machine (SVM), to classify users’ emotions as expressed in individual utterances. However, this alone fails to model the temporal and interactive aspects of conversational engagement. We therefore propose the use of a multilevel structure based on coupled hidden Markov models (HMM) to estimate engagement levels in continuous natural speech. The first level is comprised of SVM-based classifiers that recognize emotional states, which could be (e.g.) discrete emotion types or arousal/valence levels. A high-level HMM then uses these emotional states as input, estimating users’ engagement in conversation by decoding the internal states of the HMM. We report experimental results obtained by applying our algorithms to the LDC EMOTIONAL PROSODY and CALLFRIEND speech corpora.
Decline in Renal Function Following Thoracic Organ Transplantation in Children

Heart and/or lung transplantation are life‐saving treatments for end‐stage cardiopulmonary disease; however, chronic renal failure may develop. The impact of thoracic organ transplant on renal function in infants and children is not well characterized. This retrospective cohort study evaluated renal function following thoracic organ transplantation in 46 children (32 heart, 9 lung, 5 heart‐lung; median age 4.1 years) with at least 12 months of follow‐up. Glomerular filtration rate (GFR, ml/min/1.73 m2) was estimated by the Schwartz formula throughout and each GFR estimate was converted to per cent normal for age (GFR%). Changes in renal function following transplantation were analyzed using longitudinal mixed‐effects linear regression models. GFR% decreased following thoracic organ transplantation (p < 0.001). Younger age at transplant was associated with a greater decline in GFR% (p < 0.01). The decline in GFR% persisted after adjustment for nutritional status with body mass index or weight‐for‐length z‐scores. The prevalence of renal insufficiency (GFR% < 75) increased from 22% at transplant to 55% and 85% at 1 and 5 years post transplant, respectively, while 15% had a GFR% < 50 at 5 years post transplantation. Higher tacrolimus trough levels over the first 6 months correlated with a lower GFR% (p < 0.01). Renal function declined significantly following thoracic organ transplantation.
Noninvasive Imaging of Human Immune Responses in a Human Xenograft Model of Graft-Versus-Host Disease

The immune system plays a crucial role in many diseases. Activation or suppression of immunity is often related to clinical outcome. Methods to explore the dynamics of immune responses are important to elucidate their role in conditions characterized by inflammation, such as infectious disease, cancer, or autoimmunity. Immuno-PET is a noninvasive method by which disease and immune cell infiltration can be explored simultaneously. Using radiolabeled antibodies or fragments derived from them, it is possible to image disease-specific antigens and immune cell subsets. Methods: We developed a method to noninvasively image human immune responses in a relevant humanized mouse model. We generated a camelid-derived single-domain antibody specific for human class II major histocompatibility complex products and used it to noninvasively image human immune cell reconstitution in nonobese diabetic severe combined immune deficiency γ−/− mice reconstituted with human fetal thymus, liver, and liver-derived hematopoietic stem cells (BLT mice). Results: We showed imaging of infiltrating immunocytes in BLT mice that spontaneously developed a graft-versus-host–like condition, characterized by alopecia and blepharitis. In diseased animals, we showed an increased PET signal in the liver, attributable to infiltration of activated class II major histocompatibility complex+ T cells. Conclusion: Noninvasive imaging of immune infiltration and activation could thus be of importance for diagnosis and evaluation of treatment of graft-versus-host disease and holds promise for other diseases characterized by inflammation.
Reviews and syntheses: on the roles trees play in building and plumbing the critical zone

Abstract. Trees, the most successful biological power plants on earth, build and plumb the critical zone (CZ) in ways that we do not yet understand. To encourage exploration of the character and implications of interactions between trees and soil in the CZ, we propose nine hypotheses that can be tested at diverse settings. The hypotheses are roughly divided into those about the architecture (building) and those about the water (plumbing) in the CZ, but the two functions are intertwined. Depending upon one's disciplinary background, many of the nine hypotheses listed below may appear obviously true or obviously false. (1) Tree roots can only physically penetrate and biogeochemically comminute the immobile substrate underlying mobile soil where that underlying substrate is fractured or pre-weathered. (2) In settings where the thickness of weathered material, H, is large, trees primarily shape the CZ through biogeochemical reactions within the rooting zone. (3) In forested uplands, the thickness of mobile soil, h, can evolve toward a steady state because of feedbacks related to root disruption and tree throw. (4) In settings where h ≪ H and the rates of uplift and erosion are low, the uptake of phosphorus into trees is buffered by the fine-grained fraction of the soil, and the ultimate source of this phosphorus is dust. (5) In settings of limited water availability, trees maintain the highest length density of functional roots at depths where water can be extracted over most of the growing season with the least amount of energy expenditure. (6) Trees grow the majority of their roots in the zone where the most growth-limiting resource is abundant, but they also grow roots at other depths to forage for other resources and to hydraulically redistribute those resources to depths where they can be taken up more efficiently. (7) Trees rely on matrix water in the unsaturated zone that at times may have an isotopic composition distinct from the gravity-drained water that transits from the hillslope to groundwater and streamflow. (8) Mycorrhizal fungi can use matrix water directly, but trees can only use this water by accessing it indirectly through the fungi. (9) Even trees growing well above the valley floor of a catchment can directly affect stream chemistry where changes in permeability near the rooting zone promote intermittent zones of water saturation and downslope flow of water to the stream. By testing these nine hypotheses, we will generate important new cross-disciplinary insights that advance CZ science.
NKG2D‐mediated immunity underlying paroxysmal nocturnal haemoglobinuria and related bone marrow failure syndromes

It is considered that a similar immune mechanism acts in the pathogenesis of bone marrow (BM) failure in paroxysmal nocturnal haemoglobinuria (PNH) and its related disorders, such as aplastic anaemia (AA) and myelodysplastic syndromes (MDS). However, the molecular events in immune‐mediated marrow injury have not been elucidated. We recently reported an abnormal expression of stress‐inducible NKG2D (natural‐killer group 2, member D) ligands, such as ULBP (UL16‐binding protein) and MICA/B (major histocompatibility complex class I chain‐related molecules A/B), on granulocytes in some PNH patients and the granulocyte killing by autologous lymphocytes in vitro. The present study found that the expression of NKG2D ligands was common to both granulocytes and BM cells of patients with PNH, AA, and MDS, indicating their exposure to some incitement to induce the ligands. The haematopoietic colony formation in vitro by the patients’ marrow cells significantly improved when their BM cells were pretreated with antibodies against NKG2D receptor, suggesting that the antibodies rescued haematopoietic cells expressing NKG2D ligands from damage by autologous lymphocytes with NKG2D. Clinical courses of patients with PNH and AA showed a close association of the expression of NKG2D ligands with BM failure and a favourable response to immunosuppressive therapy. We therefore propose that NKG2D‐mediated immunity may underlie the BM failure in PNH and its‐related marrow diseases.