Miracle-dz/UniFAR-FTUs huggingface dataset:
Diffusion Basis Spectrum and Diffusion Tensor Imaging Detect Hippocampal Inflammation and Dendritic Injury in a Virus-Induced Mouse Model of Epilepsy

Hippocampal CA1 inflammation and dendritic loss are common in epilepsy. Quantitative detection of coexisting brain inflammation and injury could be beneficial in monitoring disease progression and assessing therapeutic efficacy. In this work, we used conventional diffusion tensor imaging (DTI, known to detect axonal injury and demyelination) and a novel diffusion basis spectrum imaging (DBSI, known to detect axonal injury, demyelination, and inflammation) to detect hippocampal CA1 lesions resulting from neuronal dendritic injury/loss and concomitant inflammation in Theiler's murine encephalomyelitis virus (TMEV)-induced seizure mice. Following the cross-sectional ex vivo diffusion magnetic resonance imaging measurements, immunohistochemistry was performed to validate DTI and DBSI findings. Both DTI and DBSI detected immunohistochemistry-confirmed dendritic injury in the hippocampal CA1 region. Additionally, DBSI-derived restricted isotropic diffusion tensor fraction correlated with 4',6-diamidine-2'-phenylindole dihydrochloride (DAPI)-positive nucleus counts, and DBSI-derived fiber fraction correlated with dendrite density assessed by microtubule-associated protein 2 staining. DTI-derived fractional anisotropy (FA) correlated with dendrite density and negatively correlated with DAPI-positive nucleus counts. Although both DTI and DBSI detected hippocampal injury/inflammation, DTI-FA was less specific than DBSI-derived pathological metrics for hippocampal CA1 dendritic injury and inflammation in TMEV-induced seizure mice.
A joint ERS/ATS policy statement: what constitutes an adverse health effect of air pollution? An analytical framework

The American Thoracic Society has previously published statements on what constitutes an adverse effect on health of air pollution in 1985 and 2000. We set out to update and broaden these past statements that focused primarily on effects on the respiratory system. Since then, many studies have documented effects of air pollution on other organ systems, such as on the cardiovascular and central nervous systems. In addition, many new biomarkers of effects have been developed and applied in air pollution studies. This current report seeks to integrate the latest science into a general framework for interpreting the adversity of the human health effects of air pollution. Rather than trying to provide a catalogue of what is and what is not an adverse effect of air pollution, we propose a set of considerations that can be applied in forming judgments of the adversity of not only currently documented, but also emerging and future effects of air pollution on human health. These considerations are illustrated by the inclusion of examples for different types of health effects of air pollution. Air pollution has many effects on health; this document provides guidance to judge the adversity of such effects http://ow.ly/T2xx304WTZp
Towards a better understanding of the cannabinoid-related orphan receptors GPR3, GPR6, and GPR12

Abstract GPR3, GPR6, and GPR12 are three orphan receptors that belong to the Class A family of G-protein-coupled receptors (GPCRs). These GPCRs share over 60% of sequence similarity among them. Because of their close phylogenetic relationship, GPR3, GPR6, and GPR12 share a high percentage of homology with other lipid receptors such as the lysophospholipid and the cannabinoid receptors. On the basis of sequence similarities at key structural motifs, these orphan receptors have been related to the cannabinoid family. However, further experimental data are required to confirm this association. GPR3, GPR6, and GPR12 are predominantly expressed in mammalian brain. Their high constitutive activation of adenylyl cyclase triggers increases in cAMP levels similar in amplitude to fully activated GPCRs. This feature defines their physiological role under certain pathological conditions. In this review, we aim to summarize the knowledge attained so far on the understanding of these receptors. Expression patterns, pharmacology, physiopathological relevance, and molecules targeting GPR3, GPR6, and GPR12 will be analyzed herein. Interestingly, certain cannabinoid ligands have been reported to modulate these orphan receptors. The current debate about sphingolipids as putative endogenous ligands will also be addressed. A special focus will be on their potential role in the brain, particularly under neurological conditions such as Parkinson or Alzheimer’s disease. Reported physiological roles outside the central nervous system will also be covered. This critical overview may contribute to a further comprehension of the physiopathological role of these orphan GPCRs, hopefully attracting more research towards a future therapeutic exploitation of these promising targets.
Do females use their sexual status to gain resource access? Investigating food-for-sex in wolves and dogs

Abstract While food sharing among related individuals can be explained by kin selection, food sharing between unrelated individuals has been more of an evolutionary puzzle. The food-for-sex hypothesis provides an explanation for the occurrence of food sharing among nonkin. However, little is known about the socio-ecological factors that can promote such a commodity exchange. A species mating system is a factor potentially influencing food-for-sex patterns of behavior. Here, we compared wolves, which form pair-bonds, with dogs, which are typically promiscuous in free-ranging contexts, to investigate the effect of reproductive stages on the behavior around a food source in 2 different contexts. Furthermore, we considered the roles of both the males and the females in the potential food-for-sex exchange. Results indicate that in both species and for both sexes the breeding period promotes decreased aggression. Additionally, females were more persistent in their attempts to access the food and were able to monopolize the resource more when in heat as compared to outside the breeding period. Finally, in dogs, but not wolves, females spent more time in proximity to the male’s bone and had a shorter latency to start eating it when in heat. Overall, this study demonstrates that the food-for-sex hypothesis plays a part in intersexual food sharing in canids, and highlights the role of females in the interaction. These effects were especially the case in dogs, suggesting a potential effect of mating system on food-for-sex responses.
Genome-Wide Association Analyses Identify QTL Hotspots for Yield and Component Traits in Durum Wheat Grown under Yield Potential, Drought, and Heat Stress Environments

Understanding the genetic bases of economically important traits is fundamentally important in enhancing genetic gains in durum wheat. In this study, a durum panel of 208 lines (comprised of elite materials and exotics from the International Maize and Wheat Improvement Center gene bank) were subjected to genome wide association study (GWAS) using 6,211 DArTseq single nucleotide polymorphisms (SNPs). The panel was phenotyped under yield potential (YP), drought stress (DT), and heat stress (HT) conditions for 2 years. Mean yield of the panel was reduced by 72% (to 1.64 t/ha) under HT and by 60% (to 2.33 t/ha) under DT, compared to YP (5.79 t/ha). Whereas, the mean yield of the panel under HT was 30% less than under DT. GWAS identified the largest number of significant marker-trait associations on chromosomes 2A and 2B with p-values 10−06 to 10−03 and the markers from the whole study explained 7–25% variation in the traits. Common markers were identified for stress tolerance indices: stress susceptibility index, stress tolerance, and stress tolerance index estimated for the traits under DT (82 cM on 2B) and HT (68 and 83 cM on 3B; 25 cM on 7A). GWAS of irrigated (YP and HT combined), stressed (DT and HT combined), combined analysis of three environments (YP + DT + HT), and its comparison with trait per se and stress indices identified QTL hotspots on chromosomes 2A (54–70 cM) and 2B (75–82 cM). This study enhances our knowledge about the molecular markers associated with grain yield and its components under different stress conditions. It identifies several marker-trait associations for further exploration and validation for marker-assisted breeding.
An efficient design strategy for logistic regression using outcome‐ and covariate‐dependent pooling of biospecimens prior to assay

Potential reductions in laboratory assay costs afforded by pooling equal aliquots of biospecimens have long been recognized in disease surveillance and epidemiological research and, more recently, have motivated design and analytic developments in regression settings. For example, Weinberg and Umbach (1999, Biometrics 55, 718–726) provided methods for fitting set‐based logistic regression models to case‐control data when a continuous exposure variable (e.g., a biomarker) is assayed on pooled specimens. We focus on improving estimation efficiency by utilizing available subject‐specific information at the pool allocation stage. We find that a strategy that we call “(y,c)‐pooling,” which forms pooling sets of individuals within strata defined jointly by the outcome and other covariates, provides more precise estimation of the risk parameters associated with those covariates than does pooling within strata defined only by the outcome. We review the approach to set‐based analysis through offsets developed by Weinberg and Umbach in a recent correction to their original paper. We propose a method for variance estimation under this design and use simulations and a real‐data example to illustrate the precision benefits of (y,c)‐pooling relative to y‐pooling. We also note and illustrate that set‐based models permit estimation of covariate interactions with exposure.
CDK1 and PLK1 coordinate the disassembly and reassembly of the nuclear envelope in vertebrate mitosis

Micronuclei (MN) arise from chromosomes or fragments that fail to be incorporated into the primary nucleus after cell division. These structures are a major source of genetic instability caused by DNA repair and replication defects coupled to aberrant Nuclear Envelope (NE). These problems ultimately lead to a spectrum of chromosome rearrangements called chromothripsis, a phenomenon that is a hallmark of several cancers. Despite its importance, the molecular mechanism at the origin of this instability is still not understood. Here we show that lagging chromatin, although it can efficiently assemble Lamin A/C, always fails to recruit Nuclear Pore Complexes (NPCs) proteins and that Polo-Like Kinase (PLK1) negatively regulates the NPC assembly. We also provide evidence for the requirement of PLK1 activity for the disassembly of NPCs, but not Lamina (A/C), at mitotic entry. Altogether this study reveals the existence of independent regulatory pathways for Lamin A/C and NPC reorganization during mitosis where Lamin A targeting to the chromatin is controlled by CDK1 activity (a clock-based model) while the NPC loading is also spatially monitored by PLK1.
On the Sublinear Convergence of Randomly Perturbed Alternating Gradient Descent to Second Order Stationary Solutions

The alternating gradient descent (AGD) is a simple but popular algorithm which has been applied to problems in optimization, machine learning, data ming, and signal processing, etc. The algorithm updates two blocks of variables in an alternating manner, in which a gradient step is taken on one block, while keeping the remaining block fixed. When the objective function is nonconvex, it is well-known the AGD converges to the first-order stationary solution with a global sublinear rate. In this paper, we show that a variant of AGD-type algorithms will not be trapped by "bad" stationary solutions such as saddle points and local maximum points. In particular, we consider a smooth unconstrained optimization problem, and propose a perturbed AGD (PA-GD) which converges (with high probability) to the set of second-order stationary solutions (SS2) with a global sublinear rate. To the best of our knowledge, this is the first alternating type algorithm which takes $\mathcal{O}(\text{polylog}(d)/\epsilon^{7/3})$ iterations to achieve SS2 with high probability [where polylog$(d)$ is polynomial of the logarithm of dimension $d$ of the problem].
The Macrophage Mannose Receptor Regulate Mannan-Induced Psoriasis, Psoriatic Arthritis, and Rheumatoid Arthritis-Like Disease Models

The injection of mannan into mice can result in the development of psoriasis (Ps) and psoriatic arthritis (PsA), whereas co-injection with antibodies toward collagen type II leads to a chronic rheumatoid-like arthritis. The critical event in all these diseases is mannan-mediated activation of macrophages, causing more severe disease if the macrophages are deficient in neutrophil cytosolic factor 1 (Ncf1), i.e., lack the capacity to make a reactive oxygen species (ROS) burst. In this study, we investigated the role of one of the receptors binding mannan; the macrophage mannose receptor (MR, CD206). MR is a C-type lectin present on myeloid cells and lymphatics. We found that mice deficient in MR expression had more severe mannan-induced Ps, PsA as well as rheumatoid-like arthritis. Interestingly, the MR-mediated protection was partly lost in Ncf1 mutated mice and was associated with an type 2 macrophage expansion. In conclusion, these results show that MR protects against a pathogenic inflammatory macrophage response induced by mannan and is associated with induction of ROS.
On falsification of the binary instrumental variable model

SUMMARY Instrumental variables are widely used for estimating causal effects in the presence of unmeasured confounding. The discrete instrumental variable model has testable implications for the law of the observed data. However, current assessments of instrumental validity are typically based solely on subject-matter arguments rather than these testable implications, partly due to a lack of formal statistical tests with known properties. In this paper, we develop simple procedures for testing the binary instrumental variable model. Our methods are based on existing techniques for comparing two treatments, such as the \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{upgreek} \usepackage{mathrsfs} \setlength{\oddsidemargin}{-69pt} \begin{document} }{}$t$\end{document}-test and the Gail–Simon test. We illustrate the importance of testing the instrumental variable model by evaluating the exogeneity of college proximity using the National Longitudinal Survey of Young Men.
Adaptive Routing and Recharging Policies for Electric Vehicles

Planning a trip with an electric vehicle requires consideration of both battery dynamics and the availability of charging infrastructure. Recharging costs for an electric vehicle, which increase as the battery’s charge level increases, are fundamentally different than refueling costs for conventional vehicles, which do not depend on the amount of fuel already in the tank. Furthermore, the viability of any route requiring recharging is sensitive to the availability of charging stations along the way. In this paper, we study the problem of finding an optimal adaptive routing and recharging policy for an electric vehicle in a network. Each node in the network represents a charging station and has an associated probability of being available at any point in time or occupied by another vehicle. We develop efficient algorithms for finding an optimal a priori routing and recharging policy and then present solution approaches to an adaptive problem that build on a priori policy. We present two heuristic methods f.
Contribution of Neural Elements to Thoracic Stability.

AIM Studies of spinal biomechanics typically do not focus on the contributions to range of motion (ROM) of the primary components of the spinal canal, dura, arachnoid, pia, spinal cord, nerve roots, ligaments, and vessels. We sought to determine the stability offered by these soft tissues in vitro. MATERIAL AND METHODS Human cadaveric segments were tested intact, after osteoligamentous destabilization, and after transection of T8-9 spinal canal components. Specimens were induced into flexion, extension, axial rotation, and lateral bending using non-constraining, non-destructive pure moment while tracking motion response stereophotogrammetrically. The range of motion (ROM) was compared in each condition after adjusting for soft tissue creep. RESULTS After spinal canal element transection, ROM increased in all directions (mean 4.7%). This increase was most pronounced during lateral bending (p=0.055). The cumulative ROM from all directions of loading showed a statistically significant mean increase of 3.3% (p=0.040). CONCLUSION Sectioning of canal elements was found to cause a measurable increase in ROM. Although nonviable tissues were tested, living tissues are also likely to contribute to spinal stability.
Distributed Anomaly Detection Using Minimum Volume Elliptical Principal Component Analysis

Principal component analysis and the residual error is an effective anomaly detection technique. In an environment where anomalies are present in the training set, the derived principal components can be skewed by the anomalies. A further aspect of anomaly detection is that data might be distributed across different nodes in a network and their communication to a centralized processing unit is prohibited due to communication cost. Current solutions to distributed anomaly detection rely on a hierarchical network infrastructure to aggregate data or models; however, in this environment, links close to the root of the tree become critical and congested. In this paper, an algorithm is proposed that is more robust in its derivation of the principal components of a training set containing anomalies. A distributed form of the algorithm is then derived where each node in a network can iterate towards the centralized solution by exchanging small matrices with neighboring nodes. Experimental evaluations on both synthetic and real-world data sets demonstrate the superior performance of the proposed approach in comparison to principal component analysis and alternative anomaly detection techniques. In addition, it is shown that in a variety of network infrastructures, the distributed form of the anomaly detection model is able to derive a close approximation of the centralized model.
Extended diversity analysis of cultivated grapevine Vitis vinifera with 10K genome-wide SNPs

Grapevine is a very important crop species that is mainly cultivated worldwide for fruits, wine and juice. Identification of the genetic bases of performance traits through association mapping studies requires a precise knowledge of the available diversity and how this diversity is structured and varies across the whole genome. An 18k SNP genotyping array was evaluated on a panel of Vitis vinifera cultivars and we obtained a data set with no missing values for a total of 10207 SNPs and 783 different genotypes. The average inter-SNP spacing was ~47 kbp, the mean minor allele frequency (MAF) was 0.23 and the genetic diversity in the sample was high (He = 0.32). Fourteen SNPs, chosen from those with the highest MAF values, were sufficient to identify each genotype in the sample. Parentage analysis revealed 118 full parentages and 490 parent-offspring duos, thus confirming the close pedigree relationships within the cultivated grapevine. Structure analyses also confirmed the main divisions due to an eastern-western gradient and human usage (table vs. wine). Using a multivariate approach, we refined the structure and identified a total of eight clusters. Both the genetic diversity (He, 0.26–0.32) and linkage disequilibrium (LD, 28.8–58.2 kbp) varied between clusters. Despite the short span LD, we also identified some non-recombining haplotype blocks that may complicate association mapping. Finally, we performed a genome-wide association study that confirmed previous works and also identified new regions for important performance traits such as acidity. Taken together, all the results contribute to a better knowledge of the genetics of the cultivated grapevine.
COPPER MOBILITY IN SOILS AS AFFECTED BY SEWAGE SLUDGE AND LOW MOLECULAR WEIGHT ORGANIC ACIDS

Copper is an essential micronutrient, but at increased concentrations, it quickly becomes toxic to plants, and remediation is needed. Because the land disposal of copper containing sewage sludge is increasing each year, there is a need to evaluate the mobility of copper in soil as affected by sewage sludge and low molecular weight organic acids (citric acid and oxalic acid). Copper mobility was studied in a Marvyn soil (fine-loamy, siliceous, subactive, thermic, Typic Kanhapludult) without or with 1 of 2 sewage sludges from the Birmingham, Alabama area. A total of 5 column experiments were performed. The columns were leached with solutions containing potassium sulfate (10−2 M/L) to maintain proper ionic strength, in addition to different combinations of copper, oxalic acid, and citric acid. The Cu2+ concentration in all applied solutions was 1000 mg Cu2+ per kg of solution. In the column experiments containing sewage sludge, the effluent copper concentration did not reach the influent concentration. In the column experiments without sewage sludge, the influent copper concentrations were easily reached in the effluent, independent of the addition of oxalic or citric acid. A batch equilibrium study showed that both sewage sludges could adsorb more than 50,000 mg of copper per kilogram of sewage sludge, compared with 1250 mg of copper per kilogram of Marvyn soil. This amount is so high that sewage sludges could possibly be used for copper detoxification in mine tailings or farm lands where copper pollution is a potential problem for vegetation.
Modification of Silicone Elastomers Using Silicone Comonomers Containing Hydrophilic Surface Active Endgroups

A facile technique was developed for a long-term increase in silicone elastomer surface hydrophilicity, eliminating the need for post-cure surface treatment (e.g. oxygen plasma or surface grafting). Well-defined silicones (1-4 kDa) with a central vinyl functionality and discrete PEG 2 , PEG 3 and tetrahydrofurfuryl (THF) pendant endgroups were synthesized, characterized and used as comonomers in addition-cure, platinum catalyzed 2-part silicone elastomer formulations. The modified silicone elastomers were optically clear and maintained the mechanical performance characteristic of this class of material with up to 20 wt. % comonomer in the 2-part formulation. Contact angle measurements of deionized water on the silicone elastomer surface showed improved wettability with comonomer content. The elastomer surface shifted from hydrophobic (contact angle ~120 o C) to hydrophilic (contact angle 5 months). Coefficient of friction measurements of the modified silicone elastomers revealed an increase in surface lubricity with comonomer loadings.
Low-Cost Nested-MIMO Array for Large-Scale Wireless Sensor Applications

In modern communication and radar applications, large-scale sensor arrays have increasingly been used to improve the performance of a system. However, the hardware cost and circuit power consumption scale linearly with the number of sensors, which makes the whole system expensive and power-hungry. This paper presents a low-cost nested multiple-input multiple-output (MIMO) array, which is capable of providing O(2N2) degrees of freedom (DOF) with O(N) physical sensors. The sensor locations of the proposed array have closed-form expressions. Thus, the aperture size and number of DOF can be predicted as a function of the total number of sensors. Additionally, with the help of time-sequence-phase-weighting (TSPW) technology, only one receiver channel is required for sampling the signals received by all of the sensors, which is conducive to reducing the hardware cost and power consumption. Numerical simulation results demonstrate the effectiveness and superiority of the proposed array.