Miracle-dz/UniFAR-FTUs huggingface dataset:
PICARA, an Analytical Pipeline Providing Probabilistic Inference about A Priori Candidates Genes Underlying Genome-Wide Association QTL in Plants

PICARA is an analytical pipeline designed to systematically summarize observed SNP/trait associations identified by genome wide association studies (GWAS) and to identify candidate genes involved in the regulation of complex trait variation. The pipeline provides probabilistic inference about a priori candidate genes using integrated information derived from genome-wide association signals, gene homology, and curated gene sets embedded in pathway descriptions. In this paper, we demonstrate the performance of PICARA using data for flowering time variation in maize – a key trait for geographical and seasonal adaption of plants. Among 406 curated flowering time-related genes from Arabidopsis, we identify 61 orthologs in maize that are significantly enriched for GWAS SNP signals, including key regulators such as FT (Flowering Locus T) and GI (GIGANTEA), and genes centered in the Arabidopsis circadian pathway, including TOC1 (Timing of CAB Expression 1) and LHY (Late Elongated Hypocotyl). In addition, we discover a regulatory feature that is characteristic of these a priori flowering time candidates in maize. This new probabilistic analytical pipeline helps researchers infer the functional significance of candidate genes associated with complex traits and helps guide future experiments by providing statistical support for gene candidates based on the integration of heterogeneous biological information.
Practical Private Range Search in Depth

We consider a data owner that outsources its dataset to an untrusted server. The owner wishes to enable the server to answer range queries on a single attribute, without compromising the privacy of the data and the queries. There are several schemes on “practical” private range search (mainly in database venues) that attempt to strike a trade-off between efficiency and security. Nevertheless, these methods either lack provable security guarantees or permit unacceptable privacy leakages. In this article, we take an interdisciplinary approach, which combines the rigor of security formulations and proofs with efficient data management techniques. We construct a wide set of novel schemes with realistic security/performance trade-offs, adopting the notion of Searchable Symmetric Encryption (SSE), primarily proposed for keyword search. We reduce range search to multi-keyword search using range-covering techniques with tree-like indexes, and formalize the problem as Range Searchable Symmetric Encryption (RSSE). We demonstrate that, given any secure SSE scheme, the challenge boils down to (i) formulating leakages that arise from the index structure and (ii) minimizing false positives incurred by some schemes under heavy data skew. We also explain an important concept in the recent SSE bibliography, namely locality, and design generic and specialized ways to attribute locality to our RSSE schemes. Moreover, we are the first to devise secure schemes for answering range aggregate queries, such as range sums and range min/max. We analytically detail the superiority of our proposals over prior work and experimentally confirm their practicality.
Transcriptomic analysis of gene cascades involved in protein kinase A and C signaling in the KGN line of human ovarian granulosa tumor cells

Abstract The developmental competence of an oocyte is its capacity to resume maturation, undergo successful fertilization, and reach the blastocyst stage. This competence is acquired through interaction with somatic cells of the follicle. Cumulus and granulosa cells support oocyte development, while the oocyte influences follicular cell growth and differentiation. Studies suggest that folliclestimulating hormone and luteinizing hormone play an essential role in oocyte competence acquisition through signaling initiated by protein kinases A and C (PKA and PKC) in granulosa cells. Using a microarray and RT-qPCR, the transcriptome of human granulosa-like tumor cells (KGN) treated for 24 h with forskolin (FSK) or phorbol 12-myristate 13-acetate (PMA) was analyzed to determine the effects of PKA and PKC stimulation on gene expression. Protein-kinase-driven signaling appeared to involve five major upstream regulators, namely epidermal growth factor (EGF), transforming growth factor beta 1 (TGFβ1), vascular endothelial growth factor (VEGF), basic fibroblast growth factor (FGF2), and hepatocyte growth factor (HGF). Gene associations with seven major ovarian functions were identified: Prostaglandin- endoperoxide synthase 2 (PTGS2), interleukin 8 (IL8), and interleukin 6 (IL6) with inflammation; Steroidogenic acute regulatory protein (STAR), cytochrome P450scc (CYP11A1), and cytochrome P450 family 19 subfamily Amember 1 (CYP19A1) with steroidogenesis; Vascular endothelial growth factor C (VEGFC), Vascular endothelial growth factor A (VEGFA), and C-X-C chemokine receptor type 4 (CXCR4) with angiogenesis; Amphiregulin (AREG), epidermal growth factor receptor (EGFR), and sprouty RTK signaling antagonist 2 (SPRY2) with differentiation, BCL2 associated X (BAX), BCL2 like 12 (BCL2L12), and caspase 1(CASP1) with apoptosis, Cyclin D1 (CCND1), cyclin B1 (CCNB1), and cyclin B2 (CCNB2) with division; and Matrix metalloproteinase-1 (MMP1), Matrix metallopeptidase 9 (MMP9), and TIMP metallopeptidase inhibitor 1 (TIMP1) with ovulation. Overall, these results indicate that signaling via both PKA and PKC potentiates gene regulation of functions such as inflammation and apoptosis, while functions such as differentiation, ovulation and angiogenesis are partial to one kinase or the other. These results improve understanding of the pathways underlying the most important changes that occur in the follicle prior to ovulation. Summary Sentence Protein kinase A and C signaling pathways play an important role in various major functions of ovarian follicle development such as cell differentiation, final maturation, luteinization, and ovulation.
Inhibition of nuclear factor of activated T cells (NFAT) c3 activation attenuates acute lung injury and pulmonary edema in murine models of sepsis

Specific therapies targeting cellular and molecular events of sepsis induced Acute Lung Injury (ALI) pathogenesis are lacking. We have reported a pivotal role for Nuclear Factors of Activated T cells (NFATc3) in regulating macrophage phenotype during sepsis induced ALI and subsequent studies demonstrate that NFATc3 transcriptionally regulates macrophage CCR2 and TNFα gene expression. Mouse pulmonary microvascular endothelial cell monolayer maintained a tighter barrier function when co-cultured with LPS stimulated NFATc3 deficient macrophages whereas wild type macrophages caused leaky monolayer barrier. More importantly, NFATc3 deficient mice showed decreased neutrophilic lung inflammation, improved alveolar capillary barrier function, arterial oxygen saturation and survival benefit in lethal CLP sepsis mouse models. In addition, survival of wild type mice subjected to the lethal CLP sepsis was not improved with broad-spectrum antibiotics, whereas the survival of NFATc3 deficient mice was improved to 40–60% when treated with imipenem. Passive adoptive transfer of NFATc3 deficient macrophages conferred protection against LPS induced ALI in wild type mice. Furthermore, CP9-ZIZIT, a highly potent, cell-permeable peptide inhibitor of Calcineurin inhibited NFATc3 activation. CP9-ZIZIT effectively reduced sepsis induced inflammatory cytokines and pulmonary edema in mice. Thus, this study demonstrates that inhibition of NFATc3 activation by CP9-ZIZIT provides a potential therapeutic option for attenuating sepsis induced ALI/pulmonary edema.
Assessing the Risk of Establishment of Rhagoletis cerasi (Diptera: Tephritidae) in the United States and Globally

Abstract The European cherry fruit fly, Rhagoletis cerasi (L.) (Diptera: Tephritidae), is a highly destructive pest of cherries (Prunus spp.) (Rosaceae) in Europe and Asia. In 2016, R. cerasi was detected in Ontario, Canada, and in 2017 in New York State, USA, the first records of this pest in North America.The initial detections in Canada caused concern for the major cherry-growing states of Michigan, Washington, Oregon, and California in the United States. Establishment of R. cerasi in the United States could restrict cherry exports to other markets and increase costs needed for fly control, but it is unknown if R. cerasi can establish in U.S. commercial cherry regions. Here, we used the CLIMEX ecological niche model to determine the risk of establishment of R. cerasi in the United States and globally. Within the United States under a no-irrigation scenario, R. cerasi would establish in the East and West Coasts; however, under an irrigation scenario, its distribution would expand to the major cherry-growing regions in the interior of central and eastern Washington and in California. Results also showed that if introduced, R. cerasi would likely establish in eastern China, Japan, the Koreas, Australia, New Zealand, South America, South Africa, Mexico, and Canada. Host plant (Prunus spp. and Lonicera spp. [Caprifoliaceae]) presence, although not included in models, would affect fly establishment. Our results stress the importance of surveying for R. cerasi to prevent its spread and establishment within the United States and other countries.
Point set registration based on multi-object metrics

In robotics and computer vision, point set registration is necessary in many tasks, for example in estimating the motion of a sensor/sensors between subsequent scans containing point/feature sets. Currently, the Iterated Closest Point (ICP) method and its variants have been presented as possible solutions to this problem. However most of these methods lack robustness when random spatial and detection errors are present. This is because ICP methods typically use an L2 metric as part of their optimization criteria, which is unable to penalize cardinality errors. Therefore, this article presents a registration technique based on the multi-object Optimal Sub-Pattern Assignment (OSPA) and Cardinalized Optimal Linear Assignment (COLA) metrics, which penalize data differences based on both cardinality and spatial errors. This allows scan registration to take place in the presence of both inter-scan translation and orientation as well as detection errors.
Two-Dimensional Whitening of Face Images for Improved PCA Performance

We address the problem of two-dimensional (2-D) whitening of face image matrices. The proposed method whitens the distribution of rows and columns of an image matrix. The main contribution of this letter is to investigate some aspects of recently published studies on this topic. We point out that existing methods on 2-D whitening for face recognition overlook the rows as potential random vectors, implying that the image matrix is only a collection of independent identically distributed column vectors. This study shows that this one-sided whitening approach relies on an incorrect assumption for image data. We show that one-sided whitening replaces the covariance matrix along one dimension with the identity matrix. Our proposed, truely 2-D, whitening transform does not enforce any such restriction on the row- or column-covariance matrices. A second contribution of our letter is to illustrate a method to confirm that the rows and columns of front-pose face images are in fact approximately normally distributed. This validation has not been addressed previously, although it plays a crucial role in deriving a linear whitening transform.
Evaluation Of Marginal Fit Of Castings Made With Nickel-chromium And Cobalt-chromium Alloys Using Varying Coats Of Die Spacers - A Laboratory Study

Objectives of the study: To study the marginal fit of artificial crowns made with two base metal alloys. To find out the effect of die-spacers on the fit of base metal alloy crowns. To evaluate comparatively the effect of number of coats of die-spacers with respect to marginal fit of crowns made with two base metal alloys. Materials and methods: For each alloy material 20 specimens were made. A standardized die was prepared and impressions were made with polyether elastomeric impression material and dies were made with die stone. Wax patters were made on the dies with varying coats of die spacer. The wax patters were invested and castings were made with 20 specimens using Ni-Cr alloy and 20 specimens using Co-Cr alloy. The marginal fit of crowns were evaluated with optical micro scope. Results: The mean and standard deviation of the marginal fit was calculated for castings made with NiCr alloy and castings made with Co-Cr alloy. It was found that maximum mean was with castings made with Co-Cr alloy and minimum with castings made with Ni-Cr alloy. Conclusion: Co-Cr alloy copings had lesser marginal fit when compared with copings of Ni-Cr alloy. Use of paint-on die spacer has the potential to ease insertion of coping without significantly affecting its marginal fit
Studies of modern Italian dog populations reveal multiple patterns for domestic breed evolution

Abstract Through thousands of years of breeding and strong human selection, the dog (Canis lupus familiaris) exists today within hundreds of closed populations throughout the world, each with defined phenotypes. A singular geographic region with broad diversity in dog breeds presents an interesting opportunity to observe potential mechanisms of breed formation. Italy claims 14 internationally recognized dog breeds, with numerous additional local varieties. To determine the relationship among Italian dog populations, we integrated genetic data from 263 dogs representing 23 closed dog populations from Italy, seven Apennine gray wolves, and an established dataset of 161 globally recognized dog breeds, applying multiple genetic methods to characterize the modes by which breeds are formed within a single geographic region. Our consideration of each of five genetic analyses reveals a series of development events that mirror historical modes of breed formation, but with variations unique to the codevelopment of early dog and human populations. Using 142,840 genome‐wide SNPs and a dataset of 1,609 canines, representing 182 breeds and 16 wild canids, we identified breed development routes for the Italian breeds that included divergence from common populations for a specific purpose, admixture of regional stock with that from other regions, and isolated selection of local stock with specific attributes.
An image-based uterus positioning interface using ADALINE networks for robot-assisted hysterectomy

Surgical manipulators are becoming more popular in modern operating theatres. Robots which work side-by-side with the surgeon and perform supportive tasks are one of the examples. However, how to allow the user to control the robot in a user-friendly manner is challenging. In this paper, we present our work on developing an image-based adaptive user interface to control a robot which assist in uterus positioning during laparoscopic hysterectomy for the hand-busy surgeon. The presented interface can be operated in two different modes, the pick and place mode, and the command specifying mode. Under the pick and place mode, the user specifies the desired starting point and ending point of the manipulation with his/her eyes and the robot drives automatically based on these points specified by the user; under the command specifying mode, the user specifies which joint and in which direction to move by looking at features of the laparoscopic monitor, then a driving command would be sent to the robot. Details of these two control approaches and the experimental results demonstrating how they work in uterus positioning are presented.
Uplink Co-Tier Interference Management in Femtocell Networks With Successive Group Decoding

We propose a new scheme to mitigate the uplink co-tier interference in dense femtocell networks, assuming that advanced receivers are employed by the femtocell base stations (FBSs). The conventional solution where interfering cells are assigned orthogonal spectrum resources leads to the inefficient spectrum usage. We exploit resource reuse by taking advantage of the successive group decoder (SGD) such that users can opportunistically access the entitled resources of nearby cells. The SGD decodes some interference signals in order to best decode the useful signal. Multi-cell uplink resource allocation with SGDs is formulated as a joint channel, rate and decoding group (CRG) allocation problem to maximize the weighted sum rates of the variable bit rate (VBR) users while meeting the rate requirements of the guaranteed bit rate (GBR) users. Due to the provable NP-hardness of the problem, we propose a greedy algorithm where the idea is to let GBR users opportunistically transmit on the channels of nearby cells and release more interference-free channels for high-rate transmission of VBR users. A semi-analytical framework is developed to provide a rough estimate of the potential throughput gain by the proposed technique. Simulation results show that the throughput gain over the conventional orthogonal resource allocation ranges from 10%-140% with different traffic proportion, number of users and rate requirement.
Complete mitochondrial genome sequence of Ussurian moose, Alces alces cameloides

Abstract Ussurian moose (Alces alces cameloides) in Northeast China, which is on the southmost edge of the species’ Eurasian range, are facing dramatic decline in population size and distribution areas. We undertook the first sequencing of the entire mitogenome of Ussurian moose, which is thought as the oldest moose subspecies to better understand the evolutionary history of this circumboreal sole extant species. The mitogenome is 16,418 bp in length, consisting of two ribosomal RNA (rRNA) genes, 22 transfer RNA (tRNA) genes, 13 protein-coding genes, and one control region. The overall base composition is A: 33.7%, T: 30.1%, C: 23.2%, and G: 13.0%, with a much higher A + T content. The phylogenetic tree of moose and 10 other most closely related Cervidae species was built.
miR-EdiTar: a database of predicted A-to-I edited miRNA target sites

MOTIVATION A-to-I RNA editing is an important mechanism that consists of the conversion of specific adenosines into inosines in RNA molecules. Its dysregulation has been associated to several human diseases including cancer. Recent work has demonstrated a role for A-to-I editing in microRNA (miRNA)-mediated gene expression regulation. In fact, edited forms of mature miRNAs can target sets of genes that differ from the targets of their unedited forms. The specific deamination of mRNAs can generate novel binding sites in addition to potentially altering existing ones. RESULTS This work presents miR-EdiTar, a database of predicted A-to-I edited miRNA binding sites. The database contains predicted miRNA binding sites that could be affected by A-to-I editing and sites that could become miRNA binding sites as a result of A-to-I editing. AVAILABILITY miR-EdiTar is freely available online at http://microrna.osumc.edu/mireditar. CONTACT alessandro.lagana@osumc.edu or carlo.croce@osumc.edu SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
FPGA synthesis of an stereo image matching architecture for autonomous mobile robots

This paper describes a hardware proposal to speed up the process of image matching in stereo vision systems like those employed by autonomous mobile robots. This proposal combines a classical window-based matching approach with a previous stage, where key points are selected from each image of the stereo pair. In this first step the key point extraction method is based on the SIFT algorithm. Thus, in the second step, the window-based matching is only applied to the set of selected key points, instead of to the whole images. For images with a 1 % of key points, this method speeds up the matching four orders of magnitude. This proposal is, on the one hand, a better parallelizable architecture than the original SIFT, and on the other, a faster technique than a full image windows matching approach. The architecture has been implemented on a lower power Virtex 6 FPGA and it achieves a image matching speed above 30 fps.
Using wide-area signals to improve the inter-area mode damping performance of static VAR compensators

A static VAR compensator (SVC) is an instrumental device in a flexible alternating current transmission system and was originally intended for voltage and reactive power control. SVCs with voltage input have poor oscillation damping performance and require both supplementary signals to effectively function in damping applications. The choice of an input signal and the design of a stabilizer exert considerable effects on the applicability and utility of SVC damping controllers. Accordingly, we identified the signal that serves as a excellent input for a damping controller by using the synthetic residue method. Given that a power system is likely to feature more than one inter-area oscillation mode, we designed a system damper on the basis of a single-input multi-output (SIMO) scheme. In other words, each oscillation mode was damped with one lead-lag controller to enable the appropriate handling of all modes. SIMO control parameters were designed using the phase compensator method. The results of a simulation conducted on a two-area power system showed that the proposed SVC damping controller exhibits improved oscillation damping
Interferon-Regulatory Factor 5-Dependent Signaling Restricts Orthobunyavirus Dissemination to the Central Nervous System

ABSTRACT Interferon (IFN)-regulatory factor 5 (IRF-5) is a transcription factor that induces inflammatory responses after engagement and signaling by pattern recognition receptors. To define the role of IRF-5 during bunyavirus infection, we evaluated Oropouche virus (OROV) and La Crosse virus (LACV) pathogenesis and immune responses in primary cells and in mice with gene deletions in Irf3, Irf5, and Irf7 or in Irf5 alone. Deletion of Irf3, Irf5, and Irf7 together resulted in uncontrolled viral replication in the liver and spleen, hypercytokinemia, extensive liver injury, and an early-death phenotype. Remarkably, deletion of Irf5 alone resulted in meningoencephalitis and death on a more protracted timeline, 1 to 2 weeks after initial OROV or LACV infection. The clinical signs in OROV-infected Irf5 −/− mice were associated with abundant viral antigen and terminal deoxynucleotidyltransferase-mediated dUTP-biotin nick end labeling (TUNEL)-positive cells in several regions of the brain. Circulating dendritic cell (DC) subsets in Irf5 −/− mice had higher levels of OROV RNA in vivo yet produced lower levels of type I IFN than wild-type (WT) cells. This result was supported by data obtained in vitro, since a deficiency of IRF-5 resulted in enhanced OROV infection and diminished type I IFN production in bone marrow-derived DCs. Collectively, these results indicate a key role for IRF-5 in modulating the host antiviral response in peripheral organs that controls bunyavirus neuroinvasion in mice. IMPORTANCE Oropouche virus (OROV) and La Crosse virus (LACV) are orthobunyaviruses that are transmitted by insects and cause meningitis and encephalitis in subsets of individuals in the Americas. Recently, we demonstrated that components of the type I interferon (IFN) induction pathway, particularly the regulatory transcription factors IRF-3 and IRF-7, have key protective roles during OROV infection. However, the lethality in Irf3 −/− Irf7 −/− (DKO) mice infected with OROV was not as rapid or complete as observed in Ifnar −/− mice, indicating that other transcriptional factors associated with an IFN response contribute to antiviral immunity against OROV. Here, we evaluated bunyavirus replication, tissue tropism, and cytokine production in primary cells and mice lacking IRF-5. We demonstrate an important role for IRF-5 in preventing neuroinvasion and the ensuing encephalitis caused by OROV and LACV.