Miracle-dz/UniFAR-FTUs huggingface dataset:
DTH8 overexpression induces early flowering, boosts yield, and improves stress recovery in rice cv IR64.

Rice yield and heading date are the two discrete traits controlled by quantitative trait loci (QTLs). Both traits are influenced by the genetic make-up of the plant as well as the environmental factors where it thrives. Drought and salinity adversely affect crop productivity in many parts of the world. Tolerance to these stresses is multigenic and complex in nature. In this study, we have characterized a QTL, DTH8 (Days to heading) from Oryza sativa L. cv IR64 that encodes a putative HAP3/NF-YB/CBF subunit of CCAAT-box binding protein (HAP complex). We demonstrate DTH8 to be positively influencing the yield, heading date, and stress tolerance in IR64. DTH8 up-regulates the transcription of RFT1, Hd3a, GHD7, MOC1, and RCN1 in IR64 at the pre-flowering stage and plays a role in early flowering increased number of tillers, enhanced panicle branching, and improved tolerance towards drought and salinity stress at the reproductive stage. The presence of DTH8 binding elements (CCAAT) in the promoter regions of all of these genes, predicted by in silico analysis of the promoter region, indicates the regulation of their expression by DTH8. In addition, DTH8 overexpressing transgenic lines showed favourable physiological parameters causing less yield penalty under stress than the WT plants. Taken together, DTH8 is a positive regulator of the network of genes related to early flowering/heading, higher yield, as well as salinity and drought stress tolerance, thus, enabling the crops to adapt to a wide range of climatic conditions. This article is protected by copyright. All rights reserved.
LncRNA NEAT1 affects endometrial receptivity by regulating HOXA10 promoter activity

ABSTRACT In vitro fertilization and embryo transfer (IVF-ET) is one of the effective methods to treat female infertility. Poor endometrial receptivity (ER) is an important factor leading to embryo implantation dysfunction, which can reduce pregnancy rate of IVF-ET. The mice model with embryo implantation dysfunction in vivo and attachment model of trophoblast (JAR) spheroids in vitro were constructed. The levels of lncRNA NEAT1, HOXA10, CTCF and markers of ER were detected. The cell proliferation was measured. The interaction between lncRNA NEAT1 and CTCF, HOXA10 promoter and CTCF were confirmed. LncRNA NEAT1 and HOXA10 levels in infertile patients and mice model with embryo implantation dysfunction were increased. In vitro experiments showed that down-regulation of lncRNA NEAT1 improved EECs proliferation and ER marker expressions. LncRNA NEAT1 could bind to CTCF, and CTCF could bind to HOXA10 promoter and down-regulate HOXA10 gene expression by regulating histone modification level. The lncRNA NEAT1/CTCF/HOXA10 signaling pathway regulated EECs proliferation and ER establishment in vitro and in vivo. Our study suggested that lncRNA NEAT1 could up-regulate HOXA10 promoter activity and its expression by combining with CTCF, thus improving EECs proliferation and ER establishment, and ultimately facilitating embryo implantation.
Separation of Heart and Lung-related Signals in Electrical Impedance Tomography Using Empirical Mode Decomposition

Background: Electrical impedance tomography (EIT) can be used for continuous monitoring of pulmonary ventilation. However, no proper method has been developed for the separation of pulmonary ventilation and perfusion signals and the measurement of the associated ventilation/perfusion (V/Q) ratio. Previously, various methods have been used to extract these components; however, these have not been able to effectively separate and validate cardiac- and pulmonary-related images. Aims: This study aims at validating and developing a novel method to separate cardiac- and pulmonary-related components based on the EIT simulation field of view and to simultaneously reconstruct the individual images instantly. Methods: Our approach combines the advantages of the principal component analysis (PCA) and processes that originally measure EIT data instead of handling a series of EIT images, thus introducing the empirical mode decomposition (EMD). The PCA template functions for cardiac-related imaging and intrinsic mode functions (IMFs) of EMD for lung-related imaging are then adapted to input signals. Results: The proposed method enables the separation of cardiac- and lung-related components by adjusting the proportion of the key components related to lung imaging, which are the fourth component (PC4) and the first component (IMF1) in PCA- and EMD-based methods, respectively. The preliminary results on the application of the method to real human EIT data revealed the consistently better performance and optimal computation compared with previous methods. Conclusion: This study proposes a novel method for applying EIT to evaluate the best time of V/Q matching on the cardiovascular and respiratory systems; this aspect can be investigated in future research.
Analyzing the economic benefits and costs of smart growth strategies

California’s Senate Bill 375, (Chapter 728, Statutes of 2008), aims to reduce transportationrelated greenhouse gas emissions through more efficient patterns of land development. Advocates claim these smart growth policies will reduce vehicle travel while benefitting residents, cities, and regions in the form of more attractive communities, more affordable housing, and healthier municipal finances. In this study, we analyzed the economic impacts of existing smart growth plans similar to those currently being considered and adopted throughout metropolitan California. Through five case studies of neighborhood-level plans already implemented in California, we examined the effects of smart growth interventions on residential development, commercial development, municipal budgets, and vehicle travel. We used a combination of quantitative and qualitative methods to estimate the net benefits and costs from the regional, municipal, and household perspectives. We found the plans, in most cases, produced net benefits for the stakeholders considered. The benefits emerged from plans that resulted in denser development in relatively central locations with good access to transit. However, in some cases the plans produced costs, and impacts were not evenly distributed. The research suggests smart growth policies can produce benefits, but planners must be aware of potential costs.
Genetic and Phenotypic Study of the Pectobacterium versatile Beta-Lactamase, the Enzyme Most Similar to the Plasmid-Encoded TEM-1

This study aimed to compare the chromosomal beta-lactamase from Pectobacterium versatile, PEC-1, with the well-known and globally distributed TEM-1 in terms of genetic and functional properties. Despite the similarities between the enzymes, we obtained no definitive proof of gene transfer for the emergence of blaPEC-1 from blaTEM-1. ABSTRACT Genus Pectobacterium bacteria include important agricultural pathogens. Pectobacterium versatile isolates contain a chromosome-borne beta-lactamase, PEC-1. This enzyme is the closest relative of TEM-1, a plasmid-borne beta-lactamase widespread in the Enterobacterales. We performed bioinformatics and phenotypic analyses to investigate the genetic and phenotypic features of PEC-1 and its frequency and ability to spread within genus Pectobacterium. We also compared the characteristics of PEC-1 and TEM-1 and evaluated the likelihood of transfer. We found that blaPEC-1 was present principally in a small number of genetic environments in P. versatile. Identical blaPEC-1 genetic environments were present in closely related species, consistent with the high frequency of genetic exchange within the genus Pectobacterium. Despite the similarities between PEC-1 and TEM-1, their genetic environments displayed no significant identity, suggesting an absence of recent transfer. Phenotypic analyses on clonal constructs revealed similar hydrolysis spectra. Our results suggest that P. versatile is the main reservoir of PEC-1, which seems to transfer to closely related species. The genetic distance between PEC-1 and TEM-1, and the lack of conserved elements in their genetic environments, suggest that any transfer that may have occurred must have taken place well before the antibiotic era. IMPORTANCE This study aimed to compare the chromosomal beta-lactamase from Pectobacterium versatile, PEC-1, with the well-known and globally distributed TEM-1 in terms of genetic and functional properties. Despite the similarities between the enzymes, we obtained no definitive proof of gene transfer for the emergence of blaPEC-1 from blaTEM-1. Indeed, given the limited degree of sequence identity and the absence of a common genetic environment, it seems unlikely that any transfer of this gene has occurred recently. However, although blaPEC-1 was found mostly in one specific clade of the P. versatile species, certain isolates from other closely related species, such as Pectobacterium brasiliense and Pectobacterium polaris, may also carry this gene inserted into common genetic environments. This observation suggests that genetic exchanges are frequent, accounting for the diffusion of blaPEC-1 between isolates from different Pectobacterium species and, potentially, to exogenous mobile genetic elements.
Genome Sequence of Campylobacter Strain 19-13652, Isolated from Breeding Pheasants

We report the whole-genome sequence of a Campylobacter strain that was isolated from breeding pheasants presenting “bulgy eyes” in Italy. Traditional molecular typing methods did not return any reliable result. Whole-genome sequencing and sequence comparison with known genomes did not meet the criteria for assignment to an existing species. ABSTRACT We report the whole-genome sequence of a Campylobacter strain that was isolated from breeding pheasants presenting “bulgy eyes” in Italy. Traditional molecular typing methods did not return any reliable result. Whole-genome sequencing and sequence comparison with known genomes did not meet the criteria for assignment to an existing species.
Fictitious Play and Best-Response Dynamics in Identical Interest and Zero-Sum Stochastic Games

This paper combines ideas from Q-learning and fictitious play to define three reinforcement learning procedures which converge to the set of stationary mixed Nash equilibria in identical interest discounted stochastic games. First, we analyse three continuous-time systems that generalize the best-response dynamics defined by Leslie et al. for zero-sum discounted stochastic games. Under some assumptions depending on the system, the dynamics are shown to converge to the set of stationary equilibria in identical interest discounted stochastic games. Then, we introduce three analog discrete-time procedures in the spirit of Sayin et al. and demonstrate their convergence to the set of stationary equilibria using our results in continuous time together with stochastic approximation techniques. Some numerical experiments complement our theoretical findings.
Hardware Discussion of a MIMO Wireless Communication System Using Orthogonal Space Time Block Codes

Although multiple-input multiple-output (MIMO) systems have become increasingly popular, the existence of real time results to compare with those predicted by theory is still surprisingly limited. In this work the hardware description of a MIMO wireless communication system using orthogonal space time block codes (OSTBC) is discussed for two antennas at both the transmitter and receiver. A numerical example for a frequency flat time correlated channel is given to show the impact of channel estimation.
Benefits of collocating vertical-axis and horizontal-axis wind turbines in large wind farms

In this study, we address the benefits of a vertically staggered (VS) wind farm, in which vertical-axis and horizontal-axis wind turbines are collocated in a large wind farm. The case study consists of 20 small vertical-axis turbines added around each large horizontal-axis turbine. Large-eddy simulation is used to compare power extraction and flow properties of the VS wind farm versus a traditional wind farm with only large turbines. The VS wind farm produces up to 32% more power than the traditional one, and the power extracted by the large turbines alone is increased by 10%, caused by faster wake recovery from enhanced turbulence due to the presence of the small turbines. A theoretical analysis based on a top-down model is performed and compared with the large-eddy simulation. The analysis suggests a nonlinear increase of total power extraction with increase of the loading of smaller turbines, with weak sensitivity to various parameters, such as size, and type aspect ratio, and thrust coefficient of the vertical-axis turbines. We conclude that vertical staggering can be an effective way to increase energy production in existing wind farms. Copyright © 2016 John Wiley & Sons, Ltd.
On-line parameter identification of SPM motors based on MRAS technique

ABSTRACT This article proposes a new parameter estimation method for surface-mounted permanent magnet (SPM) motors by employing the model reference adaptive system (MRAS) technique. The proposed algorithm is applied to an SPM motor used in washing machines. To determine washing and dewatering patterns, a washer tries to detect the size of load in the beginning of the operation. Hence it requires an accurate estimation of system parameters. The proposed estimation method identifies stator inductance and flux-linkage by using d- or q-axis current error, and its value is used for estimation independently with respect to each parameter. Therefore, the proposed scheme can get rid of the instability in inductance and flux estimation caused by the cross-coupling between d- and q- quantities. In this article, the stator resistance is detected by using the recursive least square (RLS) method to reduce measurement noises and to eliminate dead-time effect. Simulation results show that the proposed scheme tracks the parameters well even when there is transient states in rotor speed and the load conditions, and experimental results verify the validity and efficacy of the proposed algorithm.
Detecting Rogue Access Points Using Client-agnostic Wireless Fingerprints

The broadcast nature of wireless media makes WLANs easily attacked by rogue Access Points (APs). Rogue AP attacks can potentially cause severe privacy leakage and financial loss. Hardware fingerprinting is the state-of-the-art technology to detect rogue APs since an attacker would find it difficult to set up a rogue AP with specific hardware fingerprints. However, existing hardware fingerprints not only depend on the AP but also depend on the client, significantly limiting their application scenarios. In this work, we investigate two novel client-agnostic fingerprints, which can be extracted using commercial off-the-shelf WiFi devices, to detect rogue APs. One is the power amplifier non-linearity fingerprint and the other is the frame interval distribution fingerprint. These two fingerprints remain consistent over time and space for the same AP but vary across different APs even with the same brand, model, and firmware. We use the fingerprint similarity between the candidate AP and the authorized AP for device authentication in typical indoor environments. We have also proposed a threshold-improved authentication scheme to improve the robustness of our system in dynamic environments. Our schemes can be implemented without modifying the infrastructural APs and can work well with new clients without rebuilding the fingerprint database. We evaluate our scheme in both in-lab and field scenarios, by analyzing 18 million WiFi packets. Results show that our scheme achieves an overall 96.55% positive detection rate and a 4.31% false alarm rate. Moreover, the threshold-improved authentication scheme can further reduce the false alarm rate by 13.0%-44.8% for dynamic environments.
Picking winners in cell-cell collisions: wetting, speed, and contact

Groups of eukaryotic cells can coordinate their crawling motion to follow cues more effectively, stay together, or invade new areas. This collective cell migration depends on cell-cell interactions, which are often studied by colliding pairs of cells together. Can the outcome of these collisions be predicted? Recent experiments on trains of colliding epithelial cells suggest that cells with a smaller contact angle to the surface or larger speeds are more likely to maintain their direction (“win”) upon collision. When should we expect shape or speed to correlate with the outcome of a collision? We build a model for two-cell collisions within the phase field approach, which treats cells as deformable objects. We can reproduce the observation that cells with high speed and small contact angles are more likely to win with two different assumptions for how cells interact: (1) velocity-aligning, in which we hypothesize that cells sense their own velocity and align to it over a finite timescale, and (2) front-front contact repolarization, where cells polarize away from cell-cell contact, akin to contact inhibition of locomotion. Surprisingly, though we simulate collisions between cells with widely varying properties, in each case, the probability of a cell winning is completely captured by a single summary variable: its relative speed (in the velocity-aligning model) or its relative contact angle (in the contact repolarization model). Both models are currently consistent with reported experimental results, but they can be distinguished by varying cell contact angle and speed through orthogonal perturbations.
Identification of Fusarium Head Blight Resistance in Triticum timopheevii Accessions and Characterization of Wheat-T. timopheevii Introgression Lines for Enhanced Resistance

A diverse panel of wheat wild relative species was screened for resistance to Fusarium head blight (FHB) by spray inoculation. The great majority of species and accessions were susceptible or highly susceptible to FHB. Accessions of Triticum timopheevii (P95-99.1-1), Agropyron desertorum (9439957) and Elymus vaillantianus (531552) were highly resistant to FHB while additional accessions of T. timopheevii were found to be susceptible to FHB. A combination of spray and point inoculation assessments over two consecutive seasons indicated that the resistance in accession P95-99.1-1 was due to enhanced resistance to initial infection of the fungus (type 1 resistance), and not to reduction in spread (type 2 resistance). A panel of wheat-T. timopheevii (accession P95-99.1-1) introgression lines was screened for FHB resistance over two consecutive seasons using spray inoculation. Most introgression lines were similar in susceptibility to FHB as the wheat recipient (Paragon) but substitution of the terminal portion of chromosome 3BS of wheat with a similar-sized portion of 3G of T. timopheevii significantly enhanced FHB resistance in the wheat background.
Doublecortin-Like Kinase 1 Facilitates Dendritic Spine Growth of Pyramidal Neurons in Mouse Prefrontal Cortex

The L1 cell adhesion molecule NrCAM (Neuron-glia related cell adhesion molecule) functions as a co-receptor for secreted class 3 Semaphorins to prune subpopulations of dendritic spines on apical dendrites of pyramidal neurons in the developing mouse neocortex. The developing spine cytoskeleton is enriched in actin filaments but a small number of microtubules have been shown to enter the spine apparently trafficking vesicles to the membrane. Doublecortin-like kinase 1 (DCLK1) is a member of the Doublecortin (DCX) family of microtubule-binding proteins with serine/threonine kinase activity. To determine if DCLK1 plays a role in spine remodeling, we generated a tamoxifen-inducible mouse line (Nex1Cre-ERT2: DCLK1flox/flox : RCE) to delete microtubule binding isoforms of DCLK1 from pyramidal neurons during postnatal stages of spine development. Homozygous DCLK1 conditional mutant mice exhibited decreased spine density on apical dendrites of pyramidal neurons in the prefrontal cortex (layer 2/3). Mature mushroom spines were selectively decreased upon DCLK1 deletion but dendritic arborization was unaltered. Mutagenesis and binding studies revealed that DCLK1 bound NrCAM at the conserved FIGQY1231 motif in the NrCAM cytoplasmic domain, a known interaction site for the actin-spectrin adaptor Ankyrin. These findings demonstrate that DCLK1 facilitates spine growth and maturation on cortical pyramidal neurons in the mouse prefrontal cortex potentially through microtubule and NrCAM interactions.
Expression and subcellular localization of USH1C/harmonin in human retina provides insights into pathomechanisms and therapy

Abstract Usher syndrome (USH) is the most common form of hereditary deaf-blindness in humans. USH is a complex genetic disorder, assigned to three clinical subtypes differing in onset, course and severity, with USH1 being the most severe. Rodent USH1 models do not reflect the ocular phenotype observed in human patients to date; hence, little is known about the pathophysiology of USH1 in the human eye. One of the USH1 genes, USH1C, exhibits extensive alternative splicing and encodes numerous harmonin protein isoforms that function as scaffolds for organizing the USH interactome. RNA-seq analysis of human retinae uncovered harmonin_a1 as the most abundant transcript of USH1C. Bulk RNA-seq analysis and immunoblotting showed abundant expression of harmonin in Müller glia cells (MGCs) and retinal neurons. Furthermore, harmonin was localized in the terminal endfeet and apical microvilli of MGCs, presynaptic region (pedicle) of cones and outer segments (OS) of rods as well as at adhesive junctions between MGCs and photoreceptor cells (PRCs) in the outer limiting membrane (OLM). Our data provide evidence for the interaction of harmonin with OLM molecules in PRCs and MGCs and rhodopsin in PRCs. Subcellular expression and colocalization of harmonin correlate with the clinical phenotype observed in USH1C patients. We also demonstrate that primary cilia defects in USH1C patient-derived fibroblasts could be reverted by the delivery of harmonin_a1 transcript isoform. Our studies thus provide novel insights into PRC cell biology, USH1C pathophysiology and development of gene therapy treatment(s).
Concurrent spinal and brain imaging with optically pumped magnetometers

The spinal cord and its interactions with the brain are fundamental for movement control and somatosensation. However, brain and spinal cord electrophysiology in humans have largely been treated as distinct enterprises, in part due to the relative inaccessibility of the spinal cord. Consequently, there is a dearth of knowledge on human spinal electrophysiology, including the multiple pathologies of the central nervous system that affect the spinal cord as well as the brain. Here we exploit recent advances in the development of wearable optically pumped magnetometers (OPMs) which can be flexibly arranged to provide coverage of both the spinal cord and the brain concurrently in unconstrained environments. Our system for magnetospinoencephalography (MSEG) measures both spinal and cortical signals simultaneously by employing a custom-made spinal scanning cast. We evidence the utility of such a system by recording simultaneous spinal and cortical evoked responses to median nerve stimulation, demonstrating the novel ability for concurrent non-invasive millisecond imaging of brain and spinal cord.