Miracle-dz/UniFAR-FTUs huggingface dataset:
Proteomic Dissection of Seed Germination and Seedling Establishment in Brassica napus

The success of seed germination and establishment of a normal seedling are key determinants of plant species propagation. At present, only a few studies have focused on the genetic control of seed germination by using a proteomic approach in Brassica napus. In the present study, the protein expression pattern of seed germination was investigated using differential fluorescence two-dimensional gel electrophoresis in B. napus. One hundred and thirteen differentially expressed proteins (DEPs) that were mainly involved in storage (23.4%), energy metabolism (18.9%), protein metabolism (16.2%), defense/disease (12.6%), seed maturation (11.7%), carbohydrate metabolism (4.5%), lipid metabolism (4.5%), amino acids metabolism (3.6%), cell growth/division (3.6%), and some unclear functions (2.7%) were observed by proteomic analysis. Seventeen genes corresponding to 11 DEPs were identified within or near the associated linkage disequilibrium regions related to seed germination and vigor quantitative traits reported in B. napus in previous studies. The expression pattern of proteins showed that heterotrophic metabolism could be activated in the process of seed germination and that the onset of defense mechanisms might start during seed germination. These findings will help generate a more in-depth understanding of the mobilization of seed storage reserves and regulation mechanisms of the germination process in B. napus.
Optimizing Soft Vector Processing in FPGA-Based Embedded Systems

Soft vector processors can augment and extend the capability of FPGA-based embedded systems-on-chip such as the Xilinx Zynq. However, configuring and optimizing the soft processor for best performance is hard. We must consider architectural parameters such as precision, vector lane count, vector length, chunk size, and DMA scheduling to ensure efficient execution of code on the soft vector processing platform. To simplify the design process, we develop a compiler framework and an autotuning runtime that splits the optimization into a combination of static and dynamic passes that map data-parallel computations to the soft processor. We compare and contrast implementations running on the scalar ARM processor, the embedded NEON hard vector engine, and low-level streaming Verilog designs with the VectorBlox MXP soft vector processor. Across a range of data-parallel benchmarks, we show that the MXP soft vector processor can outperform other organizations by up to 4 × while saving ≈ 10% dynamic power. Our compilation and runtime framework is also able to outperform the gcc NEON vectorizer under certain conditions by explicit generation of NEON intrinsics and performance tuning of the autogenerated data-parallel code. When constrained by IO bandwidth, soft vector processors are even competitive with spatial Verilog implementations of computation.
Cytokinin Regulates the Activity of Reproductive Meristems, Flower Organ Size, Ovule Formation, and Thus Seed Yield in Arabidopsis thaliana[C][W][OA]

This work shows that the mutation of two cytokinin oxidase/dehydrogenases causes the formation of more and larger flowers and describes a previously undiscovered function of cytokinin in ovule-forming placenta tissue. Its findings support a central function of cytokinin in regulating reproductive meristems and highlight the relevance of sink strength in determining yield. The size and activity of the shoot apical meristem is regulated by transcription factors and low molecular mass signals, including the plant hormone cytokinin. The cytokinin status of the meristem depends on different factors, including metabolic degradation of the hormone, which is catalyzed by cytokinin oxidase/dehydrogenase (CKX) enzymes. Here, we show that CKX3 and CKX5 regulate the activity of the reproductive meristems of Arabidopsis thaliana. CKX3 is expressed in the central WUSCHEL (WUS) domain, while CKX5 shows a broader meristematic expression. ckx3 ckx5 double mutants form larger inflorescence and floral meristems. An increased size of the WUS domain and enhanced primordia formation indicate a dual function for cytokinin in defining the stem cell niche and delaying cellular differentiation. Consistent with this, mutation of a negative regulator gene of cytokinin signaling, ARABIDOPSIS HISTIDINE PHOSPHOTRANSFER PROTEIN 6, which is expressed at the meristem flanks, caused a further delay of differentiation. Terminal cellular differentiation was also retarded in ckx3 ckx5 flowers, which formed more cells and became larger, corroborating the role of cytokinin in regulating flower organ size. Furthermore, higher activity of the ckx3 ckx5 placenta tissue established supernumerary ovules leading to an increased seed set per silique. Together, the results underpin the important role of cytokinin in reproductive development. The increased cytokinin content caused an ~55% increase in seed yield, highlighting the relevance of sink strength as a yield factor.
Incidence, Secular Trends, and Outcomes of Prosthetic Joint Infection: A Population-Based Study, Olmsted County, Minnesota, 1969–2007

Context. The epidemiology of prosthetic joint infection (PJI) in a population-based cohort has not been studied in the United States. Objectives. To provide an accurate assessment of the true incidence, secular trends, clinical manifestations, microbiology, and treatment outcomes of PJI in a population-based cohort. Design. Historical cohort study. Setting. Olmsted County, Minnesota. Participants. Residents who underwent total knee arthroplasty (TKA) or total hip arthroplasty (THA) between January 1, 1969, and December 31, 2007. Methods. Incidence rates and trends in PJI were assessed using the Kaplan-Meier method and log-rank test, as were treatment outcomes among PJI case patients. Results. A total of 7,375 THAs or TKAs were implanted in residents of Olmsted County during the study period. Seventy-five discrete joints in 70 individuals developed PJI, during a mean ± SD follow-up of 6.8 ± 6.1 years. The cumulative incidence of PJI was 0.5%, 0.8%, and 1.4% after 1, 5, and 10 years after arthroplasty, respectively. Overall, the rate of survival free of clinical failure after treatment of PJI was 76.8% (95% confidence interval [CI], 64.3–85.2) and 65.2% (95% CI, 33.1–76.2) at 3 and 5 years, respectively. The incidence and treatment outcomes did not significantly differ by decade of implantation, patient age at implantation, gender, or joint location. Conclusions. The incidence of PJI is relatively low in a population-based cohort and is a function of age of the prosthesis. Incidence trends and outcomes have not significantly changed over the past 40 years.
Long-Term Cosmic-Ray Modulation in the Heliosphere

A time-dependent model based on a numerical solution of Parker's transport equation is used to model the modulation of cosmic-ray protons, electrons, and helium for full 11 year and 22 year modulation cycles using a compound approach. This approach incorporates the concept of propagating diffusion barriers, increases in the heliospheric magnetic field as they propagate from the Sun throughout the heliosphere, time-dependent gradient, curvature, and current-sheet drifts, and other basic modulation mechanisms. The model results are compared with those of the observed 11 year and 22 year cycles for 1.2 GV electrons and 1.2 GV helium at Earth for the period of 1975-1998. The model solutions are also compared with the observed charge-sign-dependent modulation along the Ulysses trajectory for the period of 1990-1998. This compound approach to long-term modulation, especially charge-sign-dependent modulation, is found to be remarkably successful. It is shown that the model can account for the latitude dependence of cosmic-ray protons and electrons by assuming a large perpendicular diffusion in the polar direction. This approach contributes to an improved understanding of how diffusion and drifts vary from solar minimum to maximum modulation and what the time dependence of the heliospheric diffusion coefficients may be. It is found that less than 10% of the available drifts are needed at solar maximum, when the solar magnetic field reverses, to explain, e.g., the observed electron-to-proton ratio along the Ulysses trajectory.
Water bathing alters threat perception in starlings

The majority of bird taxa perform water bathing, but little is known about the adaptive value of this behaviour. If bathing is important for feather maintenance then birds that have not bathed should have poorer feather condition, compromised escape ability and therefore increased responsiveness to cues of predation. We conducted two experiments examining the behaviour of captive starlings responding to conspecific alarm calls. Birds that had no access to bathing water showed a decreased willingness to feed and increased their vigilance behaviour following an alarm call. We argue that birds denied access to bathing water interpreted an ambiguous cue of threat as requiring more caution than birds that had access, consistent with higher levels of anxiety. Our results support the provision of bathing water for captive birds as an important welfare measure.
Mechanical properties and microstructure of recycled mortar reinforced with hybrid fiber

This study investigated the hybrid effects of two types of microfiber, namely, polypropylene and nylon, on the mechanical properties of high-strength mortar, which produced fine recycled aggregate (FRA). The amount of microfibers was maintained at a volumetric fraction of 0.6%. The microstructure and mechanical strength properties (compressive strength and flexural strength) of recycled mortar reinforced with hybrid-size microfibers were evaluated at various curing ages. Experimental results show that the inclusion of hybrid fibers significantly influenced the mechanical performance of the recycled mortar. The hybridization fiber at volume fraction 0.3% polypropylene + 0.3% nylon yielded the most promising mechanical performance. Enhancements of 8% on compressive and 11% flexural strength were achieved at 28 days. Scanning electron microscopy observations revealed that reinforcement at the microscale prohibited the initiation and growth of cracks at the micro level. High loads were required to form macrocracks within composites, thereby improving the mechanical strength of the mortar matrix.
Recovery limits in pointwise degradation

Pointwise image formation models appear in a variety of computational vision and photography problems. Prior studies aim to recover visibility or reflectance under the effects of specular or indirect reflections, additive scattering, radiance attenuation in haze and flash, etc. This work considers bounds to recovery from pointwise degradation. The analysis uses a physical model for the acquired signal and noise, and also accounts for potential post-acquisition noise filtering. Linear-systems analysis yields an effective cutoff-frequency, which is induced by noise, despite having no optical blur in the imaging model. We apply this analysis to hazy images. The result is a tool that assesses the ability to recover (within a desirable success rate) an object or feature having a certain size, distance from the camera, and radiance difference from its nearby background, per attenuation coefficient of the medium. The bounds rely on the camera specifications. The theory considers the pointwise degradation that exists in the scene during acquisition, which fundamentally limits recovery, even if the parameters of an algorithm are perfectly set.
Investigation of the Molecular Mechanism of the α7 Nicotinic Acetylcholine Receptor Positive Allosteric Modulator PNU-120596 Provides Evidence for Two Distinct Desensitized States

Although α7 nicotinic acetylcholine receptors are considered potentially important therapeutic targets, the development of selective agonists has been stymied by the α7 receptor's intrinsically low probability of opening (Popen) and the concern that an agonist-based therapeutic approach would disrupt endogenous cholinergic function. Development of α7 positive allosteric modulators (PAMs) holds promise of avoiding both issues. N-(5-Chloro-2,4-dimethoxyphenyl)-N′-(5-methyl-3-isoxazolyl)-urea (PNU-120596) is one of the most effective α7 PAMs, with a mechanism associated, at least in part, with the destabilization of desensitized states. We studied the mechanism of PNU-120596 potentiation of α7 receptors expressed in Xenopus laevis oocytes and outside-out patches from BOSC 23 cells. We identify two forms of α7 desensitization: one is destabilized by PNU-120596 (Ds), and the other is induced by strong episodes of activation and is stable in the presence of the PAM (Di). Our characterization of prolonged bursts of single-channel currents that occur with PNU-120596 provide a remarkable contrast to the behavior of the channels in the absence of the PAM. Individual channels that avoid the Di state show a 100,000-fold increase in Popen compared with receptors in the nonpotentiated state. In the presence of PNU-120596, balance between Ds and Di is dynamically regulated by both agonist and PAM binding, with maximal ion channel activity at intermediate levels of binding to both classes of sites. In the presence of high agonist concentrations, competitive antagonists may have the effect of shifting the balance in favor of Ds and increasing ion channel currents.
A Case Study of a Genetically Evolved Control System

A comparison between a genetically evolved controlled system and a standard PID controlled system is carried out. In “Method and Apparatus for Automatic Synthesis Controllers” by John Koza et al., a method for the automatic design and synthesis of controllers by means of genetic programming is proposed; several genetically evolved controllers are presented and compared with controllers designed with existing methodologies. In this paper I illustrate a possible procedure to reproduce the results claimed by Koza with regard to the two lags plant controller. The system is compared to a PID proposed in a textbook. The control problem is analysed to identify specifications, requirements and characteristics of the controlled system. The lack of some constraints and data regarding the physics of the control problem are pointed out to be initial flaws of the method. The solution is searched in a not well defined search space: inferences are drawn in order to continue the analysis. A simulation of the genetically evolved controller and the PID is carried out with Matlab. Through the data presented, the two system are compared. A substantial difference in the problem specifications seems to be partially responsible for the manifested difference of performance in favour of the genetically evolved controller. Hence a new PID controller is tuned respecting the constraints assumed for the evolved controller and a new comparison is carried out. The similar results and the comparable or better performances obtained with newly tuned PID suggest to reject the hypothesis of absolute superiority of the genetic programming controller. Though, the topic is left open to discuss the achievement of Pareto optimal classes of solutions by the genetic programming methodology with more carefully chosen control constraints.
Axon Withdrawal during Synapse Elimination at the Neuromuscular Junction Is Accompanied by Disassembly of the Postsynaptic Specialization and Withdrawal of Schwann Cell Processes

Nerve terminal withdrawal is accompanied by a loss of acetylcholine receptors (AChRs) at corresponding postsynaptic sites during the process of synapse elimination at developing (Balice-Gordon and Lichtman, 1993) and reinnervated adult (Rich and Lichtman, 1989a) neuromuscular junctions. Aside from AChR and nerve terminal loss, however, the molecular and cellular alterations that occur at sites of elimination are unknown. To gain a better understanding of the cascade of events that leads to the disassembly of synaptic sites during the synapse elimination process, we surveyed the distribution of molecular elements of the postsynaptic specialization, the basal lamina, and supporting Schwann cells during the process of synapse elimination that occurs after reinnervation. In addition, quantitative techniques were used to determine the temporal order of disappearance of molecules that were lost relative to the loss of postsynaptic AChRs. We found that the dismantling of the postsynaptic specialization was inhomogeneous, with evidence of rapid dissolution of some aspects of the postsynaptic apparatus and slower loss of others. We also observed a loss of Schwann cell processes from sites of synapse elimination, with a time course similar to that seen for nerve terminal retraction. In contrast, all of the extracellular markers that we examined were lost slowly from sites of synapse loss. We therefore conclude that the synapse elimination process is synapse-wide, removing not only nerve terminals but also Schwann cells and many aspects of the postsynaptic apparatus. The disassembly occurs in a stereotyped sequence with some synaptic elements appearing much more stable than others.
Systematic review: emergency department bedside ultrasonography for diagnosing suspected abdominal aortic aneurysm.

BACKGROUND The use of ultrasound (US) to diagnose an abdominal aortic aneurysm (AAA) has been well studied in the radiology literature, but has yet to be rigorously reviewed in the emergency medicine arena. OBJECTIVES This was a systematic review of the literature for the operating characteristics of emergency department (ED) ultrasonography for AAA. METHODS The authors searched PubMed and EMBASE databases for trials from 1965 through November 2011 using a search strategy derived from the following PICO formulation: Patients-patients (18+ years) suspected of AAA. Intervention-bedside ED US to detect AAA. Comparator-reference standard for diagnosing an AAA was a computed tomography (CT), magnetic resonance imaging (MRI), aortography, official US performed by radiology, ED US reviewed by radiology, exploratory laparotomy, or autopsy results. AAA was defined as ≥ 3 cm dilation of the aorta. Outcome-operating characteristics (sensitivity, specificity, and likelihood ratios [LR]) of ED abdominal US. The papers were analyzed using Quality Assessment of Diagnostic Accuracy Studies (QUADAS) guidelines. RESULTS The initial search strategy identified 1,238 articles; application of inclusion/exclusion criteria resulted in seven studies with 655 patients. The weighted average prevalence of AAA in symptomatic patients over the age of 50 years is 23%. On history, 50% of AAA patients will lack the classic triad of hypotension, back pain, and pulsatile abdominal mass. The sensitivity of abdominal palpation for AAA increases as the diameter of the AAA increases. The pooled operating characteristics of ED US for the detection of AAA were sensitivity 99% (95% confidence interval [CI] = 96% to 100%) and specificity 98% (95% CI = 97% to 99%). CONCLUSIONS Seven high-quality studies of the operating characteristics of ED bedside US in diagnosing AAA were identified. All showed excellent diagnostic performance for emergency bedside US to detect the presence of AAA in symptomatic patients.
Spatial-Vector Smoothing for Coherent Sources in Presence of a Reflecting Boundary

A new spatial-vector smoothing algorithm for multiple coherent sources is proposed based on the measurement model of 3-D cylindrical array with multi vector-hydrophones, which is located on or near a reflecting boundary. And the performance of the proposed algorithm is examined in two practical applications: hull-mounted and seabed array. The advantages of the spatial-vector smoothing scheme are: (1) less reduction in the overall array's spatial aperture, (2) no limit to the maximum number of coherent sources
Nonstructural Proteins 4A and 4B of Hepatitis C Virus Transactivate the Interleukin 8 Promoter

Interleukin 8 (IL‐8) is induced in many cell types by various stimuli including virus infection. It was reported that nonstructural protein 5A (NS5A) of hepatitis C virus (HCV) was involved in induction of IL‐8 expression at both mRNA and protein levels in cultured human cells. In this study, we aimed to determine whether or not another HCV protein(s) transactivates the IL‐8 gene expression, by means of an IL‐8 promoter‐driven luciferase reporter assay and measurement of endogenous IL‐8 mRNA and secreted IL‐8 protein levels. We observed that NS4B, and NS4A to a lesser extent, significantly transactivated the IL‐8 promoter, which resulted in enhanced production of IL‐8 protein. Also, the IL‐8 expression was augmented in Huh‐7 cells harboring an HCV subgenomic RNA replicon, compared with the control cells. Deletion mutational analysis of the IL‐8 promoter revealed the possible involvement of the transcription factor AP‐1 in both NS4A‐ and NS4B‐mediated IL‐8 gene activation. In addition, the IL‐8 gene activation by NS4B, but not that by NS4A, was likely to involve NF‐κB and/or NFIL‐6. The degree of the transactivation by NS4B and NS4A varied with different human cell lines, with HeLa cells showing the strongest activation followed by Huh‐7 cells, and with HepG2 cells exhibiting a marginal level of activation. Taken together, our present results suggest the possibility that NS4B and NS4A play an important role in inducing the IL‐8 gene expression under certain cellular conditions, which might be one of the strategies to establish persistent HCV infection.
High Affinity Interactions of Nucleolin with G-G-paired rDNA*

Nucleolin is a very abundant eukaryotic protein that localizes to the nucleolus, where the rDNA undergoes transcription, replication, and recombination and where rRNA processing occurs. The top (non-template) strand of the rDNA is very guanine-rich and has considerable potential to form structures stabilized by G-G pairing. We have assayed binding of endogenous and recombinant nucleolin to synthetic oligonucleotides in which G-rich regions have formed intermolecular G-G pairs to produce either two-stranded G2 or four-stranded G4 DNA. We report that nucleolin binds G-G-paired DNA with very high affinity; the dissociation constant for interaction with G4 DNA is K D = 1 nm. Two separate domains of nucleolin can interact with G-G-paired DNA, the four RNA binding domains and the C-terminal Arg-Gly-Gly repeats. Both domains bind G4 DNA with high specificity and recognize G4 DNA structure independent of sequence context. The high affinity of the nucleolin/G4 DNA interaction identifies G-G-paired structures as natural binding targets of nucleolin in the nucleolus. The ability of two independent domains of nucleolin to bind G-G-paired structures suggests that nucleolin can function as an architectural factor in rDNA transcription, replication, or recombination.
Robust adaptive beamformers: A beampattern shaping approach

Adaptive beamformers can degrade drastically in practice because they are highly sensitive to mismatches between the exploited assumptions and the actual characteristics of the sensor array, environment and sources. At low snapshots, the sidelobes can get very high due to errors in the array covariance matrix. This degrades the signal-to-interference-plus-noise-ratio (SINR). Recently, a robust adaptive beamformer based on worst-case optimization (RAB-WC), has reformulated beamforming as a second-order cone programming (SOCP) problem. It exhibits adaptive interference-rejection capability and robustness against large steering direction errors. However, the sidelobes in RAB-WC are indirectly controlled by a regularization factor and it is not clear how the factor value should be selected. In this paper, we propose a new framework based on the use of a set of beampattern shaping constraints. With this framework, the beamformer possesses not only adaptive interference-rejection capability and robustness against large steering direction errors, but also direct sidelobe control simultaneously. Unlike other state-of-the-art robust adaptive beamformers, the proposed beamformer is robust against moving interferences too. The proposed framework is generic and many beamformers can be derived to tackle specific problems.