Miracle-dz/UniFAR-FTUs huggingface dataset:
Catalase Is Differentially Expressed in Dividing and Nondividing Protoplasts

Based on our previous results that peroxidase is induced in dividing tobacco protoplasts but it is not expressed in the nondividing grapevine (Vitis vinifera L.) protoplasts during culture (C.I. Siminis, A.K. Kanellis, K.A. Roubelakis-Angelakis [1993] Physiol Plant 87: 263-270), we further tested the hypothesis that oxidative stress may be implicated in the recalcitrance of plant protoplasts. The expression of catalase, a major defense enzyme against cell oxidation, was studied during isolation and culture of mesophyll protoplasts from the recalcitrant grapevine and regenerating tobacco (Nicotiana tabacum L.). Incubation of tobacco leaf strips with cell wall-degrading enzymes resulted in a burst of catalase activity and an increase in its immunoreactive protein; in contrast, no such increases were found in grapevine. The cathodic and anodic catalase isoforms consisted exclusively of subunits [alpha] and [beta], respectively, in tobacco, and of subunits [beta] and [alpha], respectively, in grapevine. The catalase specific activity increased only in grapevine protoplasts during culture. The ratio of the enzymatic activities to the catalase immunoreactive protein declined in dividing tobacco protoplasts and remained fairly constant in nondividing tobacco and grapevine protoplasts during culture. Also, in dividing tobacco protoplasts the de novo accumulation of the catalase [beta] subunit gave rise to the acidic isoenzymes, whereas in nondividing tobacco and grapevine protoplasts, after 8 d in culture, only the basic isoenzymes remained due to de novo accumulation of the [alpha] subunit. The pattern of catalase expression in proliferating tobacco leaf cells during callogenesis was similar to that in dividing protoplasts. The different responses of catalase expression in dividing and nondividing tobacco and grapevine mesophyll protoplasts may indicate a specificity of catalase related to induction of totipotency.
A de novo missense mutation in the inositol 1,4,5‐triphosphate receptor type 1 gene causing severe pontine and cerebellar hypoplasia: Expanding the phenotype of ITPR1‐related spinocerebellar ataxia's

We report a de novo missense mutation (c.7649T>A) in the inositol, 1,4,5 triphosphate receptor type 1 (ITPR1) gene in a patient with severe pontocerebellar hypoplasia. The mutation results in an amino acid substitution of a highly conserved isoleucine by asparagine (p. I2550N) in the transmembrane domain. Mutations and deletions of the ITPR1 gene are associated with several types of autosomal dominant spinocerebellar ataxia, varying in age of onset and severity. Patients have signs of cerebellar ataxia and at most, a mild cerebellar atrophy on MRI. In contrast, the patient we report here has profound cerebellar and pontine hypoplasia. Our finding therefore further expands the spectrum of ITPR1‐related ataxias. © 2016 Wiley Periodicals, Inc.
Replication and supercoiling of simian virus 40 DNA in cell extracts from human cells

Soluble extracts prepared from the nucleus and cytoplasm of human 293 cells are capable of efficient replication and supercoiling of added DNA templates that contain the origin of simian virus 40 replication. Extracts prepared from human HeLa cells are less active than similarly prepared extracts from 293 cells for initiation and elongation of nascent DNA strands. DNA synthesis is dependent on addition of purified simian virus 40 tumor (T) antigen, which is isolated by immunoaffinity chromatography of extracts from cells infected with an adenovirus modified to produce large quantities of this protein. In the presence of T antigen and the cytoplasmic extract, replication initiates at the origin and continues bidirectionally. Initiation is completely dependent on functional origin sequences; a plasmid DNA containing an origin mutation known to affect DNA replication in vivo fails to replicate in vitro. Multiple rounds of DNA synthesis occur, as shown by the appearance of heavy-heavy, bromodeoxyuridine-labeled DNA products. The products of this reaction are resolved, but are relaxed, covalently closed DNA circles. Addition of a nuclear extract during DNA synthesis promotes the negative supercoiling of the replicated DNA molecules.
Bootstrapping ARMA Models: Some Simulations

The bootstrap is used to demonstrate the feasibility of obtaining estimates of standard errors of the parameter estimates of ARMA models. The method is applied to simulated data and to two published data sets, and the success of the bootstrap is evaluated. The simulations show the bootstrap to be an effective tool for estimating standard errors for parameter estimates in time series models. The bootstrap estimates of the standard errors are distribution free and valid for small samples.
Application of struvite precipitation coupled with biological treatment to slaughterhouse wastewaters

In this study, struvite precipitation coupled with an activated sludge process was applied to slaughterhouse wastewaters. Biological treatability characteristics of the wastewater were evaluated in a wide organic loading range of 0.06–0.42 g COD (g MLVSS)−1d−1 to assess COD removal as well as the extent of nitrification. Results of biological treatment of raw wastewater indicated that COD removal varied between 88% and 99% and complete nitrification was achieved at 0.1 g COD (g MLVSS)−1d−1 and lower organic loadings. Biological treatment of the struvite‐precipitated sample, which required no nitrification, yielded 86% COD removal at the organic removal of 0.3 g COD (g MLVSS)−1d−1. Struvite precipitation of both raw and biologically treated wastewater was at effective stoichiometric magnesium and phosphate doses to ammonia and between pH values of 9.0 and 9.5, providing ammonia concentrations of 20–30 mg N L−1 in the effluent and being independent of initial concentrations. The application of struvite precipitation both prior to and after biological treatment resulted in similar effluent qualities and provided the additional benefit of having a high‐rate activated sludge system instead of a low organic loading system with nitrification–denitrification. An additional benefit of struvite precipitation was the production of sludge which had recovery potential as a fertilizer. Among the tested treatment schemes, biological treatment following struvite precipitation seemed to be more advantageous in terms of process stability.
Real-Time Quantitative PCR for Assessment of Abundance of Pseudoalteromonas Species in Marine Samples

ABSTRACT A real-time quantitative PCR (RTQ-PCR) method for measuring the abundance of Pseudoalteromonas species in marine samples is presented. PCR primers targeting a Pseudoalteromonas-specific region of the 16S rRNA gene were tested at three different levels using database searches (in silico), a selection of pure cultures (in vitro), and a combined denaturing gradient gel electrophoresis and cloning approach on environmental DNA (in situ). The RTQ-PCR method allowed for the detection of SYBR Green fluorescence from double-stranded DNA over a linear range spanning six orders of magnitude. The detection limit was determined as 1.4 fg of target DNA (1,000 gene copies) measured in the presence of 20 ng of nontarget DNA from salmon testes. In this study, we discuss the importance of robust post-PCR analyses to overcome pitfalls in RTQ-PCR when samples from different complex marine habitats are analyzed and compared on a nonroutine basis. Representatives of the genus Pseudoalteromonas were detected in samples from all investigated habitats, suggesting a widespread distribution of this genus across many marine habitats (e.g., seawater, rocks, macroalgae, and marine animals). Three sample types were analyzed by RTQ-PCR to determine the relative abundance of Pseudoalteromonas ribosomal DNA (rDNA) compared to the total abundance of eubacterial rDNA. The rDNA fractions of Pseudoalteromonas compared to all Eubacteria were 1.55% on the green alga Ulva lactuca, 0.10% on the tunicate Ciona intestinalis, and 0.06% on the green alga Ulvaria fusca.
An evolutionary algorithm approach to poetry generation

Poetry is a unique artifact of the human language faculty, with its defining feature being a strong unity between content and form. Contrary to the opinion that the automatic generation of poetry is a relatively easy task, we argue that it is in fact an extremely difficult task that requires intelligence, world and linguistic knowledge, and creativity. We propose a model of poetry generation as a state space search problem, where a goal state is a text that satisfies the three properties of meaningfulness, grammaticality, and poeticness. We argue that almost all existing work on poetry generation only properly addresses a subset of these properties. In designing a computational approach for solving this problem, we draw upon the wealth of work in natural language generation (NLG). Although the emphasis of NLG research is on the generation of informative texts, recent work has highlighted the need for more flexible models which can be cast as one end of a spectrum of search sophistication, where the opposing end is the deterministically goal-directed planning of traditional NLG. We propose satisfying the properties of poetry through the application to NLG of evolutionary algorithms (EAs), a wellstudied heuristic search method. MCGONAGALL is our implemented instance of this approach. We use a linguistic representation based on Lexicalized Tree Adjoining Grammar (LTAG) that we argue is appropriate for EA-based NLG. Several genetic operators are implemented, ranging from baseline operators based on LTAG syntactic operations to heuristic semantic goal-directed operators. Two evaluation functions are implemented: one that measures the isomorphism between a solution’s stress pattern and a target metre using the edit distance algorithm, and one that measures the isomorphism between a solution’s propositional semantics and a target semantics using structural similarity metrics. We conducted an empirical study using MCGONAGALL to test the validity of employing EAs in solving the search problem, and to test whether our evaluation functions adequately capture the notions of semantic and metrical faithfulness. We conclude that our use of EAs offers an innovative approach to flexible NLG, as demonstrated by its successful application to the poetry generation task.
Site-directed Mutagenesis of Arginine 72 of HIV-1 Reverse Transcriptase

In order to determine the catalytic role of Arg72 of HIV-1 reverse transcriptase (RT), we carried out site-directed mutagenesis at codon 72. Two mutant proteins (R72A and R72K) were purified and characterized. With Arg to Ala substitution the kcat of the polymerase reaction was reduced by nearly 100-fold with poly(rA) template, but only about 5-15-fold with poly(rC) and poly(dC) templates. The Arg to Lys substitution exhibited a qualitatively similar pattern, although the overall reduction in kcat was less severe. Most interestingly, we noted a large difference in the rate constant of the first and second nucleotide incorporation by R72A, suggesting that Arg72 participates in the reaction after the formation of the first phosphodiester bond. We propose this step to be the pyrophosphate binding and removal step following the nucleotidyltransferase reaction. Support for this proposal is obtained from the observation that the R72A mutant (i) exhibited a pronounced translocation defect in the processivity analysis, (ii) lacked the ability to catalyze pyrophosphorolysis, and (iii) showed complete resistance to phosphonoformate, an analog of PPi. Arg72 is the first residue of HIV-1 RT proposed to be involved in the pyrophosphate binding/removal function of RT.
Effect of Disorder in the Frustrated Ising FCC Antiferromagnet: Phase Diagram and Stretched Exponential Relaxation

We study the phase transition in a face-centered-cubic antiferromagnet with Ising spins as a function of the concentration $p$ of ferromagnetic bonds randomly introduced into the system. Such a model describes the spin-glass phase at strong bond disorder. Using the standard Monte Carlo simulation and the powerful Wang-Landau flat-histogram method, we carry out in this work intensive simulations over the whole range of $p$. We show that the first-order transition disappears with a tiny amount of ferromagnetic bonds, namely $p\sim 0.01$, in agreement with theories and simulations on other 3D models. The antiferromagnetic long-range order is also destroyed with a very small $p$ ($\simeq 5%$). With increasing $p$, the system changes into a spin glass and then to a ferromagnetic phase when $p>0.65$. The phase diagram in the space ($T_c,p$) shows an asymmetry, unlike the case of the $\pm J$ Ising spin glass on the simple cubic lattice. We calculate the relaxation time around the spin-glass transition temperature and we show that the spin autocorrelation follows a stretched exponential relaxation law where the factor $b$ is equal to $\simeq 1/3$ at the transition as suggested by the percolation-based theory. This value is in agreement with experiments performed on various spin glasses and with Monte Carlo simulations on different SG models.
Pharmacokinetics of [3H]biotin bound to different avidin analogues.

The use of avidin-biotin technology in drug delivery facilitates the conjugation of biotinylated therapeutics to transport vectors that are enabled to undergo receptor-mediated transcytosis through the brain capillary endothelial wall, which makes up the blood-brain barrier (BBB) in vivo. However, the conjugation of avidin, a cationic glycosylated protein, to transport vectors greatly increases the rate of removal of the vector from the bloodstream, owing to rapid uptake of avidin by peripheral tissues such as liver and kidney. However, modified avidins may retain high affinity biotin binding properties, but may not be rapidly removed from plasma by peripheral tissues, and such avidin analogues would provide preferred plasma pharmacokinetic profiles. Therefore, the present studies investigate the pharmacokinetics of plasma removal of [3H]biotin bound to one of six different avidin analogues: streptavidin, Neutra-lite avidin, avidin, neutral avidin, Lite-avidin, and succinylated avidin. Isoelectric focusing studies show that avidin and Lite-avidin were highly cationic proteins, whereas neutral avidin, Neutra-lite avidin, and streptavidin were neutral proteins, and succinylated avidin had an acidic isoelectric point. The avidin analogues fell into two groups with respect to rate of biotin removal from plasma. The low clearance group included streptavidin and Neutra-lite avidin, which had a mean plasma clearance of 0.41 mL/min/kg. The high clearance group consisted of succinylated avidin, neutral avidin, and Lite-avidin and had a mean plasma clearance of 17 mL/min/kg, or 40-fold faster than the low clearance avidins. (ABSTRACT TRUNCATED AT 250 WORDS)
β-Trace protein and prognosis in patients with atrial fibrillation receiving anticoagulation treatment.

BACKGROUND Atrial fibrillation (AF) is associated with a high risk of mortality and morbidity and it commonly coexists with chronic kidney disease. A biomarker of renal function, β-trace protein (BTP), has been implicated in the progression of cardiovascular disease. The aim of our study was to evaluate the association of BTP with adverse cardiovascular events, bleeding, and mortality in patients with AF. METHODS In a consecutive cohort of patients with nonvalvular AF receiving anticoagulation treatment, plasma BTP was determined using an automated nephelometer BN ProSpec System (Siemens) and related to estimated glomerular filtration rate (eGFR). We recorded adverse cardiovascular events (stroke, acute coronary syndrome, and acute pulmonary edema), major bleeding, and mortality. RESULTS We included 1,279 patients (48.6% men), aged 76 years (IQR, 71-81 years), who were followed up for 996 days (IQR, 802-1,254 days). During the follow-up, there were 150 cardiovascular events (annual rate, 3.99%), 57 embolisms (annual rate, 1.54%), and 114 major bleeding events (annual rate, 3.04%), and 161 patients died (annual rate, 4.32%). BTP levels were inversely associated with eGFR (P < .001). High BTP concentrations were significantly associated with embolic events (hazard ratio [HR], 4.64 [1.98-10.86]; P < .001), composite adverse cardiovascular events (HR, 1.93 [1.31-2.85]; P = .001), and mortality (HR, 2.08 [1.49-2.90]; P < .001), even after adjusting for CHAD2DS2-VASc (congestive heart failure, hypertension, age ≥ 75 years [doubled], diabetes mellitus, stroke [doubled], vascular disease, age 65 to 74 years, sex category) score and renal function. High BTP was associated with major bleeding events (HR, 1.88 [1.18-3.00]; P = .008), even after adjusting for the HAS-BLED (hypertension, abnormal renal/liver function, stroke, bleeding history or redisposition, labile international normalized ratio, elderly [> 65 years], drugs/alcohol concomitantly) score. CONCLUSIONS We suggest that BTP, a proposed renal damage biomarker, may be a novel predictor of adverse cardiovascular events, major bleeding, and mortality in patients with AF. BTP may help refine clinical risk stratification in these patients.
Cubic B-spline approximation in scalers: Efficient design and implementation

Scaling is a very important process in digital image/video processing. This paper studies the application of cubic B-spline in image/video scaling. Cubic B-spline is very popular in image/video scaling, but in most cases it is not applied properly. We explain why a pre-filtering process is necessary when cubic B-spline kernel is applied to interpolate the image or video, and we also give a fast algorithm of the pre-filtering process. In addition, an efficient VLSI implementation of our interpolation method is proposed. To sum up, our method is not only theoretically robust but also easy to implement in hardware.
An Analysis of Pattern of Transforaminal Epidurography

고식적인 경막외 차단술의 방법은 영상증강장치의 도움 없이 맹검법에 의한 추궁간(interlaminar) 혹은 미추 접근법으 로 행해져 왔으나 시술의 정확성과 특정 병변 부위를 목표 로 할 수 없는 한계가 있다. 연구에 의하면 매우 숙련된 의 사가 시행할지라도 맹검법에 의한 경막 외 주입은 25% 이 상에서 부적절한 곳에 바늘이 위치한다고 했다. 또한 경 막외 스테로이드 주입의 유용성에 관한 과거 연구들의 주 된 문제점들은 주로 맹검법을 사용하였다는 것이다. 따라 서 경막외강 내 바늘이 정확하게 있는지 혹은 혈관 내나 척수강 내 주입을 확인하기 위해서 조영제를 사용하여 영 상증강장치로 확인하는 것은 매우 중요하다. 기술적으로 경막외강에 접근할 수 있는 방법은 추궁간, 미추 접근법과 경추간공 경막외 스테로이드 주입법(transforaminal epidural steroid injections, TFESI)이 있다. 추궁간 접근법 에는 정중 및 방정중 접근법을 포함하며 근처 추체의 가시 돌기 사이로 경막외 바늘을 삽입하여 저항소실법을 통해 경막외강에 접근하는 방법이다. TFESI는 영상증강장치 혹은 컴퓨터 단층 촬영하에 추경(vertebral pedicle)의 바로 하방에 해당하는 추간공에 바늘을 삽입하는 것이며 의심되는 신경 근에 진단 혹은 치료목적으로 국소마취제와 스테로이드를 주입하는 것이다. 비록 TFESI은 시술법이 좀 더 복잡하고 경추간공 경막외 조영술의 양상에 관한 분석
Real-time coupling coefficient estimation and maximum efficiency control on dynamic wireless power transfer using secondary DC-DC converter

Transmitting efficiency is able to be controlled by changing the input impedance on the receiving side using a DC-DC converter for static wireless power transfer system. However, the control method has never been applied for dynamic wireless power transfer system where coupling coefficient changes drastically. The information of coupling coefficient is needed constantly to achieve the control. Moreover, the considerations about dynamics of the transmitting circuit and coupling coefficient are necessary in dynamic wireless power transfer system. In this paper, a simple method of coupling coefficient estimation with RLS (Recursive least squares) filter and maximum efficiency control using a PID feedback controller are proposed. The simulation and experimental results of dynamic maximum efficiency control are provided and indicating the effectiveness of the proposed control in a real dynamic wireless power transfer system for EVs.
Drosophila Atlastin in motor neurons is required for locomotion and presynaptic function

ABSTRACT Hereditary spastic paraplegias (HSPs) are characterized by spasticity and weakness of the lower limbs, resulting from length-dependent axonopathy of the corticospinal tracts. In humans, the HSP-related atlastin genes ATL1–ATL3 catalyze homotypic membrane fusion of endoplasmic reticulum (ER) tubules. How defects in neuronal Atlastin contribute to axonal degeneration has not been explained satisfactorily. Using Drosophila, we demonstrate that downregulation or overexpression of Atlastin in motor neurons results in decreased crawling speed and contraction frequency in larvae, while adult flies show progressive decline in climbing ability. Broad expression in the nervous system is required to rescue the atlastin-null Drosophila mutant (atl2) phenotype. Importantly, both spontaneous release and the reserve pool of synaptic vesicles are affected. Additionally, axonal secretory organelles are abnormally distributed, whereas presynaptic proteins diminish at terminals and accumulate in distal axons, possibly in lysosomes. Our findings suggest that trafficking defects produced by Atlastin dysfunction in motor neurons result in redistribution of presynaptic components and aberrant mobilization of synaptic vesicles, stressing the importance of ER-shaping proteins and the susceptibility of motor neurons to their mutations or depletion. Highlighted Article: Disruption of Drosophila motor neuron Atlastin produces locomotor defects, axonal trafficking disorganization and synaptic dysfunction, providing insights into the cellular and pathological roles of neuronal atlastin in human spastic paraplegias.
A new two-layer bandpass filter using stepped impedance hairpin resonators for wireless applications

In this paper, we propose a new compact two-layer band-pass filter using stepped impedance hairpin resonators. This structure is composed of four resonators located on two microstrip stacked layer substrates, and the couplings between the resonators on the upper layer and those on the lower one are obtained by using two coupling apertures etched on a common ground plane placed between the two layers. A full-wave simulator is used to design the proposed structure and calculate the aperture coupling coefficients. To demonstrate the proposed design, a four-order band-pass filter prototype was fabricated and measured. The simulated results are compared with the measured data, and a good agreement is reported.
IL-7 Promotes T Cell Viability, Trafficking, and Functionality and Improves Survival in Sepsis

Sepsis is a highly lethal disorder characterized by widespread apoptosis-induced depletion of immune cells and the development of a profound immunosuppressive state. IL-7 is a potent antiapoptotic cytokine that enhances immune effector cell function and is essential for lymphocyte survival. In this study, recombinant human IL-7 (rhIL-7) efficacy and potential mechanisms of action were tested in a murine peritonitis model. Studies at two independent laboratories showed that rhIL-7 markedly improved host survival, blocked apoptosis of CD4 and CD8 T cells, restored IFN-γ production, and improved immune effector cell recruitment to the infected site. Importantly, rhIL-7 also prevented a hallmark of sepsis (i.e., the loss of delayed-type hypersensitivity), which is an IFN-γ– and T cell-dependent response. Mechanistically, rhIL-7 significantly increased the expression of the leukocyte adhesion markers LFA-1 and VLA-4, consistent with its ability to improve leukocyte function and trafficking to the infectious focus. rhIL-7 also increased the expression of CD8. The potent antiapoptotic effect of rhIL-7 was due to increased Bcl-2, as well as to a dramatic decrease in sepsis-induced PUMA, a heretofore unreported effect of IL-7. If additional animal studies support its efficacy in sepsis and if current clinical trials continue to confirm its safety in diverse settings, rhIL-7 should be strongly considered for clinical trials in sepsis.