Miracle-dz/UniFAR-FTUs huggingface dataset:
A novel lactococcal bacteriocin whose activity depends on the complementary action of two peptides

A lactococcal bacteriocin, termed lactococcin G, was purified to homogeneity by a simple four-step purification procedure that includes ammonium sulfate precipitation, binding to a cation exchanger and octyl-Sepharose CL-4B, and reverse-phase chromatography. The final yield was about 20%, and nearly a 7,000-fold increase in the specific activity was obtained. The bacteriocin activity was associated with three peptides, termed alpha 1, alpha 2, and beta, which were separated by reverse-phase chromatography. Judging from their amino acid sequences, alpha 1 and alpha 2 were the same gene product. Differences in their configurations presumably resulted in alpha 2 having a slightly lower affinity for the reverse-phase column than alpha 1 and a reduced bacteriocin activity when combined with beta. Bacteriocin activity required the complementary action of both the alpha and the beta peptides. When neither alpha 1 nor beta was in excess, about 0.3 nM alpha 1 and 0.04 nM beta induced 50% growth inhibition, suggesting that they might interact in a 7:1 or 8:1 ratio. As judged by the amino acid sequence, alpha 1 has an isoelectric point of 10.9, an extinction coefficient of 1.3 x 10(4) M-1 cm-1, and a molecular weight of 4,346 (39 amino acid residues long). Similarly, beta has an isoelectric point of 10.4, an extinction coefficient of 2.4 x 10(4) M-1 cm-1, and a molecular weight of 4110 (35 amino acid residues long). Molecular weights of 4,376 and 4,109 for alpha 1 and beta, respectively, were obtained by mass spectrometry. The N-terminal halves of both the alpha and beta peptides may form amphiphilic alpha-helices, suggesting that the peptides are pore-forming toxins that create cell membrane channels through a "barrel-stave" mechanism. The C-terminal halves of both peptides consist largely of polar amino acids.
Predicting Variable-Length Functional Outputs for Emulation of a NASA Flight Simulator

Adaptive flight control systems using online-learning neural networks have great promise for improving the safety of aircraft. However, these systems are difficult or perhaps even impossible to certify using current methodology, yet it is required that the systems be demonstrated to be safe. A recent approach considers the use of statistical emulation to help understand the behavior of the system. We present a statistical framework to model and predict the output of a function of multiple real variables in which the output is itself a function of a real variable using statistical emulation. This approach has the benefit that it carries statistical uncertainties with its predictions. Through our model, we can assist NASA with development of their flight control simulator.
Selective Induction of Cancer Cell Death by Targeted Granzyme B

The potential utility of immunotoxins for cancer therapy has convincingly been demonstrated in clinical studies. Nevertheless, the high immunogenicity of their bacterial toxin domain represents a critical limitation, and has prompted the evaluation of cell-death inducing proteins of human origin as a basis for less immunogenic immunotoxin-like molecules. In this review, we focus on the current status and future prospects of targeted fusion proteins for cancer therapy that employ granzyme B (GrB) from cytotoxic lymphocytes as a cytotoxic moiety. Naturally, this serine protease plays a critical role in the immune defense by inducing apoptotic target cell death upon cleavage of intracellular substrates. Advances in understanding of the structure and function of GrB enabled the generation of chimeric fusion proteins that carry a heterologous cell binding domain for recognition of tumor-associated cell surface antigens. These hybrid molecules display high selectivity for cancer cells, with cell killing activities similar to that of corresponding recombinant toxins. Recent findings have helped to understand and circumvent intrinsic cell binding of GrB and susceptibility of the enzyme to inhibition by serpins. This now allows the rational design of optimized GrB derivatives that avoid sequestration by binding to non-target tissues, limit off-target effects, and overcome resistance mechanisms in tumor cells.
Defuzzified clustering algorithms derived from the method of entropy-based fuzzy c-means

A class of hard c-means algorithms is derived from 'defuzzifying' objective functions of the entropy-based fuzzy c-means and the KL-information based fuzzy c-means. Namely an entropy term is deleted from the objective functions while other parameters of cluster sizes and covariances are preserved. As a result, the objective function becomes linear with respect to the membership whereby a hard c-means algorithm is derived. Variations of the basic hard c-means algorithms are moreover proposed and reduction of computation using iterative matrix inversion is considered. Numerical examples are shown to compare results of proposed algorithms. Finally, a cluster validity measure is used whereby stability of clusters by different algorithms is compared.
Paraneoplastic motor neuron disease with type 1 Purkinje cell antibodies

Autoimmune serological testing is a useful aid for identifying a paraneoplastic basis for sporadic motor neuron disease. A 67‐year‐old woman with ovarian carcinoma presented with progressive weakness. Neurological examination was suggestive of motor neuron disease with signs of upper motor neuron disorder. Electromyography revealed severe motor neuronopathy of the upper extremities. Characteristic type 1 Purkinje cell antibodies (anti‐Yo antibody) was detected in the serum diluted at 1:61,400. © 1998 John Wiley & Sons, Inc. Muscle Nerve 21:943–945, 1998.
Molecular Mechanism of Photoperiodic Time Measurement in the Brain of Japanese Quail

In most organisms living in temperate zones, reproduction is under photoperiodic control. Although photoperiodic time measurement has been studied in organisms ranging from plants to vertebrates, the underlying molecular mechanism is not well understood. The Japanese quail (Coturnix japonica) represents an excellent model to study this problem because of the rapid and dramatic photoperiodic response of its hypothalamic‐pituitary‐gonadal axis. Recent investigations of Japanese quail show that long‐day‐induced type 2 deiodinase (Dio2) expression in the mediobasal hypothalamus (MBH) plays an important role in the photoperiodic gonadal regulation by catalyzing the conversion of the prohormone thyroxine (T4) to bioactive 3,5,3′‐triiodothyronine (T3). The T3 content in the MBH is approximately 10‐fold higher under long than short days and conditions, and the intracerebroventricular infusion of T3 under short days and conditions mimics the photoperiodic gonadal response. While Dio2 generates active T3 from T4 by outer ring deiodination, type 3 deiodinase (Dio3) catalyzes the conversion of both T3 and T4 into inactive forms by inner ring deiodination. In contrast to Dio2 expression, Dio3 expression in the MBH is suppressed under the long‐day condition. Photoperiodic changes in the expression of both genes during the photoinduction process occur before the changes in the level of luteinizing hormone (LH) secretion, suggesting that the reciprocal changes in Dio2 and Dio3 expression act as gene switches of the photoperiodic molecular cascade to trigger induction of LH secretion.
Diffuse Gallbladder Wall Thickening on Computed Tomography in Patients With Liver Cirrhosis: Correlation With Clinical and Laboratory Variables

Objectives: The objective of the study was to retrospectively evaluate (a) which clinical/laboratory features are associated with the presence of diffuse gallbladder wall thickening (DGWT) in cirrhotic patients and (b) whether the degree of DGWT is correlated with such clinical/laboratory variables. Methods: After excluding patients with DGWT or laboratory test abnormalities from known causes unrelated to liver cirrhosis, a retrospective review of liver computed tomography obtained from 242 consecutive cirrhotic patients was performed by 2 radiologists in consensus to determine the presence of DGWT of greater than 3 mm in thickness and, if present, to measure the degree of DGWT defined as maximal thickness. Univariate and multivariate analysis were performed to evaluate association between presence/degree of DGWT and clinical/laboratory features. Results: Of 242 patients, 73 (30.2%) had DGWT. Diffuse gallbladder wall thickening was seen in 7.6% (12/157) of patients with Child-Pugh class A, 61.1% (33/54) of class B, and 90.3% (28/31) of class C (P < 0.001). The presence of ascites, lower platelet count, and lower albumin level were independently associated with the presence of DGWT (P < 0.01, P = 0.01, and P = 0.02, respectively). However, these factors did not show significant correlation with the degree of DGWT. Conclusions: The presence of DGWT in cirrhotic patients is associated with the presence of ascites, lower platelet count, and lower albumin level. The degree of DGWT is not correlated with such variables.
Optimization of Recombinant Bacteriophage Lysin of Streptococcus Expression in Escherichia coli

To improve the expression level of bacteriophage lysin of Streptococcus (PlyC), the growth conditions of the engineering strains, that confirmed by transforming the recombinant plasmids pET-32a(+)-PlyCA and pET-32a(+)-PlyCB (PlyCA and PlyCB are two genes of PlyC) which constructed in our laboratory into E. coli BL21 (DE3) were studied. Some key parameters such as isopropyl-&#946;-D- thiogalactopyranoside (IPTG) concentration, induction time, induction temperature and induction opportunity have been investigated to explore optimal fermentation conditions for expressing the recombinant protein. The results indicated that the best expression condition was as follows: induction started as OD600 reached about 0.3 (PlyCA) and 0.7 (PlyCB) by adding IPTG to a final concentration of 0.7mmol/L and then continued incubation for 7 h at 30&#8451; in the 2×YT medium. The maximum yield of PlyCA and PlyCB were above 30% of the total cell proteins. This result laid the foundation for the further application study.
A Revised Mechanism for Human Cyclooxygenase-2*

The mechanism of ω-6 polyunsaturated fatty acid oxidation by wild-type cyclooxygenase 2 and the Y334F variant, lacking a conserved hydrogen bond to the catalytic tyrosyl radical/tyrosine, was examined for the first time under physiologically relevant conditions. The enzymes show apparent bimolecular rate constants and deuterium kinetic isotope effects that increase in proportion to co-substrate concentrations before converging to limiting values. The trends exclude multiple dioxygenase mechanisms as well as the proposal that initial hydrogen atom abstraction from the fatty acid is the first irreversible step in catalysis. Temperature dependent kinetic studies reinforce the novel finding that hydrogen transfer from the reduced catalytic tyrosine to a terminal peroxyl radical is the first irreversible step that controls regio- and stereospecific product formation.
Energy Efficient Power Management for 4 G Heterogeneous Cellular Networks

Heterogeneous network is a promising solution to improve the energy efficiency of the cellular system. In this work, an energy efficient power management scheme designed for LTE femtocells is presented. Using user and service classification, the proposed algorithm balances the network coverage, average data rate and energy consumption. Simulation results confirms the superiority of proposed algorithm in energy efficiency and coverage. Keywords—Energy efficiency, femtocell, LTE, channel quality indicator
Non-invasive measurement of blood sugar level by millimeter waves

Measurement of blood sugar level by noninvasive method is highly desirable. Nevertheless, a practical non-invasive technique has not been reported. In this paper, to measure blood sugar level using millimeter wave noninvasively, complex permittivity of glucose and sodium chloride solution is measured and the change of transmission coefficient in millimeter wave region is obtained. An applicator system to measure blood sugar level in vivo is designed and optimized by simulation using transmission line modeling (TLM) method.
A Study on Autonomic Nervous System Responses and Feauture Selection for Emotion Recognition - Emotion Recognition using Machine Learning Algorithms

This study is related with emotion recognition based on autonomic nervous system responses. Three different emotional states, fear, surprise and stress, are evoked by stimuli and the autonomic nervous system responses for the induced emotions are measured as physiological signals such as skin temperature, electrodermal activity, electrocardiogram, and photoplethysmography. Twenty-eight features are analysed and extracted from these signals. The results of one-way ANOVA toward each parameter, there are significant differences among three emotions in some features. Therefore we select eight features from 28 features for emotion recognition. The comparative results of emotion recognition are discussed in view point of feature space with the selected features. For emotion recognition, we use four machine learning algorithms, namely, linear discriminant analysis, classification and regression tree, self-organizing map and naive bayes, and those are evaluated by only training, 10-fold cross-validation and repeated random sub-sampling validation. This can be helpful to provide the basis for the emotion recognition technique in human computer interaction as well as contribute to the standardization in emotion-specific ANS responses.
Heterogeneous modular deep neural network for diabetic retinopathy detection

This paper proposes heterogeneous modular deep neural network (DNN) to address a complex problem of detection of diabetic retinopathy and simultaneously the five types of abnormalities. The modular approach gives the advantage to extract class specific features for the classifier, which helps to outperform the classical convolutional neural networks. Moreover, the heterogeneous nature of modular DNN provides the economy in the overall architecture and also enables to extract region specific features which further contribute to higher accuracy of detection. Extensive simulation studies were performed using benchmark dataset DIARETDB0 and results show that the proposed approach performs better or equivalently good than the other standard approaches.
Surface location and high affinity for calcium of a 500‐kd liver membrane protein closely related to the LDL‐receptor suggest a physiological role as lipoprotein receptor.

We describe a cell surface protein that is abundant in liver and has close structural and biochemical similarities to the low density lipoprotein (LDL) receptor. The complete sequence of the protein containing 4544 amino acids is presented. From the sequence a remarkable resemblance to the LDL‐receptor and epidermal growth factor (EGF) precursor is apparent. Three types of repeating sequence motifs entirely account for the extracellular domain of the molecule. These are arranged in a manner resembling four copies of the ligand binding and the EGF‐precursor homologous region of the LDL‐receptor. Following a proline‐rich segment of 17 amino acids are found six consecutive repeats with close homology to EGF. A single membrane‐spanning segment precedes a carboxy‐terminal ‘tail’ of 100 amino acids. This contains two seven‐amino acid sequences with striking homology to the cytoplasmic tail of the LDL‐receptor in the region that contains the signal for clustering into coated pits. The mRNA for this protein is most abundant in liver, brain and lung. By using an antibody raised against a 13‐amino acid peptide corresponding to the deduced amino acid sequence of the carboxy‐terminus of the protein we have demonstrated its existence on the cell surface and its abundance in liver. Like the LDL‐receptor this protein also strongly binds calcium, a cation absolutely required for binding of apolipoproteins B and E to their receptors. We propose that this LDL‐receptor related protein (LRP) is a recycling lipoprotein receptor with possible growth‐modulating effects.
Body-Centered Cubic Iron-Nickel Alloy in Earth's Core

Cosmochemical, geochemical, and geophysical studies provide evidence that Earth's core contains iron with substantial (5 to 15%) amounts of nickel. The iron-nickel alloy Fe0.9Ni0. 1 has been studied in situ by means of angle-dispersive x-ray diffraction in internally heated diamond anvil cells (DACs), and its resistance has been measured as a function of pressure and temperature. At pressures above 225 gigapascals and temperatures over 3400 kelvin, Fe0.9Ni0. 1 adopts a body-centered cubic structure. Our experimental and theoretical results not only support the interpretation of shockwave data on pure iron as showing a solid-solid phase transition above about 200 gigapascals, but also suggest that iron alloys with geochemically reasonable compositions (that is, with substantial nickel, sulfur, or silicon content) adopt the bcc structure in Earth's inner core.
Distributed Feedback Laser Diode and Module for CATV Systems

Harmonic distortion of distributed feedback laser diodes (DFB-LDs) for analog transmission systems is investigated. It is shown that, under a modulation frequency of less than 1 GHz, the harmonic distortion depends on the nonlinearity of the light output power-current (P-I) curve under the continuous wave (CW) condition, which is determined by the coupling constant kappa L, and that the distortion can be minimized at kappa L approximately 1. A 1.3 mu m wavelength InGaAsP DFB-PPIBH (p-substrate partially inverted buried heterostructure) LD and its module, with low distortion by the control of a coupling constant, have been developed. >
Targeted phosphoproteomics of insulin signaling using data-independent acquisition mass spectrometry

A mass spectrometry method may enable the simultaneous and rapid quantification of multiple phosphorylation events in multiple samples. Cross sample proteomics Nontargeted proteomic approaches are not well suited for comparisons of different samples and have detection limits, meaning that many biologically important but low abundance proteins are not detected. By applying a proteomic approach called DIA-MS (data-independent acquisition mass spectrometry) to an adipocyte cell line, Parker et al. showed that this method successfully mapped the phosphorylation events that occurred in response to insulin in a quantitative manner. Furthermore, by comparing the quantification of phosphorylation in cells exposed to various kinase inhibitors, the authors assigned specific kinases to many of phosphorylation events, which identified points of crosstalk between signaling pathways. This study provides proof of principle that this approach enables simultaneous analysis of phosphorylation events in multiple samples from different time points, doses, or patients. A major goal in signaling biology is the establishment of high-throughput quantitative methods for measuring changes in protein phosphorylation of entire signal transduction pathways across many different samples comprising temporal or dose data or patient samples. Data-independent acquisition (DIA) mass spectrometry (MS) methods, which involve tandem MS scans that are collected independently of precursor ion information and then are followed by targeted searching for known peptides, may achieve this goal. We applied DIA-MS to systematically quantify phosphorylation of components in the insulin signaling network in response to insulin as well as in stimulated cells exposed to a panel of kinase inhibitors targeting key downstream effectors in the network. We accurately quantified the effect of insulin on phosphorylation of 86 protein targets in the insulin signaling network using either stable isotope standards (SIS) or label-free quantification (LFQ) and mapped signal transmission through this network. By matching kinases to specific phosphorylation events (based on linear consensus motifs and temporal phosphorylation) to the quantitative phosphoproteomic data from cells exposed to inhibitors, we investigated predicted kinase-substrate relationships of AKT and mTOR in a targeted fashion. Furthermore, we applied this approach to show that AKT2-dependent phosphorylation of GAB2 promoted insulin signaling but inhibited epidermal growth factor (EGF) signaling in a manner dependent on 14-3-3 binding. Because DIA-MS can increase throughput and improve the reproducibility of peptide detection across multiple samples, this approach should facilitate more accurate, comprehensive, and quantitative assessment of signaling networks under various experimental conditions than are possible using other MS proteomic methods.
Factors Associated With Screen Time Among School-Age Children in Korea

The purpose of this study was to investigate the association of sociodemographic, psychosocial, and behavioral characteristics with screen time among school-age children in Korea. This study employed a nonexperimental, cross-sectional study design. A total of 370 children attending four elementary schools participated in the study. Self-report method was used, and instruments included screen time (time spent on TV/video/computer/video games), sleep duration, eating behavior, pros and cons of exercise, and exercise self-efficacy. According to the results, 45.7% of the children had screen time of 1–2.9 hr/day and 8.9% had 3 or more hr/day. Increased screen time showed an association with gender (boy), higher body mass index, fast food consumption, higher cons of exercise, having a working mother, and attendance at a school in an inner city area (p < .05). Understanding the factors associated with screen time may provide useful information in the development of health promotion programs aimed at decreasing sedentary behaviors.
Reduced Function of a Phenylacetate-Oxidizing Cytochrome P450 Caused Strong Genetic Improvement in Early Phylogeny of Penicillin-Producing Strains

ABSTRACT The single-copy pahA gene from Penicillium chrysogenum encodes a phenylacetate 2-hydroxylase that catalyzes the first step of phenylacetate catabolism, an oxidative route that decreases the precursor availability for penicillin G biosynthesis. PahA protein is homologous to cytochrome P450 monooxygenases involved in the detoxification of xenobiotic compounds, with 84% identity to the Aspergillus nidulans homologue PhacA. Expression level of pahA displays an inverse correlation with the penicillin productivity of the strain and is subject to induction by phenylacetic acid. Gene expression studies have revealed a reduced oxidative activity of the protein encoded bypahA genes from penicillin-overproducing strains ofP. chrysogenum compared to the activity conferred byphacA of A. nidulans. Sequencing and expression of wild-type pahA from P. chrysogenum NRRL 1951 revealed that an L181F mutation was responsible for the reduced function in present industrial strains. The mutation has been tracked down to Wisconsin 49–133, a mutant obtained at the Department of Botany of the University of Wisconsin in 1949, at the beginning of the development of the Wisconsin family of strains.