Miracle-dz/UniFAR-FTUs huggingface dataset:
Aminoacylation of the N-terminal Cysteine Is Essential for Lol-dependent Release of Lipoproteins from Membranes but Does Not Depend on Lipoprotein Sorting Signals*

Lipoproteins are present in a wide variety of bacteria and are anchored to membranes through lipids attached to the N-terminal cysteine. The Lol system of Escherichia colimediates the membrane-specific localization of lipoproteins. Aspartate at position 2 functions as a Lol avoidance signal and causes the retention of lipoproteins in the inner membrane, whereas lipoproteins having residues other than aspartate at position 2 are released from the inner membrane and localized to the outer membrane by the Lol system. Phospholipid:apolipoprotein transacylase, Lnt, catalyzes the last step of lipoprotein modification, converting apolipoprotein into mature lipoprotein. To reveal the importance of this aminoacylation for the Lol-dependent membrane localization, apolipoproteins were prepared by inhibiting lipoprotein maturation. Lnt was also purified and used to convert apolipoprotein into mature lipoproteinin vitro. The release of these lipoproteins was examined in proteoliposomes. We show here that the aminoacylation is essential for the Lol-dependent release of lipoproteins from membranes. Furthermore, lipoproteins with aspartate at position 2 were found to be aminoacylated both in vivo and in vitro, indicating that the lipoprotein-sorting signal does not affect lipid modification.
Alternative Translation of OCT4 by an Internal Ribosome Entry Site and its Novel Function in Stress Response

OCT4 is a pivotal transcription factor in maintaining the pluripotency and self‐renewal capacities of embryonic stem (ES) cells. Human OCT4 can generate two isoforms by alternative splicing, termed OCT4A and OCT4B. OCT4A confers the stemness properties of ES cells, whereas the function of OCT4B is unknown. We present here the diverse protein products and a novel function of OCT4 gene. A single OCT4B mRNA can encode three isoforms by alternative translation initiation at AUG and CUG start codons, respectively. A putative internal ribosome entry site (IRES) has been identified in OCT4B mRNA accounting for the translation mechanism. The OCT4B‐190 is upregulated under stress conditions and it may protect cell against apoptosis under stress. This work evokes the significance to distinguish the biological function of the protein products of OCT4. The OCT4 gene, by the regulation of alternative splicing and alternative translation initiation, may carry out more crucial roles in many biological events. STEM CELLS 2009;27:1265–1275
Detection of ascending and descending stairways by surface normal vectors

Persons with walking frames are often limited with respect to visual acuity and they are depending on assistance. To give them the possibility to move free and autonomous in their environment an intelligent assistance system is proposed which can be mounted on a walking frame is used to observe the scene in walking direction, and obstacles have to be detected. Especially, stairways represent a high risk of injury if a collapse occurs. For stairway recognition, an algorithm is proposed which estimates normal vectors by using a covariance matrix and this makes it possible to segment the point cloud data provided by the Kinect sensor. The calculation of surface normal vectors of these regions helps to detect ascending and descending stairways.
Higher level of circulating estradiol is associated with lower frequency of cognitive impairment in Southeast China

Abstract Background: Estrogen has been proved to have positive effects on the brain cognitive function. However, many clinical studies investigating the associations between cognitive functions and circulating estrogen levels in perimenopausal and postmenopausal women demonstrated controversial results. Method: Circulating estradiol and follicle stimulating hormone (FSH) levels were obtained from 199 perimenopausal and postmenopausal women (mean age: 49.61 years). The cognitive function has been assessed using the Beijing version of the Montreal Cognitive Assessment. Results: Results revealed that higher estradiol levels were associated with better cognitive function (p < 0.05) both in perimenopausal and postmenopausal women and levels of FSH were unrelated to cognitive performance. Conclusions: In perimenopausal and postmenopausal women, higher levels of circulating estradiol are associated with lower risk of cognitive impairment.
2-Bromoethanesulfonate, Sulfate, Molybdate, and Ethanesulfonate Inhibit Anaerobic Dechlorination of Polychlorobiphenyls by Pasteurized Microorganisms

ABSTRACT Dechlorination of Aroclor 1242 by pasteurized microorganisms was inhibited by 2-bromoethanesulfonate (BES), sulfate, molybdate, and ethanesulfonate. Consumption of these anions and production of sulfide from BES were detected. The inhibition could not be relieved by hydrogen. Taken together these results suggest that pattern M dechlorination is mediated by spore-forming sulfidogenic bacteria. These results also suggest that BES may inhibit anaerobic dechlorination by nonmethanogens by more than one mechanism.
The COP9 signalosome controls jasmonic acid synthesis and plant responses to herbivory and pathogens.

The COP9 signalosome (CSN) is a multi-protein complex that regulates the activities of cullin-RING E3 ubiquitin ligases (CRLs). CRLs ubiquitinate proteins in order to target them for proteasomal degradation. The CSN is required for proper plant development. Here we show that the CSN also has a profound effect on plant defense responses. Silencing of genes for CSN subunits in tomato plants resulted in a mild morphological phenotype and reduced expression of wound-responsive genes in response to mechanical wounding, attack by Manduca sexta larvae, and Prosystemin over-expression. In contrast, expression of pathogenesis-related genes was increased in a stimulus-independent manner in these plants. The reduced wound response in CSN-silenced plants corresponded with reduced synthesis of jasmonic acid (JA), but levels of salicylic acid (SA) were unaltered. As a consequence, these plants exhibited reduced resistance against herbivorous M. sexta larvae and the necrotrophic fungal pathogen Botrytis cinerea. In contrast, susceptibility to tobacco mosaic virus (TMV) was not altered in CSN-silenced plants. These data demonstrate that the CSN orchestrates not only plant development but also JA-dependent plant defense responses.
How to reduce the false alarm rate beyond voting system for financial distress prediction

Financial distress prediction has increasingly become a hot topic. To enhance the predictive performance, this paper includes support vector machines, particle swarm optimization, fuzzy c-means and back propagation artificial neural network into the two-stage modelling process of business failure research. This paper use an empirical research which studies sixty-six failing corporation and sixty-six one-to-one matching non-falling corporation in Taiwan during 1971 to 2014 through utilizing existing data for the six years before bankruptcy. The developed two-stage prediction model in this research is 97.7% accurate on a validation sample. These findings protrude the efficacy of two-stage prediction models for commerce financial distress forecast and specially the importance of Support Vector Machines, Particle swarm optimization and Fuzzy c-means and coupled with back propagation artificial neural network in business failure research.
High-Frequency Magnetic Thin-Film Inductor Integrated on Flexible Organic Substrates

This paper presents integrated inductors with Co-Zr-Ta-B (CZTB) thin films on flexible organic substrates for MHz–GHz applications. This paper demonstrated the fabrication and characterization of magnetic thin-film inductors on flexible organic substrates, such as polyimide and Ajinomoto build-up film thin films. These films have thicknesses of only tens of micrometer and thus are very flexible compared to the same inductor structures fabricated on rigid substrates, such as quartz. The magnetic films on flexible substrates were observed to maintain similar magnetic properties compared with those on Si substrate, but with greater coercivity likely due to the increased roughness of the substrate surface. The fabricated thin-film inductors on organic substrates with inductance $L$ , measured by RF characteristics, have shown significantly increased inductance compared to air-core inductors (without magnetic core materials). This paper also demonstrated a high frequency response, clearly over GHz, consistent with the CZTB type of materials. The frequency response, as well as inductance and Q values, remains similar even after many iterations of bending to a large degree, indicating the robustness of the inductor on flexible organic substrates, as well as that of the magnetic thin films.
Expression of KLF5 is a Prognostic Factor for Disease-Free Survival and Overall Survival in Patients with Breast Cancer

Purpose: Kruppel-like factor (KLF5) is a cell growth mediator in various epithelial cells. Higher KLF5 increases cell growth rate and leads to transformed phenotypes. Because tumor cell proliferation is tightly associated with tumor progression, and consequently, with survival of cancer patients, we wanted to examine the prognostic value of KLF5 gene expression for patients with breast cancer. Experimental Design: The gene expression levels of KLF5, ER, PR, HER2, and MKI67 were quantified in the tumor tissues of 90 patients with breast cancer and correlated with disease-free survival and overall survival of the patients. The correlations of gene expression between KLF5 and ER, PR, HER2, and MKI67 were analyzed. In addition, KLF5 expression was also compared with clinical data and age of patients. Results: Statistically significant correlations were found between gene expression of KLF5 and both disease-free survival (univariate analysis) and overall survival (univariate and multivariate analysis). Patients with higher KLF5 expression had shorter disease-free survival and overall survival time, whereas patients with lower KLF5 expression had better survival. Moreover, KLF5 was also found to be positively correlated with HER2 and MKI67, and negatively correlated with age of the patients at diagnosis. Conclusion: The gene expression of KLF5 is directly correlated with cell proliferation in vivo and is a prognostic factor for patients with breast cancer. Patients with higher KLF5 expression have shorter disease-free survival and overall survival than patients with lower KLF5 expression. In addition, KLF5 has higher expression in patients ages ≤50 years old than in patients >50 years old.
Chaperone-assisted translocation

We investigate the translocation of a stiff polymer through a nanopore in a membrane, in the presence of binding particles (chaperones) that bind reversibly to the polymer on both sides of the membrane. A bound chaperone covers one (univalent binding) or many (multivalent binding) binding sites. Assuming that the diffusion of the chaperones is fast compared to the rate of translocation we describe the process by a one-dimensional master equation. We expand previous models by a detailed study of the effective force in the master equation, which is obtained by the appropriate statistical mechanical average over the chaperone states. The dependence of the force on the degree of valency (the number of binding sites occupied by a chaperone) is studied in detail. We obtain finite size corrections (to the thermodynamical expression for the force), which, for univalent binding, can be expressed analytically. We finally investigate the mean velocity for translocation as a function of chaperone binding strength and size. For both univalent and multivalent binding simple results are obtained for the case of a sufficiently long translocating polymer.
Research on the evaluation of security risk for e-government information system

This paper presents a risk assessment method which combines wavelet neural network (WNN) and entropy-grey correlation, creates a WNN model and has done simulation experiments by Matlab7.1. In addition, comparisons between WNN and other traditional estimation methods are made in terms of convergent speed, training precision and forecasting effect. The experiment results indicate that, with this method, subjective judgment in previous research is avoided effectively and the evaluation results are more scientific and reasonable. The study of the case shows that the method can be easily applied to the security risk assessment of e-government information system to produce objective results.
Brain metabolite changes in patients with type 2 diabetes and cerebral infarction using proton magnetic resonance spectroscopy

The aim of this study was to investigate the possible brain metabolic alterations in patients with type 2 diabetes mellitus (T2DM) and cerebral infarction (DMCI) using proton magnetic resonance spectroscopy (MRS). Thirty-four patients with T2DM and DMCI were scanned together with 33 patients with nondiabetic cerebral infarction (NDCI) on a 1.5-T MRI/MRS imager. Voxels were placed in the infarcted area and the contralateral normal area in the basal ganglia. N-acetylaspartate (NAA)/creatine (Cr), choline (Cho)/Cr, and lactate (Lac)/Cr ratios were calculated. Cerebral NAA/Cr ratios in the infarcted area were lower than those in the contralateral normal area of the NDCI group. There was a significant decrease in NAA/Cr in the infarcted area of the DMCI group as compared with the infarcted area of the NDCI group. NAA/Cr ratios in the contralateral normal area of DMCI group were lower than those of the NDCI group. Lac/Cr ratios were increased in the infarcted area of both the DMCI group and NDCI group, and Lac/Cr ratios tended to be higher in the infarcted area of the DMCI group than those of the NDCI group. Glycosylated hemoglobin (HbA1c) levels were negatively correlated with NAA/Cr ratios. The study suggested that the metabolite changes were different between DMCI patients and NDCI patients, which may provide important information in the treatment of DMCI.
Bagging likelihood-based belief decision trees

To embed ensemble techniques into belief decision trees for performance improvement, the bagging algorithm is explored. Simple belief decision trees based on entropy intervals extracted from evidential likelihood are constructed as the base classifiers, and a combination of individual trees promises to lead to a better classification accuracy. Requiring no extra querying cost, bagging belief decision trees can obtain good classification performance by simple belief tree combination, making it an alternative to single belief tree with querying. Experiments on UCI datasets verify the effectiveness of bagging approach. In various uncertain cases, the bagging method outperforms single belief tree without querying, and is comparable in accuracy to single tree with querying.
Two‐dimensional fluorescence difference gel electrophoresis analysis of the urine proteome in human diabetic nephropathy

Urinary proteins may provide clues regarding pathogenesis of kidney disease as well as providing markers of disease activity. We employed two‐dimensional differential in‐gel electrophoretic analysis (2‐D DIGE) to assess multiple urine samples in patients with diabetic nephropathy. Patient samples were collected as timed overnight collections. All the patients had longstanding diabetes, impaired renal function, and overt proteinuria. Control and patient urinary protein were analyzed by 2‐D DIGE and DeCyder analysis. Ninety‐nine spots were significantly regulated in the urine proteome of the diabetic samples, with 63 up‐ and 36 down‐regulated. One spot corresponding to a pI 5–6 and a molecular weight between 45 and 66 kDa was consistently up‐regulated by 19‐fold across individuals in the diabetic group. Surface‐enhanced laser desorption/ionization‐time of flight analysis of in‐gel tryptic digest of this spot identified this protein as alpha 1 antitrypsin (AAT). ELISA of urine samples from a separate group of patients and controls confirmed a marked increase of AAT in diabetic patients. Immunostaining of human diabetic kidneys revealed up‐regulation of AAT in areas of renal fibrosis. In conclusion, we developed a method to analyze numerous urine samples from patients and allowed for detection and identification of regulated urine protein spots.
Martin Boundaries and Random Walks

The first three sections give a quick overview of Martin boundary theory and state the main results. The succeeding sections will flesh out the details, and give proofs and examples. Virtually all of the results below are classical. The article Doob (1959) and the book by Kemeny, Snell, and Knapp (1976) are good sources for additional details. A recent survey article by Wolfgang Woess (1994) has an immense amount of information (both modern and classical) about Martin boundaries and random walks in general. Finally, Doob (1984) is an excellent source for classical Martin boundary theory for Brownian motion and the Laplacian.
Noise removal in ECG signals using the quadratic filter

This article studies the capability of applying the quadratic filter (QF) for removing noise in ECG R-peak detection preprocessing. The important advantage of the QF, which is a 2D filter, over linear filtering is that it has two degrees of freedom for optimizing noise removal in ECG signals. The QF is designed in the frequency domain based on the sum of two 2D Gaussian filters. Subsequently, the filter coefficients can be obtained using the inverse Fourier transform. The QF from proposed algorithm was evaluated with ECG signals from the MIT-BIH arrhythmia database (MITDB). Results show that the QF provides the SNR value better than that from the conventional linear filtering 20 dB in ECG noise removal. This opens the opportunity for the QF as a preprocessing step to increase accuracy in ECG R-peak detection.
Effects of the combination of metyrapone and oxazepam on cocaine craving and cocaine taking: a double-blind, randomized, placebo-controlled pilot study

Although cocaine dependence affects an estimated 1.6 million people in the USA, there are currently no medications approved for the treatment of this disorder. Experiments performed in animal models have demonstrated that inhibitors of the stress response effectively reduce intravenous cocaine self-administration. This exploratory, double-blind, placebo-controlled study was designed to assess the safety and efficacy of combinations of the cortisol synthesis inhibitor metyrapone, and the benzodiazepine oxazepam, in 45 cocaine-dependent individuals. The subjects were randomized to a total daily dose of 500 mg metyrapone/20 mg oxazepam (low dose), a total daily dose of 1500 mg metyrapone/20 mg oxazepam (high dose), or placebo for 6 weeks of treatment. The outcome measures were a reduction in cocaine craving and associated cocaine use as determined by quantitative measurements of the cocaine metabolite benzoylecgonine (BE) in urine at all visits. Of the randomized subjects, 49% completed the study. The combination of metyrapone and oxazepam was well tolerated and tended to reduce cocaine craving and cocaine use, with significant reductions at several time points when controlling for baseline scores. These data suggest that further assessments of the ability of the metyrapone and oxazepam combination to support cocaine abstinence in cocaine-dependent subjects are warranted.
On a One Time-Step SABR Simulation Approach: Application to European Options

In this work, we propose a one time-step Monte Carlo method for the SABR model. We base our approach on an accurate approximation of the cumulative distribution function of the integrated variance (conditional on the SABR volatility process), using Fourier techniques and a copula. Resulting is a fast simulation algorithm which can be employed to price European options under the SABR dynamics. Our approach can thus be seen as an alternative to Hagan's analytic formula for short maturities that may be employed for model calibration purposes.
THE INFLUENCE OF DEVELOPMENT ON THE NUMBER AND APPEARANCE OF SILVER GRAINS IN ELECTRON MICROSCOPIC RADIOAUTOGRAPHY

Under conditions similar to those in electron microscopic radioautography, the development of three different nuclear track emulsions—Ilford L4, Gevaert 307 and Kodak NTE—was investigated by varying the type of developer, duration of action and temperature. These three factors influence: (1) the number of silver grains produced from exposed silver bromide crystals and, therefore, the sensitivity of the emulsion; (2) the production of a few silver grains from silver bromide crystals, unexposed to radiation from the specimen, that is, the background fog; and (3) the size and shape of the developed silver grains, thus influencing the resolving power. The developed silver grains increase in number and in size with increasing duration of development. After complete development in most developers, the silver grains consist of highly convoluted silver filaments and are 2 or 3 times as large as the original silver bromide crystals. However, small grains may be obtained by brief development in Loveland's and p-phenylenediamine developers, in which case only development centers are revealed. Such small grain development improves resolving power, but decreases the number of developed silver grains, thus reducing sensitivity. The most satisfactory emulsion-developer combination under the conditions of the experiment appears to be Gevaert 307 emulsion developed for 2 min in D-19b. Data are also presented to facilitate the selection of the optimal emulsion-developer combination for various experimental situations.
Ethics and the computer world: a new challenge for philosophers

I shall assume that our job as moral philosophers is to follow the time-honored tradition set by Socrates and to serve as gadflies. In ethics, the pursuit of Socratic questioning has been called critical ethics. Its task is to subject commonly accepted conventions, popular superstitions, social prejudices and prevailing mythologies to critical ethical scrutiny. Its method consists of persistent and uncompromising questioning of concepts, premises, arguments and presuppositions and applying logical and conceptual analysis to commonly accepted and seldom challenged opinions. For that reason, Collingwood aptly described philosophy as the critique of presuppositions. In order to carry out this challenging task philosophers, good philosophers, must of necessity be outsiders. Spinoza, one of the Netherland's most eminent sons is a prototype. I am glad to see some veteran outsiders on the program. Even Kant, whom most people do not recognize to be the radical thinker that he was, remarked in a handwritten note in the Bemerhungen that a philosopher is useless as far as ordinary morality is concerned but, on the other hand, most useful, even indispensable in confronting "oppression from superstition and from the use of violence and power. " As far as computers are concerned, there is a lot both of superstition and power--as I shall briefly try to show.