Miracle-dz/UniFAR-FTUs huggingface dataset:
Role of FAST Kinase Domains 3 (FASTKD3) in Post-transcriptional Regulation of Mitochondrial Gene Expression*

The Fas-activated serine/threonine kinase (FASTK) family of proteins has recently emerged as a central regulator of mitochondrial gene expression through the function of an unusual RNA-binding domain named RAP (for RNA-binding domain abundant in Apicomplexans), shared by all six members of the family. Here we describe the role of one of the less characterized members, FASTKD3, in mitochondrial RNA metabolism. First, we show that, in contrast to FASTK, FASTKD2, and FASTKD5, FASTKD3 does not localize in mitochondrial RNA granules, which are sites of processing and maturation of mtRNAs and ribosome biogenesis. Second, we generated FASTKD3 homozygous knock-out cell lines by homologous recombination and observed that the absence of FASTKD3 resulted in increased steady-state levels and half-lives of a subset of mature mitochondrial mRNAs: ND2, ND3, CYTB, COX2, and ATP8/6. No aberrant processing of RNA precursors was observed. Rescue experiments demonstrated that RAP domain is required for FASTKD3 function in mRNA stability. Besides, we describe that FASTKD3 is required for efficient COX1 mRNA translation without altering mRNA levels, which results in a decrease in the steady-state levels of COX1 protein. This finding is associated with reduced mitochondrial complex IV assembly and activity. Our observations suggest that the function of this family of proteins goes beyond RNA processing and ribosome assembly and includes RNA stability and translation regulation within mitochondria.
Digital Media Tampering Detection Techniques: An Overview

Digital media has played a critical role in today information system. With emerging of easy-to-use media manipulating tools which can be found anywhere on the internet, a user can now alter the content of their digital media (e.g. digital image, audio or video) in order to achieve his/her personal goal without leaving no traces detectable by human’s basic perceptions. Hence, the authenticity of the digital media can no longer be guaranteed. This leads to the serious problem regarding digital crime investigation. In this paper, an overview on forgery attacks and techniques used to fight against these attacks are present and discussed.
Software security characteristics for function point analysis

Software cost estimation (SCE) has been an important but difficult task since the beginning of the computer era. It considers list of parameters to estimate accurately the software cost. However, security cost is always excluded in most of the parametric cost estimation models. It is because of the security aspect is normally considered late in the software development. To overcome this problem, we proposed an enhancement to one of the parametric estimation models, which is Function Point Analysis (FPA), to address the security concerns. The enhancement suggests potential software security characteristics during system development life cycle (SDLC). These characteristics are then integrated into FPA calculation to encounter the security cost estimation. This paper also points to the validation of a survey findings and calibration of the FPA calculation.
Glucose interactions with a model peptide

Molecular dynamics simulations have been conducted of the helical polypeptide melittin, in concentrated aqueous solutions of the alpha and beta anomers of D‐glucopyranose. Glucose is an osmolyte, and it is expected to be preferentially excluded from the surfaces of proteins. This was indeed found to be the case in the simulations. The results indicate that the observed exclusion may have a contribution from an under‐representation of hydrogen bonding interactions between glucose groups and exposed side chains, compared to water. However, glucose was found to bind quite specifically to melittin by stacking its hydrophobic face, consisting of aliphatic protons, against the flat hydrophobic face of the indole group of the tryptophan‐19 side chain. Although the binding site for this interaction is localized, the binding is weak for both anomers, with a binding free energy estimated as only ∼0.5 kcal/mol (i.e. near kBT). The face of the sugar stacked against the Trp indole ring is different for the two anomers of glucose, due to the disruption of the H1‐H3‐H5 hydrophobic triad of the beta anomer by the axial C1 hydroxyl group in the alpha anomer. The measurable affinity of the sugar for the Trp side chain is consistent with the very frequent occurrence of this group in the binding sites of proteins that complex with sugars. Proteins 2011; © 2011 Wiley‐Liss, Inc.
Identification of the UDP-N-Acetylglucosamine 4-Epimerase Involved in Exosporium Protein Glycosylation in Bacillus anthracis

ABSTRACT Spores of Bacillus anthracis, the causative agent of anthrax, are enclosed by a loosely fitting exosporium composed of a basal layer and an external hair-like nap. The filaments of the nap are formed by trimers of the collagen-like glycoprotein BclA. The side chains of BclA include multiple copies of two linear rhamnose-containing oligosaccharides, a trisaccharide and a pentasaccharide. The pentasaccharide terminates with the unusual deoxyamino sugar anthrose. Both oligosaccharide side chains are linked to the BclA protein backbone through an N-acetylgalactosamine (GalNAc) residue. To identify the gene encoding the epimerase required to produce GalNAc for BclA oligosaccharide biosynthesis, three annotated UDP-glucose 4-epimerase genes of B. anthracis were cloned and expressed in Escherichia coli. The candidate proteins were purified, and their enzymatic activities were assessed. Only two proteins, encoded by the BAS5114 and BAS5304 genes (B. anthracis Sterne designations), exhibited epimerase activity. Both proteins were able to convert UDP-glucose (Glc) to UDP-Gal, but only the BAS5304-encoded protein could convert UDP-GlcNAc to UDP-GalNAc, indicating that BAS5304 was the gene sought. Surprisingly, spores produced by a mutant strain lacking the BAS5304-encoded enzyme still contained normal levels of BclA-attached oligosaccharides. However, monosaccharide analysis of the oligosaccharides revealed that GlcNAc had replaced GalNAc. Thus, while GalNAc appears to be the preferred amino sugar for the linkage of oligosaccharides to the BclA protein backbone, in its absence, GlcNAc can serve as a substitute linker. Finally, we demonstrated that the expression of the BAS5304 gene occurred in a biphasic manner during both the early and late stages of sporulation.
High‐resolution diffusion tensor imaging of the human pons with a reduced field‐of‐view, multishot, variable‐density, spiral acquisition at 3 T

Diffusion tensor imaging of localized anatomic regions, such as brainstem, cervical spinal cord, and optic nerve, is challenging because of the existence of significant susceptibility differences, severe physiologic motion in the surrounding tissues, and the need for high spatial resolution to resolve the underlying complex neuroarchitecture. The aim of the methodology presented here is to achieve high‐resolution diffusion tensor imaging in localized regions of the central nervous system that is motion insensitive and immune to susceptibility while acquiring a set of two‐dimensional images with more than six diffusion encoding directions within a reasonable total scan time. We accomplish this aim by implementing self‐navigated, multishot, variable‐density, spiral encoding with outer volume suppression. We establish scan protocols for achieving equal signal‐to‐noise ratio at 1.2 mm and 0.8 mm in‐plane resolution for reduced field‐of‐view diffusion tensor imaging of the brainstem. In vivo application of the technique on the human pons of three subjects shows a clear delineation of the multiple local neural tracts. By comparing scans acquired with varying in‐plane resolution but with constant signal‐to‐noise ratio, we demonstrate that increasing the resolution and reducing the partial volume effect result in higher fractional anisotropy values for the corticospinal tracts. Magn Reson Med, 2009. © 2009 Wiley‐Liss, Inc.
Managing the generalised tonic–clonic seizure and preventing progress to status epilepticus: a stepwise approach

Seizures are a commonly encountered medical problem. Seizure protocols have been shown to be effective by avoiding inappropriate over‐ and undertreatment, but are not presently utilised in many centres in Australia. We outline a stepwise approach to effective seizure management based on timely investigation and escalating treatment with an appropriate choice of medications. Because large‐scale clinical trials are lacking, we base our approach on the underlying seizure pathophysiology and the pharmacological properties of the available drugs. Early management consists of finding and correcting possible reversible causes and ensuring patient safety. With ongoing seizure length, spontaneous resolution becomes unlikely, necessitating administration of anti‐epileptic drugs. Benzodiazepines are the agents of first choice, with a preference of short‐acting drugs. With ongoing seizures, other agents (i.e. valproate, levetiracetam, phenobarbitone, phenytoin) are utilised. Refractory status epilepticus requires aggressive treatment in an intensive care setting. Novel approaches and agents, including ketamine, topiramate, lacosamide, pregabalin and intravenous immunoglobulins, are discussed. We provide our own recently developed hospital protocol as a guide. This protocol relies on a time‐based four‐step escalating approach to seizure management, ranging from supportive management of the initial simple seizure to the use of multiple agents for established status epilepticus.
A protein deacetylase SIRT1 is a negative regulator of metalloproteinase‐9

Inappropriate elevation of matrix metalloproteinase‐9 (MMP9) is reported to be involved in the pathogenesis of chronic obstructive pulmonary disease (COPD). The object of this study was to identify the molecular mechanism underlying this increase of MMP9 expression, and here we show that oxidative stress‐dependent reduction of a protein deacetylase, SIRT1, known as a putative antiaging enzyme, causes elevation of MMP9 expression. A sirtuin inhibitor, splitomycin, and SIRT1 knockdown by RNA interference led an increase in MMP9 expression in human monocytic U937 cells and in primary sputum macrophages, which was detected by RT‐PCR, Western blot, activity assay, and zymography. In fact, the SIRT1 level was significantly decreased in peripheral lungs of patients with COPD, and this increase was inversely correlated with MMP9 expression and MMP9 promoter activation detected by a chromatin immunoprecipitation assay. H2O2 reduced SIRT1 expression and activity in U937 cells;furthermore, cigarette smoke exposure also caused reduction of SIRT1 expression in lung tissue of A/J mice, with concomitant elevation of MMP9. Intranasal treatment of a selective and novel SIRT1 small molecule activator, SRT2172, blocked the increase of MMP9 expression in the lung as well as pulmonary neutrophilia and the reduction in exercise tolerance. Thus, SIRT1 is a negative regulator of MMP9 expression, and SIRT1 activation is implicated as a novel therapeutic approach to treating chronic inflammatory diseases, in which MMP9 is abundant. — Nakamaru, Y. , Vuppusetty, C. , Wada, H. , Milne, J. C. , Ito, M. , Rossios, C. , Elliot, M. , Hogg, J., Kharitonov, S. , Goto, H. , Bemis, J. E. , Elliott, P., Barnes, P. J., Ito, K. A protein deacetylase SIRT1 is a negative regulator of metalloproteinase‐9. FASEB J. 23, 2810–2819 (2009). www.fasebj. org
Stimulation of the P 6 Acupuncture Point for Prophylaxis of Nausea and Vomiting in Pregnant Women Submitted to Cesarean Section : A Blinded Clinical Trial

In pregnant women subjected to spinal anesthesia for a Cesarean section, episodes of nausea and vomiting are common both during and following surgery. Acupuncture for the prophylaxis and treatment of these complications has been gaining in popularity due to its low cost, simplicity, absence of side effects and confirmed efficacy. This study investigated the efficacy of stimulating the P6 acupoint in conjunction with the use of dexamethasone as prophylaxis for nausea and vomiting in pregnant women submitted to spinal anesthesia for a Cesarean section. The patients (n = 100) were randomly distributed into two groups. In the first group (n = 50), a site located one centimeter laterally from P6 was stimulated. This is not a true acupuncture point (sham acupuncture). In the second group (n = 50), P6 was stimulated. In both groups, 4 mg of dexamethasone were administered intravenously. A questionnaire was used to obtain information on the occurrence of nausea and vomiting during surgery and in the first 12 hours postpartum. The chi-square test and Fisher’s exact test were used to assess differences between the groups. Age and physical status were similar in both groups. The incidence of nausea during surgery was 32% (n = 16) in the control group and 22% (n = 11) in the P6 group (p > 0.05). In the first 12 hours following surgery, nausea occurred in 16% of the women in the control group (n = 6) and in 4% in the P6 group (n = 4) (p = 0.045). The incidence of vomiting in the control group was 12% (n = 6) during surgery and 10% (n = 5) in the postoperative period compared to 8% (n = 4) and 4% (n = 2), respectively, in the P6 group (p > 0.05). Although these differences were not statistically significant with the exception of the incidence of nausea in the first 12 hours postpartum, a reduction occurred in the incidence of all the outcomes evaluated in the P6 group.
Fusion of RSS and Phase Shift Using the Kalman Filter for RFID Tracking

Radio frequency identification (RFID)-based indoor tracking system has been used for the localization and tracking of forklift and automated guided vehicles in warehouses. Most of the existing tracking methods rely on either received signal strength (RSS) or phase shift alone. This paper presents a new RFID tracking method that fuses the RSS and phase shift together to predict the instant position of a mobile target. The fingerprints database is first constructed by collecting the RSS values at reference points. After data normalization, the fingerprints are fed into the extreme learning machine for the rough position estimation. The radial speed of the RFID tag can be calculated by measuring the phase difference between two consecutive time steps. Then, the linear least squares method is exploited to fit the instant speed of the mobile tag. On the assumption that the trajectory of the mobile tag could be approximated by a series of line segments, the Kalman filter is utilized afterward to enhance the position estimation by combing the rough location estimation and the instant velocity. The performance of our method is studied in simulations and experimentally verified in our lab. The results demonstrate that our method is feasible and achieves higher accuracy than traditional tracking methods.
The resting potential of moth muscle fibre

1. The membrane of the moth muscle fibre was tested for resting permeability to various ions: it is not permeable to Mg2+ or Ca2+; it is slightly permeable to Na+ and NH4+; it is appreciably permeable to Cl−, but Cl− is passively distributed; it is apparently permeable to H+ but effects of HCO3− are not ruled out; and it is primarily permeable to K+.
Computational aspects of the matrix sign function solution to the ARE

Roberts matrix sign function solution to the ARE is defined so as to speed convergence and reduce storage requirements; our work extends ideas proposed by R. Byers, ref(8). Features of the sign function presented here are: (a) our formulation of the Roberts-Byers algorithm recurses on the symmetric transformed Hamiltonian, which reduces storage requirements, (b) the symmetric indefinite matrix inversion required by the algorithm is carried out using LINPACK (and our excellent numerical results reflect the wisdom of this choice); corrections to the computed (approximate) solution are obtained by applying the same algorithms to the translated problem (which improves upon the linear Lyapunov equation correction that has been used), and (d) simple (but somewhat ad hoc) convergence criteria are proposed to reduce computation. The algorithm described in this work has been tested on a variety of continuous time ARE test problems, and the results have been very satisfactory. Tests on numerically ill-conditioned problems produced results of comparable accuracy with those obtained by the Shur vector RICPACK method. Our sign function iterative ARE solution demonstrates numerical robustness, accurate results, rapid (super linear) convergence, algorithmic simplicity, and modest storage requirements. Our work shows that iterative ARE solutions offer a viable alternative to the Shur eigenvector approach that is a generally accepted reference.
Sustained benefit of left ventricular remodelling after valve replacement for aortic stenosis.

BACKGROUND Valve replacement for aortic stenosis (AS) determines negative ventricular remodelling. We used cross sectional and Doppler echocardiography to check how rapidly it occurs and to assess if these changes are sustained over time. METHODS We evaluated in 34 patients subjected to aortic valve replacement for AS morphological and functional (ejection fraction and E:A ratio) left ventricular data by echocardiography prior to surgery and 2 postoperative studies: early after surgery (pQ1) and at mid-term evolution (pQ2). RESULTS Left ventricular mass index was reduced at pQ1 (from 152 +/- 47 g/m2 to 113 +/- 31 g/m2; p < 0.01) as well as end-diastolic (from 51.3 mm to 48.3 mm; p < 0.03), end-systolic (from 32.2 mm to 29.4 mm; p < 0.02), interventricular septum (from 12.9 mm to 10.3 mm; p < 0.01), and posterior wall (from 12.5 mm to 11 mm; p < 0.01) dimensions. Left ventricular ejection fraction (from 61.2% to 65.2%; p < 0.04) and E:A ratio (from 0.94 to 0.98; p < 0.01) increased significantly at pQ1. There were no significant differences in measurements between pQ1 and pQ2. CONCLUSIONS Aortic valve replacement surgery leads to a rapid negative left ventricular remodelling during the first 7 months, including a decrease in myocardial hypertrophy and an improvement in systolic and diastolic function. These beneficial hemodynamic changes are sustained for at least 3 years.
Mexico's experience with a flexible exchange rate regime

The availability of a nominal anchor and increased trade and investment flows are considered key benefits from a fixed exchange rate, while a floating exchange rate ensures freedom to use monetary policy. We show that having a flexible exchange rate has not hurt Mexico's ability to reduce inflation, develop trade, and attract foreign investment. Moreover, monetary policy has been used to address shocks on the economy with good results, while the elimination of explicit and implicit exchange rate guarantees has prevented the emergence of currency and maturity mismatches in capital flows and balance sheets.
The RNA binding domain of ribosomal protein L11: three-dimensional structure of the RNA-bound form of the protein and its interaction with 23 S rRNA.

The three-dimensional solution structure has been determined by NMR spectroscopy of the 75 residue C-terminal domain of ribosomal protein L11 (L11-C76) in its RNA-bound state. L11-C76 recognizes and binds tightly to a highly conserved 58 nucleotide domain of 23 S ribosomal RNA, whose secondary structure consists of three helical stems and a central junction loop. The NMR data reveal that the conserved structural core of the protein, which consists of a bundle of three alpha-helices and a two-stranded parallel beta-sheet four residues in length, is nearly the same as the solution structure determined for the non-liganded form of the protein. There are however, substantial chemical shift perturbations which accompany RNA binding, the largest of which map onto an extended loop which bridges the C-terminal end of alpha-helix 1 and the first strand of parallel beta-sheet. Substantial shift perturbations are also observed in the N-terminal end of alpha-helix 1, the intervening loop that bridges helices 2 and 3, and alpha-helix 3. The four contact regions identified by the shift perturbation data also displayed protein-RNA NOEs, as identified by isotope-filtered three-dimensional NOE spectroscopy. The shift perturbation and NOE data not only implicate helix 3 as playing an important role in RNA binding, but also indicate that regions flanking helix 3 are involved as well. Loop 1 is of particular interest as it was found to be flexible and disordered for L11-C76 free in solution, but not in the RNA-bound form of the protein, where it appears rigid and adopts a specific conformation as a result of its direct contact to RNA.
Winner determination problem with loss-averse buyers in reverse auctions

Reverse auctions have been widely adopted for purchasing goods and services. This paper considers a novel winner determination problem in a multiple-object reverse auction in which the buyer involves loss-averse behavior due to uncertain attributes. A corresponding winner determination model based on cumulative prospect theory is proposed. Due to the NP-hard characteristic, a loaded route strategy is proposed to ensure the feasibility of the model. Then, an improved ant colony algorithm that consists of a dynamic transition strategy and a Max-Min pheromone strategy is designed. Numerical experiments are conducted to illustrate the effectiveness of the proposed model and algorithm. We ﬁ nd that under the loaded route strategy, the improved ant colony algorithm performs better than the basic ant colony algorithm. In addition, the proposed model can effectively characterize the buyer ’ s loss-averse behavior.
Identification of two ancillary subunits of Escherichia coli type 1 fimbriae by using antibodies against synthetic oligopeptides of fim gene products

We have chemically synthesized oligopeptides corresponding to the NH2-terminal stretch of two gene products, designated FimG and FimH, of the fim gene cluster of Escherichia coli. These synthetic peptides, designated S-T1FimG(1-16) and S-T1FimH(1-25)C, evoked antibodies in rabbits that reacted with 14- and 29-kilodalton subunits, respectively, of dissociated fimbriae encoded by the recombinant plasmid pSH2 carrying the genetic information for the synthesis and expression of functional type 1 fimbriae. Neither of these fimbrial proteins was detected in dissociated fimbrial preparations from nonadhesive E. coli cells carrying the mutant plasmid pUT2002, containing a restriction site-specific deletion of fimG and fimH. Anti-S-T1FimH(1-25)C inhibited the adherence of type 1 fimbriated E. coli to epithelial cells. Immunoelectron microscopy revealed that anti-S-T1FimH(1-25)C, but not anti-S-T1FimG(1-16), bound to intact type 1 fimbriae of E. coli at the fimbrial tips and at long intervals along the fimbrial filaments. Anti-S-T1FimG(1-16) appeared to be directed at epitopes not accessible on the intact fimbriae and consequently failed to bind to intact fimbriae or to block fimbrial attachment. Our results suggest that the fimG and fimH gene products are components of type 1 fimbriae and that FimH may be the tip adhesin mediating the binding of type 1 fimbriated E. coli to D-mannose residues on mucosal surfaces.