Miracle-dz/UniFAR-FTUs huggingface dataset:
Tools for Interpreting Large-scale Protein Profiling in Microbiology

Quantitative proteomic analysis of microbial systems generates large datasets that can be difficult and time-consuming to interpret. Fortunately, many of the data display and gene-clustering tools developed to analyze large transcriptome microarray datasets are also applicable to proteomes. Plots of abundance ratio vs. total signal or spectral counts can highlight regions of random error and putative change. Displaying data in the physical order of the genes in the genome sequence can highlight potential operons. At a basic level of transcriptional organization, identifying operons can give insights into regulatory pathways as well as provide corroborating evidence for proteomic results. Classification and clustering algorithms can group proteins together by their abundance changes under different conditions, helping to identify interesting expression patterns, but often work poorly with noisy data such as typically generated in a large-scale proteomic analysis. Biological interpretation can be aided more directly by overlaying differential protein abundance data onto metabolic pathways, indicating pathways with altered activities. More broadly, ontology tools detect altered levels of protein abundance for different metabolic pathways, molecular functions, and cellular localizations. In practice, pathway analysis and ontology are limited by the level of database curation associated with the organism of interest.
A multi-level design methodology of multistage interconnection network for MPSOCs

In this paper, we propose a design methodology of Multistage Interconnection Networks (MINs) for multiprocessor system on chip. The framework covers the design step from algorithm level to RTL. We first develop a functional formalisation of MIN-based on-chip network at a high level of abstraction. The specification and the validation of the model have been defined in the logic of ACL2 proving system. The main objective in this step is to provide a formal description of the network that integrates architectural parameters, which have a huge impact on design costs. After validating the functional model, step 2 consists in the design and the implementation of the Delta multistage NoC dedicated to multiprocessor architectures on reconfigurable platforms FPGA. In the last step, we propose an evaluation methodology based on performance and cost metrics to evaluate different topologies of dynamic network through applications with different numbers of cores. We also show in the proposed framework that MIN will become future general-purpose communication architecture for MPSOCs.
Challenges in Getting Flash Drives Closer to CPU

The PCI Express Solid State Disks (PCIe SSDs) blur the difference between block and memory access semantic devices. Since these SSDs leverage PCIe bus as storage interface, their interfaces are different from conventional memory system interconnects as well as thin storage interfaces. This leads to a new SSD architecture and storage software stack design. Unfortunately, there are not many studies focusing on the system characteristics of these emerging PCIe SSD platforms. In this paper, we quantitatively analyze the challenges faced by PCIe SSDs in getting flash memory closer to CPU and study two representative PCIe SSD architectures (from-scratch SSD and bridge-based SSD) using state-of-the-art real SSDs from two different vendors. Our experimental analysis reveals that 1) while the from-scratch SSD approach offers remarkable performance improvements, it requires enormous host-side memory and computation resources which may not be acceptable in many computing systems; 2) the performance of the from-scratch SSD significantly degrades in a multi-core system; 3) redundant flash software and controllers should be eliminated from the bridge-based SSD architecture; and 4) latency of PCIe SSDs significantly degrade with their storage-level queueing mechanism. Finally, we discuss system implications including potential PCIe SSD applications such as all-flash array.
Power flow modeling and analysis of voltage source converter-based plug-in electric vehicles

This paper presents a novel plug-in electric vehicle (PEV) model in a voltage controlled bus formulation, suitable to carry out efficient power flow studies of large vehicular fleets. The PEV model comprises a voltage source converter (VSC) and it is different from the family of PEV models based on a PQ bus with unity power factor concept. While active power is regulated at the storage device according to the charging and discharging status of battery, the voltage magnitude at the point of common coupling is regulated by the VSC. In addition, a comprehensive VSC-based PEV equivalent model that accurately reflects the behavior of a distributed vehicular fleet is proposed in this work to carry out efficient steady-state analyses. Consequently, power flow studies of electric power networks including large vehicular fleets can be performed with a low computational effort and without losing accuracy. A Tesla Roadster PEV including a lithium-ion battery pack and a single phase inverter is modeled with the proposal presented in this paper, considering both active and reactive power transfer conditions. The impact of a plug-in vehicular fleet in the voltage profile is analyzed for the IEEE 14-node test system.
Prevention of Fungal Peritonitis with Nystatin Prophylaxis in Patients Receiving CAPD

Objective Fungal peritonitis (FP) is a serious complication of continuous ambulatory peritoneal dialysis (CAPD), being associated with significant morbidity and mortality. The role of nystatin prophylaxis during antibiotic therapy in the prevention of FP remains controversial, especially in programs with a modest or low baseline FP rate. The aim of the present study was to evaluate the effect of nystatin prophylaxis on the occurrence of FP in programs with a relatively modest baseline FP rate. Patients and Methods Incident and prevalent patients receiving CAPD between April 1995 and April 2005 at our center were included and divided into 2 groups. The control group included 320 patients (total follow-up 8875 patient-months) being treated without nystatin before October 1999; the nystatin group included 481 patients (total follow-up 13725 patient-months) being treated after October 1999. Nystatin tablets (500000 units, 4 times per day) were given orally during whatever use of antibiotics to cover the whole course of antibiotic therapy. Occurrence of FP and antibiotic-related FP (AR-FP) in patients with and without nystatin prophylaxis was compared. Results The two groups were of similar age but the nystatin group had a significantly higher percentage of diabetics. In addition, the nystatin group had a higher proportion of patients using disconnecting twin-bag exchange systems and had a significantly lower peritonitis rate compared with the control. There were 13 and 14 episodes of FP in the nystatin and control groups respectively. The fungal peritonitis rate of the nystatin group was slightly lower than that of the control group (0.011 vs 0.019 per patient-year) but it did not reach statistical significance. There was, however, a significant decrease in the incidence and proportion of AR-FP in the nystatin group compared with the control group, which persisted even after adjustment for the peritonitis rate. Kaplan–Meier analysis further demonstrated significantly better AR-FP-free survival in the nystatin group compared with the control group. No significant side effects were observed for nystatin. Subgroup analyses in patients of the 2 different connecting systems revealed a similar but nonsignificant trend toward reduction of AR-FP in patients given nystatin prophylaxis. Conclusion Oral nystatin prophylaxis might prevent the occurrence of AR-FP in CAPD patients, resulting in a trend toward reduction in the incidence of FP even in programs with a modest baseline FP rate. A large scale, prospective, randomized controlled trial is needed to further examine this issue.
Body image and depression in women with early and late onset obesity.

ABSTRACT Three groups of women (N = 27 in each group) were compared: women of normal weight and asymptomatic for eating disorders (M = 125.5 lb); women with early onset obesity—before 13 years (M = 182.4 lb); and women with adult onset obesity—17 years or over (M = 172.4 lb). Subjects (M age = 40.7 years) were obtained through church and business groups. Body image and depression were assessed, respectively, by three scales of the Body-Self Relations Questionnaire (Winstead & Cash, 1983) and by the Beck Depression Inventory (Beck, 1967). The combined group of obese subjects rated their bodies as less fit than normal weight subjects (p<.01). However, there were no other significant differences between obese and normal weight subjects. Also, no significant differences were found between the early and late onset groups. Results showed that (a) there is a subpopulation of obese women who are relatively satisfied with their bodies and whose psychological adjustment is no different from that of other women, and.
Dual-gate silicon nanowire transistors with nickel silicide contacts

The formation of nickel silicide contacts in silicon nanowire transistors and its impact on the electrical device characteristics is investigated. The authors notice that silicide formation at low temperature converts substantial portions of the silicon wire into a metallic source/drain extension. The study also shows the impact of these contacts in a dual-gate field-effect transistor design and discusses the importance of carrier injection from the contacts even for devices with substantial scattering inside the channel
A Preliminary Assessment of Contamination of Emergency Service Helicopters with MRSA and Multi-Resistant Staphylococcus aureus

Objective: To detect the presence of methicillin-resistant Staphylococcus aureus (MRSA) and multi-resistant S. aureus (Multi-RSA) in emergency service helicopters. Methods: This proof-of-concept study used a convenience sample of two emergency service helicopters located in different Australian towns. Over a three-month period ending January 31 2015, within each helicopter five areas of perceived high contact were sampled by taking swabs on an approximately weekly basis. The precise occasions varied based on timings of cases and maintenance schedules. Swabs were analysed for the presence of MRSA, Multi-RSA and other bacteria. Results: Presumptive MRSA and other colonies were recovered from each helicopter. Of those presumptive colonies tested, 18.7% were identified as Staphylococcus aureus, 76.0% were other staphylococci (such as S. epidermidis), and 5.3% were other genera of bacteria. Further testing of these colonies detected no MRSA or Multi- RSA. Over the period of this study, high total numbers of bacteria were recovered in both helicopters. Typically, the floor of the helicopters had higher counts than the seat belts and the blood pressure cuff containers, whereas the radio and cardiac equipment had comparatively lower counts. Conclusions: Since a total of 94.7% of the colonies tested were identified as Staphylococcus spp. the potential for the existence of MRSA in emergency service helicopters is apparent. Our findings highlight the importance of regular cleaning in emergency service vehicles to promote the reduction of infectious disease transmission. We recommend the implementation of a standard operating procedure for cleaning and disinfection across all emergency service providers, reinforced by appropriate infection control training. For quality control, random intermittent swab testing of selected surfaces within all helicopters is advised. The implications of our findings may assist emergency medical service providers to reduce infectious disease transmission risks, and may help to minimise exposure to pathogenic microorganisms during disaster events including pandemics and bioterrorism.
Mutagenic analysis of the nucleation propensity of oxidized Alzheimer's β‐amyloid peptide

The formation of polypeptide aggregates represents a nucleated polymerization reaction in which an initial nucleation event (lag phase) is followed by the extension of newly formed nuclei into larger aggregates, including fibrils (growth phase). The efficiencies of these reactions relate to the lag time (lag phase) and to the rate of aggregation (growth phase), which can be determined from experimental aggregation curves. Here we present a mutagenic analysis in which we replace valine 18 of the Alzheimer's Aβ (1–40) peptide with 17 different amino acids and determine its effect on the lag time, and therefore, on the propensity of nucleation. Comparison with various physico‐chemical properties shows that nucleation is affected in a predictable manner depending on the β‐sheet propensity and hydrophobicity of residue 18. In addition, we observe a direct proportionality between the lag time and the rate of aggregation. These data imply that the two reactions, nucleation and polymerization, are governed by very similar physicochemical principles and that they involve the formation of the same types of noncovalent interactions.
La Protein Is Associated with Terminal Oligopyrimidine mRNAs in Actively Translating Polysomes*

La is an abundant, mostly nuclear, RNA-binding protein that interacts with regions rich in pyrimidines. In the nucleus it has a role in the metabolism of several small RNAs. A number of studies, however, indicate that La protein is also implicated in cytoplasmic functions such as translation. The association of La in vivo with endogenous mRNAs engaged with polysomes would support this role, but this point has never been addressed yet. Terminal oligopyrimidine (TOP) mRNAs, which code for ribosomal proteins and other components of the translational apparatus, bear a TOP stretch at the 5′ end, which is necessary for the regulation of their translation. La protein can bind the TOP sequence in vitro and activates TOP mRNA translation in vivo. Here we have quantified La protein in the cytoplasm of Xenopus oocytes and embryo cells and have shown in embryo cells that it is associated with actively translating polysomes. Disruption of polysomes by EDTA treatment displaces La in messenger ribonucleoprotein complexes sedimenting at 40–60 S. The results of polysome treatment with either low concentrations of micrococcal nuclease or with high concentrations of salt indicate, respectively, that La association with polysomes is mediated by mRNA and that it is not an integral component of ribosomes. Moreover, the analysis of messenger ribonucleoprotein complexes dissociated from translating polysomes shows that La protein associates with TOP mRNAs in vivo when they are translated, in line with a positive role of La in the translation of this class of mRNAs previously observed in cultured cells.
A revised boundary condition for the numerical analysis of Schottky barrier diodes

A new boundary condition for the computer simulation of Schottky barrier diodes is proposed. In this model the electron transport analysis can be extended to higher bias voltages by utilizing a current-dependent surface recombination velocity which is based on a drifted Maxwellian distribution of carrier velocities. Calculations based on this revised boundary condition predict a depletion of electrons at the Schottky boundary compared with an accumulation predicted in previously published calculations.
Title Roles of MIWI , MILI and PLD 6 in small RNA regulation inmouse growing oocytes

The mouse PIWI-interacting RNA (piRNA) pathway produces a class of 26–30-nucleotide (nt) small RNAs and is essential for spermatogenesis and retrotransposon repression. In oocytes, however, its regulation and function are poorly understood. In the present study, we investigated the consequences of loss of piRNA-pathway components in growing oocytes. When MILI (or PIWIL2), a PIWI family member, was depleted by gene knockout, almost all piRNAs disappeared. This severe loss of piRNA was accompanied by an increase in transcripts derived from specific retrotransposons, especially IAPs. MIWI (or PIWIL1) depletion had a smaller effect. In oocytes lacking PLD6 (or ZUCCHINI or MITOPLD), a mitochondrial nuclease/phospholipase involved in piRNA biogenesis in male germ cells, the piRNA level was decreased to 50% compared to wild-type, a phenotype much milder than that in males. Since PLD6 is essential for the creation of the 5′ ends of primary piRNAs in males, the presence of mature piRNA in PLD6depleted oocytes suggests the presence of compensating enzymes. Furthermore, we identified novel 21–23-nt small RNAs, termed spiRNAs, possessing a 10-nt complementarity with piRNAs, which were produced dependent on MILI and independent of DICER. Our study revealed the differences in the biogenesis and function of the piRNA pathway between sexes.
Novel nuclear and mitochondrial glycosylases revealed by disruption of the mouse Nth1 gene encoding an endonuclease III homolog for repair of thymine glycols

Endonuclease III, encoded by nth in Escherichia coli, removes thymine glycols (Tg), a toxic oxidative DNA lesion. To determine the biological significance of this repair in mammals, we established a mouse model with mutated mNth1, a homolog of nth, by gene targeting. The homozygous mNth1 mutant mice showed no detectable phenotypical abnormality. Embryonic cells with or without wild‐type mNth1 showed no difference in sensitivity to menadione or hydrogen peroxide. Tg produced in the mutant mouse liver DNA by X‐ray irradiation disappeared with time, though more slowly than in the wild‐type mouse. In extracts from mutant mouse liver, we found, instead of mNTH1 activity, at least two novel DNA glycosylase activities against Tg. One activity is significantly higher in the mutant than in wild‐type mouse in mitochondria, while the other is another nuclear glycosylase for Tg. These results underscore the importance of base excision repair of Tg both in the nuclei and mitochondria in mammals.
Performance of Convolution Coded Multicarrier CDMA System in Frequency Selective Rayleigh Channel

The paper describes the performance of convolution coded Multicarrier Code Division Multiple Access (MC-CDMA) system evaluated for different equalization techniques i.e. Maximal Ratio Combining (MRC) and Equal Gain Combining (EGC) in frequency selective Rayleigh channel in detail. For symbol mapping two modulation techniques: Binary Phase Shift Keying (BPSK) and Quadrature Phase Shift Keying (QPSK) is used. The comparison is done between the performances of MC-CDMA system with convolution codes and without convolution codes for different equalization and modulation techniques in terms of Bit Error Rate (BER) and Signal to Noise Ratio (SNR) using MATLAB based simulation. Simulation results reveal better SNRs when 1⁄2 rate convolution coding is used with different modulation techniques.
Genome Sequence of Rhizobium grahamii CCGE502, a Broad-Host-Range Symbiont with Low Nodulation Competitiveness in Phaseolus vulgaris

ABSTRACT Here we present the genome sequence of Rhizobium grahamii CCGE502. R. grahamii groups with other newly described broad-host-range species, which are not very efficient Phaseolus vulgaris symbionts, with a wide geographic distribution and which constitutes a novel Rhizobium clade.
An image quality evaluation tool simulating image sensors including quantum efficiency off-axis effect

The image quality evaluation of CMOS sensors is a big challenge for camera module manufacturers. In this paper, we present an update of the Image Quality Evaluation Tool, a graphical user interface simulating image sensors to assess the performance of a pixel. The simulated images are computed from operating conditions and sensor's characteristics like Quantum Efficiency including off-axis effect. Simulation of QE off-axis impact has been based on characterization data. The method does not require optics, making it suitable for early design phases as for optimizations and investigations. Both measurement and implementation in the tool will be explained. The QE degradation with angle effect will be highlighted on simulated images. A uniform gray scene or coloured image simulation from QE off-axis measurement will help engineers to calculate post-processing digital correction like colour shading correction or colour correction matrix versus pixel position.
Using Adaptive Neural Networks in Self-Healing Systems

Self-healing in systems is one of the main characteristics of Autonomic Computing (AC). In this regard the challenge is how to implement self-healing systems in real time, since online learning is required so that the running system is tuned and adapted automatically, based on the current changes of the system's behavior. In this paper, to overcome the challenges associated with self-healing comprising monitoring, interpretation, resolution, and adaptation (MIRA); a novel technique is implemented using pipelined recursive neural networks (PRNN) with a modification of the original algorithm. This method enables us to deal with several independent signals instead of one input; also on the fly learning is achieved in order to address the problems of providing system self-healing. For example instigating continuous learning rather that supervised learning which is not suitable for real systems. Traditional Predefined methods were used, but in this paper an external approach of self-adaptation is implemented to suit the changes of real time systems.
Tyrosine 192 in Apolipoprotein A-I Is the Major Site of Nitration and Chlorination by Myeloperoxidase, but Only Chlorination Markedly Impairs ABCA1-dependent Cholesterol Transport*

High density lipoprotein (HDL) isolated from human atherosclerotic lesions and the blood of patients with established coronary artery disease contains elevated levels of 3-nitrotyrosine and 3-chlorotyrosine. Myeloperoxidase (MPO) is the only known source of 3-chlorotyrosine in humans, indicating that MPO oxidizes HDL in vivo. In the current studies, we used tandem mass spectrometry to identify the major sites of tyrosine oxidation when lipid-free apolipoprotein A-I (apoA-I), the major protein of HDL, was exposed to MPO or peroxynitrite (ONOO-). Tyrosine 192 was the predominant site of both nitration and chlorination by MPO and was also the major site of nitration by ONOO-. Electron paramagnetic spin resonance studies of spin-labeled apoA-I revealed that residue 192 was located in an unusually hydrophilic environment. Moreover, the environment of residue 192 became much more hydrophobic when apoA-I was incorporated into discoidal HDL, and Tyr192 of HDL-associated apoA-I was a poor substrate for nitration by both myeloperoxidase and ONOO-, suggesting that solvent accessibility accounted in part for the reactivity of Tyr192. The ability of lipid-free apoA-I to facilitate ATP-binding cassette transporter A1 cholesterol transport was greatly reduced after chlorination by MPO. Loss of activity occurred in concert with chlorination of Tyr192. Both ONOO- and MPO nitrated Tyr192 in high yield, but unlike chlorination, nitration minimally affected the ability of apoA-I to promote cholesterol efflux from cells. Our results indicate that Tyr192 is the predominant site of nitration and chlorination when MPO or ONOO- oxidizes lipid-free apoA-I but that only chlorination markedly reduces the cholesterol efflux activity of apoA-I. This impaired biological activity of chlorinated apoA-I suggests that MPO-mediated oxidation of HDL might contribute to the link between inflammation and cardiovascular disease.