Miracle-dz/UniFAR-FTUs huggingface dataset:
Phylogenetic and Evolutionary Patterns in Microbial Carotenoid Biosynthesis Are Revealed by Comparative Genomics

Background Carotenoids are multifunctional, taxonomically widespread and biotechnologically important pigments. Their biosynthesis serves as a model system for understanding the evolution of secondary metabolism. Microbial carotenoid diversity and evolution has hitherto been analyzed primarily from structural and biosynthetic perspectives, with the few phylogenetic analyses of microbial carotenoid biosynthetic proteins using either used limited datasets or lacking methodological rigor. Given the recent accumulation of microbial genome sequences, a reappraisal of microbial carotenoid biosynthetic diversity and evolution from the perspective of comparative genomics is warranted to validate and complement models of microbial carotenoid diversity and evolution based upon structural and biosynthetic data. Methodology/Principal Findings Comparative genomics were used to identify and analyze in silico microbial carotenoid biosynthetic pathways. Four major phylogenetic lineages of carotenoid biosynthesis are suggested composed of: (i) Proteobacteria; (ii) Firmicutes; (iii) Chlorobi, Cyanobacteria and photosynthetic eukaryotes; and (iv) Archaea, Bacteroidetes and two separate sub-lineages of Actinobacteria. Using this phylogenetic framework, specific evolutionary mechanisms are proposed for carotenoid desaturase CrtI-family enzymes and carotenoid cyclases. Several phylogenetic lineage-specific evolutionary mechanisms are also suggested, including: (i) horizontal gene transfer; (ii) gene acquisition followed by differential gene loss; (iii) co-evolution with other biochemical structures such as proteorhodopsins; and (iv) positive selection. Conclusions/Significance Comparative genomics analyses of microbial carotenoid biosynthetic proteins indicate a much greater taxonomic diversity then that identified based on structural and biosynthetic data, and divides microbial carotenoid biosynthesis into several, well-supported phylogenetic lineages not evident previously. This phylogenetic framework is applicable to understanding the evolution of specific carotenoid biosynthetic proteins or the unique characteristics of carotenoid biosynthetic evolution in a specific phylogenetic lineage. Together, these analyses suggest a “bramble” model for microbial carotenoid biosynthesis whereby later biosynthetic steps exhibit greater evolutionary plasticity and reticulation compared to those closer to the biosynthetic “root”. Structural diversification may be constrained (“trimmed”) where selection is strong, but less so where selection is weaker. These analyses also highlight likely productive avenues for future research and bioprospecting by identifying both gaps in current knowledge and taxa which may particularly facilitate carotenoid diversification.
A graph pattern matching approach to software architecture recovery

This paper presents a technique for recovering the high level design of legacy software systems based on pattern matching and user defined architectural patterns. Architectural patterns are represented using a description language that is mapped to an attributed relational graph and allows to specify the legacy system components and their data and control flow interactions. Such pattern descriptions are viewed as queries that are applied against an entity-relation graph that represents information extracted from the source code of the software system. A multi-phase branch and bound search algorithm with a forward checking mechanism controls the matching process of the two graphs by which, the query is satisfied and its variables are instantiated. An association based scoring mechanism is used to rank the alternative results generated by the matching process. Experimental results of applying the technique on the Xfig system are also presented.
Acute Phase Proteins in Racehorses with Inflammatory Airway Disease

Background Systemic inflammation is observed in horses with heaves and could also be present in horses with a lesser degree of pulmonary inflammation. Hypothesis/Objectives It was hypothesized that racehorses with inflammatory airway disease (IAD) have increased concentration of circulating acute phase proteins. The objective of this study was to compare serum acute phase proteins of racehorses with and without lower airway inflammation. Animals Serum from 21 client‐owned Standardbred racehorses with exercise intolerance and lower airway inflammation and serum from 10 client‐owned Standardbred racehorses with exercise intolerance without lower airway inflammation. Methods In a case–control study, serum samples from previously characterized horses presented for exercise intolerance with or without lower airway inflammation based on bronchoalveolar lavage fluid cytology were analyzed for serum amyloid A protein (SAA), C‐reactive protein (CRP), and haptoglobin using commercial ELISAs. Results There was no significant differences between groups for SAA (non‐IAD versus IAD, median (range): 3.47 (0.06–34.94) versus 6.33 (0.06–80) μg/mL, P = . 49), CRP (10.87 (2.05–29.03) versus 4.63 (0.02–31.81) μg/mL, P = . 23) or haptoglobin (900.36 (607.99–2018.84) versus 749.54 (530.81–1076.95) μg/mL, P = . 09). Conclusions and Clinical Importance In this population of poorly performing racehorses in training, serum SAA, CRP, and haptoglobin were not helpful in distinguishing between horses with IAD from horses with exercise intolerance from other causes.
Area and power reduction in DFT based channel estimators for OFDM systems

This paper presents a new hardware implementation proposal for Discrete Fourier Transform (DFT) based channel estimators. The presented algorithm uses the high time correlation property of the channel estimates to reduce the complexity and the power consumption by utilizing a lower number of bits for the FFT, compared to a traditional approach. The idea is that the channel estimator processes the the difference between channel estimates from two Orthogonal Frequency Division Multiplexing (OFDM) symbols. The paper shows that the resulting HW could be reduced by 30 percent for logic and 15 percent for memory without performance loss in an Long Term Evolution (LTE) channel with up to 300 Hz Doppler. The algorithm has been tested in realistic environments with 3GPP channel models.
Effects of Astragaloside IV Against the TGF-β1-Induced Epithelial-to-Mesenchymal Transition in Peritoneal Mesothelial Cells by Promoting Smad 7 Expression

Background/Aims: To investigate the effect of Astragaloside IV (AS-IV) on the regulation of the TGF-β1/Smad signaling pathway in peritoneal mesothelial cells with an epithelial-to-mesenchymal transition (EMT). Methods: EMT of human peritoneal mesothelial cells (HMrSV5) was induced using 2 ng/ml TGF-β1. Cells were randomly divided into a vehicle group, a vehicle group with AS-IV, a TGF-β1 treated group, and a TGF-β1 treated group receiving varied doses of AS-IV or NAC. Real-time quantitative PCR and western blot were used to detect the expression of genes and proteins associated with the TGF-β1/Smad signaling pathway and EMT. DCFH-DA was used to detect the generation of ROS in HMrSV5 cells, and a transwell migration assay was used to verify the capacity of AS-IV to inhibit EMT in HMrSV5 cells. Lentiviruses were used as carriers for the overexpression or knockdown of the Smad7 gene. Results: Expression levels of E-cadherin (epithelial marker) was decreased and vimentin, α-SMA (EMT markers) and collagen I (extracellular matrix protein) phospho-Smad2/3, Snail1 and Snail2 was increased significantly in the TGF-β1-treated HMrSV5 cells. AS-IV was associated with downregulated expression of vimentin and phospho-Smad2/3 in a dose-dependent manner, while the expression of Smad7 increased. Silenced or forced expression of Smad7 verified its role in the inhibitory effect of AS-IV on TGF-β1-induced EMT in HMrSV5 cells. Conclusion: AS-IV effectively promotes the upregulation of Smad7 in the TGF-β1/Smad signaling pathway during the EMT of HMrSV5 cells, indicating its potential therapeutic effect for the control of PF.
Magnetic Bead-Based Colorimetric Immunoassay for Aflatoxin B1 Using Gold Nanoparticles

A competitive colorimetric immunoassay for the detection of aflatoxin B1 (AFB) has been established using biofunctionalized magnetic beads (MBs) and gold nanoparticles (GNPs). Aflatoxin B1-bovine serum albumin conjugates (AFB-BSA) modified MBs were employed as capture probe, which could specifically bind with GNP-labeled anti-AFB antibodies through immunoreaction, while such specific binding was competitively inhibited by the addition of AFB. After magnetic separation, the supernatant solution containing unbound GNPs was directly tested by UV-Vis spectroscopy. The absorption intensity was directly proportional to the AFB concentration. The influence of GNP size, incubation time and pH was investigated in detail. After optimization, the developed method could detect AFB in a linear range from 20 to 800 ng/L, with the limit of detection at 12 ng/L. The recoveries for spiked maize samples ranged from 92.8% to 122.0%. The proposed immunoassay provides a promising approach for simple, rapid, specific and cost-effective detection of toxins in the field of food safety.
Convex sensing-reporting optimization for cooperative spectrum sensing

We consider the cooperative spectrum sensing problem in cognitive radio with energy detection. Secondary users with non-identical, independent sensing channels make 1-bit sensing decisions and report their decisions to the secondary base station over orthogonal fading channels. The base station acts as a fusion center by combining the decisions with OR-rule. We allow the secondary users to trade sensing time slots for additional reporting time slots. We derive the corresponding false alarm and missed detection probabilities, which are functions of the secondary sensor decision thresholds and the durations for sensing and reporting. Furthermore, we bound these probabilities and impose a practical convex region that enables convex optimization to minimize the false alarm probability for a target missed detection probability. Allowing secondary users to trade sensing time slots for additional reporting time slots is shown to significantly improve sensing performance, even with poor sensing channels and a small number of secondary users.
UvA-DARE ( Digital Academic Repository ) SecA is required for membrane targeting of the cell division protein DivIVA in vivo

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NUMERICAL EVALUATION OF FLOW THROUGH A 5X5 PWR ROD BUNDLE: EFFECT OF THE VANE ARRANGEMENT IN A SPACER GRID

Spacer grids along the fuel assembly of Pressurized Water Reactors (PWR) maintain rod bundles arranged in a regular square configuration. The mixing vanes present in the spacer grids promote cross and swirl flow between and within the subchannels, enhancing the heat transfer performance in the grid vicinity, but also causing an adverse increase of the pressure drop in the rod bundle due the constriction on the coolant flow area. Therefore, the thermal hydraulic design of the grid must allow for both low pressure loss and high coolant mixing, which means it is important to optimize the design of the grid in relation to the mixing vane. More recently, Computational Fluid Dynamics (CFD) using three dimensional Reynolds Averaged Navier Stokes (RANS) analysis has been used efficiently as an auxiliary tool in the development of spacer grids. The influence of some geometric characteristics of spacer grids on the flow through a rod bundle have been numerically evaluated and are still a subject of discussion. This work analyses the influence of the vanes arrangement in the spacer grid on the flow through a PWR 5 x 5 rod bundle segment. The Numerical simulations were performed with the commercial code CFX 11.0. To make the simulation possible with a limited computational capacity and acceptable mesh refinement, the computational domain was divided in 7 subdomains. The subdomains were simulated sequentially applying the outlet results of a previous subdomain as inlet condition for the next. In this study the k-� turbulence model with scalable wall function was used. Five different vane arrangements were simulated at reactor level power and flow characteristics. The same grid and vane geometry were used in all simulations. The results of this study were divided in two parts. In the first part the presence of peripheral vanes on 5 x 5 rod bundle spacer grid tests were evaluated. The results showed that peripheral vanes should be avoided in experiments and simulations in order to obtain a closer to the real flow distribution at the center subchannels. In the second part the vane arrangement effects were assessed. Results showed that the grid pressure drop and secondary flow is only slightly influenced by the vane arrangement, however heat transfer and mixing downstream the grids are enhanced by vane arrangement that develop a cross flow behavior.
Correcting errors in synthetic DNA through consensus shuffling

Although efficient methods exist to assemble synthetic oligonucleotides into genes and genomes, these suffer from the presence of 1–3 random errors/kb of DNA. Here, we introduce a new method termed consensus shuffling and demonstrate its use to significantly reduce random errors in synthetic DNA. In this method, errors are revealed as mismatches by re-hybridization of the population. The DNA is fragmented, and mismatched fragments are removed upon binding to an immobilized mismatch binding protein (MutS). PCR assembly of the remaining fragments yields a new population of full-length sequences enriched for the consensus sequence of the input population. We show that two iterations of consensus shuffling improved a population of synthetic green fluorescent protein (GFPuv) clones from ∼60 to >90% fluorescent, and decreased errors 3.5- to 4.3-fold to final values of ∼1 error per 3500 bp. In addition, two iterations of consensus shuffling corrected a population of GFPuv clones where all members were non-functional, to a population where 82% of clones were fluorescent. Consensus shuffling should facilitate the rapid and accurate synthesis of long DNA sequences.
Adaptive wavelet graph model for Bayesian tomographic reconstruction

We introduce an adaptive wavelet graph image model applicable to Bayesian tomographic reconstruction and other problems with nonlocal observations. The proposed model captures coarse-to-fine scale dependencies in the wavelet tree by modeling the conditional distribution of wavelet coefficients given overlapping windows of scaling coefficients containing coarse scale information. This results in a graph dependency structure which is more general than a quadtree, enabling the model to produce smooth estimates even for simple wavelet bases such as the Haar basis. The inter-scale dependencies of the wavelet graph model are specified using a spatially nonhomogeneous Gaussian distribution with parameters at each scale and location. The parameters of this distribution are selected adaptively using nonlinear classification of coarse scale data. The nonlinear adaptation mechanism is based on a set of training images. In conjunction with the wavelet graph model, we present a computationally efficient multiresolution image reconstruction algorithm. This algorithm is based on iterative Bayesian space domain optimization using scale recursive updates of the wavelet graph prior model. In contrast to performing the optimization over the wavelet coefficients, the space domain formulation facilitates enforcement of pixel positivity constraints. Results indicate that the proposed framework can improve reconstruction quality over fixed resolution Bayesian methods.
Quality of Life Assessment in Multiple Myeloma Patients Undergoing Dose Tandem Autologous Stem Cell Transplantation

Few studies exist that consider multiple myeloma (MM) undergoing tandem autologous stem cell transplantation (TASCT). Eighteen patients with advanced MM who underwent dose study between March 2006 and March 2008. Patients <60 year old (10) received conditioning with melphalan 140 mg/m and patients who were was 57.5 years (range 35-69). We conducted the European Organization of Research and Treatment of Cancer (EORTC) QLQ presentation, after each ASCT and thereafter every 3 months for 24 months. Mean global health measure improved from 3.44 before transplant to 4.50 subsequent follow-up visits (P<0.001) and the mean global quality of life score improved from 3.61 to 4.71 (P<0.001). Pain symptom (P<0.001) throughout the period of post TASCT is well tolerated with low toxicity albeit the transient reduction in QoL during both transplants. Post-transplant follow reflects positively on the overall disease does not adequately provide indication regarding the tolerability and effectiveness of a proposed treatment on the patient’s perceived quality of life. As clinicians, our primary c toward patient-welfare as well as survival. Therefore, we should employ the tools of QoL in conjunction with overall survival in order to deliver the best possible patient outcomes. The EORTC-QLQ-MY24 is a practical tool in measuring QoL
The Fiscal Theory of the Price Level - Identification and Testing for the UK in the 1970s

We investigate whether the Fiscal Theory of the Price Level (FTPL) can explain UK inflation in the 1970s. We confront the identification problem involved by setting up the FTPL as a structural model for the episode and pitting it against an alternative Orthodox model; the models have a reduced form that is common in form but, because each model is over-identified numerically distinct. We use indirect inference to test which model could be generating the VECM approximation to the reduced form that we estimate on the data for the episode. Neither model is rejected, though the Orthodox model outperforms the FTPL. But the best account of the period assumes that expectations were a probability-weighted combination of the two regimes.
Dynamic Characterization of the Incidence Angle Dependence of Backscatter Using Metop ASCAT

Observing a target from different look and incidence angles is one of the key features of the Advanced Scatterometer (ASCAT) on-board the series of Metop satellites. The incidence angle dependency of backscatter plays an important role in extracting useful information for the retrieval of geophysical parameters. The TU Wien change detection algorithm exploits the multiangle measurement capabilities of ASCAT to retrieve relative surface soil moisture content. In the TU Wien algorithm, the incidence angle dependence of backscatter is characterized with a second-order polynomial and its coefficients are estimated from several years of data due to robustness. Recently, however, it has been shown by Melzer [1], that a kernel smoother (KS) holds promise to characterize the polynomial coefficients on an interannual basis. In this study, we tested the performance and robustness of the KS globally, by comparing the results obtained from ASCAT on-board Metop-A and Metop-B independently. Overall, a good agreement has been found between Metop-A and Metop-B confirming a robust interannual estimation of the incidence angle dependence of backscatter using the KS. However, in two cases, the prevailing conditions on the ground complicated the estimation: areas with very low signal variation and sandy deserts. An analysis of Hovmöller diagrams provided insight into seasonal variations, also revealing small remaining biases between the instruments. The dynamic characterization of the incidence angle dependence of backscatter allows to study the temporal evolution in more detail and, at the same time, moving a step further on the vegetation correction in the TU Wien soil moisture algorithm.
Effects of green tea catechin extract on serum lipids in postmenopausal women: a randomized, placebo-controlled clinical trial.

BACKGROUND Green tea has been suggested to improve cardiovascular disease risk factors, including circulating lipid variables. However, current evidence is predominantly based on small, short-term randomized controlled trials conducted in diverse populations. OBJECTIVE The aim of this study was to examine the efficacy and impact of green tea extract (GTE) supplementation high in epigallocatechin gallate (EGCG) on blood lipids in healthy postmenopausal women. DESIGN This was an ancillary study of a double-blind, randomized, placebo-controlled, parallel-arm trial investigating the effects of a GTE supplement containing 1315 mg catechins (843 mg EGCG) on biomarkers of breast cancer risk. Participants were randomly assigned to receive GTE (n = 538) or placebo (n = 537) and were stratified by catechol-O-methyltransferase (COMT) genotype activity (high COMT compared with low or intermediate COMT genotype activity). They consumed either 4 GTE or identical placebo capsules daily for 12 mo. A total of 936 women completed this substudy. Circulating lipid panels including total cholesterol (TC), HDL cholesterol, and triglycerides were measured at baseline and at months 6 and 12. RESULTS Compared with placebo, 1-y supplementation with GTE capsules resulted in a significant reduction in circulating TC (-2.1% compared with 0.7%; P = 0.0004), LDL cholesterol (-4.1% compared with 0.9%; P < 0.0001) and non-HDL cholesterol (-3.1% compared with 0.4%; P = 0.0032). There was no change in HDL-cholesterol concentration, but triglyceride concentrations increased by 3.6% in the GTE group, whereas they decreased by 2.5% in the placebo group (P = 0.046). A significant reduction in TC was observed only among women with high (i.e., ≥200 mg/dL) baseline TC concentrations (P-interaction = 0.01) who consumed GTE capsules. The effect of GTE on the increase in triglycerides was mainly observed among obese women and statin users (P-interaction = 0.06). CONCLUSION Supplementation with GTE significantly reduced circulating TC and LDL-cholesterol concentrations, especially in those with elevated baseline TC concentrations. This trial was registered at clinicaltrials.gov as NCT00917735.
Prevalence of diagnosed and undiagnosed diabetes mellitus in adults aged 19 years and older in Basrah, Iraq

Background Six of the top ten countries in the world with the highest prevalence of diabetes mellitus are in the Middle East. The objective of this investigation was to evaluate the prevalence of diabetes in Basrah, Southern Iraq. Methods A population-based, cross-sectional, simple random study screened 5,445 persons aged 19–94 years in Basrah, with glycated hemoglobin measured in 88.3% of the population and fasting plasma glucose in 18.7%. Body mass index and other demographic parameters were also measured. Results Of the 5,445 persons screened, 8.7% had already been diagnosed with diabetes and 11% were found by screening to have undiscovered diabetes, giving an age-adjusted prevalence of diabetes of 19.7%, with 55.7% of those with diabetes being previously undiagnosed. In addition, 29.1% of the screened population had prediabetes, giving a prevalence of dysglycemia of 48.8%, with only 51.2% of the persons screened being normoglycemic. The prevalence of diabetes in both sexes peaked at age 46–60 years. Diabetes was slightly more prevalent in females than in males, and about 70.3% of diabetic individuals had a body mass index ≥25 kg/m2. Conclusion The prevalence of diabetes in Basrah, Iraq, is very high, affecting one in five adults. The epidemic of diabetes will result in strain on the financial resources of health care systems.