Miracle-dz/UniFAR-FTUs huggingface dataset:
Rapid Microcystis Cyanophage Gene Diversification Revealed by Long- and Short-Term Genetic Analyses of the Tail Sheath Gene in a Natural Pond

ABSTRACT Viruses influence the abundance of host populations through virus-mediated host cell lysis. Viruses contribute to the generation and maintenance of host diversity, which also results in viral diversity throughout their coevolution. Here, to determine the phage gene diversification throughout the coevolution of host and phage in a natural environment, we investigated the genetic diversity and temporal changes in Microcystis cyanophage populations using a total of 810 sequences of the Ma-LMM01-type cyanophage tail sheath gene (g91) from 2006 to 2011 in a natural pond. The sequences obtained were highly diverse and assigned to 419 different genotypes (GT1 to GT419) clustered at 100% nucleotide sequence similarity. A maximum-parsimony network showed that the genotypes were largely divided into three sequence groups, which were dominated by major genotypes (more than 24 sequences: GT2, GT53, and GT163 in group I; GT25 in group II; and GT1 in group III). These major genotypes coexisted and oscillated throughout the sampling periods, suggesting that the Microcystis-cyanophage coevolution was partly driven by a negative frequency-dependent selection. Meanwhile, the high viral genetic diversity observed was derived from a large number of the variants of each major and moderately frequent genotype (including 7 to 18 sequences: GT7, GT26, GT56, GT149, and GT182 in group I; GT152 in group II) (1 or 2 nucleotide substitutions). The variants almost always co-occurred with their origin genotypes. This manner of variant emergence suggests that increased contact frequency within a host-phage population promotes rapid coevolution in a form of “arms race. ”
Analysis of fuzzy multi-objective location problems by using open georeferenced data

This paper presents a general solution approach to solve location problems under imprecise criteria based on exploiting open georeferenced data by using a Geographic Information System. The suitability of this approach is assessed on a new practical multi-objective optimization problem arisen in the context of the location theory. It seeks to determine the locations of a known number of electric vehicle sharing stations in the city of San Francisco while considering fuzzy criteria. These new stations are the departure points of touristic routes aimed at visiting the most representative points of interest around the city. The computational experiments indicate that the solution approach can be easily used as an effective tool to support decision making processes in related problems.
A phase-comparison monopulse system based on a 4D antenna array

Conventional monopulse systems based on sum and difference patterns produced by traditional arrays face the contradiction of angle-resolution and angle-searching range, and a compromise between them usually has to be made. In four-dimensional (4D) antenna arrays, multiple pairs of sum and difference patterns can be produced simultaneously at the center frequency and low sidebands. By designing the time sequences reasonably, the multiple sum and difference patterns point in different directions, covering a much wider angle-range. In this paper, the conventional phase-comparison monopulse is introduced into a 4D array to form a novel monopulse system by which both high angle-resolution and wide angel-searching range are realized. Theoretical analysis shows that the novel monopulse system covers a ±60o angle-searching range without beam-scanning. An experiment system based on an 8-element 4D array is established, and measurement results validate the effectiveness of the proposed system.
Analysis of population structure of the chestnut blight fungus based on vegetative incompatibility genotypes.

Vegetative incompatibility is a self/nonself-recognition system in fungi that has often been used for describing phenotypic diversity in fungal populations. A common hypothesis is that vegetative incompatibility polymorphisms are maintained by balancing selection. However, understanding the evolutionary significance of vegetative incompatibility and the factors that maintain these polymorphisms has been limited by a lack of knowledge of the underlying genetics of vegetative compatibility (vc) types. Genotypes of 64 vc types, controlled by six unlinked vegetative incompatibility (vic) loci, have been identified in the chestnut blight fungus, Cryphonectria parasitica. By interpreting vc type survey data in terms of vic genotypes, we estimated vic-allele frequencies and analyzed the multilocus genetic structure of 13 populations in Europe and 3 populations in the U.S. European populations have less vc type diversity than the US populations because of a combination of lower vic-allele diversity and limited recombination. Genotypic diversity of 10 populations in Italy correlated to the abundance of sexual structures; however, significant deviations from random mating suggest that either sexual reproduction may not contribute many offspring in these populations or that vic genes (or vic genotypes) are under selection. Most vic-allele frequencies deviated from 0.5, the equilibrium frequency predicted under frequency-dependent selection, providing no evidence for selection acting on these loci.
Simvastatin: present and future perspectives

Simvastatin is lipophilic statin with a short half-life that is primarily metabolized by CYP450 3A4. At doses of 5 – 80 mg, simvastatin lowers LDL cholesterol by 25 – 50%. Simvastatin has been shown to reduce the risk of cardiovascular disease by 35% and overall mortality by up to 30% over 5 years. The recommended starting dose of simvastatin 40 mg is approved as a lipid-lowering agent and for all high-risk patients, including those with cardiovascular disease and diabetes, regardless of the baseline LDL level. Simvastatin dose should be adjusted in those receiving CYP3A4 inhibitors, gemfibrozil, or ciclosporin, amiodarone, or in those with severe renal insufficiency. Coformulation of simvastatin with ezetimibe is now available, and coformulation with extended release niacin is under development.
Field evaluation of a real-time fluorescence loop-mediated isothermal amplification assay, RealAmp, for the diagnosis of malaria in Thailand and India.

BACKGROUND To eliminate malaria, surveillance for submicroscopic infections is needed. Molecular methods can detect submicroscopic infections but have not hitherto been amenable to implementation in surveillance programs. A portable loop-mediated isothermal amplification assay called RealAmp was assessed in 2 areas of low malaria transmission. METHODS RealAmp was evaluated in 141 patients from health clinics in India (passive surveillance) and in 127 asymptomatic persons in Thailand (active surveillance). The diagnostic validity, precision, and predictive value of RealAmp were determined using polymerase chain reaction (PCR) as the reference method. A pilot study of RealAmp was also performed on samples from patients presenting at a Thai health center. RESULTS A total of 96 and 7 positive cases were detected in India and Thailand, respectively, via PCR. In comparison with nested PCR, the sensitivity and specificity of RealAmp in India were 94.8% (95% confidence interval [CI], 88.3%-98.3%) and 100% (95% CI, 92.1%-100%), respectively, with correct identification of all 5 Plasmodium vivax cases. In Thailand, compared with pooled real-time PCR, RealAmp demonstrated 100% sensitivity (95% CI, 59.0%-100%) and 96.7% specificity (95% CI, 91.7%-99.1%). Testing at the health center demonstrated RealAmp's potential to serve as a point-of-care test with results available in 30-75 minutes. CONCLUSION RealAmp was comparable to PCR in detecting malaria parasites and shows promise as a tool to detect submicroscopic infections in malaria control and elimination programs worldwide.
Multifunctional Role of Choline Binding Protein G in Pneumococcal Pathogenesis

ABSTRACT Members of the choline binding protein (Cbp) family are noncovalently bound to phosphorylcholine residues on the surface of Streptococcus pneumoniae. It has been suggested that CbpG plays a role in adherence and increase virulence both at the mucosal surface and in the bloodstream, but the function of this protein has been unclear. A new sequence analysis indicated that CbpG is a possible member of the S1 family of multifunctional surface-associated serine proteases. Clinical isolates contained two alleles of cbpG, and one-third of the strains expressed a truncated protein lacking the C-terminal, cell wall-anchoring choline binding domain. CbpG on the surface of pneumococci (full length) or released into the supernatant (truncated) showed proteolytic activity for fibronectin and casein, as did CbpG expressed on lactobacilli or as a purified full-length or truncated recombinant protein. Recombinant CbpG (rCbpG)-coated beads adhered to eukaryotic cells, and TIGR4 mutants lacking CbpG or having a truncated CbpG protein showed decreased adherence in vitro and attenuation of disease in mouse challenge models of colonization, pneumonia, and bacteremia. Immunization with rCbpG was protective in an animal model of colonization and sepsis. We propose that CbpG is a multifunctional surface protein that in the cell-attached or secreted form cleaves host extracellular matrix and in the cell-attached form participates in bacterial adherence. This is the first example of distinct functions in virulence that are dependent on natural variation in expression of a choline binding domain.
Hierarchical Multiview Rigid Registration

Registration is a key step in the 3D reconstruction of real‐world objects. In this paper, we propose a hierarchical method for the rigid registration of multiple views. The multiview registration problem is solved via hierarchical optimization defined on an undirected graph. Each node or edge in this graph represents a single view or a connection between two overlapped views, respectively. The optimizations are performed hierarchically on the edges, the loops, and the entire graph. First, each overlapped pair of views is locally aligned. Then, a loop‐based incremental registration algorithm is introduced to refine the initial pairwise alignments. After a loop is registered, the views in the loop are merged into a metaview in the graph. Finally, global error diffusion is applied to the entire graph to evenly distribute the accumulated errors to all views. In addition, a new objective function is defined to describe the loop closure problem; it improves the accuracy and robustness of registration by simultaneously considering transformation and registration errors. The experimental results show that the proposed hierarchical approach is accurate, efficient and robust for initial view states that are not well posed.
A Novel Adaptive, Real-Time Algorithm to Detect Gait Events From Wearable Sensors

A real-time, adaptive algorithm based on two inertial and magnetic sensors placed on the shanks was developed for gait-event detection. For each leg, the algorithm detected the Initial Contact (IC), as the minimum of the flexion/extension angle, and the End Contact (EC) and the Mid-Swing (MS), as minimum and maximum of the angular velocity, respectively. The algorithm consisted of calibration, real-time detection, and step-by-step update. Data collected from 22 healthy subjects (21 to 85 years) walking at three self-selected speeds were used to validate the algorithm against the GaitRite system. Comparable levels of accuracy and significantly lower detection delays were achieved with respect to other published methods. The algorithm robustness was tested on ten healthy subjects performing sudden speed changes and on ten stroke subjects (43 to 89 years). For healthy subjects, F1-scores of 1 and mean detection delays lower than 14 ms were obtained. For stroke subjects, F1-scores of 0.998 and 0.944 were obtained for IC and EC, respectively, with mean detection delays always below 31 ms. The algorithm accurately detected gait events in real time from a heterogeneous dataset of gait patterns and paves the way for the design of closed-loop controllers for customized gait trainings and/or assistive devices.
Impact of Interpolation Techniques on Statistical Properties and Speed of Fading Channel Simulators

Interpolation filters are considered to be computationally intensive sections of fading channel simulators. They can be implemented by using linear interpolation or zero-padding followed by low-pass IIR or polyphase filtering. In this work, we will investigate how different interpolation techniques affect statistical properties and speed of the simulator. We will show that use of linear interpolation results in 3 to 6 times improvement in simulation speed while there is negligible degradation in desired statistical accuracy. We will validate this claim by designing a fading channel simulator that uses the above mentioned three interpolation techniques and observing their impact on its first order (probability density functions) and second order (correlation functions) statistical properties. We will also compare the impact of interpolation techniques on the level crossing rate (LCR) and bit error rate (BER) of the fading signal. Finally, we will emphasize our claim by using an advance multiple-tap channel model (gsmTUX6C1) with our simulator (using linear interpolation) and showing that its performance is comparable to corresponding Matlab model that uses polyphase interpolation. We will conclude this work with a recommendation to use linear interpolation for efficient and statistically correct fading channel simulators.
Significance of endotension, endoleak, and aneurysm pulsatility after endovascular repair.

OBJECTIVE The lack of aneurysm pulsatility after endovascular aneurysm repair (EVAR) is deemed by some an important guide to the effectiveness of exclusion. However, factors that contribute to aneurysm pulsatility after EVAR have not been elucidated. This study quantitatively analyzed the effects of systemic pressure, aneurysm sac pressure, endoleak, branch outflow from aneurysm sac, and intra-sac thrombus on aneurysm pulsatility after EVAR. METHODS In an ex vivo model, an artificial aneurysm sac was incorporated within a mock circulation comprised of rubber tubing and a pulsatile pump. The aneurysm sac was then completely excluded from the circulatory circuit with two types of stent-grafts, ie, supported and unsupported, and heparinized canine blood was circulated. Systemic circulation and aneurysm sac pressure was recorded in the absence and presence of endoleaks, and simulated open and closed lumbar branch outflow from the aneurysm sac. The aneurysm sac was then filled with organized human thrombus, and all pressure measurements were repeated. Two observers blinded to the above-mentioned variables independently evaluated aneurysm sac pulsatility with palpation in five separate experiments. Analysis of variance was performed, with significance accepted at P =. 05. RESULTS Systemic pressure was simulated in the artificial circulation to range from 100/60 to 180/60 mm Hg. Regardless of the simulated lumbar branch outflow from the aneurysm, sac pressure was directly related to the presence of endoleak (P <.001). Aneurysm sac pulsatility was present only when the lumbar branch outflow was patent and not dependent on sac pressures. Aneurysm sac thrombosis or type of stent-graft did not influence sac pressure and pulsatility. CONCLUSIONS In this model, after EVAR pulsatility depends on aneurysm sac outflow, regardless of endoleak, sac thrombosis, sac pressure, or stent-graft. Furthermore, persistent pulsatility does not predict systemic intra-sac pressure, nor does lack of pulsatility reflect freedom of the aneurysm sac from systemic pressurization. This ex vivo model suggests that aneurysm pulsatility is an unreliable guide for predicting aneurysm sac pressurization after EVAR. Other diagnostic methods must be used to assess successful aneurysm exclusion.
Decreased Coronary Vascular Reserve in Watanabe Heritable Hyperlipidemic Rabbits

Watanabe heritable hyperlipidemic (WHHL) rabbits have severe hypercholesterolemla due to a genetic defect In their low density llpoproteln receptors. Therefore, they develop severe premature atherosclerosis of the large arteries Including the coronary arteries. In the present study, we measured the coronary vascular reserve of these rabbits to evaluate the total cross-sectional coronary surface area. This method allowed us to quantify the functional consequences of the coronary atherosclerotic lesions. To evaluate coronary vascular reserve, we measured coronary blood flow with the radioactive mlcrosphere technique before and after Induction of maximal coronary vasodilation by an Intravenous dose of 9 mg/kg of carbocromen. A group of pure-bred WHHL rabbits was compared to a group of normal Burgundy rabbits at ages of 100 and 300 days. At 100 days, there was no difference In coronary vascular reserve between the two groups. However, at 300 days, the coronary vascular reserve In WHHL rabbits was 48% smaller than in the normal Burgundy rabbits (p < 0.01). In addition, by making corrosion casts and morphological studies, we were able to show that at 300 days nearly all the WHHL rabbits had severe coronary atherosclerotic lesions located mainly at the origin of the large coronary arteries. We conclude that WHHL rabbits at 300 days have a severe Impairment of their coronary vascular reserve due to proximal atherosclerotic lesions in the coronary arteries.
C-Reactive Protein May Influence Decisively the Prescription of Prophylactic Antibiotics in Acute Pancreatitis: A Population-Based Cohort Study

Objectives Prescription of prophylactic antibiotics in acute pancreatitis (AP) is controversial. We aimed to identify the patients’ characteristics that may prompt clinicians to prescribe prophylactic antibiotics in AP. Methods This single-center retrospective cohort study included 299 consecutive patients with AP from a Portuguese hospital in 2009 to 2010. Logistic regression was used to study the association of patients’ characteristics with prescription of prophylactic antibiotics in AP. Results Persistent organ failure developed in 7% of patients (9/136). The median C-reactive protein at 48 hours after hospital admission was 154 mg/L (interquartile range, 55–271 mg/L). Bedside Index for Severity in AP score greater than or equal to 3 occurred in 14% of patients (42/299). Pancreatic necrosis was diagnosed in 21% of the patients (35/169). Computerized Tomography Severity Index score greater than 3 occurred in 23% of patients (38/169). In-hospital mortality rate was 4% (10/299). Prophylactic antibiotics were prescribed to 14% of patients (42/299). After adjusting for persistent organ failure and Computerized Tomography Severity Index score greater than 3, C-reactive protein at 48 hours after hospital admission greater than or equal to 150 mg/L was significantly associated with higher likelihood of receiving prophylactic antibiotics (odds ratio, 12.2). Prophylactic antibiotics did not improve in-hospital mortality rate (P = 0.637). Conclusions C-reactive protein was the most influential in prescribing prophylactic antibiotics in AP. Clinicians may need better tools to support the decision to prescribe prophylactic antibiotics in AP.
Pulmonary surfactant composition early in development of acute lung injury after cardiopulmonary bypass: prophylactic use of surfactant therapy.

Cardiopulmonary bypass surgery (CPB) causes lung injury and at least 2% of adult patients and more children develop the most severe form acute respiratory distress syndrome (ARDS). Pulmonary surfactant deficiency contributes to the pathogenesis of ARDS. It has been proposed that surfactant therapy immediately after CPB might arrest progression to ARDS. However, many patients develop only mild lung injury after CPB. Thus early markers are needed to identify those patients at highest risk to guide selection for treatment. The aim of this study was to determine whether changes in surfactant phospholipids occur, and reflect severity of lung injury within the first few hours after bypass. Because of the relatively low incidence of ARDS in adult patients, this study was conducted using young pigs highly susceptible to bypass‐induced lung injury. Eight pigs were given 2 hours bypass. Six controls underwent ‘sham’ bypass. At 3 h after bypass pulmonary vascular endothelial permeability was assessed by transcapillary leakage of radiolabelled transferrin. A 4 hour broncho‐alveolar lavage (BAL) was used to assess intra‐alveolar levels of surfactant, inflammatory cells and oedema protein. Bypass caused falls in arterial oxygenation and lung compliance (P < 0.01), but at this early stage in progression of lung injury BAL surfactant phospholipid and albumin levels were within the control range indicating that the alveolar epithelium had not yet suffered major damage.The main abnormalities were increases in vascular endothelial permeability (P < 0.01), BAL neutrophils (P < 0.01), total protein and sphingomyelin (SM) (P < 0.05). Lung histology showed that the main damage was interstitial oedema located around the bronchioles and their associated vessels. A single instilled dose of surfactant phospholipids in 5 animals caused excess in vivo supplementation and did not reduce the early pathophysiologic changes. Our findings suggest that surfactant phospholipid deficiency does not make a major contribution in the initial stages of lung injury after CPB, and that excessive phospholipid supplementation at this stage can be deleterious.
Zebrafish tiggy‐winkle hedgehog promoter directs notochord and floor plate green fluorescence protein expression in transgenic zebrafish embryos

Zebrafish tiggy‐winkle hedgehog (twhh) is a member of the hedgehog gene family that plays an important role in patterning brain, neural tube, somites, and eyes. To better understand the regulation of its tissue‐specific expression, the activity of the twhh promoter was determined in zebrafish embryos by transient and transgenic expression analysis. Transient expression studies revealed that the 5.2‐kb twhh promoter drove green fluorescence protein (GFP) expression in the notochord, floor plate, and branchial arches. Deletion analysis showed that distinct regions of the twhh promoter regulated the respective notochord or floor plate specific expression. To confirm the tissue specificity of the twhh promoter, transgenic zebrafish containing the twhh‐GFP transgene were generated. GFP expression was analyzed in the F1, F2, and F3 generations of the transgenic embryos. The results confirmed the tissue‐specific expression of the transgene in the notochord, floor plate, and branchial arches. In addition, GFP expression was also found in the pectoral fin buds, retina, and epithelial lining cells of the Kupffer's vesicle in the transgenic fish embryos. The expression pattern of the twhh‐GFP transgene mimicked the expression of the endogenous twhh mRNAs in the floor plate, fin buds, branchial arches, retina, and epithelial lining cells of the Kupffer's vesicle. The expression in the notochord, however, did not mimic the pattern of the endogenous twhh expression. To determine whether no tail (ntl) or floating head (flh) mutants that have developmental defect in the notochord or the Kupffer's vesicle may affect the GFP expression in these regions, GFP expression was analyzed in ntl or flh transgenic embryos. No GFP expression could be detected in the midline region of the ntl transgenic embryos. However, in flh transgenic embryos, although GFP expression was affected in the midline region, its expression in the Kupffer's vesicle appeared normal. Together, these data indicated that the 5.2‐kb twhh promoter contains regulatory elements for tissue‐specific expression of twhh in the floor plate, pectoral fin bud, branchial arches, retina, and Kupffer's vesicle. © 2001 Wiley‐Liss, Inc.