Miracle-dz/UniFAR-FTUs huggingface dataset:
Influence of fungal endophyte infection on phenolic content and antioxidant activity in grasses: interaction between Lolium perenne and different strains of Neotyphodium lolii.

Lolium perenne is a major forage and turf grass, which is often naturally infected with a "wild-type" strain (E(WT)) of the fungal endophyte Neotyphodium lolii , establishing a symbiotic relationship. In this study, the impacts of different strains wild type E(WT), AR1 (E(AR1)) and AR37 (E(AR37)), of N. lolii on the phenolic profile, phenolic content, and antioxidant capacity of L. perenne were examined. Samples could be ranked according to their phenol content as follows: E(AR1) > E(AR37) ≥ E(-) > E(WT). Radical-scavenging assays showed the same relative ranking of extracts. Flavonoid glycosides and hydroxycinnamic acids were the most abundant polyphenols in L. perenne extracts. Chlorogenic acid and its derivatives were the major compounds responsible for the antioxidant activity. Infection with N. lolii significantly influenced L. perenne phenolic content and antioxidant activity. In conclusion, changes in phenolic composition were merely quantitative. Endophyte infection can have zero, positive, or negative effect on phenol content depending on the endophyte strain.
Free energy reconstruction from irreversible single- molecule pulling experiments

Recent developments in nonequilibrium statistical mechanics, including Jarzynski's equality and the Crooks Fluctuation Theorem, have made the calculation of equilibrium free energy differences from irreversible processes possible. Building off these theorems, two approaches have been developed to calculate the free energy surface, or potential of mean force, along a continuous reaction coordinate: the stiff spring approximation and the Hummer-Szabo method. In this thesis, we extend the Hummer-Szabo method to encompass pulling experiments performed with different biasing protocols and to calculate multidimensional potentials of mean force. These extensions are tested on toy one-dimensional and two -dimensional systems. Next, we compare the efficacy of the stiff spring approximation and the Hummer-Szabo method in interpreting pulling experiments at different spring stiffnesses and using dynamic force spectroscopy on the model peptide deca-alanine. We find that analysis based on the stiff spring approximation fails when weaker springs are used. The Hummer-Szabo method is generally more effective for interpreting dynamic force spectroscopy. For both methods, the second cumulant expansion is found to be a good way to make the best of a limited sample. We anticipate that the methods and analysis presented in this thesis will be useful to experimentalists seeking to design and interpret irreversible single-molecule pulling experiments
The Anolis Lizard Genome: An Amniote Genome without Isochores

Isochores are large regions of relatively homogeneous nucleotide composition and are present in the genomes of all mammals and birds that have been sequenced to date. The newly sequenced genome of Anolis carolinensis provides the first opportunity to quantify isochore structure in a nonavian reptile. We find Anolis to have the most compositionally homogeneous genome of all amniotes sequenced thus far, a homogeneity exceeding that for the frog Xenopus. Based on a Bayesian algorithm, Anolis has smaller and less GC-rich isochores compared with human and chicken. Correlates generally associated with GC-rich isochores, including shorter introns and higher gene density, have all but disappeared from the Anolis genome. Using genic GC as a proxy for isochore structure so as to compare with other vertebrates, we found that GC content has substantially decreased in the lineage leading to Anolis since diverging from the common ancestor of Reptilia ∼275 Ma, perhaps reflecting weakened or reversed GC-biased gene conversion, a nonadaptive substitution process that is thought to be important in the maintenance and trajectory of isochore evolution. Our results demonstrate that GC composition in Anolis is not associated with important features of genome structure, including gene density and intron size, in contrast to patterns seen in mammal and bird genomes.
Inheritance of plumage colour variations in a large flock of Japanese quail

1. The inheritance of various plumage colour variants and their underlying interactions were investigated in a large flock of Japanese quail maintained at CARI (India) by conducting reciprocal crosses between four breeding stocks inheriting Pharaoh, White Breasted, White and Brown plumages, followed by test crosses. 2. Based on the proportion of plumage-colour types in the progeny, putative genotypes were determined for parents and offspring for each of the crosses. 3. The White and Brown phenotypes were attributed to the Panda (S) and Roux (Br) loci respectively in agreement with contemporary quail stocks. 4. The White Breasted plumage type present in our stock was caused by a novel mutation with dominant gene action at an autosomal locus that was not allelic to either Panda or the White feather locus. 5. A recessive epistatic action of the Panda locus (S) on White Breasted (Wb) resulted in a White colour phenotype. 6. A novel phenotype, White Breasted-Brown was co-expressed with the Br and Wb loci. 7. It was concluded that breeding for customized feather colour phenotypes in Japanese quail using colour mutations was feasible and would be advantageous in order to overcome the limitations of legislation to protect wildlife in India.
Short Bouts of Vocalization Induce Long-Lasting Fast Gamma Oscillations in a Sensorimotor Nucleus

Performance evaluation is a critical feature of motor learning. In the vocal system, it requires the integration of auditory feedback signals with vocal motor commands. The network activity that supports such integration is unknown, but it has been proposed that vocal performance evaluation occurs offline. Recording from NIf, a sensorimotor structure in the avian song system, we show that short bouts of singing in adult male zebra finches (Taeniopygia guttata) induce persistent increases in firing activity and coherent oscillations in the fast gamma range (90–150 Hz). Single units are strongly phase locked to these oscillations, which can last up to 30 s, often outlasting vocal activity by an order of magnitude. In other systems, oscillations often are triggered by events or behavioral tasks but rarely outlast the event that triggered them by more than 1 s. The present observations are the longest reported gamma oscillations triggered by an isolated behavioral event. In mammals, gamma oscillations have been associated with memory consolidation and are hypothesized to facilitate communication between brain regions. We suggest that the timing and persistent nature of NIf's fast gamma oscillations make them well suited to facilitate the integration of auditory and vocal motor traces associated with vocal performance evaluation.
The infective endocarditis team: recommendations from an international working group

Infective endocarditis (IE) is uncommon but important because it is difficult to manage and universally fatal unless appropriately treated. The estimated incidence is 3–10 episodes each year per 100 000 population.1 In industrially developed countries, IE increasingly occurs in older adults with intracardiac devices (pacemakers and implantable defibrillators), replacement heart valves and medical interventions such as haemodialysis.2–4 Younger age groups are also affected, particularly intravenous drug users and those with adult congenital heart disease.5 Staphylococci are now the most common causative organisms in international series and streptococci the second most common.6 Resistance to antimicrobial agents, particularly vancomycin, is increasing.1 ,7 Patients with IE remain in hospital for a median of 4–6 weeks8 ,9 and approximately a half require inpatient cardiac surgery.1 ,10 ,11 The inhospital mortality rate is about 20%8 ,12 but varies widely according to age, comorbidity, heart failure, the presence of prosthetic material and the organism.13 For example, in prosthetic valve IE with associated renal failure, the reported mortality may be 40%–50%14 ,15 and with severe heart failure as high as 64%. 15 The outcome can be improved by prompt diagnosis and antibiotic therapy and by early surgery when indicated.8 ,10 ,16 ,17 Despite this, the diagnosis may be delayed, mistakes may be made in the type, duration or dose of antibiotic18 or the antibiotic may be started before blood cultures are obtained.11 Patients are still frequently referred to a specialist only at an advanced stage with heart failure6 ,11 ,18–20 or may not receive surgery even when indicated.8 As expected, non-compliance with guidelines is associated with a worse outcome.20 A multidisciplinary team (MDT) approach is increasingly seen as best practice where decision …
Node cooperation in hybrid ad hoc networks

A hybrid ad hoc network is a structure-based network that is extended using multihop communications. Indeed, in this kind of network, the existence of a communication link between the mobile station and the base station is not required: A mobile station that has no direct connection with a base station can use other mobile stations as relays. Compared with conventional (single-hop) structure-based networks, this new generation can lead to a better use of the available spectrum and to a reduction of infrastructure costs. However, these benefits would vanish if the mobile nodes did not properly cooperate and forward packets for other nodes. In this paper, we propose a charging and rewarding scheme to encourage the most fundamental operation, namely packet forwarding. We use "MAC layering" to reduce the space overhead in the packets and a stream cipher encryption mechanism to provide "implicit. authentication" of the nodes involved in the communication. We analyze the robustness of our protocols against rational and malicious attacks. We show that-using our solution-collaboration is rational for selfish nodes. We also show that our protocols thwart rational attacks and detect malicious attacks.
Maturation and the Evolution of Imitative Learning in Artificial Organisms

The traditional explanation of delayed maturation age, as part of an evolved life history, focuses on the increased costs of juvenile mortality due to early maturation. Prior quantitative models of these trade-offs, however, have addressed only morphological phenotypic traits, such as body size. We argue that the development of behavioral skills prior to reproductive maturity also constitutes an advantage of delayed maturation and thus should be included among the factors determining the trade-off for optimal age at maturity. Empirical support for this hypothesis from animal field studies is abundant. This article provides further evidence drawn from simulation experiments. Latent energy environments (LEE) are a class of tightly controlled environments in which learning organisms are modeled by neural networks and evolve according to a type of genetic algorithm. An advantage of this artificial world is that it becomes possible to discount all nonbehavioral costs of early maturity in order to focus exclusively on behavioral consequences. Despite large selective costs imposed on parental fitness due to prolonged immaturity, the optimal age at maturity is shown to be significantly delayed when offspring learn from their parents' behavior via imitation.
Two distinct pools of recirculating T lymphocytes: migratory characteristics of nodal and intestinal T lymphocytes

A pronounced asymmetry in the recirculation from blood to lymph of resting small recirculating T lymphocytes is described. When 51Cr- labeled small T-recirculating lymphocytes (TRL) from intestinal lymph were infused intravenously their relative recovery in intestinal lymph was about twice that in nodal lymph. In contrast, the relative recovery in nodal lymph of 51Cr-labeled nodal TRL was twice that in intestinal lymph. Intestinal TRL migrated in large numbers through the small intestine. Nodal TRL did not. It is proposed that the pool of recirculating small T lymphocytes consists of two major subdivisions, an intestinal pool and a nodal pool. The nodal circulation comprises small TRL which traverse PCV in all lymph nodes (LN) but not the small intestine. The intestinal circulation comprises small TRL which do not traverse PCV in LN, but which do recirculate through the small intestine from which they pass via afferent lymphatics to the mesenteric LN and subsequently via the thoracic duct into the blood. It is suggested that the intestinal circulation is present in the fetus and that its initial development is independent of extrinsic antigen.
Perspectives on: Ion selectivity: Origins of ion selectivity in potassium channels from the perspective of channel block

Potassium channels play crucial roles in physiology, and one of their more important roles is to repolarize the membrane after an action potential in excitable cells (Hille, 2001). During an action potential, Na+ channels open first and depolarize the cell membrane, which is followed closely by their inactivation and subsequent opening of K+ channels that repolarize the cell membrane by allowing K+ to flow out of the cell. If Na+ were allowed to move through K+ channels, the influx of Na+ would compete with the outflow of K+, and the sharp membrane repolarization would no longer occur. It is then paramount that K+ channels select keenly against Na+ ions.
Fast Optimal Motion Estimation Based on Gradient-Based Adaptive Multilevel Successive Elimination

In this paper, we propose a fast and optimal solution for block motion estimation based on an adaptive multilevel successive elimination algorithm. This algorithm is accomplished by applying a modified multilevel successive elimination algorithm (SEA) with the elimination order determined by the sum of the gradient magnitudes of each subblock and the elimination process terminated by comparing the above sum with a threshold. In addition a fast approximate motion estimation method and the accumulated distortion scheme are employed to make the proposed algorithm even more efficiently. Experimental results show that the proposed adaptive multilevel successive elimination strategy (AdaMSEA) algorithm significantly outperforms other previous optimal motion estimation algorithms, including SEA, MSEA, and FGSE on a wide variety of video sequences. Finally, we modify the proposed AdaMSEA to an approximate motion estimation algorithm to achieve very fast computational speed, and the experimental results show superior performance of this approximate algorithm over some fast motion estimation algorithms.
Microscale solution IEF combined with 2‐D DIGE substantially enhances analysis depth of complex proteomes such as mammalian cell and tissue extracts

Current gel‐based protein profiling methods such as 2‐DE and fluorescent 2‐D difference in gel electrophoresis (DIGE) evaluate small portions of complex proteomes. Hence, sample prefractionation is essential for more comprehensive proteome coverage and detection of low‐abundant proteins. In this study, we describe the combination of DIGE labeling with microscale solution IEF (MicroSol‐IEF) fractionation and subsequent analysis on slightly overlapping narrow pH range 2‐D gels. By fluorescently tagging and mixing samples and controls prior to prefractionation, complications resulting from minor run‐to‐run variations during MicroSol‐IEF separations of multiple samples are avoided. This greatly improves the reliability of quantitative comparisons. To illustrate its utility, this 3‐D DIGE strategy was applied to analysis of human melanoma cells and mouse lung tissue extracts. Approximately 1000 reproducible spots can be obtained from narrow range 2‐D gels of individual MicroSol‐IEF fractions, and approximately 6000 spots can be obtained from entire proteomes. Quantitative changes in closely related samples could be more reliably detected and the method has a greatly increased capacity to distinguish between closely related protein isoforms. Thus the 3‐D DIGE strategy produces a powerful method for more comprehensive and more reliable quantitative comparisons of protein profiles of very complex proteomes.
Propositional Dynamic Logic with Converse and Repeat for Message-Passing Systems

The model checking problem for propositional dynamic logic (PDL) over message sequence charts (MSCs) and communicating finite state machines (CFMs) asks, given a channel bound B, a PDL formula ϕ and a CFM $\mathcal{C}$, whether every existentially B-bounded MSC M accepted by $\mathcal{C}$ satisfies ϕ. Recently, it was shown that this problem is PSPACE-complete. In the present work, we consider CRPDL over MSCs which is PDL equipped with the operators converse and repeat. The former enables one to walk back and forth within an MSC using a single path expression whereas the latter allows to express that a path expression can be repeated infinitely often. To solve the model checking problem for this logic, we define global message sequence chart automata (gMSCAs) which are multi-way alternating parity automata walking on MSCs. By exploiting a new concept called concatenation states, we are able to inductively construct, for every CRPDL formula ϕ, a finite set of gMSCAs $\mathfrak{G}$ such that the set of models of ϕ equals the union of the languages of the gMSCAs from $\mathfrak{G}$. As a result, we obtain that the model checking problem for CRPDL and CFMs is still in PSPACE.
Spontaneous networks: Trust in a world of equals

Protecting data interchange through wireless nets is one of the greatest problems requiring solution before these technologies can be considered totally trustworthy. Studies to determine the security of the protocols used at present (WEP, 802.11X) show that they continue to have too many weak points. Security measures are needed to make these transmissions reliable. Moreover as we concentrate on the study of ad-hoc nets, formed by a group of autonomous mobile nodes, these protocols are not useful. Ad-hoc nets do not use any type of fixed infrastructure or centralized administration and they offer communication without any type of external infrastructure. This work presents a solution based on a trusted net. We try to extrapolate network behaviour from human behaviour, where trust on both sides is very important when we want to obtain reliable data and protect our own information
Incidence of sexually transmitted hepatitis C virus infection in HIV-positive men who have sex with men

Objective:The epidemiology of the incidence of sexually transmitted hepatitis C virus (HCV) infection in HIV-positive men who have sex with men (MSM) is only partially understood. In the presence of HIV, HCV infection is more likely to become chronic and liver fibrosis progression is accelerated. Design:A systematic review and meta-analysis was used to synthesize data characterizing sexually transmitted HCV in HIV-positive MSM. Methods:Electronic and other searches of medical literature (including unpublished reports) were conducted. Eligible studies reported on HCV seroconversion or on reinfection postsuccessful HCV treatment in HIV-positive MSM who were not injecting drugs. Pooled incidence rates were calculated using random-effects meta-analysis, and meta-regression was used to assess study-level moderators. Attributable risk measures were calculated from statistically significant associations between exposures and HCV seroconversion. Results:More than 13 000 HIV-positive MSM in 17 studies were followed for more than 91 000 person-years between 1984 and 2012; the pooled seroconversion rate was 0.53/100 person-years. Calendar time was a significant moderator of HCV seroconversion, increasing from an estimated rate of 0.42/100 person-years in 1991 to 1.09/100 person-years in 2010, and 1.34/100 person-years in 2012. Reinfection postsuccessful HCV treatment (n = 2 studies) was 20 times higher than initial seroconversion rates. Among the seroconverters, a large proportion of infections were attributable to high-risk behaviours including mucosally traumatic sex and sex while high on methamphetamine. Conclusion:The high reinfection rates and the attributable risk analysis suggest the existence of a subset of HIV-positive MSM with recurring sexual exposure to HCV. Approaches to HCV control in this population will need to consider the changing epidemiology of HCV infection in MSM.
Using Diagnoses to Describe Populations and Predict Costs

The Diagnostic Cost Group Hierarchical Condition Category (DCG/HCC) payment models summarize the health care problems and predict the future health care costs of populations. These models use the diagnoses generated during patient encounters with the medical delivery system to infer which medical problems are present. Patient demographics and diagnostic profiles are, in turn, used to predict costs. We describe the logic, structure, coefficients and performance of DCG/HCC models, as developed and validated on three important data bases (privately insured, Medicaid, and Medicare) with more than 1 million people each.
Design and Implementation of Low Power Smart PV Energy System for Portable Applications Using Synchronous Buck Converter

In this paper, synchronous buck converter based PV energy system for portable applications, especially low power device applications such as charging mobile phone batteries are considered. The converter topology used here is soft switching technique to reduce the switching losses which is found prominently in the conventional buck converter, thus efficiency of the system is improved and the heating of MOSFETs due to switching losses reduce and the MOSFETs have a longer life. The dc power extracted from the PV array is synthesized and modulated by the converter to suit the load requirements. Further, a charging method is studied with controller to regulate the battery voltage and current without overheating. As a result, the charging efficiency can be improved by soft switching technique. Besides, the performance is obtained less number of components and the developed system is cost effective and highly portable. The proposed system is simulated in the MATLAB-Simulink environment and the practical implementation of the proposed converter is done to validate the theoretical results.
Methodology of brain perfusion imaging

Numerous techniques have been proposed in the last 15 years to measure various perfusion‐related parameters in the brain. In particular, two approaches have proven extremely successful: injection of paramagnetic contrast agents for measuring cerebral blood volumes (CBV) and arterial spin labeling (ASL) for measuring cerebral blood flows (CBF). This review presents the methodology of the different magnetic resonance imaging (MRI) techniques in use for CBV and CBF measurements and briefly discusses their limitations and potentials. J. Magn. Reson. Imaging 2001;13:496–520. © 2001 Wiley‐Liss, Inc.