Miracle-dz/UniFAR-FTUs huggingface dataset:
Unravelling angiosperm genome evolution by phylogenetic analysis of chromosomal duplication events

L are assigned values to give a basic reproduction number, R 0 , for local transmission in a patch of 5, R 0 for mass-action transmission in a patch of 0.4, and an R 0 of 0.02 between any two patches. Seasonal variation in contact rates is characterized by 1 p , and is assumed to be opposite in phase for the Northern and Southern hemispheres (represented by setting 1 p ¼ þ0:25 for 1 , p # M=2; and 1 p ¼ 20:25 for M=2 , p # M). The probability that a host is infected upon exposure depends on the strain s, and the host's immune history. Each strain is characterized by A epitopes, each consisting of C codons (three nucleotide bases). Immunity is assumed to be specific to the set of amino acids to which the host has been exposed at each codon, and for simplicity, no functional constraints are imposed on the amino acid sequences. For the default values of A ¼ 4 and C ¼ 3 used here, a total of 4 £ 10 15 strains are possible. Antigenic distance, d(s,H) between a strain s and the immune history of a host, H, is then simply defined as the number of codons in strain s for which the amino acid has not been previously encountered by the host. The level of cross-protection from infection provided at a certain antigenic distance is given by the function f (d), where we assume f ðdÞ ¼ v 1 þ ðv 0 2 v 1 Þðd 2 n t Þ=ðAC 2 n t Þ for d $ n t ; f ðdÞ ¼ v 1 for 0 , d , n t ; and f(d) ¼ 1 for d ¼ 0. n t (¼2) is the threshold level of change necessary for cross-protection to drop below the maximal level set by v 1 (¼0.99), and v 0 (¼0.25) is the minimal level of cross-protection mounted against a strain with no similarity to a previously encountered strain at the codons modelled (¼0 for no cross-protection). These assumptions reflect empirical studies suggesting that two or more substitutions at key antigenic sites are required to escape pre-existing immunity 26,27. The probability that a host will be infected by a strain following exposure is given by where t (¼270 days) is the decay timescale (half-life ¼ t 1/2 ¼ 187 days < 6 …
New types of McKibben artificial muscles

Actuators are devices that exhibit reversible change in their shape or volume or generate force when externally stimulated. Because of their very similar operation style to biological muscles, actuator materials are also known as artificial muscles. These materials are in demand for many applications, such as medical devices and robotics. These applications normally require an inexpensive actuator system that can offer high force, high strain, and high power density in a relatively short period of time. The device packaging and size of the actuator are also important parameters as currently most of the applications desire very compact and lightweight systems. Furthermore, low electricity consumption also as a last requirement has a significant effect on the actuation system by increasing the efficiency of the entire system. Producing all of the above requirements in one device is currently a challenge for engineers and scientists. In this thesis, a new contractile artificial muscle system is introduced than can offer most of the above requirements to satisfy the current expectations of these devices. Chapter 1 of this thesis focuses on a literature review of prominent available artificial muscles and comparing them with biological muscle performance for better understanding of their advantages and disadvantages. Chapter 2 investigates the effect of the inner tube material and muscle geometry on a small hydraulic McKibben artificial muscle as well as the possibility of running this system with a compact, low voltage water pump. This chapter also introduces a new equation that is able to predict static muscle performance notably more accurately than previous models. Chapter 3 illuminates the possibility of three-dimensional printing the braided sleeve used in McKibben artificial muscles to have more control on the manufacturing process of such devices. In Chapter 4, the fluid normally used in conventional McKibben muscles is substituted with a temperature sensitive material to eliminate the need V of the pump/compressor and piping to introduce a more compact device. The new muscles were stimulated either by immersing in a hot water bath or using a heating filament. A contraction strain of 9 % and 2 N isometric force were produced. A new equation is also introduced to predict the performance of this type of McKibben muscles with temperature as the driving force. Chapter 5 introduces a novel miniature type of McKibben artificial muscle by using a conductive braided sleeve and eliminating the need for the inner tube. The electricity consumption of this muscle is as low as 2.5 V. The muscle weight is only 0.14 gr with a diameter of 1.4 mm. The muscle generates a tensile stress of 50 kPa and contraction strain of 10%. Finally, Chapter 6 concludes this study and also represents some potential future works.
Stiffness Comparison of Tissue Phantoms using Optical Coherence Elastography without a Load Cell

Mechanical property of tissue is closely related to diseases such as breast cancer, prostate cancer, cirrhosis of the liver, and atherosclerosis. Therefore measurement of tissue mechanical property is important for a better diagnosis. Ultrasound elastography has been developed as a diagnostic modality for a number of diseases that maps mechanical property of tissue. Optical coherence elastography (OCE) has a higher spatial resolution than ultrasound elastography. OCE, therefore, could be a great help for early diagnosis. In this study, we made tissue phantoms and measured their compressive moduli with a rheometer measuring the response to applied force. Uniaxial strain of the tissue phantom was also measured with OCE by using cross-correlation of speckles and compared with the results from the rheometer. In order to compare stiffness of tissue phantoms by OCE, the applied force should be measured in addition to the strain. We, however, did not use a load cell that directly measures the applied force for each sample. Instead, we utilized one silicone film (called as reference phantom) for all OCE measurements that indirectly indicated the amount of the applied force by deformation. Therefore, all measurements were based on displacement, which was natural and effective for image-based elastography such as OCE.
Stability of roundness measurement system

In order to improve measurement capabilities and to ensure good foundation for further research in the field of roundness measurements National laboratory for length has implemented several modifications on a commercially available roundness measurement device Mahr MMQ3. Furthermore, dedicated measurement software which includes all modern algorithms for out of roundness error calculation has been developed. These improvements to the measurement system provide a new possibility to perform a large number of consecutive measurements over extended time period. Result of those measurements provides insight into temperature and mechanical stability of the measurement system. Mechanical stability and temperature influence by the means of temperature drift are discussed.
Epidemics in Partially Overlapped Multiplex Networks

Many real networks exhibit a layered structure in which links in each layer reflect the function of nodes on different environments. These multiple types of links are usually represented by a multiplex network in which each layer has a different topology. In real-world networks, however, not all nodes are present on every layer. To generate a more realistic scenario, we use a generalized multiplex network and assume that only a fraction of the nodes are shared by the layers. We develop a theoretical framework for a branching process to describe the spread of an epidemic on these partially overlapped multiplex networks. This allows us to obtain the fraction of infected individuals as a function of the effective probability that the disease will be transmitted . We also theoretically determine the dependence of the epidemic threshold on the fraction of shared nodes in a system composed of two layers. We find that in the limit of the threshold is dominated by the layer with the smaller isolated threshold. Although a system of two completely isolated networks is nearly indistinguishable from a system of two networks that share just a few nodes, we find that the presence of these few shared nodes causes the epidemic threshold of the isolated network with the lower propagating capacity to change discontinuously and to acquire the threshold of the other network.
Annotation transfer between genomes: protein-protein interologs and protein-DNA regulogs.

Proteins function mainly through interactions, especially with DNA and other proteins. While some large-scale interaction networks are now available for a number of model organisms, their experimental generation remains difficult. Consequently, interolog mapping--the transfer of interaction annotation from one organism to another using comparative genomics--is of significant value. Here we quantitatively assess the degree to which interologs can be reliably transferred between species as a function of the sequence similarity of the corresponding interacting proteins. Using interaction information from Saccharomyces cerevisiae, Caenorhabditis elegans, Drosophila melanogaster, and Helicobacter pylori, we find that protein-protein interactions can be transferred when a pair of proteins has a joint sequence identity >80% or a joint E-value <10(-70). (These "joint" quantities are the geometric means of the identities or E-values for the two pairs of interacting proteins.) We generalize our interolog analysis to protein-DNA binding, finding such interactions are conserved at specific thresholds between 30% and 60% sequence identity depending on the protein family. Furthermore, we introduce the concept of a "regulog"--a conserved regulatory relationship between proteins across different species. We map interologs and regulogs from yeast to a number of genomes with limited experimental annotation (e.g., Arabidopsis thaliana) and make these available through an online database at http://interolog.gersteinlab. org. Specifically, we are able to transfer approximately 90,000 potential protein-protein interactions to the worm. We test a number of these in two-hybrid experiments and are able to verify 45 overlaps, which we show to be statistically significant.
HIV-1 Gag-Virus-Like Particles Induce Natural Killer Cell Immune Responses via Activation and Maturation of Dendritic Cells

Despite the extensive efforts that have been made to combat acquired immune deficiency syndrome (AIDS), the number of people infected each year with human immunodeficiency virus type 1 (HIV-1) is still increasing worldwide, and a safe and effective vaccine to control HIV infection is urgently needed. Recently, the natural killer (NK) cell-mediated innate immune response, which represents the first line of defense against infections, has attracted attention for its role in combating HIV infection and disease progression. In the present study, we investigated the immunogenic ability of HIV-1 Gag-virus-like particles (Gag-VLPs) to induce NK cell immune responses in vitro and in vivo. Gag-VLPs efficiently activated human monocyte-derived dendritic cells (MDDCs), eliciting MDDC maturation with an associated increase in the surface expression of CD80, CD86 and MHC classes I and II, MDDC proliferation and proinflammatory cytokine production. Gag-VLP-treated MDDCs subsequently activated autologous NK cells, leading to their proliferation and production of interferon-γ and to the upregulation of NK cell cytotoxicity against YAC-1 cells and HIV-1-infected CD4+ T cells. In addition, we introduced a 2-phase immunization strategy in BALB/c mice to assess the role of DCs in the induction of NK cell immune responses by Gag-VLPs in vivo. Our findings reveal that Gag-VLPs efficiently activate DCs, which in turn induce innate and Gag-specific immune responses in NK cells.
Spectral analysis for periodic solutions of the Cahn–Hilliard equation on R

We consider the spectrum associated with the linear operator obtained when the Cahn–Hilliard equation on R is linearized about a stationary periodic solution. Our analysis is particularly motivated by the study of spinodal decomposition, a phenomenon in which the rapid cooling (quenching) of a homogeneously mixed binary alloy causes separation to occur, resolving the mixture into regions of different crystalline structure, separated by steep transition layers. In this context, a natural problem regards the evolution of solutions initialized by small, random (in some sense) perturbations of the pre-quenching homogeneous state. Solutions initialized in this way appear to evolve transiently toward certain unstable periodic solutions, with the rate of evolution described by the spectrum associated with these periodic solutions. In the current paper, we use Evans function methods and a perturbation argument to locate the spectrum associated with such periodic solutions. We also brieﬂy discuss a heuristic method due to Langer for relating our spectral information to coarsening rates.
The State of the Art in Interactive Global Illumination

The interaction of light and matter in the world surrounding us is of striking complexity and beauty. Since the very beginning of computer graphics, adequate modelling of these processes and efficient computation is an intensively studied research topic and still not a solved problem. The inherent complexity stems from the underlying physical processes as well as the global nature of the interactions that let light travel within a scene. This paper reviews the state of the art in interactive global illumination (GI) computation, i.e., methods that generate an image of a virtual scene in less than 1 s with an as exact as possible, or plausible, solution to the light transport. Additionally, the theoretical background and attempts to classify the broad field of methods are described. The strengths and weaknesses of different approaches, when applied to the different visual phenomena, arising from light interaction are compared and discussed. Finally, the paper concludes by highlighting design patterns for interactive GI and a list of open problems.
Is There Any Association Between Use of Antidepressants and Preeclampsia or Gestational Hypertension?: A Systematic Review of Current Studies

Objective Hypertension in pregnant women is an important medical problem, which can cause morbidity and mortality in the fetus. This study reviewed the current literature examining the potential relationship between use of antidepressants during pregnancy and preeclampsia or gestational hypertension. Methods PubMed was searched for English-language reports between January 1, 1995, and December 31, 2015, by using combinations of key words pregnancy, pregnancy complications, preeclampsia, gestational hypertension, and antidepressants. Studies that reported the diagnosis of preeclampsia or gestational hypertension and use of antidepressant were included in the review. Results A total of 7 relevant studies that met the review criteria were examined. The studies reported that compared with nonusers adjusted relative risk of preeclampsia or gestational hypertension in antidepressant users was 1.28 to 1.53 for any antidepressant, 1.05 to 3.16 for selective serotonin reuptake inhibitors, 1.49 to 1.95 for selective serotonin-norepinephrine reuptake inhibitors, and 0.35 to 3.23 for tricyclic antidepressants. Consistently, antidepressant use during the second trimester of pregnancy was associated with increased risk of preeclampsia or gestational hypertension. However, possible contribution of severity, type, and comorbidity of underlying anxiety or depressive disorders is unclear in the current studies. Conclusions Although some studies have suggested a moderately increased risk in pregnancy-specific hypertensive disorders with antidepressant treatment, the current data do not allow a definitive conclusion on this topic, because the studies have many methodological limitations. In addition, the effects of untreated depression or anxiety disorders cannot be disentangled from the results.
Summary of the NHLBI Working Group on Research on Hypertension During Pregnancy

A Working Group on Research in Hypertension in Pregnancy was recently convened by the National Heart Lung and Blood Institute to determine the state of knowledge in this area and suggest appropriate directions for research. Hypertensive disorders in pregnancy, especially preeclampsia, are a leading cause of maternal mortality worldwide and even in developed countries increase perinatal mortality five‐fold. Much has been learned about preeclampsia but gaps in the knowledge necessary to direct therapeutic strategies remain. Oxidative stress is a biologically plausible contributor to the disorder that may be amenable to intervention. Hypertension that antedates pregnancy (chronic hypertension) bears many similarities to hypertension in nonpregnant women but the special setting of pregnancy demands information to guide evidence based therapy. The recommendations of the Working Group are to attempt a clinical trial of antioxidant therapy to prevent preeclampsia that is be complemented by mechanistic research to increase understanding of the genetics and pathogenesis of the disorder. For chronic hypertension clinical trials are recommended to direct choice of drugs, evaluate degree of control and assess implications to the mother and fetus. Recommendations to increase participation in this research are also presented.
The association of workflow interruptions and hospital doctors' workload: a prospective observational study

Background Subjective workload in healthcare employees is suspected to be important for the performance and safety of healthcare delivery. This study investigates associations between workflow interruptions and hospital doctors' capability to manage their perceived workload in a safe and efficient manner. Aim To examine the relationship of observed workflow interruptions with hospital doctors' perceived workload during day clinical shifts. Methods A prospective study of 43 full shift observations with 29 doctors working in internal medicine and surgical specialties. Workflow interruptions were assessed via observation using a previously validated observation instrument. Doctors assessed their workload twice throughout their day shift using three items of the validated NASA-Task Load Index (NASA-TLX; mental demands, effort, frustration). Results Hospital doctors were on average disrupted 3.66 times per hour. Most frequent were interruptions by nursing staff, telephone/beeper interruptions and by fellow doctors. Senior doctors reported higher workload than their junior colleagues. Overall workflow interruptions were significantly related to doctors' workload (β=0.22; p=0.03). Further analyses revealed that doctors' workload was associated particularly with interruptions by nursing personnel (β=0.23; p=0.03). Conclusions Frequent workflow interruptions may be linked with increased workload in doctors. Healthcare environments need to be better designed to reduce unnecessary interruptions and distractions so that hospital doctors can manage clinical work efficiently and safely.
Structural and dielectric properties of hot-pressed poly(vinylidene fluoride)-based composites

The characterization of ceramic/polymer composites was performed on zinc oxide/poly(vinylidene fluoride) – ZnO/PVDF and barium titanate/poly(vinylidene fluoride) composites with varying filler concentration in order to evaluate the main interactions responsible for the composite dielectric behavior. The materials, poly(vinylidene fluoride) and its composites, were melt-blended using a two-roller mixer and then hot-pressed. The permittivity of composites was enhanced compared with that of the pure poly(vinylidene fluoride) with the addition of 20 w/w% of ZnO particles. However, samples with 40 or 60 w/w% of ZnO registered a diminution in the real permittivity values which was connected to particle-matrix adhesion problems. On the other hand, barium titanate composites presented a more homogeneous morphology with less presence of voids and a better adhesion between the filler and the polymer, where real permittivity increased with the addition of barium titanate particles.
Parallel Evolutionary Algorithms Performing Pairwise Comparisons

We study mathematically and experimentally the convergence rate of differential evolution and particle swarm optimization for simple unimodal functions. Due to parallelization concerns, the focus is on lower bounds on the runtime, i.e. upper bounds on the speed-up, as a function of the population size. Two cases are particularly relevant: A population size of the same order of magnitude as the dimension and larger population sizes. We use the branching factor as a tool for proving bounds and get, as upper bounds, a linear speed-up for a population size similar to the dimension, and a logarithmic speed-up for larger population sizes. We then propose parametrizations for differential evolution and particle swarm optimization that reach these bounds.
Prognostic significance of age and tonsillectomy in uvulopalatopharyngoplasty

The objective of this study was to analyze the results of uvulopalatopharyngoplasty on 133 adult patients with sleep apnea. This group of patients was subjected to computer analysis by a statistician. Two previously unreported observations were revealed: There was a straight line decline in measurable improvement with advancing age so, by age 60, there were no patients with improvement; and patients who had tonsillectomy as a part of the uvulopalatopharyngoplasty had a markedly increased success rate compared to those who did not have tonsils.
No zero match browsing of hierarchically categorized information entities

The two main ways to search for information in electronic document collections are by using free-text retrieval search engines or browsing information that has been organized into predefined organizational structures. However, each of these approaches has limitations. Using word or phrase search, users are faced with a compromise between overly broad searches returning an excessive amount of information or overly narrow searches that may fail to return relevant information. Browsing organizational structures is dependent on the user's knowledge of the structures, and a user may find it difficult to refine searches. This paper introduces a user interface based approach to the browsing of hierarchically organized information entities that avoids these problems by allowing the incremental narrowing down of a set of search results and by pruning the organizational structure after each user selection to show the consequences of the selection. The effect is to present to the user at all times only that part of the organizational structure that will lead to a nonnull selection. The approach is called no zero match (NZM) browsing. The paper presents the computational basis of NZM browsing before describing a trial implementation of the approach and presenting three case studies, which represent common search situations in an engineering context.