Miracle-dz/UniFAR-FTUs huggingface dataset:
Clonal Integration of Fragaria orientalis in Reciprocal and Coincident Patchiness Resources: Cost-Benefit Analysis

Clonal growth allows plants to spread horizontally and to experience different levels of resources. If ramets remain physiologically integrated, clonal plants can reciprocally translocate resources between ramets in heterogeneous environments. But little is known about the interaction between benefits of clonal integration and patterns of resource heterogeneity in different patches, i.e., coincident patchiness or reciprocal patchiness. We hypothesized that clonal integration will show different effects on ramets in different patches and more benefit to ramets under reciprocal patchiness than to those under coincident patchiness, as well as that the benefit from clonal integration is affected by the position of proximal and distal ramets under reciprocal or coincident patchiness. A pot experiment was conducted with clonal fragments consisting of two interconnected ramets (proximal and distal ramet) of Fragaria orientalis. In the experiment, proximal and distal ramets were grown in high or low availability of resources, i.e., light and water. Resource limitation was applied either simultaneously to both ramets of a clonal fragment (coincident resource limitation) or separately to different ramets of the same clonal fragment (reciprocal resource limitation). Half of the clonal fragments were connected while the other half were severed. From the experiment, clonal fragments growing under coincident resource limitation accumulated more biomass than those under reciprocal resource limitation. Based on a cost-benefit analysis, the support from proximal ramets to distal ramets was stronger than that from distal ramets to proximal ramets. Through division of labour, clonal fragments of F. orientalis benefited more in reciprocal patchiness than in coincident patchiness. While considering biomass accumulation and ramets production, coincident patchiness were more favourable to clonal plant F. orientalis.
The performance of the spatiotemporal Kalman filter and LORETA in seizure onset localization

The assumption of spatial-smoothness is often used to solve the bioelectric inverse problem during electroencephalographic (EEG) source imaging, e.g., in low resolution electromagnetic tomography (LORETA). Since the EEG data show a temporal structure, the combination of the temporal-smoothness and the spatial-smoothness constraints may improve the solution of the EEG inverse problem. This study investigates the performance of the spatiotemporal Kalman filter (STKF) method, which is based on spatial and temporal smoothness, in the localization of a focal seizure's onset and compares its results to those of LORETA. The main finding of the study was that the STKF with an autoregressive model of order two significantly outperformed LORETA in the accuracy and consistency of the localization, provided that the source space consists of a whole-brain volumetric grid. In the future, these promising results will be confirmed using data from more patients and performing statistical analyses on the results. Furthermore, the effects of the temporal smoothness constraint will be studied using different types of focal seizures.
Exogenous β-Hydroxybutyrate Treatment and Neuroprotection in a Suckling Rat Model of Hypoxic-Ischemic Encephalopathy

β-Hydroxybutyrate (BHB) is a representative ketone body that may play a role in the mitigation of neonatal hypoxic-ischemic encephalopathy by altering energy metabolism. This study aimed to investigate the neuroprotective efficacy of exogenous BHB administration in a suckling rat model after hypoxia-ischemia (HI). Thirteen-day-old (P13) rat pups were subjected to 120 min of hypoxia according to the Rice-Vannucci model. BHB (5.0 mmol/kg, HI-BHB) or vehicle (0.9% saline, HI-Veh) was administered 0, 2, 4, and 6 h after HI induction. Pathologic injury scores and the number of TUNEL-positive cells were evaluated on P15. Residual hemispheric volume was measured with T2-weighted MRI (on P27) and functional tests, such as the negative geotaxis test, rope suspension test, rotarod test, novel object recognition test, and cylinder test, were performed. Systemic ketosis (approx. 2.0–3.0 mM/L) was well tolerated by the rat pups with no difference in the mortality rate between both groups. Compared with the HI-Veh group, the HI-BHB group demonstrated significantly lower pathological scores as well as fewer TUNEL-positive cells. The intact residual hemispheric and hippocampal volumes were greater in the HI-BHB group than the HI-Veh group. However, the results of functional tests did not differ between both groups. Postischemic BHB administration reduced brain injury in suckling rats after HI. The safe clinical application of our animal model to human infants with HI requires further investigation.
Virtual Network Embedding via Monte Carlo Tree Search

Network virtualization helps overcome shortcomings of the current Internet architecture. The virtualized network architecture enables coexistence of multiple virtual networks (VNs) on an existing physical infrastructure. VN embedding (VNE) problem, which deals with the embedding of VN components onto a physical network, is known to be ${\mathcal {NP}}$ -hard. In this paper, we propose two VNE algorithms: MaVEn-M and MaVEn-S. MaVEn-M employs the multicommodity flow algorithm for virtual link mapping while MaVEn-S uses the shortest-path algorithm. They formalize the virtual node mapping problem by using the Markov decision process (MDP) framework and devise action policies (node mappings) for the proposed MDP using the Monte Carlo tree search algorithm. Service providers may adjust the execution time of the MaVEn algorithms based on the traffic load of VN requests. The objective of the algorithms is to maximize the profit of infrastructure providers. We develop a discrete event VNE simulator to implement and evaluate performance of MaVEn-M, MaVEn-S, and several recently proposed VNE algorithms. We introduce profitability as a new performance metric that captures both acceptance and revenue to cost ratios. Simulation results show that the proposed algorithms find more profitable solutions than the existing algorithms. Given additional computation time, they further improve embedding solutions.
Epidermal growth factor receptor and integrins control force-dependent vinculin recruitment to E-cadherin junctions

ABSTRACT This study reports novel findings that link E-cadherin (also known as CDH1)-mediated force-transduction signaling to vinculin targeting to intercellular junctions via epidermal growth factor receptor (EGFR) and integrins. These results build on previous findings that demonstrated that mechanically perturbed E-cadherin receptors activate phosphoinositide 3-kinase and downstream integrins in an EGFR-dependent manner. Results of this study show that this EGFR-mediated kinase cascade controls the force-dependent recruitment of vinculin to stressed E-cadherin complexes – a key early signature of cadherin-based mechanotransduction. Vinculin targeting requires its phosphorylation at tyrosine 822 by Abl family kinases (hereafter Abl), but the origin of force-dependent Abl activation had not been identified. We now present evidence that integrin activation, which is downstream of EGFR signaling, controls Abl activation, thus linking E-cadherin to Abl through a mechanosensitive signaling network. These findings place EGFR and integrins at the center of a positive-feedback loop, through which force-activated E-cadherin signals regulate vinculin recruitment to cadherin complexes in response to increased intercellular tension. This article has an associated First Person interview with the first author of the paper. Summary: E-cadherin force transduction activates a kinase cascade via epidermal growth factor receptor and integrins that regulates force-dependent recruitment of VCL to stressed cadherin adhesions.
Population Pharmacokinetics of Intravenous Polymyxin B from Clinical Samples

ABSTRACT A retrospective study was conducted in hospitalized patients receiving intravenous polymyxin B who underwent therapeutic drug monitoring during treatment. The aim of this study was to assess the population pharmacokinetics (PK) of intravenous polymyxin B in patients with variable total body weights and create a population model for clinical use. Nonlinear mixed-effects modeling analyses were performed. A total of 43 patients were included, and 70% of these patients were male. The median age was 58 years, and the median weight was 78 kg. The median polymyxin B dose was 180 mg/day or 2.8 mg/kg/day. A one-compartment model described the polymyxin B PK well with conditional mean parameter estimates of a clearance (CL) of 2.37 liters/h and a volume of distribution of 34.4 liters and can be employed for clinical population modeling. Total body weight was not significantly associated with CL (Akaike information criterion, 361.6 for the weight-based model versus 359.5 for the non-weight-based model). These data suggest that dosing according to patient body weight requires further exploration. Greater study is needed to assess the relationships between polymyxin B exposures and efficacy and toxicity.
High‐pressure metamorphism in the southern New England Orogen: Implications for long‐lived accretionary orogenesis in eastern Australia

New geochemical, metamorphic, and isotopic data are presented from high‐pressure metamorphic rocks in the southern New England Orogen (eastern Australia). Conventional and optimal thermobarometry are augmented by U‐Pb zircon and 40Ar/39Ar phengite dating to define pressure‐temperature‐time (P‐T‐t) histories for the rocks. The P‐T‐t histories are compared with competing geodynamic models for the Tasmanides, which can be summarized as (i) a retreating orogen model, the Tasmanides formed above a continuous, west dipping, and eastward retreating subduction zone, and (ii) a punctuated orogen model, the Tasmanides formed by several arc accretion, subduction flip, and/or transference events. Whereas both scenarios are potentially supported by the new data, an overlap between the timing of metamorphic recrystallization and key stages of Tasmanides evolution favors a relationship between a single, long‐lived subduction zone and the formation, exhumation, and exposure of the high‐pressure rocks. By comparison with the retreating orogen model, the following links with the P‐T‐t histories emerge: (i) exhumation and underplating of oceanic eclogite during the Delamerian Orogeny, (ii) recrystallization of underplated and exhuming high‐pressure rocks at amphibolite facies conditions coeval with a period of rollback, and (iii) selective recrystallization of high‐pressure rocks at blueschist facies conditions, reflecting metamorphism in a cooled subduction zone. The retreating orogen model can also account for the anomalous location of the Cambrian‐Ordovician high‐pressure rocks in the Devonian‐Carboniferous New England Orogen, where sequential rollback cycles detached and translated parts of the leading edge of the overriding plate to the next, younger orogenic cycle.
Imagen: runtime migration of browser sessions for javascript web applications

Due to the increasing complexity of web applications and emerging HTML5 standards, a large amount of runtime state is created and managed in the user's browser. While such complexity is desirable for user experience, it makes it hard for developers to implement mechanisms that provide users ubiquitous access to the data they create during application use. This paper presents our research into browser session migration for JavaScript-based web applications. Session migration is the act of transferring a session between browsers at runtime. Without burden to developers, our system allows users to create a snapshot image that captures all runtime state needed to resume the session elsewhere. Our system works completely in the JavaScript layer and thus snapshots can be transfered between different browser vendors and hardware devices. We report on performance metrics of the system using five applications, four different browsers, and three different devices.
Antimicrobial Efficacy of Multipurpose Disinfecting Solutions in the Presence of Contact Lenses and Lens Cases

Objective: The aim of this study was to use antimicrobial efficacy endpoint methodology to determine compatibility of multipurpose disinfecting solutions (MPSs), lens cases, and hydrogel lenses for disinfection (AEEMC) against International Organization for Standardization (ISO)–specified microorganisms and clinical ocular isolates of Stenotrophomonas maltophilia. Methods: Six MPSs (PQ/Aldox 1, 2, and 3; PQ/Alexidine; PQ/PHMB; and PHMB) were challenged against ISO-specified microorganisms and S. maltophilia using the AEEMC test. AEEMC tests were performed with and without balafilcon A, etafilcon A, and senofilcon A lenses in lens cases with organic soil. Exposure times included disinfection time (DT) and 24 hr. Additionally, all six MPSs were challenged with two strains of S. maltophilia, based on the ISO Stand-alone test. Results: The efficacy against bacteria for PQ/Aldox and PQ/Alexidine MPSs was not diminished by the presence of lenses. The efficacy of PQ/PHMB and PHMB MPSs against Serratia marcescens was significantly reduced compared with the no-lens control at DT for at least one lens type. The PHMB MPS with lenses present also demonstrated reduced efficacy against Staphylococcus aureus at DT versus the control. PQ/Aldox MPSs retained activity against Fusarium solani with lenses present; however, all other test MPSs demonstrated reduced F. solani efficacy at DT with lenses present. With lenses, all MPSs showed reduced efficacy against Candida albicans. Conclusions: AEEMC antimicrobial efficacy test results vary based on challenge microorganism, contact lenses, and MPS biocide systems. This study highlights the importance of evaluating MPSs for compatibility with lenses and lens cases.
Development of a standardized protein immunomarking protocol for insect mark–capture dispersal research

A field study was conducted to test the marking efficiency of broadcast spray applications of protein marks on stationary (represented by cadavers) and free‐roaming lady beetles Hippodamia convergens Guérin‐Méneville that were strategically placed in blooming alfalfa plots. The marks tested included three different concentrations of egg albumin from chicken egg white, casein from bovine milk and trypsin inhibitor from soy milk. The cadaver and free‐roaming beetle treatments served to measure the acquisition and retention of each protein treatment regime by direct contact with the spray solution and by residual contact with protein‐marked residue on alfalfa, respectively. In addition, the vertical distribution of marking efficacy was determined by sampling alfalfa plant tissue and beetle cadavers that were located on the upper and lower portion of the plant canopy. The data indicated that the backpack spray apparatus was very effective at uniformly administering the various protein marks, regardless of the concentration, throughout the entire plant canopy. Also, the free‐roaming beetles readily self‐marked by contact exposure to protein‐treated plants. We also identified concentrations of each protein type that will mark about 90% of the resident beetle population. Moreover, if a mark–capture‐type study only requires two unique protein marks, we determined that concentrations of 25% for egg white and 100% for bovine milk could be used to mark 98% of the population. Our results provide a significant step towards standardizing protein immunomarking protocols for insect mark–capture dispersal research. In addition, we identify several areas of research that are needed to further standardize the protein mark–capture procedure.
Rapid, pervasive genetic differentiation of urban white‐footed mouse (Peromyscus leucopus) populations in New York City

We investigated genetic diversity and structure of urban white‐footed mouse, Peromyscus leucopus, populations in New York City (NYC) using variation at 18 microsatellite loci. White‐footed mice are ‘urban adapters’ that occur at higher population densities as habitat fragments are reduced in area but have a limited ability to disperse through urbanized areas. We hypothesized that this combination of traits has produced substantial genetic structure but minimal loss of genetic variation over the last century in NYC. Allelic diversity and heterozygosity in 14 NYC populations were high, and nearly all of our NYC study sites contained genetically distinct populations of white‐footed mice as measured by pairwise FST, assignment tests, and Bayesian clustering analyses performed by Structure and baps. Analysis of molecular variance revealed that genetic differences between populations separated by a few kilometres are more significant than differences between prehistorically isolated landmasses (i.e. Bronx, Queens, and Manhattan). Allele size permutation tests and lack of isolation by distance indicated that mutation and migration are less important than drift as explanations for structure in urban, fragmented P. leucopus populations. Peromyscus often exhibit little genetic structure over even regional scales, prompting us to conclude that urbanization is a particularly potent driver of genetic differentiation compared to natural fragmentation.
Step-up fecal microbiota transplantation (FMT) strategy

ABSTRACT Gut dysbiosis is a characteristic of inflammatory bowel disease (IBD) and is believed to play a role in the pathogenesis of IBD. Fecal microbiota transplantation (FMT) is an effective strategy to restore intestinal microbial diversity and has been reported to have a potential therapeutic value in IBD. Our recent study reported a holistic integrative therapy called “step-up FMT strategy,” which was beneficial in treating steroid-dependent IBD patients. This strategy consists of scheduled FMTs combined with steroids, anti-TNF-α antibody treatment or enteral nutrition. Herein, we will elaborate the strategy thoroughly, introducing the concept, potential indication, methodology, and safety of “step-up FMT strategy” in detail.
Synthetic generation of handwritten signatures based on spectral analysis

A new method to generate synthetic online signatures is presented. The algorithm uses a parametrical model to generate the synthetic Discrete Fourier Transform (DFT) of the trajectory signals, which are then refined in the time domain and completed with a synthetic pressure function. Multiple samples of each signature are created so that synthetic databases may be produced. Quantitative and qualitative results are reported, showing that, in addition to presenting a very realistic appearance, the synthetically generated signatures have very similar characteristics to those that enable the recognition of real signatures.
HIV Infection: Implications on Surgical Practice

The human immune deficiency virus (HIV) may have had its origins in Africa; a large percentage of those infected live in sub-Saharan African. HIV is thought to have started and spread unnoticed through the 1960s and 1970s, developing into epidemic proportions in the 1980s. The HIV/AIDS pandemic is currently a global phenomenon that has especially impacted on sub-Saharan Africans because of the large numbers of those affected, as well as poverty and illiteracy so rampant in the continent. The initial hopelessness of the 1980s and early 1990s because of the social stigma and lack of affordable anti-retroviral therapy was replaced with fresh hope, as a result of on-going initiatives that have over the last decade availed anti-retroviral drugs to a population that had would have had no other possibility of accessing this treatment; health education, civic activism, advocacy, government and international recognition and support. The recognition of the threat that HIV/AIDS poses to the survival of mankind, and the measures taken to counter this threat have significantly eroded the social stigma and other complications associated with HIV/AIDS. Fear of whole populations being wiped out, as suggested by the large number of HIV orphans in the 1980s and 1990s was transformed into hope by the availability of ARVs, translating into a large population of patients surviving way beyond what was previously possible. Opportunistic infections, which in the pre-ARV era caused so many deaths, have seen a significant reduction since the introduction of HAART. This improved survival has introduced a number of aspects that have, and are impacting on the practice of surgery globally. The challenge of availing ARVs to the eligible patient population still exists; of an estimated 2.24 million people living with HIV/AIDS in Latin America and the Caribbean in 2008, only 54% were on ARVs (Fink et al. 2011).
Modeling the non-elastic stretch deformation of cloth based on creep analysis

This work proposes a method to model the non-elastic components in the fabric stretch deformation in the context of physically based fabric simulator. This paper finds that the above problem can be made tractable if we decompose the stretch deformation into the immediate elastic, viscoelastic, and plastic components. A non-trivial job is the decomposition of the deformation itself. For the purpose of the simulator development, the decomposition must be possible at any stage of deformation and any occurrence of loading and unloading. Based on the observations of various constant force creep measurements, this paper makes an assumption that, within a particular fabric, the viscoelastic and plastic components are proportional to each other and their ratio is invariant over time. Experimental results produced with the proposed method match with general expectations, and show that the method can represent the non-elastic stretch deformation for arbitrary time-varying force.
Shaping Health Policy for Low-Income Populations: An Assessment of Public Comments in a New Medicaid Waiver Process.

Since the Supreme Court decided that the Affordable Care Act's (ACA) Medicaid expansion is optional for the states, several have obtained federal approval to use Section 1115 waivers to expand Medicaid while changing its coverage and benefits design. There has long been concern that policy making for Medicaid populations may lack meaningful engagement with low-income constituents, and therefore the ACA established a new process under which the public can submit comments on pending Medicaid waiver applications. We analyzed 291 comment letters submitted to federal regulators pertaining to Medicaid Section 1115 waiver applications in the first five states to seek such waivers: Arkansas, Indiana, Iowa, Michigan, and Pennsylvania. We found that individual citizens, including those who identified as Medicaid-eligible, submitted a sizable majority of the comment letters. Comment letters tended to mention controversial provisions of the waivers and reflected the competing political rhetoric of "personal responsibility" versus "vulnerable populations. " Despite the fact that the federal government seemed likely to approve the waiver applications, we found robust public engagement, reflecting the salience of the issue of Medicaid expansion under the ACA. Our findings are consistent with the argument that Medicaid is a program of growing centrality in US health politics.