Miracle-dz/UniFAR-FTUs huggingface dataset:
Antimicrobial peptides modulate bilayer barrier properties using a variety of mechanisms of actions

Various antimicrobial peptides (AMPs) are active in changing the biophysical properties of cell membranes. AMPs often interact with lipids and create AMP-lipid complexes which lead to the creation ofprotein-lined or lipid-lined well structured ion channels, less structured ion flowing pores, localized disorders or defects, etc. in membranes. Such special structuresrequire various AMP specific mechanisms. The complexes often appear with various distinguishable structures. A few of them are,for example, linear β-helix created by e.g. gramicidin A, barrel-stave pore created by e.g. alamethicin, toroidal pore created by e.g.magainin, melittin, etc.,lipidic channels created by e.g. ceramides (example of a non AMPinduced channel), defects created by e.g. gramicidin S, etc. In this minireview we shall address about the primary mechanisms which dictate the formation and function of the mentioned ion flowing events. The AMP effects on membrane depend mainly onphysical properties such as geometric, electrical, mechanical, etc. of membrane and AMPs. Also, the regulation of AMP or general membrane protein (MP) functions depend on the hydrophobic coupling between membrane and the integral AMPs/MPs. Specifically, the AMP-membrane hydrophobic coupling dependent regulation of membrane properties and AMP functions depend mainly on the electrostatic and mechanical energetic AMP-membrane couplings. Both of these energetics emerge from a common calculation of screened Coulomb interaction between AMPs and the host membrane.It is also important to mention that the electrostatic energetic coupling is found to be the diminant contributor while mechanical energetic coupling is found to serve as seconday role in the mentioned energetic coupling regulation of both membrane and AMP functions. Experimental, theoretical and computational results will be used to address the problems and support our remarks.
At-issueness Does Not Predict Projection

The notion of PROJECTION was introduced in Langendoen & Savin (1971) and has since been employed to describe the ability of certain implications to survive embedding under entailment-canceling operators, e.g. negation or modals. The term has traditionally been applied to presupposed inferences (Karttunen 1973; 1974; Heim 1983; Beaver 2001; a.o.) and has more recently been discussed in the context of non-presupposed projective content, including inferences triggered by appositives, expressives, and evidentials (Potts 2005; Koev 2013; 2016; Murray 2014; AnderBois et al. 2015). In turn, Potts (2005) introduced the term AT-ISSUE content to describe implications that constitute the main point of an utterance. In a series of recent papers, David Beaver, Craige Roberts, Mandy Simons, and Judith Tonhauser (henceforth BRST) made the influential proposal that projection can be explained in terms of at-issueness, hypothesizing that there is a perfect correlation between these two linguistic categories, in the sense that semantic content projects if and only if it is not at issue (see especially Simons et al. 2010 and Beaver et al. 2017). This squib critically evaluates BRST’s proposal and raises several theoretical and empirical issues. I argue that although projection and not-at-issueness appear to be strongly correlated, there is no perfect overlap in the way envisaged by BRST. In particular, semantic content may project and be at issue, and it may not project but be not at issue. 1. Defining and Diagnosing Projection Projection is the ability of semantic content to remain unaffected by the presence of entailmentcanceling operators such as negation, modals, etc. Simons et al. (2010) define this notion as follows.
QCD on the Light-Front A Systematic Approach to Hadron Physics

Light-Front Hamiltonian theory, derived from the quantization of the QCD Lagrangian at fixed light-front time x = x + x, provides a rigorous frame-independent framework for solving nonperturbative QCD. The eigenvalues of the light-front QCD Hamiltonian HLF predict the hadronic mass spectrum, and the corresponding eigensolutions provide the light-front wavefunctions which describe hadron structure, providing a direct connection to the QCD Lagrangian. In the semiclassical approximation the valence Fock-state wavefunctions of the light-front QCD Hamiltonian satisfy a single-variable relativistic equation of motion, analogous to the nonrelativistic radial Schrödinger equation, with an effective confining potential U which systematically incorporates the effects of higher quark and gluon Fock states. Remarkably, the potential U has a unique form of a harmonic oscillator potential if one requires that the chiral QCD action remains conformally invariant. A mass gap and the color confinement scale also arises when one extends the formalism of de Alfaro, Fubini and Furlan to light-front Hamiltonian theory. In the case of mesons, the valence Fock-state wavefunctions of HLF for zero quark mass satisfy a single-variable relativistic equation of motion in the invariant variable ζ = b⊥x(1−x), which is conjugate to the invariant mass squared M qq̄. The result is a nonperturbative relativistic light-front quantum mechanical wave equation which incorporates color confinement and other essential spectroscopic and dynamical features of hadron physics, including a massless pion for zero quark mass and linear Regge trajectories M(n,L, S) = 4κ(n+L+S/2) with the same slope in the radial quantum number n and orbital angular momentum L. Only one mass parameter κ appears. The corresponding light-front Dirac equation provides a dynamical and spectroscopic model of nucleons. The same light-front equations arise from the holographic mapping of the soft-wall model modification of AdS5 space with a unique dilaton profile to QCD (3+1) at fixed light-front time. Light-front holography thus provides a precise relation between the bound-state amplitudes in the fifth dimension of AdS space and the boost-invariant light-front wavefunctions describing the internal structure of hadrons in physical space-time. We also discuss the implications of the underlying conformal template of QCD for renormalization scale-setting and the implications of light-front quantization for the value of the cosmological constant.
SPECIAL ISSUE : Scaling Effects Regulating Plant Response to Global Change Responses of sap flow , leaf gas exchange and growth of hybrid aspen to elevated atmospheric humidity under field conditions

An increase in average air temperature and frequency of rain events is predicted for higher latitudes by the end of the 21st century, accompanied by a probable rise in air humidity. We currently lack knowledge on how forest trees acclimate to rising air humidity in temperate climates. We analysed the leaf gas exchange, sap flow and growth characteristics of hybrid aspen (Populus tremula × P. tremuloides) trees growing at ambient and artificially elevated air humidity in an experimental forest plantation situated in the hemiboreal vegetation zone. Humidification manipulation did not affect the photosynthetic capacity of plants, but did affect stomatal responses: trees growing at elevated air humidity had higher stomatal conductance at saturating photosynthetically active radiation (gs sat) and lower intrinsic water-use efficiency (IWUE). Reduced stomatal limitation of photosynthesis in trees grown at elevated air humidity allowed slightly higher net photosynthesis and relative current-year height increments than in trees at ambient air humidity. Tree responses suggest a mitigating effect of higher air humidity on trees under mild water stress. At the same time, trees at higher air humidity demonstrated a reduced sensitivity of IWUE to factors inducing stomatal closure and a steeper decline in canopy conductance in response to water deficit, implying higher dehydration risk. Despite the mitigating impact of increased air humidity under moderate drought, a future rise in atmospheric humidity at high latitudes may be disadvantageous for trees during weather extremes and represents a potential threat in hemiboreal forest ecosystems.
Image retrieval and ranking through Deep Comparative Neural Networks

We focus our work on instance-level image retrieval. We approach this problem from the point of view of learning to rank. We explore the idea of using the pairwise ranking model instead of providing a similarity measure between a query and a candidate document. We also investigate the ability of this model to learn high level query-document joint features. Our preliminary results show that the end-to-end approach is not only able to learn a better preference function, but also to drive the model to learn better high level features.
Title A Genome Scan for Genes Underlying Microgeographic-ScaleLocal Adaptation in a Wild Arabidopsis Species

Adaptive divergence at the microgeographic scale has been generally disregarded because high gene flow is expected to disrupt local adaptation. Yet, growing number of studies reporting adaptive divergence at a small spatial scale highlight the importance of this process in evolutionary biology. To investigate the genetic basis of microgeographic local adaptation, we conducted a genome-wide scan among sets of continuously distributed populations of Arabidopsis halleri subsp. gemmifera that show altitudinal phenotypic divergence despite gene flow. Genomic comparisons were independently conducted in two distinct mountains where similar highland ecotypes are observed, presumably as a result of convergent evolution. Here, we established a de novo reference genome and employed an individual-based resequencing for a total of 56 individuals. Among 527,225 reliable SNP loci, we focused on those showing a unidirectional allele frequency shift across altitudes. Statistical tests on the screened genes showed that our microgeographic population genomic approach successfully retrieve genes with functional annotations that are in line with the known phenotypic and environmental differences between altitudes. Furthermore, comparison between the two distinct mountains enabled us to screen out those genes that are neutral or adaptive only in either mountain, and identify the genes involved in the convergent evolution. Our study demonstrates that the genomic comparison among a set of genetically connected populations, instead of the commonly-performed comparison between two isolated populations, can also offer an effective screening for the genetic basis of local adaptation. PLOS Genetics | DOI:10.1371/journal.pgen.1005361 July 14, 2015 1 / 26 OPEN ACCESS Citation: Kubota S, Iwasaki T, Hanada K, Nagano AJ, Fujiyama A, Toyoda A, et al. (2015) A Genome Scan for Genes Underlying Microgeographic-Scale Local Adaptation in a Wild Arabidopsis Species. PLoS Genet 11(7): e1005361. doi:10.1371/journal. pgen.1005361 Editor: Rodney Mauricio, University of Georgia, UNITED STATES Received: November 4, 2014 Accepted: June 15, 2015 Published: July 14, 2015 Copyright: © 2015 Kubota et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Data Availability Statement: Raw short read sequences are available in the DDBJ Sequenced Read Archive under the accession number DRA003268. Draft reference genome of A. halleri subsp. gemmifera is available at https://drive.google. com/open? id=0B3zal5FswpDBR04wUzJyZ25EUlk. Funding: This work was funded by the Environment Research and Technology Development Fund (S9) of the Ministry of the Environment, KAKENHI (No. 22114504, 22770013, 24770014), Inamori Foundation, Environmental Information Projects, Green Network of Excellence of MEXT (GRENE-ei),
Performance evaluation of parallel computing and Big Data processing with Java and PCJ library

—In this paper, we present PCJ (Parallel Computing in Java), a novel tool for scalable high-performance computing and big data processing in Java. PCJ is Java library implementing PGAS (Partitioned Global Address Space) programming paradigm. It allows for the easy and feasible development of computational applications as well as Big Data processing. The use of Java brings HPC and Big Data type of processing together and enables running on the different types of hardware. In particular, the high scalability and good performance of PCJ applications have been demonstrated using Cray XC40 systems. We present performance and scalability of PCJ library measured on Cray XC40 systems with standard benchmarks such as ping-pong, broadcast, and random access. We describe parallelization of example applications of different characteristics including FFT and 2D stencil. Results for standard Big Data benchmarks such as word count are presented. In all cases, measured performance and scalability conﬁrm that PCJ is a good tool to develop parallel applications of different type.
Model for Quantitative Analysis of Communication in Heterogeneous Codesign Environment

Various research groups have contributed different frameworks, models, methodologies and tools to cover the general or specific aspects of the design. In our research, we have focused on the modeling and quantitative analysis of communication aspect of the design in a heterogeneous target environment. The objective is twofold – (i) to support early design space exploration, and (ii) to suggest behavior level modifications in given application modules to support the communication requirements for the given target architecture, and architectural mappings. A model to capture the detailed communication scenario for a given application on a given target architecture and selected resource mappings, is proposed. The model is used to create abstract views of the communication scenario and to work on relevant abstraction level for the specific objective. The algorithms used in the model have been implemented and run on several data sets. The results of our analysis have been discussed to show the utility of the proposed model.
Using Edutainment to Facilitate Mathematical Thinking and Learning : An Exploratory Study

The focus of the study is to ascertain levels of student creative-critical mathematical thinking and problem solving when the element of edutainment is introduced as a pedagogical tool. As in-class activities, seven participants viewed three randomly selected episodes of Numb3rs, completed associated activities/assignments, and participated in evaluating their learning experiences based on the episodes and associated activities/assignments. Two artifacts, video and student work, were used to determine levels of critical-creative thinking after completing edutainment-related mathematics activities. The results indicated that utilizing Numb3rs as a teaching and learning tool generally facilitated movement of students’ thought processes to levels of critical-creative thinkers, increased engagement and promoted transition from fixed mindsets to growth mindsets. Intrinsic and extrinsic variables which may have contributed to ratings and student learning were included in the discussion.
BIOT THEORY OF POROELASTICITY

This document verifies that groundwater flow principles are correctly implemented in PLAXIS. Poroelasticity theory, first introduced by Biot (1941), counts for coupled hydro-mechanical processes. The present verification example studies the case of a drilled vertical borehole in saturated soil formation (porous rock), subjected to non-hydrostatic in situ stress. PLAXIS results are compared to the analytical solution provided by Detournay & Cheng (1988).
DYNAMIC PRICE AND LEAD TIME QUOTATION UNDER SEMICONDUCTOR INDUSTRY RELATED CHALLENGES

We consider the dynamic price and lead time quotation problem in the practical context of the semiconductor industry. Our model considers an inventory decoupled supply chain and accounts for a limited capacity, stochastic demand and processing times and quote-sensitive customers. We focus on performance evaluation under two decision making strategies. The first is lead time based pricing (LTBP). It follows a sequential approach where the firm decides first on the lead time quote (manufacturing) and then quotes the price under the given lead time (marketing). The second strategy suggests determining the lead time and the price quotes simultaneously. From the practical view-point, it is interesting to first understand the system performance under LTBP and then look for the ways to realize it. Based on our numerical results, we elaborate on the effect of LTBP on the key performance indicators and discuss conditions for close performance to a simultaneous decision strategy.
Who Goes to Preschool and Why Does it Matter? (Updated)

In a world shaped by global competition, preschool education programs play an increasingly vital role in child development and school readiness. There is growing awareness that early learning’s impacts persist across children’s life spans, affecting educational achievement, adult earning and even crime and delinquency. Preschool education is increasingly seen as a middleincome essential. In 2005, two-thirds of 4-year-olds and more than 40 percent of 3-year-olds were enrolled in a preschool education program. This represents a substantial increase over earlier decades, particularly at age 4. The evidence indicates the increase in enrollment has not reached all segments of the population equally and there are variations in participation rates regionally within the U.S. This report seeks to identify these important differences and shed light on how income, education, ethnicity, family structure, maternal employment and geography relate to preschool education program participation.
Identification and Characterization of the UL 24 Gene Product of Herpes Simplex Virus Type 2

The UL24 gene of herpes simplex virus type 2 (HSV-2) is predicted to encode a 281 amino acid protein with a molecular mass of 30.5 kDa. In this study, the HSV-2 UL24 gene product has been identified by using a rabbit polyclonal antiserum produced against a recombinant protein containing the full-length UL24 gene product of HSV-2 fused to glutathione-S-transferase. The antiserum reacted specifically with a 32 kDa protein in HSV-2 186-infected Vero cells and with 31 and 32 kDa proteins in UL24-expressing Cos-7 cells. Accumulation of UL24 protein to detectable levels required viral DNA synthesis, indicating that the protein was regulated as a late gene. UL24 protein was found to be associated with purified HSV-2 virions and C capsids. Indirect immunofluorescence analysis demonstrated that the UL24-specific fluorescence was detected in perinuclear regions of the cytoplasm and/or in the nucleus as small discrete granules from 9 h post infection (hpi). Furthermore, the UL24 protein expressed singly was detected predominantly in the nucleus and slightly in the cytoplasm at 24 h after transfection, with branch-like cytoplasmic protruding structures. Strong nucleolus staining was visible in partial cells.
A framework for testing the in fl uence of Aboriginal burning on grassy ecosystems in lowland , mesic south – eastern Australia

The complex interactions among climate, soils, fire and humans in the biogeography of natural grasslands has long been debated in Australia. On the one hand, ecological models assume the primacy of climate and soils. On the other, Aboriginal burning is hypothesised to have altered the entire continent since before the last glacial maximum. The present paper develops a framework to test for the ‘fingerprint’ of Aboriginal burning in lowland, mesic grassy ecosystems of south-eastern Australia, using ecological theory, and the ethno-historical record. It is clear that fire-stick farming was used to promote staple roots in south-eastern Australia and, in some instances, it has been shown to influence grassland–woodland boundaries. The framework comprises the following three evidence lines: (1) archival benchmarking and palaeoecology; (2) phytoecology; and (3) ethnology and archaeology. That fire-stick farming was likely instrumental in grassland formation and maintenance must be supported by evidence that shows that ‘natural’ grasslands exist in climatically–edaphically unexpected places, that fine-scale patterns and dynamics are at least partly due to fire and that the fire regime has been influenced by Aboriginal burning. Application of the framework indicated that widespread Aboriginal burning for staple foods likely extended the area of temperate grasslands and influenced their structure and function. Additional keywords: ethno-historical record, grassland–woodland boundaries. Received 20 April 2016, accepted 17 October 2016, published online 15 November 2016
Distributed House-Hunting in Ant Colonies Citation

We introduce the study of the ant colony house-hunting problem from a distributed computing perspective. When an ant colony’s nest becomes unsuitable due to size constraints or damage, the colony relocates to a new nest. The task of identifying and evaluating the quality of potential new nests is distributed among all ants. They must additionally reach consensus on a final nest choice and transport the full colony to this single new nest. Our goal is to use tools and techniques from distributed computing theory in order to gain insight into the house-hunting process. We develop a formal model for the house-hunting problem inspired by the behavior of the Temnothorax genus of ants. We then show a Ω(logn) lower bound on the time for all n ants to agree on one of k candidate nests. We also present two algorithms that solve the house-hunting problem in our model. The first algorithm solves the problem in optimal O(logn) time but exhibits some features not characteristic of natural ant behavior. The second algorithm runs in O(k logn) time and uses an extremely simple and natural rule for each ant to decide on the new nest.
Compact Printed Band-Notched UWB Antenna With 90 Degree Rotation Angle

─ A novel band-notched ultrawideband monopole antenna is presented. The proposed antenna consists of a swallow shape radiating patch, two novel 90 degree rotation angle complementary splitring resonator (CSRR) structures for generating band-notched function instead of changing the patchor feeding shapes, and a trapezoidal ground plane that provides a wide usable bandwidth of more than 143 % (2 GHz – 11.2 GHz). With two novel 90 degree rotation angle complementary SRR structures, band-stop frequency performance is realized, and some key characteristics such as band-notched frequency and bandwidth can be controlled easily. The designed antenna has a small size of 25 × 27.9 mm,showing the band-rejection performance in the frequency band of 3.9 GHz / 5.9GHz. The antenna demonstrates omni-directional and stable radiation patterns across all the relevant bands. Moreover, a prototype of the proposed antenna is fabricated, and the measured results are shown to be in good agreement with the simulated results. Index Terms ─ Complementary split ring resonator (CSRR), multiband, notch bands, and ultra-wideband (UWB).