Miracle-dz/UniFAR-FTUs huggingface dataset:
Early/recycling endosomes-to-TGN transport involves two SNARE complexes and a Rab6 isoform

The molecular mechanisms underlying early/recycling endosomes-to-TGN transport are still not understood. We identified interactions between the TGN-localized putative t-SNAREs syntaxin 6, syntaxin 16, and Vti1a, and two early/recycling endosomal v-SNAREs, VAMP3/cellubrevin, and VAMP4. Using a novel permeabilized cell system, these proteins were functionally implicated in the post-Golgi retrograde transport step. The function of Rab6a' was also required, whereas its closely related isoform, Rab6a, has previously been implicated in Golgi-to-endoplasmic reticulum transport. Thus, our study shows that membrane exchange between the early endocytic and the biosynthetic/secretory pathways involves specific components of the Rab and SNARE machinery, and suggests that retrograde transport between early/recycling endosomes and the endoplasmic reticulum is critically dependent on the sequential action of two members of the Rab6 subfamily.
Structured Output Prediction for Semantic Perception in Autonomous Vehicles

A key challenge in the realization of autonomous vehicles is the machine's ability to perceive its surrounding environment. This task is tackled through a model that partitions vehicle camera input into distinct semantic classes, by taking into account visual contextual cues. The use of structured machine learning models is investigated, which not only allow for complex input, but also arbitrarily structured output. Towards this goal, an outdoor road scene dataset is constructed with accompanying fine-grained image labelings. For coherent segmentation, a structured predictor is modeled to encode label distributions conditioned on the input images. After optimizing this model through max-margin learning, based on an ontological loss function, efficient classification is realized via graph cuts inference using alpha-expansion. Both quantitative and qualitative analyses demonstrate that by taking into account contextual relations between pixel segmentation regions within a second-degree neighborhood, spurious label assignments are filtered out, leading to highly accurate semantic segmentations for outdoor scenes.
Nonlinear Dynamic Analysis of Atomic Force Microscopy Under Bounded Noise Parametric Excitation

When the vibrating microcantilever in an atomic force microscope (AFM) is close to the sample surface, the nonlinear tip-sample interaction will greatly influence the dynamics of the cantilever. In this paper, the effect of the bounded noise parametric excitation on the nonlinear dynamic behavior of dynamic AFM system is investigated. The microcantilever is modeled by a single-lumped-mode approximation and the interactions between the microcantilever and sample are described by the Lennard-Jones (LJ) potential. Numerical simulations are carried out to study the coupled nonlinear dynamic system in terms of bifurcation diagram, Poincaré maps, largest Lyapunov exponent, phase portraits, and time histories in detail. Effects of the density of the random disturbance with bounded noise, material property, and contact angle of the meniscus force are analyzed and discussed. The results indicate that periodic and chaotic motions occur in the dynamic AFM system. It is demonstrated that the coupled dynamic system goes through a complex nonlinear behavior as the system parameters change and the effect of bounded noise cannot be ignored in the further design of an AFM.
Dual-Phase Lock-In Amplifier Based on FPGA for Low-Frequencies Experiments

Photothermal techniques allow the detection of characteristics of material without invading it. Researchers have developed hardware for some specific Phase and Amplitude detection (Lock-In Function) applications, eliminating space and unnecessary electronic functions, among others. This work shows the development of a Digital Lock-In Amplifier based on a Field Programmable Gate Array (FPGA) for low-frequency applications. This system allows selecting and generating the appropriated frequency depending on the kind of experiment or material studied. The results show good frequency stability in the order of 1.0 × 10−9 Hz, which is considered good linearity and repeatability response for the most common Laboratory Amplitude and Phase Shift detection devices, with a low error and standard deviation.
TAZ Servers and the Rewebber Network: Enabling Anonymous Publishing on the World Wide Web

The World Wide Web has recently matured enough to provide everyday users with an extremely cheap publishing mechanism. However, the current WWW architecture makes it fundamentally difficult to provide content without identifying yourself. We examine the problem of anonymous publication on the WWW, propose a design suitable for practical deployment, and describe our implementation. Some key features of our design include universal accessibility by preexisting clients, short persistent names, security against social, legal, and political pressure, protection against abuse, and good performance.
Computational study of self-assembly in block copolymer/superparamagnetic nanoparticle composites under external magnetic fields

This computational and theoretical study investigates the self-assembly of superparamagnetic nanoparticles and block copolymers under external magnetic fields. A variety of morphological transitions are observed based on the field orientation, nanoparticle loading, and selectivity of the nanoparticles for the blocks. For symmetric block copolymers, chaining of superparamagnetic nanoparticles under in-plane magnetic fields is shown to achieve long range orientational order of the block copolymer nanodomains and is found to be dependent on nanoparticle size, volume fraction and magnetization strength. A critical selectivity of the particles for one nanodomain is observed, above which strong alignment results and below which comparatively disordered structures are formed. Higher magnetization strengths are found to reduce equilibrium defect densities in the nematic-isotropic ordering of lamellar thin films, as corroborated by scaling arguments. For asymmetric coil fractions forming hexagonal block copolymer nanostructure, the inplane field induced chaining of the nanoparticles selective for the minority block, leads to the formation of stripe phases oriented parallel to the magnetic field. Furthermore, in-plane field induced chaining of nanoparticles selective for the majority block leads to alignment of hexagonal morphology with direction oriented parallel to the external magnetic field. Out of plane magnetic fields induce repulsive dipolar interactions between the nanoparticles that annihilate the defects in the hexagonal morphology of the block copolymer when the nanoparticle is selective for the minority block. Honeycomb lattices are obtained using nanoparticles selective for majority block under out of plane magnetic fields for certain specific nanoparticle loadings. Commensurability of nanoparticle size and loadings with the block copolymer structure is critical in optimizing the ordering of the final composite. Kinetics of alignment in block copolymer nanocomposites is studied using External Potential Dynamics (EPD) method, wherein an equivalent evolution equation for potential fields is solved instead of conservation equation for the monomer segments. The dynamics study reveals an interesting interplay of nanoparticle mobility, dipolar interaction strength and nanoparticle-polymer interaction strength on the rate of alignment of domains.
Meeting Report from the Genomic Standards Consortium (GSC) Workshop 10

This report summarizes the proceedings of the 10th workshop of the Genomic Standards Consortium (GSC), held at Argonne National Laboratory, IL, USA. It was the second GSC workshop to have open registration and attracted over 60 participants who worked together to progress the full range of projects ongoing within the GSC. Overall, the primary focus of the workshop was on advancing the M5 platform for next-generation collaborative computational infrastructures. Other key outcomes included the formation of a GSC working group focused on MIGS/MIMS/MIENS compliance using the ISA software suite and the formal launch of the GSC Developer Working Group. Further information about the GSC and its range of activities can be found at http://gensc.org/.
Volume Transmission Hologram Gratings — Basic Properties, Energy Channelizing, Effect of Ambient Temperature and Humidity

The present paper offers the authors’ view of such an important problem as classification of volume holograms, which has currently no generally accepted clear-cut principles and ter‐ minology; discussion of parameters of volume recording media that have been developed in S.I. Vavilov State Optical Institute, Russia, and show principal directions in the field of de‐ sign of volume recording media for holography; description of the results of the authors’ ex‐ periments to study the impact of ambient temperature and humidity on parameters of polymeric hologram gratings.
Utility of the trnH–psbA Intergenic Spacer Region and Its Combinations as Plant DNA Barcodes: A Meta-Analysis

Background The trnH–psbA intergenic spacer region has been used in many DNA barcoding studies. However, a comprehensive evaluation with rigorous sequence preprocessing and statistical testing on the utility of trnH–psbA and its combinations as DNA barcodes is lacking. Methodology/Principal Findings Sequences were searched from GenBank for a meta-analysis on the usefulness of trnH–psbA and its combinations as DNA barcodes. After preprocessing, we constructed full and matching data sets that contained 17 983 trnH–psbA sequences and 2190 sets of trnH–psbA, matK, rbcL, and ITS2 sequences from the same sample, repectively. These datasets were used to analyze the ability of trnH–psbA and its combinations to discriminate species by the BLAST and BLAST+P methods. The Fisher's exact test was used to evaluate the significance of performance differences. For the full data set, the identification success rates of trnH–psbA exceeded 70% in 18 families and 12 genera, respectively. For the matching data set, the identification rates of trnH–psbA were significantly higher than those of the other loci in two families and four genera. Similarly, the identification rates of trnH–psbA+ITS2 were significantly higher than those of matK+rbcL in 18 families and 21 genera. Conclusion/Significane This study provides valuable information on the higher utility of trnH–psbA and its combinations. We found that trnH–psbA+ITS2 combination performs better or equally well compared with other combinations in most taxonomic groups investigated. This information will guide the optimal usage of trnH–psbA and its combinations for species identification.
Requirement of Pax6 for the integration of guidance cues in cell migration

The intricate patterns of cell migration that are found throughout development are generated through a vast array of guidance cues. Responding integratively to distinct, often conflicting, migratory signals is probably crucial for cells to reach their correct destination. Pax6 is a master transcription factor with key roles in neural development that include the control of cell migration. In this study, we have investigated the ability of cells derived from cortical neurospheres from wild-type (WT) and Pax6−/− mouse embryos to integrate diverging guidance cues. We used two different cues, either separately or in combination: substratum nanogrooves to induce contact guidance, and electric fields (EFs) to induce electrotaxis. In the absence of an EF, both WT and Pax6−/− cells aligned and migrated parallel to grooves, and on a flat substrate both showed marked electrotaxis towards the cathode. When an EF was applied in a perpendicular orientation to grooves, WT cells responded significantly to both cues, migrating in highly oblique trajectories in the general direction of the cathode. However, Pax6−/− cells had an impaired response to both cues simultaneously. Our results demonstrate that these neurosphere derived cells have the capacity to integrate diverging guidance cues, which requires Pax6 function.
A density-based approach for mining movement patterns from semantic trajectories

In this paper, we study the problem of discovering all movement patterns from semantic trajectory databases. We propose a two-step method to solve this problem efficiently. We first retrieve frequent movement patterns of categories from the transformed database of sequential categories, and then cluster dense trajectories in a growth-type way for all movement patterns. Moreover, we define a new metric distance function on trajectories. We also use M-tree to cluster trajectories more efficiently. Our experimental results demonstrate the efficiency of the proposed method.
Further evidence for an association between the gamma-aminobutyric acid receptor A, subunit 4 genes on chromosome 4 and Fagerström Test for Nicotine Dependence.

AIMS A previous association analysis identified polymorphisms in gamma-aminobutyric acid receptor A, subunit 4 (GABRA4) and GABRA2 to be associated with nicotine dependence, as assessed by a score of 4 or more on the Fagerström Test for Nicotine Dependence (FTND). In the present report, we extend the previous study by expanding our genotyping efforts significantly for these two genes. DESIGN In 1049 cases (FTND of 4 or more) and 872 controls (smokers with FTND of 0) from the United States and Australia, we examine the association between 23 GABRA4 and 39 GABRA2 recently genotyped single nucleotide polymorphisms (SNPs) and nicotine dependence using logistic regression-based association analyses using the genomic analysis package PLINK. RESULTS Two and 18 additional SNPs in GABRA4 and GABRA2, respectively, were associated with nicotine dependence. The SNPs identified in GABRA4 (P-value = 0.002) were restricted to introns 1 and 2, exon 1 and the 5' end of the gene, while those in GABRA2 localized to the 3' end of the gene and spanned introns 9-3, and were in moderate to high linkage disequilibrium (as measured by r(2)) with each other and with previously studied polymorphisms. CONCLUSION Our findings demonstrate consistently the role of GABRA4 and GABRA2 in nicotine dependence. However, further research is needed to identify the biological influence of these intronic variations and to isolate functionally relevant polymorphisms neighboring them.
A Comparison of the KTP/532-Laser Tonsillectomy Vs. Traditional Dissection/Snare Tonsillectomy

This study compared tonsillectomy by potassium-titanyl-phosphate (KTP/532) laser with tonsillectomy by traditional dissection and snare. Eighty-three consecutive patients who were candidates for a tonsillectomy were randomly assigned to one of four groups in a prospective study. The four treatments were bilateral traditional dissection/snare tonsillectomy, bilateral KTP/532-laser tonsillectomy, left laser tonsillectomy and right dissection/snare tonsillectomy, and left dissection/snare tonsillectomy and right laser tonsillectomy. Intraoperative comparisons were made between the two methods with regard to blood loss and operating time. Postoperatively bleeding and healing time were also recorded. A questionnaire answered on a daily basis assessed the patient's pain. Disadvantages of the KTP/532 tonsillectomy included increased cost, increased total operating time as a result of increased setup time and laser malfunctions, delayed healing, and no statistically significant improvement in level of pain. The sole advantage associated with the KTP/532 laser tonsillectomy was decreased blood loss, which may be significant for patients with a coagulopathy.
Multicast Linear Precoding for MIMO-OFDM Systems

Multiple-input multiple-output (MIMO) orthogonal-frequency division multiplexing (OFDM) multicasting system is considered. For a real-time multicast MIMO-OFDM system, we propose a non-iterative and simple linear precoding that consists of a linear sum (LS) of the corresponding channels. Through numerical results, we show that a minimum user rate of the proposed LS precoding is almost identical to its performance upper bound, which can be obtained through max-min rate maximization.
Everything you wanted to know about double auctions , but were afraid to ( bid or ) ask

With the rise of ecommerce on the internet and, especially, the increase in volume of business procurement carried out electronically, double auctions have received much attention in the economics and, increasingly, computer science literature. However, there is no such thing as “the double auction”. Instead there is a profusion of terminology and a wide variety of different market institutions that are all, confusingly, described as “double auctions”. This paper aims to bring some order to this profusion. First, the paper documents the terminology and to identify the variety of market institutions that are grouped under the “double auction” heading. Second, the paper describes some of the theoretical and experimental work that has been carried out on double auctions. Finally, the paper sketches some of our recent work which aims to synthesize a common set fo experiments from those detailed in the literature.
SNX5 is essential for efficient macropinocytosis and antigen processing in primary macrophages

Summary Macropinocytosis mediates the bulk endocytosis of solute molecules, nutrients and antigens. As this endocytic pathway is considered important in functions associated with immune responses, the molecular mechanisms regulating this pathway in immune cells is of particular significance. However, the regulators of macropinocytosis in primary cells remain poorly defined. Members of the sorting nexin (SNX) family have been implicated in macropinosome biogenesis in cultured cells and here we have analyzed the role of two SNX family members, SNX1 and its binding partner SNX5, in macropinocytosis of mouse primary macrophages. We show that endogenous SNX1 and SNX5 are localised to newly-formed macropinosomes in primary mouse macrophages and, moreover, demonstrate that SNX5 plays an essential role in macropinosome biogenesis. Depletion of SNX5 in bone marrow-derived macrophages dramatically decreased both the number and size of macropinosomes. Depletion of SNX5 also resulted in dramatic reduction in uptake and processing of soluble ovalbumin in macrophages, indicating that the majority of antigen uptake and delivery to late endosomes is via macropinocytosis. By contrast, the absence of SNX1 had no effect on endogenous SNX5 localisation and macropinosome biogenesis using macrophages from SNX1 knockout mice. Therefore, SNX5 can function independently of SNX1 and is a modulator of macropinocytosis that influences the uptake and processing of soluble antigen in primary mouse macrophages.
A smooth particle mesh Ewald method

The previously developed particle mesh Ewald method is reformulated in terms of efficient B‐spline interpolation of the structure factors. This reformulation allows a natural extension of the method to potentials of the form 1/rp with p≥1. Furthermore, efficient calculation of the virial tensor follows. Use of B‐splines in place of Lagrange interpolation leads to analytic gradients as well as a significant improvement in the accuracy. We demonstrate that arbitrary accuracy can be achieved, independent of system size N, at a cost that scales as N log(N). For biomolecular systems with many thousands of atoms this method permits the use of Ewald summation at a computational cost comparable to that of a simple truncation method of 10 A or less.
Drug Delivery: Engineering Principles for Drug Therapy

Synthetic materials are a tremendous potential resource for treating human disease. For the rational design of many of these biomaterials it is necessary to have an understanding of polymer chemistry and polymer physics. Equally important to those two fields is a quantitative understanding of the principles that govern rates of drug transport, reaction, and disappearance in physiological and pathological situations. This book is a synthesis of these principles, providing a working foundation for those in the field of drug delivery. It covers advanced drug delivery and contemporary biomaterials.
FLOWERING LOCUS C EXPRESSOR Family Proteins Regulate FLOWERING LOCUS C Expression in Both Winter-Annual and Rapid-Cycling Arabidopsis1[C][W][OPEN]

FLX4 physically interacts with FLX to form a transcription activation module in the FRIGIDA complex, which is required for the activation of FLC expression in winter-annual Arabidopsis. Many naturally occurring Arabidopsis (Arabidopsis thaliana) are very late flowering, unless flowering is promoted by a prolonged period of cold (e.g. winter) known as vernalization. In these winter-annual strains, flowering prior to winter is blocked by the synergistic interaction of FRIGIDA (FRI) and FLOWERING LOCUS C (FLC). FLC acts as a strong floral inhibitor, and FRI is required for high levels of FLC expression. Vernalization, in turn, leads to an epigenetic down-regulation of FLC expression. Most rapid-cycling Arabidopsis carry loss-of-function mutations in FRI, leading to low levels of FLC and rapid flowering in the absence of vernalization. Recent work has shown that FRI acts as a scaffolding protein for the assembly of a FRI complex (FRI-C) that includes both general transcription and chromatin-modifying factors, as well as FRI-specific components such as FRI-LIKE1, FRI ESSENTIAL1 (FES1), SUPPRESSOR OF FRI4 (SUF4), and FLC EXPRESSOR (FLX). Here, we show that FLX-LIKE4 (FLX4) is a novel component of the FRI-C and is essential for the activation of FLC by FRI. Both FLX and FLX4 contain leucine zipper domains that facilitate interaction with FRI. In addition, FLX and FLX4 interact with each other and show synergistic transcription activation activity. Interestingly, we show that FLX, FLX4, FES1, and SUF4 are required for basal levels of FLC expression in the absence of FRI. Thus, components of the FRI-C play a role in the regulation of FLC expression in both FRI-containing winter annuals, as well as fri-null rapid-cycling strains.
An Aspect-Oriented Visual Ontology Editor with Edit-Time Consistency Checking

Semantic computing relies on knowledge. Ontologies are a most common means for knowledge representation and they are widely used in numerous semantic applications. While ontologies are both useful and easy-to-use, they are not easy to build and edit. Ontologies can represent complex real-world domains and concepts, much like a code in a modern programming language. Also, much like program code, descriptions easily become hard to read and complex to edit as elements' semantics are highly interconnected. Unlike modern code editors, most ontology editors do not come with edit time consistency checking and highlighting for inconsistent inputs. This paper introduces an ontology editor that incorporates edittime consistency checking for a subset of OWL Lite constraints. The editor also borrows the idea of aspect-oriented editing from software engineering in that it allows for editing and visualizing arbitrary subsets of an ontologies elements and connections with contextually meaningful names (e.g. Superman in one aspect is Clark Kent in another). The ontology itself is represented in an editable visual language that covers all semantic aspects of OWL Lite. Non-semantic information such as versioning can be edited in a text-based manner.
High Confinement and High Density with Stationary Plasma Energy and Strong Edge Radiation in the TEXTOR-94 Tokamak.

Stationary high energy confinement is observed on TEXTOR-94 for times limited only by the flux swing of the transformer using strong edge radiation cooling. Necessary tools are the feedback control of the radiated power and of the plasma energy content. At the highest densities obtained (up to 1.2 times the Greenwald limit), energy confinement exceeds the edge-localized-mode-free H-mode scaling ITERH93-P by more than 20%. beta limits of TEXTOR-94 are reached with f(H89)/q(a) approximate to 0.6 No detrimental effect of the seeded impurity is seen. These high confinement discharges meet many conditions necessary for a fusion reactor regime.