Miracle-dz/UniFAR-FTUs huggingface dataset:
Capturing protein sequence–structure specificity using computational sequence design

It is well known that protein fold recognition can be greatly improved if models for the underlying evolution history of the folds are taken into account. The improvement, however, exists only if such evolutionary information is available. To circumvent this limitation for protein families that only have a small number of representatives in current sequence databases, we follow an alternate approach in which the benefits of including evolutionary information can be recreated by using sequences generated by computational protein design algorithms. We explore this strategy on a large database of protein templates with 1747 members from different protein families. An automated method is used to design sequences for these templates. We use the backbones from the experimental structures as fixed templates, thread sequences on these backbones using a self‐consistent mean field approach, and score the fitness of the corresponding models using a semi‐empirical physical potential. Sequences designed for one template are translated into a hidden Markov model‐based profile. We describe the implementation of this method, the optimization of its parameters, and its performance. When the native sequences of the protein templates were tested against the library of these profiles, the class, fold, and family memberships of a large majority (>90%) of these sequences were correctly recognized for an E‐value threshold of 1. In contrast, when homologous sequences were tested against the same library, a much smaller fraction (35%) of sequences were recognized; The structural classification of protein families corresponding to these sequences, however, are correctly recognized (with an accuracy of >88%). Proteins 2013; © 2013 Wiley Periodicals, Inc.
Method to reduce blur distortion from EEG's using a realistic head model

A mathematical procedure, called deblurring, was developed to reduce spatial blur distortion of scalp-recorded brain potentials due to transmission through the skull and other tissues. Deblurring estimates potentials at the superficial cerebral cortical surface from EEGs recorded at the scalp using a finite-element model of each subject's scalp, skull, and cortical surface constructed from their magnetic resonance images (MRIs). Simulations indicate that deblurring is numerically stable, and a comparison of deblurred data with a direct cortical recording from a neurosurgery patient suggests that the procedure is valid. Application of deblurring to somatosensory evoked potential data recorded at 124 scalp sites suggests that the method greatly improves spatial detail and merits further development. <<ETX>>
Assembly of One-Patch Colloids into Clusters via Emulsion Droplet Evaporation

We study the cluster structures of one-patch colloidal particles generated by droplet evaporation using Monte Carlo simulations. The addition of anisotropic patch–patch interaction between the colloids produces different cluster configurations. We find a well-defined category of sphere packing structures that minimize the second moment of mass distribution when the attractive surface coverage of the colloids χ is larger than 0.3. For χ < 0.3, the uniqueness of the packing structures is lost, and several different isomers are found. A further decrease of χ below 0.2 leads to formation of many isomeric structures with less dense packings. Our results could provide an explanation of the occurrence of uncommon cluster configurations in the literature observed experimentally through evaporation-driven assembly.
LEA: A Summarization Web Environment Based on Human Instructors' Behaviour

This paper presents LEA a Web application for summarization exercise development. Appropriate for learners on different summarization ability levels as well as for various learning domains. The summarization environment provides edition facilities and aid tools to support learning. It assists during the summarization task and performs automatic assessment. The automatic summary grading process is based on expert performance, to emulate the evaluation behaviour underneath. Expert criterion is represented by a grading decision making model. In addition, discourse analysis and comprehension measures are modelled by means of natural language processing (NLP) techniques and latent semantic analysis (LSA).
Assessing DNA Barcoding as a Tool for Species Identification and Data Quality Control

In recent years, the number of sequences of diverse species submitted to GenBank has grown explosively and not infrequently the data contain errors. This problem is extensively recognized but not for invalid or incorrectly identified species, sample mixed-up, and contamination. DNA barcoding is a powerful tool for identifying and confirming species and one very important application involves forensics. In this study, we use DNA barcoding to detect erroneous sequences in GenBank by evaluating deep intraspecific and shallow interspecific divergences to discover possible taxonomic problems and other sources of error. We use the mitochondrial DNA gene encoding cytochrome b (Cytb) from turtles to test the utility of barcoding for pinpointing potential errors. This gene is widely used in phylogenetic studies of the speciose group. Intraspecific variation is usually less than 2.0% and in most cases it is less than 1.0%. In comparison, most species differ by more than 10.0% in our dataset. Overlapping intra- and interspecific percentages of variation mainly involve problematic identifications of species and outdated taxonomies. Further, we detect identical problems in Cytb from Insectivora and Chiroptera. Upon applying this strategy to 47,524 mammalian CoxI sequences, we resolve a suite of potentially problematic sequences. Our study reveals that erroneous sequences are not rare in GenBank and that the DNA barcoding can serve to confirm sequencing accuracy and discover problems such as misidentified species, inaccurate taxonomies, contamination, and potential errors in sequencing.
INTERRELATIONSHIPS OF PARASITES OF WHITE-WINGED DOVES AND MOURNING DOVES IN FLORIDA1

The parasites of indigenous populations of mourning doves (Zenaida macroura) in north and south Florida were compared with those of an introduced population of white-winged doves (Z. asiatica) in south Florida. Thirty-two species of parasites including 5 protozoans, 7 nematodes, 2 trematodes, 2 cestodes, 7 acarines, 7 mallophagans, and 2 dipterans were found. Of these, 16 were common to both species of doves. Mourning doves from north Florida showed a more diverse parasite fauna than did the white-winged or mourning dove populations from south Florida. Nematodes were the most common parasites in all three populations; infected doves contained one or two nematode species per dove. Total helminth burdens per infected dove averaged 13.1 for white-winged doves, 19.9 for mourning doves in south Florida, and 6.6 for mourning doves in north Florida. The prevalence of infections by Trichomonas gallinae was higher in white-winged doves (97%) than in mourning doves in south Florida (17%) or in mourning doves in north Florida (1%). The high prevalence of this parasite in expanding populations of white-winged doves may pose a threat to mourning dove populations since some strains of T. gallinae are pathogenic.
Microbiologically Influenced Corrosion on Seabed Chain in the North Sea

The last years Statoil has replaced some of our seabed mooring chain segments. Some of these chains have corrosion pits caused by Microbiologically Influenced Corrosion (MIC). In 2016 and 2017 one full length of a seabed chain segment, including anchor, was retrieved from a SEMI at approximately 300m water depth in the North Sea. The chain has been 20 years on the seabed. The corrosion on the chain was carefully documented, and showed significant levels of MIC. The extent of the MIC showed a strong dependency on seabed contact and how well the chain was buried in the sediments. The observed MIC is caused by Sulphate Reducing Bacteria (SRB). After corrosion identification, the chain has also been subject to full scale fatigue testing. This paper presents the technical condition of the seabed mooring chain, describing the different levels of MIC, typical SRB corrosion attacks, and the results from the fatigue testing.
THE EFFECTS OF LOCATION ELEMENTS ON HOME PURCHASE PRICES AND RENTS : Evidence from the San Francisco Bay Area

THE EFFECTS OF LOCATION ELEMENTS ON HOME PURCHASE PRICES AND RENTS: Evidence from the San Francisco Bay Area Author: Kara M. Kockelman Land-market theory emphasizes travel savings as well as access to amenities as the underlying determinants of land prices (e.g., von Thünen 1826 and Alonso 1964). This research investigates a series of hedonic models (which postulate a good's price to be a linear function of its multiple attributes) for implicit estimation of land values, along with explicit estimation of median housing price and monthly contract rent across the San Francisco Bay Area’s census tracts. The benefits and valuation of location are assessed by including a variety of travel-based explanatory variables (including average trip characteristics and automobile ownership) as well as measures of local land-use patterns after controlling for a variety of the dwelling units’ structural characteristics. In many of the models, lot size is interacted with location attributes in order to elucidate the direct dependence, if any, of land values on location. The results indicate that changes in accessibility and travel costs affect land and dwelling-unit values in highly statistically and economically significant ways. For example, the coefficient estimates associated with travel-time reductions suggest values of travel-time savings to be roughly five dollars per hour across all adult-traveller trip types (in 1989$). Furthermore, a high proximity to industrial land uses and very local commercial activity depress land (and dwelling unit) values, often substantially; and simple distance-to-CBD variables prove to be effective price predictors. The results also reveal that heteroskedasticity (a non-constant variance of the dependent variables' mean values) plays an important role in consistent and efficient estimation of model parameters and should thus be accommodated explicitly.
Bluehive - A field-programable custom computing machine for extreme-scale real-time neural network simulation

Bluehive is a custom 64-FPGA machine targeted at scientific simulations with demanding communication requirements. Bluehive is designed to be extensible with a reconfigurable communication topology suited to algorithms with demanding high-bandwidth and low-latency communication, something which is unattainable with commodity GPGPUs and CPUs. We demonstrate that a spiking neuron algorithm can be efficiently mapped to Bluehive using Bluespec System Verilog by taking a communication-centric approach. This contrasts with many FPGA-based neural systems which are very focused on parallel computation, resulting in inefficient use of FPGA resources. Our design allows 64k neurons with 64M synapses per FPGA and is scalable to a large number of FPGAs.
Harvesting Short-Rotation Poplar Plantations for Biomass Production

Nacrtak In Italy, short rotation forest has become very popular in recent years, with over 4,000 hectares already planted – almost exclusively with clone poplar. The study models the performance of modified forage harvesters on a range of short-rotation poplar plantations, identifies technical obstacles to the deployment of these machines and suggests solutions that may expand the capability of modified forage harvesters when treating short-rotation poplar. Data were collected from 16 operations, covering a total of 50 hectares and producing over 1000 green tonnes of wood chips. The average yield of the fields harvested during the trials was about 20 green tonnes/ha year, equivalent to 8 oven-dry tonnes/ha for a 60% average moisture content, measured in the laboratory. Gross machine productivity ranged from 9 to 44 green tonnes/scheduled machine hour (gt/SMH), with an average value of 25 gt/SMH. Of course, this result is affected by other factors than just forager performance, which is potentially much higher. A model was developed to predict harvesting performance and cost, showing that harvesting cost can be maintained below the 15 Euro/green tonne (2 Euro/GJ) ceiling only if field stocking exceeds 40 or 50 gt/ha when rows are long 300 and 100 m, respectively. The study also shows the need to optimize operations. Over a quarter of the total worksite time is occupied by unproductive delays, which may be reduced with improved planning and maintenance.
A multi-perspective approach for web service composition

The new paradigm for distributed computing over the Internet is that of Web services (WSs). One of the key ideas of this new paradigm is the ability to create value-added Service-Based Applications (SBAs) by composing pre-existing services. Building SBAs necessitates the discovery and the selection of the most appropriate WSs that fit closely users' functional and non-functional requirements. Due to the large number of WSs that are advertised over public and private registries and the various functional and non-functional capabilities that are required by users, discovery and selection of WSs have become a real challenge nowadays. In this paper, we present a WS composition approach that is built upon both perspectives: intentional and operational. In the intentional perspective, we propose to model users' requirements for SBAs using the MAP formalism and specify the required WSs using an Intentional Service Model (ISM). In the operational perspective, we propose to discover the required WSs by querying the service search engine Service-Finder and select the most appropriate WSs by using many-valued concept lattices. To validate our approach, we use an analytical technique that is the monitoring to verify that the selected WSs assure the required users' non-functional capabilities.
A domain shared by the Polycomb group proteins Scm and ph mediates heterotypic and homotypic interactions

The Sex comb on midleg (Scm) and polyhomeotic (ph) proteins are members of the Polycomb group (PcG) of transcriptional repressors. PcG proteins maintain differential patterns of homeotic gene expression during development in Drosophila flies. The Scm and ph proteins share a homology domain with 38% identity over a length of 65 amino acids, termed the SPM domain, that is located at their respective C termini. Using the yeast two-hybrid system and in vitro protein-binding assays, we show that the SPM domain mediates direct interaction between Scm and ph. Binding studies with isolated SPM domains from Scm and ph show that the domain is sufficient for these protein interactions. These studies also show that the Scm-ph and Scm-Scm domain interactions are much stronger than the ph-ph domain interaction, indicating that the isolated domain has intrinsic binding specificity determinants. Analysis of site-directed point mutations identifies residues that are important for SPM domain function. These binding properties, predicted alpha-helical secondary structure, and conservation of hydrophobic residues prompt comparisons of the SPM domain to the helix-loop-helix and leucine zipper domains used for homotypic and heterotypic protein interactions in other transcriptional regulators. In addition to in vitro studies, we show colocalization of the Scm and ph proteins at polytene chromosome sites in vivo. We discuss the possible roles of the SPM domain in the assembly or function of molecular complexes of PcG proteins.
Wavelength converters for deflection routing networks

Deflection routing may become an appealing routing principle in the metropolitan area because of the increasing gap between the WDM transmission capacities and the processing power available in the nodes. Deflection routing is fast, simple, naturally copes with local transient or permanent congestion states and may easily be tailored for service differentiation. Deflection routing however suffers from a limited throughput and relatively large delay jitters as compared to the classical store-and-forward approach, especially if the traffic is uniform and uniformly distributed. In this article we have shown how the use of wavelength converters dramatically improves the deflection routing performance for both synchronous and asynchronous deflection routing. Therefore, the larger the number of wavelengths, the better the network performance, a property which indeed makes deflection routing a future-proof paradigm in the metropolitan area. We have also shown that this improvement is stronger in the case of asynchronous deflection routing networks; this is a very important result since it allows to make use the full flexibility of deflection routing with variable packet lengths (encapsulated IP datagrams for instance) without sacrificing much performance in terms of throughput or jitter.
Characterization of a multimode coplanar waveguide parametric amplifier

We characterize a Josephson parametric amplifier based on a flux-tunable quarter-wavelength resonator. The fundamental resonance frequency is ∼1 GHz, but we use higher modes of the resonator for our measurements. An on-chip tuning line allows for magnetic flux pumping of the amplifier. We investigate and compare degenerate parametric amplification, involving a single mode, and nondegenerate parametric amplification, using a pair of modes. We show that we reach quantum-limited noise performance in both cases.
Exploring the Influence of Nature Relatedness and Perceived Science Knowledge on Proenvironmental Behavior

This study was undertaken to investigate the factors influencing proenvironmental behavior of individuals residing in the Northern Rocky Mountains (N = 267). Measures of relatedness to nature and perceived science knowledge were collected through a convenience sample approach using multiple avenues such as city email lists, organizational newsletters, and social media channels. Analysis of the data was conducted using both partial least squares and covariance based structural equation modeling to explore the relationships between the constructs. Additionally, qualitative definitions of proenvironmental behavior were investigated in order to address potential gaps between self-reported and observed behaviors. Quantitative findings show a renewed positive connection between science education, nature relatedness, and proenvironmental behaviors. Furthermore, qualitative findings suggest positive relationships between how publicly people are willing to share their passion for the outdoors and their willingness to engage in proenvironmental behaviors.
Demand Uncertainty and the Bayesian Effect in Markdown Pricing with Strategic Customers

This paper studies the role of demand uncertainty in temporal discrimination when the retailer applies markdown pricing facing strategic customers. We consider a model in which a retail firm announces a pair of declining prices for two selling periods, and customers with heterogeneous valuations each decide whether to buy a unit early, later or never. In this model, if the demand function is linear and its parameters are common knowledge, there never exist any markdown prices that achieve temporal discrimination for any feasible model parameters. Either all buying customers wait, or all buy early. By contrast, if the demand level is unknown, there always exists a temporally discriminating markdown pricing scheme for all feasible model parameters. We derive qualitative insights to the way demand uncertainty and Bayesian updating contribute to temporal discrimination, which broadly apply to nonlinear demand functions as well. We also show that in case of demand uncertainty, there always exists a temporally discriminating pricing scheme that yields a strictly higher profit to the retailer than the optimal static pricing scheme. Ironically, however, the retailer cannot implement the optimal scheme due to the same demand uncertainty.
Effects of Feature Variations on Attributions for Schematic Faces

31 subjects classified 16 schematic faces on six dimensions. Attractiveness was generally associated with widely separated eyes, a short nose, and high feature placement. When features were considered in combination, faces with low placement were judged attractive, although the effect was mitigated by a narrow mouth. Previous findings concerning perceived age and gender were partially replicated, but folk wisdom linking intelligence to low placement (high forehead) was refuted. It is suggested that the relationship between individual features and attributions is nonlinear and interactive, and that researchers should investigate these hypotheses by exercising finer control over feature variations.
40Ar/39Ar ages and zircon petrochronology for the rear arc of the Izu-Bonin-Marianas intra-oceanic subduction zone

ABSTRACT Long-lived intra-oceanic arcs of Izu-Bonin-Marianas (IBM)-type are built on thick, granodioritic crust formed in the absence of pre-existing continental crust. International Ocean Discovery Program Expedition 350, Site U1437, explored the IBM rear arc to better understand continental crust formation in arcs. Detailed petrochronological (U–Pb geochronology combined with trace elements, oxygen and hafnium isotopes) characterizations of zircon from Site U1437 were carried out, taking care to exclude potential contaminants by (1) comparison of zircon ages with ship-board palaeomagnetic and biostratigraphic ages and 40Ar/39Ar geochronology, (2) analysing zircon from drill muds for comparison, (3) selectively carrying out in situ analysis in petrographic thin sections, and (4) minimizing potential laboratory contamination through using pristine equipment during mineral separation. The youngest zircon ages in Site U1437 are consistent with 40Ar/39Ar and shipboard ages to a depth of ~1390 m below sea floor (mbsf) where Igneous Unit Ig 1 yielded an 40Ar/39Ar age of 12.9 ± 0.3 Ma (all errors 2σ). One single zircon (age 15.4 ± 1.0 Ma) was recovered from the deepest lithostratigraphic unit drilled, Unit VII (1459.80–1806.5 mbsf). Site U1437 zircon trace element compositions are distinct from those of oceanic and continental arc environments and differ from those generated in thick oceanic crust (Iceland-type) where low-δ18O evolved melts are produced via re-melting of hydrothermally altered mafic rocks. Ti-in-zircon model temperatures are lower than for mid-ocean ridge rocks, in agreement with low zircon saturation temperatures, suggestive of low-temperature, hydrous melt sources. Zircon oxygen (δ18O = 3.3–6.0‰) and hafnium (εHf = + 10–+16) isotopic compositions indicate asthenospheric mantle sources. Trace element and isotopic differences between zircon from Site U1437 rear-arc rocks and the Hadean detrital zircon population suggest that preserved Hadean zircon crystals were probably generated in an environment different from modern oceanic convergent margins underlain by depleted mantle.
Almost-commutative geometries beyond the standard model II: new colours

We will present an extension of the standard model of particle physics in its almost-commutative formulation. This extension is guided by the minimal approach to almost-commutative geometries employed by Iochum et al (2004 J. Math. Phys.45 5003 (Preprint hep-th/0312276)), Jureit and Stephan (2005 J. Math. Phys.46 043512 (Preprint hep-th/0501134)), Schücker (2005 Preprint hep-th/0501181), Jureit et al (2005 J. Math. Phys.46 072303 (Preprint hep-th/0503190)) and Jureit and Stephan (2006 Preprint hep-th/0610040), although the model presented here is not minimal itself. The corresponding almost-commutative geometry leads to a Yang–Mills–Higgs model which consists of the standard model and two new fermions of opposite electromagnetic charge which may possess a new colour-like gauge group. As a new phenomenon, grand unification is no longer required by the spectral action.