Miracle-dz/UniFAR-FTUs huggingface dataset:
Adenovirus polypeptide IX revealed as capsid cement by difference images from electron microscopy and crystallography.

Particles of adenovirus type 2 (ad2), when disassembled, consistently yield groups‐of‐nine (GON) hexons, which are the major virion shell component. The location of a minor component (6%) of the GON has been determined using a novel combination of electron microscopy and X‐ray crystallography. The Brookhaven Scanning Transmission Electron Microscope (STEM) was used to estimate the distribution of protein in the GON to a resolution of 15‐18 A. The relative hexon positions then were determined to within 1 A using a model of the hexon derived from the X‐ray crystal structure to search the STEM image. The difference image between the STEM image and a model hexon group reveals individual monomers of polypeptide IX extending along the hexon‐‐hexon interfaces. The distribution confirms our earlier proposal that four trimers of polypeptide IX are embedded in the large cavities in the upper surface of the GON to cement hexons into a highly‐stable assembly.
Characteristics of Water Masses in the Atlantic Ocean based on GLODAPv2 data

Abstract. The characteristics of the main water masses in the Atlantic Ocean are investigated and defined as Source Water Types (SWTs) from their formation area by six key properties based on the GLODAPv2 observational data. These include both conservative (potential temperature and salinity) and non-conservative (oxygen, silicate, phosphate and nitrate) variables. For this we divided the Atlantic Ocean into four vertical layers by distinct potential densities in the shallow and intermediate water column, and additionally by concentration of silicate in the deep waters. The SWTs in the upper/central water layer originates from subduction during winter and are defined as central waters, formed in four distinct areas; East North Atlantic Central water (ENACW), West North Atlantic Central Water (WNACW), East South Atlantic Central Water (ESACW) and West South Atlantic Central Water (WSACW). Below the upper/central layer the intermediate layer consist of three main SWTs; Antarctic Intermediate Water (AAIW), Subarctic Intermediate Water (SAIW) and Mediterranean Overflow Water (MOW). The North Atlantic Deep Water (NADW) is the dominating SWT in the deep and overflow layer, and is divided into upper and lower NADW based on the different origins and properties. The origin of both the upper and lower NADW is the Labrador Sea Water (LSW), the Iceland–Scotland Overflow Water (ISOW) and Denmark Strait Overflow Water (DSOW). Antarctic Bottom Water (AABW) is the only natural SWT in the bottom layer and this SWT is redefined as North East Atlantic Bottom Water (NEABW) in the north of equator due to the change of key properties, especial silicate. Similar with NADW, two additional SWTS, Circumpolar Deep Water (CDW) and Weddell Sea Bottom Water (WSBW), are defined in the Weddell Sea in order to understand the origin of AABW. The definition of water masses in biogeochemical space is useful for, in particular, chemical and biological oceanography to understand the origin and mixing history of water samples.
Comparison of Clean-Up Methods for Ochratoxin A on Wine, Beer, Roasted Coffee and Chili Commercialized in Italy

The most common technique used to detect ochratoxin A (OTA) in food matrices is based on extraction, clean-up, and chromatography detection. Different clean-up cartridges, such as immunoaffinity columns (IAC), molecular imprinting polymers (MIP), Mycosep™ 229, Mycospin™, and Oasis® HLB (Hydrophilic Lipophilic balance) as solid phase extraction were tested to optimize the purification for red wine, beer, roasted coffee and chili. Recovery, reproducibility, reproducibility, limit of detection (LOD) and limit of quantification (LOQ) were calculated for each clean-up method. IAC demonstrated to be suitable for OTA analysis in wine and beer with recovery rate >90%, as well as Mycosep™ for wine and chili. On the contrary, MIP columns were the most appropriate to clean up coffee. A total of 120 samples (30 wines, 30 beers, 30 roasted coffee, 30 chili) marketed in Italy were analyzed, by applying the developed clean-up methods. Twenty-seven out of 120 samples analyzed (22.7%: two wines, five beers, eight coffees, and 12 chili) resulted positive to OTA. A higher incidence of OTA was found in chili (40.0%) more than wine (6.6%), beers (16.6%) and coffee (26.6%). Moreover, OTA concentration in chili was the highest detected, reaching 47.8 µg/kg. Furthermore, three samples (2.5%), two wines and one chili, exceeded the European threshold.
Speech-on-speech masking with variable access to the linguistic content of the masker speech.

It has been reported that listeners can benefit from a release in masking when the masker speech is spoken in a language that differs from the target speech compared to when the target and masker speech are spoken in the same language [Freyman, R. L. et al. (1999). J. Acoust. Soc. Am. 106, 3578-3588; Van Engen, K. , and Bradlow, A. (2007), J. Acoust. Soc. Am. 121, 519-526]. It is unclear whether listeners benefit from this release in masking due to the lack of linguistic interference of the masker speech, from acoustic and phonetic differences between the target and masker languages, or a combination of these differences. In the following series of experiments, listeners' sentence recognition was evaluated using speech and noise maskers that varied in the amount of linguistic content, including native-English, Mandarin-accented English, and Mandarin speech. Results from three experiments indicated that the majority of differences observed between the linguistic maskers could be explained by spectral differences between the masker conditions. However, when the recognition task increased in difficulty, i.e., at a more challenging signal-to-noise ratio, a greater decrease in performance was observed for the maskers with more linguistically relevant information than what could be explained by spectral differences alone.
Highly Mobile Gapless Excitations in a Two-Dimensional Candidate Quantum Spin Liquid

Quantum Spin Liquid In antiferromagnets, the lowest-energy state is reached when neighboring spins on the underlying lattice point in opposite directions. Because of geometric constraints on some lattices (such as the two-dimensional triangular lattice), this magnetic ordering cannot be achieved even at temperatures close to absolute zero, and these compounds are predicted to be in a quantum spin liquid state. Yamashita et al. (p. 1246) measured the thermal conductivity of a recently identified candidate quantum spin liquid, the organic compound EtMe3Sb[Pd(dmit)2]2, and characterized its lowest-lying excitations. Two types of excitations were observed: ballistically propagating gapless excitations and excitations associated with a finite spin gap. These results contribute to our understanding of this unusual state of matter, which is potentially relevant to other two-dimensional quantum systems. Thermal conductivity measurements on a novel organic insulator help describe its microscopic electronic structure. The nature of quantum spin liquids, a novel state of matter where strong quantum fluctuations destroy the long-range magnetic order even at zero temperature, is a long-standing issue in physics. We measured the low-temperature thermal conductivity of the recently discovered quantum spin liquid candidate, the organic insulator EtMe3Sb[Pd(dmit)2]2. A sizable linear temperature dependence term is clearly resolved in the zero-temperature limit, indicating the presence of gapless excitations with an extremely long mean free path, analogous to excitations near the Fermi surface in pure metals. Its magnetic field dependence suggests a concomitant appearance of spin-gap–like excitations at low temperatures. These findings expose a highly unusual dichotomy that characterizes the low-energy physics of this quantum system.
Yelp User Rating Prediction

Yelp is a popular crowd-sourced local business reviews and social networking platform. For each individual business, users can submit a review on their products or services using a one to five star rating system while interacting with each other through following users and voting on reviews. Having accumulated an enormous amount of data on information, reviews, and ratings of businesses, Yelp has become an important reference for making consumer decision. However, going through a large quantity of raw data can be time consuming. In order to overcome information overload, we would like to create a more efficient option that gives users suggestions that are tailored to their personal preferences.
Implementation of ICF in goal setting in rehabilitation of children with chronic disabilities at Beitostolen Healthsports Centre

Purpose: Develop an International Classification of Functioning, Disability and Health (ICF) Code Set, useful in goal oriented rehabilitation of a study population of children with chronic disabilities. Method: A triangulation of methods, using an interview to identify the main needs and goals of the study population, and a questionnaire to identify the main problems, with a registration of the frequency within each category. After qualitative and quantitative analyses this resulted in two sets of ICF categories. These two sets were then compared and merged into a proposed ICF Code Set for goal setting. Results: Thirty categories were identified from the interviews and the following linking process. Problems were reported in all suggested categories within the ICF questionnaire, resulting in 49 categories. The comparison of the two sets of categories resulted in a proposed ICF Code Set of 40 categories. Conclusions: Through a triangulation of methods, we developed a tailored code set for the goal setting process in rehabilitation for children with a disability, taking into account both individual preferences and the health professionals’ perspective. Although the external validity is limited, our methodological procedures may have relevance for the implementation of ICF in other clinical settings and populations. Implications for Rehabilitation ICF is increasingly used as the framework for goal setting in rehabilitation. Development of ICF Code Sets could provide a basis for individualized treatments through a structured goal planning process. A triangulation of methods in the development of such code sets, combining qualitative and quantitative methodology could be of value, seeing the health professionals’ perspective being enriched and deepened by the patients’ preferences.
Maximum Entropy Production as an Inference Algorithm that Translates Physical Assumptions into Macroscopic Predictions: Don't Shoot the Messenger

Is Maximum Entropy Production (MEP) a physical principle? In this paper I tentatively suggest it is not, on the basis that MEP is equivalent to Jaynes’ Maximum Entropy (MaxEnt) inference algorithm that passively translates physical assumptions into macroscopic predictions, as applied to non-equilibrium systems. MaxEnt itself has no physical content; disagreement between MaxEnt predictions and experiment falsifies the physical assumptions, not MaxEnt. While it remains to be shown rigorously that MEP is indeed equivalent to MaxEnt for systems arbitrarily far from equilibrium, work in progress tentatively supports this conclusion. In terms of its role within non-equilibrium statistical mechanics, MEP might then be better understood as Messenger of Essential Physics.
Unobserved Heterogeneity and Reserve Prices in Auctions

type="main"> This article shows how reserve prices can be used to control for unobserved object heterogeneity to identify and estimate the distribution of bidder values in auctions. Reserve prices are assumed to be monotonic in the realization of unobserved heterogeneity, but not necessarily set optimally. The model is estimated using transaction prices from a used car auction platform to show that the platform enables sellers to capture a large fraction of the potential value from selling their vehicle. Individual sellers benefit mostly from access to a large set of buyers, but the magnitude depends on accounting for unobserved heterogeneity.
Developing a Framework for Describing Relations among Language Resources

In this paper, we study relations holding between language resources as implemented in activities concerned with their documentation. We envision the term language resources with an inclusive definition covering datasets (corpora, lexica, ontologies, grammars, etc.), tools (including web services, workflows, platforms etc.), related publications and documentation, specifications and guidelines. However, the scope of the paper is limited to relations holding for datasets and tools. The study fosuses on the META-SHARE infrastructure and the Linguistic Data Consortium and takes into account the ISOcat DCR relations. Based on this study, we propose a taxonomy of relations, discuss their semantics and provide specifications for their use in order to cater for semantic interoperability. Issues of granularity, redundancy in codification, naming conventions and semantics of the relations are presented.
Causality-constrained multiple shift sequential matrix diagonalisation for parahermitian matrices

This paper introduces a causality constrained sequential matrix diagonalisation (SMD) algorithm, which generates a causal paraunitary transformation that approximately diagonalises and spectrally majorises a parahermitian matrix, and can be used to determine a polynomial eigenvalue decomposition. This algorithm builds on a multiple shift technique which speeds up diagonalisation per iteration step based on a particular search space, which is constrained to permit a maximum number of causal time shifts. The results presented in this paper show the performance in comparison to existing algorithms, in particular an unconstrained multiple shift SMD algorithm, from which our proposed method derives.
Load-dependency in mechanical properties of subepicardial and subendocardial cardiomyocytes

Electrical and mechanical properties of myocardium vary transmurally in the left ventricular wall. Regional differences in the mechanical environment of cardiomyocytes may potentially contribute to this heterogeneity due to mechano-electric feedback. In the present study, we investigate transmural differences in active and passive tensions at different preloads between the subepicardial (EPI) and subendocardial (ENDO) cells isolated from mouse left ventricle, using our recently developed single cell stretch method where each cell end was held by a pair of carbon fibers to apply various extent of preload to the cells. To predict underlying mechanisms of the transmural differences, we used our electromechanical EPI and ENDO cell models to simulate experimentally obtained results. Wet experiments showed that both passive and active tensions at different preloads are higher in ENDO cardiomyocytes, indicating higher stiffness and contractility in ENDO cells compared to EPI cells. Our mathematical models reproduce experimental results, suggesting differences in the kinetics of cross bridges and calcium-troponin C complexes in ENDO and EPI models may essentially contribute to the differences in mechanical properties between the cells.
Coupling Assembly of the E-Cadherin/β-Catenin Complex to Efficient Endoplasmic Reticulum Exit and Basal-lateral Membrane Targeting of E-Cadherin in Polarized MDCK Cells

The E-cadherin/catenin complex regulates Ca++-dependent cell–cell adhesion and is localized to the basal-lateral membrane of polarized epithelial cells. Little is known about mechanisms of complex assembly or intracellular trafficking, or how these processes might ultimately regulate adhesion functions of the complex at the cell surface. The cytoplasmic domain of E-cadherin contains two putative basal-lateral sorting motifs, which are homologous to sorting signals in the low density lipoprotein receptor, but an alanine scan across tyrosine residues in these motifs did not affect the fidelity of newly synthesized E-cadherin delivery to the basal-lateral membrane of MDCK cells. Nevertheless, sorting signals are located in the cytoplasmic domain since a chimeric protein (GP2CAD1), comprising the extracellular domain of GP2 (an apical membrane protein) and the transmembrane and cytoplasmic domains of E-cadherin, was efficiently and specifically delivered to the basal-lateral membrane. Systematic deletion and recombination of specific regions of the cytoplasmic domain of GP2CAD1 resulted in delivery of <10% of these newly synthesized proteins to both apical and basal-lateral membrane domains. Significantly, >90% of each mutant protein was retained in the ER. None of these mutants formed a strong interaction with β-catenin, which normally occurs shortly after E-cadherin synthesis. In addition, a simple deletion mutation of E-cadherin that lacks β-catenin binding is also localized intracellularly. Thus, β-catenin binding to the whole cytoplasmic domain of E-cadherin correlates with efficient and targeted delivery of E-cadherin to the lateral plasma membrane. In this capacity, we suggest that β-catenin acts as a chauffeur, to facilitate transport of E-cadherin out of the ER and the plasma membrane.
Parametric timing and power macromodels for high level simulation of low-swing interconnects

The impact of global on-chip interconnections on power consumption and speed of integrated circuits is becoming a serious concern. Designers need therefore to quickly estimate how performance and power are affected by a given choice of the interconnection parameters (length, voltage swing, driver and receiver schematics and sizing). This work focuses on the entire communication channel (driver, interconnect, receiver), and provides high level parametric VHDL simulation models for low-swing signaling schemes. These SPICE-derived power and timing macromodels transfer electrical-level information to the RTL simulation in an event-driven fashion, as transitions occur at the input of the interconnect driver. The accuracy reached by this back-annotation technique is within 5% with respect to SPICE results, with only 4% simulation speed penalty in the worst case.
Software based Low Rate DoS Attack Detection Mechanism

Existing DoS attack detection tools are unable to detect Low rate DoS (LDoS) attacks. Many researchers have proposed mechanisms to detect LdoS attack. But they require modifications to the existing infrastructure or protocols which is not practical. There should be a lightweight mechanism which could be integrated with existing Intrusion Detection Systems. This paper proposes a lightweight software-based approach for LdoS detection which could be integrated with existing Intrusion detection system and does not require any change in existing infrastructure and protocol.Experimental results are provided to support the effectiveness and efficiency of proposed mechanism.
Composite Rigid-Foldable Curved Origami Structure

Summary: In this study, we show a family of multilayered rigid-foldable and flat-foldable vault structures. A vault can be designed by constructing a rigid-foldable curved folded tubular arch and assembling the arches to construct a multilayered surface. The resulting vault is also rigidly flat-foldable. We first show the process involved in the geometric construction of the tubular structure from a given space curve defined by curvature and torsion functions. Next, we show a single-DOF rigid-folding motion that is enabled by the curved folded tube. Finally, we show the parametric design of a vault structure and discuss its design parameters and the resulting form.
A problem of overlap

Abstract Here we propose that earlier-demonstrated details in the primate visual cortical map may account for an otherwise puzzling (and problematic) finding in the current human fMRI literature. Specifically, the well-known regions LO and MT(+) reportedly overlap in the human cortical visual map, when those two regions are localized using standard stimulus comparisons in conventional fMRI experiments. Here we describe evidence supporting the idea that the apparent functional overlap between LO and MT arises from a third area (the MT crescent: “MTc”), which is well known to surround posterior MT based on earlier histological, neuroanatomical, and electrophysiological studies in nonhuman primates. If we assume that MTc also exists in human visual cortex, and that it has a location and functional properties intermediate to those in LO and MT, simplistic modeling confirmed that this arrangement could produce apparent overlap between localizers for LO and MT in conventional fMRI maps in human visual cortex.
Prevention or Modification of Epileptogenesis after Brain Insults: Experimental Approaches and Translational Research

Diverse brain insults, including traumatic brain injury, stroke, infections, tumors, neurodegenerative diseases, and prolonged acute symptomatic seizures, such as complex febrile seizures or status epilepticus (SE), can induce “epileptogenesis,” a process by which normal brain tissue is transformed into tissue capable of generating spontaneous recurrent seizures. Furthermore, epileptogenesis operates in cryptogenic causes of epilepsy. In view of the accumulating information about cellular and molecular mechanisms of epileptogenesis, it should be possible to intervene in this process before the onset of seizures and thereby either prevent the development of epilepsy in patients at risk or increase the potential for better long-term outcome, which constitutes a major clinical need. For identifying pharmacological interventions that prevent, interrupt or reverse the epileptogenic process in people at risk, two groups of animal models, kindling and SE-induced recurrent seizures, have been recommended as potentially useful tools. Furthermore, genetic rodent models of epileptogenesis are increasingly used in assessing antiepileptogenic treatments. Two approaches have been used in these different model categories: screening of clinically established antiepileptic drugs (AEDs) for antiepileptogenic or disease-modifying potential, and targeting the key causal mechanisms that underlie epileptogenesis. The first approach indicated that among various AEDs, topiramate, levetiracetam, carisbamate, and valproate may be the most promising. On the basis of these experimental findings, two ongoing clinical trials will address the antiepileptogenic potential of topiramate and levetiracetam in patients with traumatic brain injury, hopefully translating laboratory discoveries into successful therapies. The second approach has highlighted neurodegeneration, inflammation and up-regulation of immune responses, and neuronal hyperexcitability as potential targets for antiepileptogenesis or disease modification. This article reviews these areas of progress and discusses the challenges associated with discovery of antiepileptogenic therapies.