Structural Hints Research Articles

StructNeRF: Neural Radiance Fields for Indoor Scenes With Structural Hints.

Neural Radiance Fields (NeRF) achieve photo-realistic view synthesis with densely captured input images. However, the geometry of NeRF is extremely under-constrained given sparse views, resulting in significant degradation of novel view synthesis quality. Inspired by self-supervised depth estimation methods, we propose StructNeRF, a solution to novel view synthesis for indoor scenes with sparse inputs. StructNeRF leverages the structural hints naturally embedded in multi-view inputs to handle the unconstrained geometry issue in NeRF. Specifically, it tackles the texture and non-texture regions respectively: a patch-based multi-view consistent photometric loss is proposed to constrain the geometry of textured regions; for non-textured ones, we explicitly restrict them to be 3D consistent planes. Through the dense self-supervised depth constraints, our method improves both the geometry and the view synthesis performance of NeRF without any additional training on external data. Extensive experiments on several real-world datasets demonstrate that StructNeRF shows superior or comparable performance compared to state-of-the-art methods (e.g. NeRF, DSNeRF, RegNeRF, Dense Depth Priors, MonoSDF, etc.) for indoor scenes with sparse inputs both quantitatively and qualitatively.

The engineer and the ocean. Structural hints for John Tzetzes’ ‘Homeric Allegories

The engineer and the ocean. Structural hints for John Tzetzes’ ‘Homeric Allegories

Two‐stream spatiotemporal networks for skeleton action recognition

AbstractSkeleton‐based neural networks have been considered a focus for human action recognition (HAR). It is noteworthy that the existing skeleton‐based methods are not capable of combining the spatial and temporal features reasonably to derive more effective high‐level representations, and it continues to be a challenging task of learning and representing the skeleton action discriminatively. In this study, a novel two‐stream spatiotemporal network (TSTN) is proposed, which is capable of processing the spatial and temporal features respectively and collectively to achieve a better representation and understanding of human action. The temporal branch stacks three gate recurrent unit (GRU) blocks in a new architecture to encode the temporal correlations from different aspects of human action, achieving high‐level temporal semantic feature expressions. The spatial branch encodes the spatial features with multi‐stacked graph convolutional network (GCN) blocks. Self‐attention mechanisms incorporated with the graph structure of the skeleton are explored to add weight influence and structural hints to further enhance the performance. The experimental results verify the effectiveness and superiority of the proposed model in skeleton action recognition; the model reaches state‐of‐the‐art on specific datasets.

Predictable Liquid Chromatography Quadrupole Time-of-Flight Mass Spectrometry Fragmentation of Ozone-Reactive N-Nitrosodimethylamine Precursors Coupled with In Silico Fragmentation and Ion Mobility-Quadrupole Time-of-Flight Facilitates Their Identification in Sewage

This study investigated the liquid chromatography quadrupole time-of-flight mass spectrometry (LC-QTOF/MS) fragmentation of 10 potent model ozone (O3)-reactive N-nitrosodimethylamine (NDMA) precursors bearing (CH3)2N-N or (CH3)2N-(SO2)-N. Fragments (m/z 61.0766, 60.0688 Da loss, and 72.0688 Da loss) were discovered as pertinent diagnostic fragments for precursors bearing (CH3)2N-N, whereas a loss of 108.0119 Da was consistent for precursors bearing (CH3)2N-S(O2)-N. Using the fragments as structural hints on a sewage fraction with a high concentration of O3-reactive precursors, peaks of precursors sharing m/z 61.0766, a 60.0688 Da loss, or both were flagged. Then, using in silico fragmenters and (CH3)2N-N as a substructure filter on online-chemical structure databases, we identified PubChem's compound identifier (PCCID) 141210417 and 1,1,1',1'-tetramethyl-4,4'-(methylene-di-p-phenylene)disemicarbazide (TMDS). TMDS was confirmed using an authentic standard, and ion mobility (IM)-QTOF/MS confirmed its rider peak as PCCID 141210417. PCCID 141210417 is an isomer of TMDS, and its environmental occurrence is associated with technical-grade TMDS and industrial effluents. The estimated contribution of TMDS to the total NDMA formation potential of the sewage fraction was 20-24%, which was suggestive of the significance of PCCID 141210417 and other precursors.

From Gargamelle to MINERvA: exploring the structure of the nucleon with neutrinos

Neutrino scattering experiments have been exploring the structure of the nucleon with Deep-Inelastic Scattering for over 50 years. Although hints of nucleon structure were available using CERN’s first neutrino beam in the 1960s, the study actually started quantitatively in the early 1970s with the Gargamelle heavy liquid bubble chamber that produced first neutrino confirmation of scaling. This study of nucleon structure continued with both bubble chambers and more massive electronic detectors that, with higher energy neutrino beams and \(Q^2\) reach, examined the breaking of this scaling while testing Quantum Chromodynamics. A significant factor when including neutrino explorations of nucleon structure in the overall picture is that to gather significant statistics, neutrino experiments have had to use heavier nuclear targets. It has been experimentally demonstrated that the structure of the nucleon in the nuclear environment is indeed different than the free nucleon structure. Understanding this modified structure has played an important part in the experimental and theoretical exploration of nucleon structure by neutrinos and is one of the important goals of the on-going MINERvA experiment at Fermilab.

Inter-hairpin linker sequences determine the structure of the ββ-solenoid fold: a “bottom-up” study of pneumococcal LytA choline-binding module

The ββ-solenoid structures are part of many proteins involved in the recognition of bacterial cell wall. They are elongated polypeptides consisting of repeated β-hairpins connected by linker sequences and disposed around a superhelical axis stabilised by short-range interactions. Among the most studied ββ-solenoids are those belonging to the family of choline-binding modules (CBMs) from the respiratory pathogen Streptococcus pneumoniae (pneumococcus) and its bacteriophages, and their properties have been employed to develop several biotechnological and biomedical tools. We have carried out a theoretical, spectroscopic and thermodynamic study of the ββ-solenoid structure of the CBM from the pneumococcal LytA autolysin using peptides of increasing length containing 1–3 repeats of this structure. Our results show that hints of native-like tertiary structure are only observed with a minimum of three β-hairpins, corresponding to one turn of the solenoid superhelix, and identify the linker sequences between hairpins as the major directors of the solenoid folding. This study paves the way for the rational structural engineering of ββ-solenoids aimed to find novel applications.

Destruction of Refractory Carbon Grains Drives the Final Stage of Protoplanetary Disk Chemistry

Abstract Here we aim to explore the origin of the strong C2H lines to reimagine the chemistry of protoplanetary disks. There are a few key aspects that drive our analysis. First, C2H is detected in young and old systems, hinting at a long-lived chemistry. Second, as a radical, C2H is rapidly destroyed, within <1000 yr. These two statements hint that the chemistry responsible for C2H emission must be predominantly in the gas phase and must be in equilibrium. Combining new and published chemical models, we find that elevating the total volatile (gas and ice) C/O ratio is the only natural way to create a long-lived, high C2H abundance. Most of the C2H resides in gas with an F UV/n gas ∼ 10−7 G 0 cm3. To elevate the volatile C/O ratio, additional carbon has to be released into the gas to enable equilibrium chemistry under oxygen-poor conditions. Photoablation of carbon-rich grains seems the most straightforward way to elevate the C/O ratio above 1.5, powering a long-lived equilibrium cycle. The regions at which the conditions are optimal for the presence of high C/O ratio and elevated C2H abundances in the gas disk set by the F UV/n gas condition lie just outside the pebble disk as well as possibly in disk gaps. This process can thus also explain the (hints of) structure seen in C2H observations.

PB28, the Sigma-1 and Sigma-2 Receptors Modulator With Potent Anti-SARS-CoV-2 Activity: A Review About Its Pharmacological Properties and Structure Affinity Relationships.

These unprecedented times have forced the scientific community to gather to face the COVID-19 pandemic. Efforts in diverse directions have been made. A multi-university team has focused on the identification of the host (human) proteins interacting with SARS-CoV-2 viral proteins, with the aim of hampering these interactions that may cause severe COVID-19 symptoms. Sigma-1 and sigma-2 receptors surprisingly belong to the “druggable” host proteins found, with the pan-sigma receptor modulator PB28 displaying the most potent anti–SARS-CoV-2 activity in in vitro assays. Being 20-fold more active than hydroxychloroquine, without cardiac side effects, PB28 is a promising antiviral candidate worthy of further investigation. Our research group developed PB28 in 1996 and have thoroughly characterized its biological properties since then. Structure–affinity relationship (SAfiR) studies at the sigma receptor subtypes were also undertaken with PB28 as the lead compound. We herein report our knowledge of PB28 to share information that may help to gain insight into the antiviral action of this compound and sigma receptors, while providing structural hints that may speed up the translation into therapeutics of this class of ligands.

Article of Significant Interest in This Issue

PrfA is the major virulence regulator in the human pathogen Listeria monocytogenes. Hansen and coworkers (e00115-20) have used a novel growth-based selection strategy to identify new constitutively active PrfA mutant proteins. The mutants showed different levels of activation based on virulence gene expression, fosfomycin sensitivity, infectivity, and DNA binding. Interestingly, the medium-activation PrfA mutants had one monomer in an activated state and the other monomer in an inactive state, suggesting that these mutants represent an intermediately active form of the protein. Altogether, this study offers structural hints of how PrfA becomes activated during Listeria monocytogenes infection.

Novel O/W nanoemulsions for nasal administration: Structural hints in the selection of performing vehicles with enhanced mucopenetration

We propose novel oil-in-water nanoemulsions (O/W NEs) including PEGylated surfactants and chitosan, showing good biocompatibility and optimization for nasal administration of drugs or vaccines. The transmucosal route has been shown to be ideal for a fast and efficient absorption and represents a viable alternative when the oral administration is problematic. The critical structural features in view of optimal encapsulation and transmucosal delivery were assessed by characterizing the NEs with complementary scattering techniques, i.e. dynamic light scattering (DLS), small angle X-ray (SAXS) and neutron scattering (SANS). Combined results allowed for selecting the formulations with the best suited structural properties and in addition establishing their propensity to enter the mucus barrier. To this scope, mucin was used as a model system and the effect of adding chitosan to the NEs, as adjuvant, was investigated. Remarkably, the presence of chitosan had a positive impact on the diffusion of the NE particles through the mucin matrix. We can infer that chitosan-mucin interaction induces density inhomogeneity and an increase in the pore size within the gel matrix that enhances the PEGylated NEs mobility. The coupling of mucoadhesive and mucopenetrating agents is shown to be a promising strategy for innovative transmucosal delivery systems.

Characterization of the High-Affinity Drug Ligand Binding Site of Mouse Recombinant TSPO.

The optimization of translocator protein (TSPO) ligands for Positron Emission Tomography as well as for the modulation of neurosteroids is a critical necessity for the development of TSPO-based diagnostics and therapeutics of neuropsychiatrics and neurodegenerative disorders. Structural hints on the interaction site and ligand binding mechanism are essential for the development of efficient TSPO ligands. Recently published atomic structures of recombinant mammalian and bacterial TSPO1, bound with either the high-affinity drug ligand PK 11195 or protoporphyrin IX, have revealed the membrane protein topology and the ligand binding pocket. The ligand is surrounded by amino acids from the five transmembrane helices as well as the cytosolic loops. However, the precise mechanism of ligand binding remains unknown. Previous biochemical studies had suggested that ligand selectivity and binding was governed by these loops. We performed site-directed mutagenesis to further test this hypothesis and measured the binding affinities. We show that aromatic residues (Y34 and F100) from the cytosolic loops contribute to PK 11195 access to its binding site. Limited proteolytic digestion, circular dichroism and solution two-dimensional (2-D) NMR using selective amino acid labelling provide information on the intramolecular flexibility and conformational changes in the TSPO structure upon PK 11195 binding. We also discuss the differences in the PK 11195 binding affinities and the primary structure between TSPO (TSPO1) and its paralogous gene product TSPO2.

The approximate entropy concept extended to three dimensions for calibrated, single parameter structural complexity interrogation of volumetric images

Reconstructive volumetric imaging permeates medical practice because of its apparently clear depiction of anatomy. However, the tell tale signs of abnormality and its delineation for treatment demand experts work at the threshold of visibility for hints of structure. Hitherto, a suitable assistive metric that chimes with clinical experience has been absent. This paper develops the complexity measure approximate entropy (ApEn) from its 1D physiological origin into a three-dimensional (3D) algorithm to fill this gap. The first 3D algorithm for this is presented in detail. Validation results for known test arrays are followed by a comparison of fan-beam and cone-beam x-ray computed tomography image volumes used in image guided radiotherapy for cancer. Results show the structural detail down to individual voxel level, the strength of which is calibrated by the ApEn process itself. The potential for application in machine assisted manual interaction and automated image processing and interrogation, including radiomics associated with predictive outcome modeling, is discussed.

African Arrow sees hints of structure in the fabric of space

In April 2016 Physics Today challenged its readers to write a fictional news story about a discovery made in 2116. Pavel Kornilovich’s runner-up entry describes the revelation in muon–antimuon collisions of the cellular nature of space.

The Borinquen geothermal system (Cañas Dulces caldera, Costa Rica)

The geotectonic location of Costa Rica has allowed the development of an active volcanic arc, geological context associated with hydrothermal systems with geothermal potential. In the northwest of the country, on the Pacific slope of the Rincon de la Vieja volcano, inside the Cañas Dulces caldera, the presence of thermal manifestations motivated the development of geoscientific studies that culminated with the drilling of 4 geothermal exploration wells to depths of 2078–2594m, as part of the research that seeks to corroborate the existence of a commercially geothermal reservoir. A date has explored an area of 31km2 known as Borinquen where information on lithostratigraphy, mineralogy, electric resistivity and thermal gradients, as well as on the geochemical and isotopic composition of the fluids derived from the meteoric water, surface hydrothermal manifestation and exploration wells, was obtained. The distribution of the secondary mineral assemblages observed in the exploration wells suggests an increase in temperature with depth, which is confirmed by the distribution of the thermal gradient. The geoelectric structure hints at the existence of a cap rock and a geothermal reservoir, and the geochemistry and isotopic composition of the samples obtained from the exploration wells reveal the existence of neutral sodium chloride fluids with high enthalpy. This suggests exploitation could be economically viable, particularly in light of comparisons with similar reservoirs already being exploited in the neighbouring calderas of San Vicente and Guayabo. Taking into account all the available information, we provide a conceptual model of the Borinquen geothermal area that explains the main elements of its high enthalpy geothermal system – heat source, distribution of the thermal anomaly, recharge zone, reservoir, cap rock, main flow paths and flow directions. This will be useful as a guide for the exploration and future development and exploitation of this geothermal resource.

Airy Equation for the Topological String Partition Function in a Scaling Limit

We use the polynomial formulation of the holomorphic anomaly equations governing perturbative topological string theory to derive the free energies in a scaling limit to all orders in perturbation theory for any Calabi-Yau threefold. The partition function in this limit satisfies an Airy differential equation in a rescaled topological string coupling. One of the two solutions of this equation gives the perturbative expansion and the other solution provides geometric hints of the non-perturbative structure of topological string theory. Both solutions can be expanded naturally around strong coupling.

Observation and Spectroscopy of New Proton-Unbound Isotopes ³⁰Ar and ²⁹Cl: An Interplay of Prompt Two-Proton and Sequential Decay.

Previously unknown isotopes (30)Ar and (29)Cl have been identified by measurement of the trajectories of their in-flight decay products (28)S+p+p and (28)S+p, respectively. The analysis of angular correlations of the fragments provided information on decay energies and the structure of the parent states. The ground states of (30)Ar and (29)Cl were found at 2.25(-0.10)(+0.15) and 1.8±0.1 MeV above the two- and one-proton thresholds, respectively. The lowest states in (30)Ar and (29)Cl point to a violation of isobaric symmetry in the structure of these unbound nuclei. The two-proton decay has been identified in a transition region between simultaneous two-proton and sequential proton emissions from the (30)Ar ground state, which is characterized by an interplay of three-body and two-body decay mechanisms. The first hint of a fine structure of the two-proton decay of (30)Ar*(2(+)) has been obtained by detecting two decay branches into the ground and first-excited states of the (28)S fragment.

Concept extraction from business documents for software engineering projects

Acquiring relevant business concepts is a crucial first step for any software project for which the software experts are not domain experts. The wealth of information buried within an organization's written documentation is a precious source of concepts, relationships and attributes which can be used to model the enterprise's domain. The lack of targeted extraction tools can make perusing through this type of resource a lengthy and costly process. We propose a domain model focused extraction process aimed at the rapid discovery of knowledge relevant to the software expert. To avoid undesirable noise from high-level linguistic tools, the process is mainly composed of positive and negative base filters that are less error prone and more robust. The extracted candidates are then reordered using a weight propagation algorithm based on structural hints from source documents. When tested on French text corpora from public organizations, our process performs 2.7 times better than a statistical baseline for relevant concept discovery. A new metric to assess the performance discovery speed of relevant concepts is introduced. The annotation of a gold standard definition of software engineering oriented concepts for knowledge extraction tasks is also presented.

Methods to identify the unexplored diversity of microbial exopolysaccharides

Microbial exopolysaccharides (EPS) are a structurally very diverse class of molecules. A number of them have found their application in rather diverging fields that extend from medicine, food, and cosmetics on the one side to construction, drilling, and chemical industry on the other side. The analysis of microbial strains for their competence in polysaccharide production has therefore been a major issue in the past, especially in the search for new polysaccharide variants among natural strain isolates. Concerning the fact that nearly all microbes carry the genetic equipment for the production of polysaccharides under specific conditions, the naturally provided EPS portfolio seems to be still massively underexplored. Therefore, there is a need for high throughput screening techniques capable of identifying novel variants of bacterial EPS with properties superior to the already described ones, or even totally new ones. A great variety of different techniques has been used in screening approaches for identifying microorganisms that are producing EPS in substantial amounts. Mucoid growth is often the method of choice for visual identification of EPS producing strains. Depending on the thickening characteristics of the polysaccharide, observation of viscosity in culture broth can also be an option to evaluate EPS production. Precipitation with different alcohols represents a common detection, isolation, and purification method for many EPS. A more quantitative approach is found in the total carbohydrate content analysis, normally determined, e.g., by phenol-sulfuric-acid-method. In addition, recently a new and reliable method for the detailed analysis of the monomeric composition and the presence of rare sugars and sugar substitutions has become available, which could give a first hint of the polymer structure of unknown EPS. This minireview will compare available methods and novel techniques and discuss their benefits and disadvantages.

Note on the newly observedY(4220)resonance

The BES III Collaboration has recently observed a vector resonance in the ${\ensuremath{\chi}}_{c0}\ensuremath{\omega}$ channel, at a mass of about 4220 MeV, named $Y(4220)$. Hints of a similar structure appear in the ${h}_{c}{\ensuremath{\pi}}^{+}{\ensuremath{\pi}}^{\ensuremath{-}}$ channel. We find that the two observations are likely due to the same state, which we identify with one of the expected diquark-antidiquark resonances with orbital quantum number $L=1$. This assignment fulfills heavy quark spin conservation. The measured branching ratio of the $Y(4220)$ into ${\ensuremath{\chi}}_{c0}\ensuremath{\omega}$ and ${h}_{c}{\ensuremath{\pi}}^{+}{\ensuremath{\pi}}^{\ensuremath{-}}$ is compatible with the prediction for such a tetraquark state.

Effective keyword query structuring using NER for XML retrieval

Purpose – The purpose of this paper is to propose and evaluate XKQSS, a query structuring method that relegates the task of generating structured queries from a user to a search engine while retaining the simple keyword search query interface. A more effective way for searching XML database is to use structured queries. However, using query languages to express queries prove to be difficult for most users since this requires learning a query language and knowledge of the underlying data schema. On the other hand, the success of Web search engines has made many users to be familiar with keyword search and, therefore, they prefer to use a keyword search query interface to search XML data. Design/methodology/approach – Existing query structuring approaches require users to provide structural hints in their input keyword queries even though their interface is keyword base. Other problems with existing systems include their inability to put keyword query ambiguities into consideration during query structuring and how to select the best generated structure query that best represents a given keyword query. To address these problems, this study allows users to submit a schema independent keyword query, use named entity recognition (NER) to categorize query keywords to resolve query ambiguities and compute semantic information for a node from its data content. Algorithms were proposed that find user search intentions and convert the intentions into a set of ranked structured queries. Findings – Experiments with Sigmod and IMDB datasets were conducted to evaluate the effectiveness of the method. The experimental result shows that the XKQSS is about 20 per cent more effective than XReal in terms of return nodes identification, a state-of-art systems for XML retrieval. Originality/value – Existing systems do not take keyword query ambiguities into account. XKSS consists of two guidelines based on NER that help to resolve these ambiguities before converting the submitted query. It also include a ranking function computes a score for each generated query by using both semantic information and data statistic, as opposed to data statistic only approach used by the existing approaches.