The extent of representation,the relationships of artifacts and the anthropology of art

This paper provides an account of the potential roles that artifacts can occupy and distinguishes their occurrence as instruments of representation from other types of relationship of artifact use. When artifacts are employed as instruments of representation there is a deliberately constructed causal connection between the artifact and what it represents. This is in contrast to relationships of association in which the artifact takes on features of the context of its occurrence. Anthropological studies of artifact use in the native societies of Africa, America, the Indian Subcontinent and the Pacific are reviewed by comparing “dominant functions” that artifacts can serve.     

Phantom based qualitative and quantitative evaluation of artifacts in MR images of metallic hip prostheses

PurposeTo develop methods for qualitative and quantitative evaluation of MRI artifacts near metallic prostheses, and to compare the efficiency of different artifact suppression techniques with different types of hip prostheses.MethodsThree hip prostheses of cobalt-chromium, stainless steel, and titanium were embedded in agarose gel together with a rectilinear grid. Coronal MR images of the prostheses were acquired on a 1.5T scanner. Three pulse sequences were evaluated; TSE: a high-bandwidth turbo spin echo; VAT: TSE with view angle tilting, SEMAC: TSE with both VAT and slice distortion correction (6, 10 or 16 z-phase-encoding steps). Through-plane distortions were assessed as the length of visible gridlines, in-plane artifacts as the artifact area, and total artifacts by subtraction of an ideal, undistorted image from the actual image.ResultsVAT reduced in-plane artifacts by up to 50% compared to TSE, but did not reduce through-plane artifacts. SEMAC reduced through-plane artifacts by 60–80% compared to TSE and VAT. SEMAC in-plane artifacts were from 20% higher (6 encoding steps) to 50% lower (16 steps) than VAT. Total artifacts were reduced by 60–80% in the best sequence (SEMAC, 16 steps) compared to the worst (TSE). The titanium prosthesis produced 3–4 times lower artifact scores than the other prostheses.ConclusionsA rectilinear grid phantom is useful for qualitative and quantitative evaluation of artifacts provoked by different MRI protocols and prosthesis models. VAT and SEMAC were superior to TSE with high bandwidth. A proper number of z-encoding steps in SEMAC was critical. The titanium prosthesis caused least artifacts.     

Antler Tine Scraper Handles in the Central Plains

Abstract

In the perspectives of archaeology, it is evident that the widespread antler-handled fleshing adz used by most historic Plains Indian tribes was preceded in the region by other types of hafted skin-working tools. These, inferentially, varied in construction and materials from area to area, but were everywhere provided with planoconvex chipped stone blades - the familiar and omnipresent end scraper of the Plains. In early historic times in the Central Plains, curved antler handles with stone blades are thought from archaeological evidence to have been used not in adz fashion but with a pushing motion, away from the operator. The relative abundance, variety in size and form, and longevity as an artifact type of the plano-convex end scraper raises various questions that invite further inquiry.     

Deep learning-based metal artifact reduction using cycle-consistent adversarial network for intensity-modulated head and neck radiation therapy treatment planning

PurposeTo develop a deep learning-based metal artifact reduction (DL-MAR) method using unpaired data and to evaluate its dosimetric impact in head and neck intensity-modulated radiation therapy (IMRT) compared with the water density override method.MethodsThe data set comprised the data of 107 patients who underwent radiotherapy. Fifteen patients with dental fillings were used as the test data set. The computed tomography (CT) images of the remaining 92 patients were divided into two domains: the metal artifact and artifact-free domains. CycleGAN was used for domain translation. The artifact index of the DL-MAR images was compared with that of the original uncorrected (UC) CT images. The dose distributions of the DL-MAR and UC plans were created by comparing the reference clinical plan with the water density override method (water plan) in each dataset. Dosimetric deviation in the oral cavity from the water plan was evaluated.ResultsThe artifact index of the DL-MAR images was significantly smaller than that of the UC images in all patients (13.2 ± 4.3 vs. 267.3 ± 113.7). Compared with the reference water plan, dose differences of the UC plans were greater than those of the DL-MAR plans. DL-MAR images provided dosimetric results that were more similar to those of the water plan than the UC plan.ConclusionsWe developed a fast DL-MAR method using CycleGAN for head and neck IMRT. The proposed method could provide consistent dose calculation against metal artifact and improve the efficiency of the planning process by eliminating manual delineation.     

Machine Assisted Encoding Of Artifact Characteristics

Abstract

A computer encoding device known as a RAND Tablet can be applied in archeological researchto read off of an artifact, such as a flint projectile point, certain points of data that when used by a computer program to provide measurements from the artifact, can provide a basis for classification.     

MMO: P450 in wolf's clothing?

 Methane monooxygenase (MMO) catalyzes the oxidation of stable hydrocarbons that are not attacked by cytochrome P450 monooxygenase. A key transient intermediate in the catalytic cycle of the soluble form of MMO termed compound Q (Q) has been trapped and characterized through spectroscopic comparisons with novel high valent model complexes. Q appears to contain a non-heme dinuclear Fe(IV) cluster bridged by at least two single oxygen atoms to form a so-called diamond core. Q has the ability to react directly with unactivated hydrocarbons to yield oxidized products. Several types of experiments indicate that this reaction involves formation of an intermediate, probably with radical character. This is consistent with a hydrogen atom abstraction mechanism analogous to that ascribed to cytochrome P450. However, these same experiments show that a pure hydrogen atom abstraction mechanism is unlikely for many substrates without an additional interaction between the intermediate that is formed and the high valent cluster. The results may be of general relevance to monooxygenase catalysis. Received: 15 January 1998 / Accepted: 9 March 1998     

Quantifying near metal visibility using dual energy computed tomography and iterative metal artifact reduction in a fracture phantom

PurposeTo quantitatively assess CT image quality and fracture visibility using virtual monochromatic imaging and iterative metal artifact reduction (iMAR) in a femoral bone fracture phantom with different fixation implants.MethodsA custom made phantom was scanned at 120-kVp and 140-kVp single-energy and 100/150-kVp dual-energy. Three stainless steel and two titanium implants with different thicknesses were placed on the phantom containing simulated one and two mm fractures. Single-energy CT images were reconstructed with and without iMAR, while DECT images were reconstructed at monochromatic energies between 70 and 190 keV. Non-metal scans were used as a reference. A Fourier power spectrum method and fracture model were used to analyze several anatomical areas.ResultsCT-value deviations of titanium implants were much lower compared to stainless steel implants. These deviations decreased for both DECT and iMAR. Fracture visibility, measured with the fracture model, improved the most when DECT was used while artifact reduction benefitted more from iMAR. The optimal monochromatic energy for metal artifact reduction, based on CT-value deviation, varied for each metal between 130 and 150 keV. The fracture model provided a signal-to-noise ratio for the near metal fracture visibility, providing the optimal keV.ConclusioniMAR and high keV monochromatic images extracted from DECT both reduce metal artifacts caused by different metal fixation implants. Quantitative femoral phantom results show that DECT is superior to iMAR regarding fracture visualization adjacent to metal fixation implants. The introduction of new artifacts when using iMAR impedes its value in near metal fixation implant imaging.     

Technical note: Unexpected external markers artifact in 3D k-space based parallel imaging turbo spin-echo magnetic resonance imaging

PurposeMRI for radiotherapy planning requires spatial referencing using immobilization devices and markers. Clinical images of a difficult-to-interpret artifact are presented, resembling a metastasis, which occurs when combining CAIPIRINHA k-space-based parallel imaging (PI), 3D distortion correction, and external markers.MethodsA 3D variable flip angle Turbo Spin Echo sequence was used on a 1.5 T and 3 T MRI using flexible and head and neck coils. Two types of markers were tested: Liquimark LM1 and Spee-D-Mark. A silicone oil phantom was used that represents low signal intensity, such as gray matter. 3D Fourier transforms were also used to show the issue’s origin.ResultsThe markers can appear in an unexpected region of a patient, not in the same original or reconstructed slice nor in a rectilinear direction in a slice, especially when using CAIPIRINHA acceleration with 3D distortion correction. The probability of occurrence was respectively 13% and 80% for distances of <=2 mm and >2 mm between marker and patient, for example when using thermoplastic masks. Clinical cases are shown where this semi-randomly occurring artifact appears post contrast only, and thus can be interpreted as metastases. The artifact did not appear when using compressed sensing acceleration.ConclusionMarkers used for radiotherapy MRI application can introduce additional artifacts that can be interpreted as metastases. However, other high signal intensity structures on the surface of a patient, such as the ear, can lead to an equivalent error.     

Insights into the interaction of the N-terminal amyloidogenic polypeptide of ApoA-I with model cellular membranes

BackgroundAbout twenty variants of apolipoprotein A-I (ApoA-I) are associated to hereditary systemic amyloidoses. Although the molecular bases of this disease are still largely unknown, it has been hypothesized that ApoA-I proteolysis is a key event in pathogenesis, since it triggers the release of an N-terminal fragment (80–100 residue long) that misfolds to form amyloid deposits in peripheral organs and tissues. It is also known that cell membrane lipids play a key role in the fibrillogenic pathway. In the case of ApoA-I related amyloidosis caused by L174S mutation, the 93-residue N-terminal fragment of ApoA-I ([1-93]ApoA-I) was found to be the major constituent of ex vivo fibrils.MethodsWith the main goal to investigate the interaction of either [1-93]ApoA-I and ApoA-I with biomimetic membranes, we set-up an experimental system based on the Raman Tweezers methodology. We tested GUVs composed by two types of zwitterionic lipids with a different fluidity degree, i.e. dioleoylphosphatidylcholine (DOPC) and dipalmitoylphosphatidylcholine (DPPC).ResultsWe found that [1-93]ApoA-I induces conformational disorder in an ordered lipid bilayer. When interacting with fluid phases, instead, the fragment was found to be able to penetrate the membrane bilayer inducing an alignment of lipid chains.ConclusionsThe interaction features of [1-93]ApoA-I with biomimetic membranes strongly depend on the lipid phase. Full-length ApoA-I was found to have similar effects, even if significantly less pronounced.General significanceOur observations shed light on still largely unknown molecular bases of ApoA-I fibrillogenic domain interaction with membranes.     

Enhancing fine-grained intra-urban dengue forecasting by integrating spatial interactions of human movements between urban regions

BackgroundAs a mosquito-borne infectious disease, dengue fever (DF) has spread through tropical and subtropical regions worldwide in recent decades. Dengue forecasting is essential for enhancing the effectiveness of preventive measures. Current studies have been primarily conducted at national, sub-national, and city levels, while an intra-urban dengue forecasting at a fine spatial resolution still remains a challenging feat. As viruses spread rapidly because of a highly dynamic population flow, integrating spatial interactions of human movements between regions would be potentially beneficial for intra-urban dengue forecasting.MethodologyIn this study, a new framework for enhancing intra-urban dengue forecasting was developed by integrating the spatial interactions between urban regions. First, a graph-embedding technique called Node2Vec was employed to learn the embeddings (in the form of an N-dimensional real-valued vector) of the regions from their population flow network. As strongly interacting regions would have more similar embeddings, the embeddings can serve as “interaction features.” Then, the interaction features were combined with those commonly used features (e.g., temperature, rainfall, and population) to enhance the supervised learning–based dengue forecasting models at a fine-grained intra-urban scale.ResultsThe performance of forecasting models (i.e., SVM, LASSO, and ANN) integrated with and without interaction features was tested and compared on township-level dengue forecasting in Guangzhou, the most threatened sub-tropical city in China. Results showed that models using both common and interaction features can achieve better performance than that using common features alone.ConclusionsThe proposed approach for incorporating spatial interactions of human movements using graph-embedding technique is effective, which can help enhance fine-grained intra-urban dengue forecasting.     

Dose distribution comparison in volumetric-modulated arc therapy plans for head and neck cancers with and without an external body contour extended technique

AimThis study compared volumetric-modulated arc therapy (VMAT) plans for head and neck cancers with and without an external body contour extended technique (EBCT).BackgroundDose calculation algorisms for VMAT have limitations in the buildup region.Materials and methodsThree VMAT plans were enrolled, with one case having a metal artifact from an artificial tooth. The proper dose was calculated using Eclipse version 11.0. The body contours were extended 2 cm outward from the skin surface in three-dimensional space, and the dose was recalculated with an anisotropic analytical algorithm (AAA) and Acuros XB (AXB). Monitor units (MUs) were set, and the dose distributions in the planning target volume (PTV), clinical target volume, and organ at risk (OAR) and conformity index (CI) with and without an EBCT were compared. The influence of a metal artifact outside of the thermoplastic head mask was also compared.ResultsThe coverage of PTV by the 95% dose line near the patient’s skin was increased drastically by using an EBCT. Plan renormalization had a negligible impact on MUs and doses delivered to OARs. CI of PTV with a 6-MV photon beam was closer to 1 than that with a 10-MV photon beam when both AAA and AXB were used in all cases. Metal artifacts outside the head mask had no effect on dose distribution.ConclusionsAn EBCT is needed to estimate the proper dose at object volumes near the patient’s skin and can improve the accuracy of the calculated dose at target volumes.     

Recombinant expression and characterization of yeast Mrc1, a DNA replication checkpoint mediator

Abstract

In Saccharomyces cerevisiae, Mrc1 (homolog of human Claspin and mediator of replication checkpoint) is not only a part of the replication machine, but also participates in the replication stress response when DNA replication is blocked by hydroxyurea. Since Mrc1 is expressed in a small amount in cells and has many proteins interacting with it as a mediator, it is difficult to obtain Mrc1 with high concentration and purity. This article reports the purification of a stable truncation of Mrc1 and the full length Mrc1. High concentration and high purity of Mrc1 was obtained and the three-dimensional structure of Mrc1 was analyzed, which is a ring with a hole in the center. At the same time, we found that Mrc1 has an interaction with Rad24-RFC a clamp loader in the replication checkpoint, and can form a complex with it, implying that we can assemble large replication checkpoint complexes in vitro. These results initially reveal the ring structure of Mrc1 and its interaction with Rad24-RFC in replication checkpoints in S. cerevisiae.     

Drug response prediction using graph representation learning and Laplacian feature selection

Background

Essential proteins are indispensable to the development and survival of cells. The identification of essential proteins not only is helpful for the understanding of the minimal requirements for cell survival, but also has practical significance in disease diagnosis, drug design and medical treatment. With the rapidly amassing of protein–protein interaction (PPI) data, computationally identifying essential proteins from protein–protein interaction networks (PINs) becomes more and more popular. Up to now, a number of various approaches for essential protein identification based on PINs have been developed.

Results

In this paper, we propose a new and effective approach called iMEPP to identify essential proteins from PINs by fusing multiple types of biological data and applying the influence maximization mechanism to the PINs. Concretely, we first integrate PPI data, gene expression data and Gene Ontology to construct weighted PINs, to alleviate the impact of high false-positives in the raw PPI data. Then, we define the influence scores of nodes in PINs with both orthological data and PIN topological information. Finally, we develop an influence discount algorithm to identify essential proteins based on the influence maximization mechanism.

Conclusions

We applied our method to identifying essential proteins from saccharomyces cerevisiae PIN. Experiments show that our iMEPP method outperforms the existing methods, which validates its effectiveness and advantage.

     

Extending MAM5 Meta-Model and JaCalIV E Framework to Integrate Smart Devices from Real Environments

This paper presents the extension of a meta-model (MAM5) and a framework based on the model (JaCalIVE) for developing intelligent virtual environments. The goal of this extension is to develop augmented mirror worlds that represent a real and virtual world coupled, so that the virtual world not only reflects the real one, but also complements it. A new component called a smart resource artifact, that enables modelling and developing devices to access the real physical world, and a human in the loop agent to place a human in the system have been included in the meta-model and framework. The proposed extension of MAM5 has been tested by simulating a light control system where agents can access both virtual and real sensor/actuators through the smart resources developed. The results show that the use of real environment interactive elements (smart resource artifacts) in agent-based simulations allows to minimize the error between simulated and real system.     

Some Consequences of Animal Domestication for Humans

ABSTRACT

Throughout human evolution our species has had many kinds of interactions with others, including predatory, competitive, parasitic, mutualistic, and commensal. We still have such interactions in the modern world, with the most important resulting from our domestication of other species. Domestication created new kinds of interaction by which we controlled the freedom and reproduction of certain animals. Because domesticated populations became dependent on humans various adaptations by humans were necessary, and it is argued that these influenced the cultural, and possibly biological, evolution of our species.     

Fifteenth annual research symposium University of Glasgow, 1975

Background: All human land use (LU) affects the distribution of plant species; however, the impacts vary with the type/intensity of LU. For managing ecosystems, it is therefore essential to understand the effects of LU types on the distribution of plant species on a macroscale.

Aims: The objectives of our study were to quantify the effects of various LU types on the distribution of vascular plant species in Japan and to determine in particular the extent to which LU was an important factor for the distribution of common species.

Methods: Based on a logistic regression model and variation partitioning being applied to each plant species, we evaluated the partial deviance by six LU types, four climatic types and three topographic and geological factors for 647 plant species at 14,412 sites in Japan.

Results: The effect of LU was significant for species present at multiple sites. Of the six LU types, secondary vegetation and plantation were the most important factors determining species distribution for many species.

Conclusions: Our results suggest that distribution of the common species is largely affected by LU on macroscale. The design of LU relating to secondary vegetation and plantations will thus be important in determining changes in the vegetation composition within Japan.     

Algorithm-based artifact reduction in patients with arms-down positioning in computed tomography

PurposeArm-artifact, a type of streak artifact frequently observed in computed tomography (CT) images obtained at arms-down positioning in polytrauma patients, is known to degrade image quality. This study aimed to develop a novel arm-artifact reduction algorithm (AAR) applied to projection data.MethodsA phantom resembling an adult abdomen with two arms was scanned using a 16-row CT scanner. The projection data were processed by AAR, and CT images were reconstructed. The artifact reduction for the same phantom was compared with that achieved by two latest iterative reconstruction (IR) techniques (IR1 and IR2) using a normalized artifact index (nAI) at two locations (ventral and dorsal side). Image blurring as a processing side effect was compared with IR2 of the model-based IR using a plastic needle phantom. Additionally, the projection data of two clinical cases were processed using AAR, and the image noise was evaluated.ResultsAAR and IR2 significantly reduced nAI by 87.5% and 74.0%, respectively at the ventral side and 84.2% and 69.6%, respectively, at the dorsal side compared with each filtered back projection (P < 0.01), whereas IR1 did not. The proposed algorithm mostly maintained the original spatial resolution, compared with IR2, which yielded apparent image blurring. The image noise in the clinical cases was also reduced significantly (P < 0.01).ConclusionsAAR was more effective and superior than the latest IR techniques and is expected to improve the image quality of polytrauma CT imaging with arms-down positioning.     

The Evolutionary Emergence of Vertebrates From Among Their Spineless Relatives

The evolutionary origin of vertebrates has been debated ad nauseam by anatomists, paleontologists, embryologists, and physiologists, but it is only now that molecular phylogenetics is providing a more rigorous framework for the placement of vertebrates among their invertebrate relatives that we can begin to arrive at concrete conclusions concerning the nature of ancient ancestors and the sequence in which characteristic anatomical features were acquired. Vertebrates tunicates and cephalochordates together comprise the chordate phylum, which along with echinoderms and hemichordates constitute the deuterostomes. The origin of vertebrates and of jawed vertebrates is characterized by a doubling of the vertebrate genome, leading to hypotheses that this genomic event drove organismal macroevolution. However, this perspective of evolutionary history, based on living organisms alone, is an artifact. Phylogenetic trees that integrate fossil vertebrates among their living relatives demonstrate the gradual and piecemeal assembly of the gnathostome body plan. Unfortunately, it has not been possible to demonstrate gradual assembly of the vertebrate body plan. This is not because vertebrates are irreducibly complex but because many of the characters that distinguish vertebrates from invertebrates are embryological and cellular and, therefore, inherently unfossilizable.

Application of ITC in foods: A powerful tool for understanding the gastrointestinal fate of lipophilic compounds

BackgroundIsothermal titration calorimetry (ITC) is a biophysical technique widely used to study molecular interactions in biological and non-biological systems. It can provide important information about molecular interactions (such as binding constant, number of binding sites, free energy, enthalpy, and entropy) simply by measuring the heat absorbed or released during an interaction between two liquid solutions.Scope of the reviewIn this review, we present an overview of ITC applications in food science, with particular focus on understanding the fate of lipids within the human gastrointestinal tract. In this area, ITC can be used to study micellization of bile salts, inclusion complex formation, the interaction of surface-active molecules with proteins, carbohydrates and lipids, and the interactions of lipid droplets.Major conclusionsITC is an extremely powerful tool for measuring molecular interactions in food systems, and can provide valuable information about many types of interactions involving food components such as proteins, carbohydrates, lipids, surfactants, and minerals. For systems at equilibrium, ITC can provide fundamental thermodynamic parameters that can be used to establish the physiochemical origin of molecular interactions.General significanceIt is expected that ITC will continue to be utilized as a means of providing fundamental information about complex materials such as those found in foods. This knowledge may be used to create functional foods designed to behave in the gastrointestinal tract in a manner that will improve human health and well-being. This article is part of a Special Issue entitled Microcalorimetry in the BioSciences — Principles and Applications, edited by Fadi Bou-Abdallah.     

Cardiovascular Disorder Severity Detection Using Myocardial Anatomic Features Based Optimized Extreme Learning Machine Approach

ObjectivesThis study focuses on integration of anatomical left ventricle myocardium features and optimized extreme learning machine (ELM) for discrimination of subjects with normal, mild, moderate and severe abnormal ejection fraction (EF). The physiological alterations in myocardium have diagnostic relevance to the etiology of cardiovascular diseases (CVD) with reduced EF.Materials and MethodsThis assessment is carried out on cardiovascular magnetic resonance (CMR) images of 104 subjects available in Kaggle Second Annual Data Science Bowl. The Segment CMR framework is used to segment myocardium from cardiac MR images, and it is subdivided into 16 sectors. 86 clinically significant anatomical features are extracted and subjected to ELM framework. Regularization coefficient and hidden neurons influence the prediction accuracy of ELM. The optimal value for these parameters is achieved with the butterfly optimizer (BO). A comparative study of BOELM framework with different activation functions and feature set has been conducted.ResultsAmong the individual feature set, myocardial volume at ED gives a better classification accuracy of 83.3% compared to others. Further, the given BOELM framework is able to provide higher multi-class accuracy of 95.2% with the entire feature set than ELM. Better discrimination of healthy and moderate abnormal subjects is achieved than other sub groups.ConclusionThe combined anatomical sector wise myocardial features assisted BOELM is able to predict the severity levels of CVDs. Thus, this study supports the radiologists in the mass diagnosis of cardiac disorder.