bluuebunny/crossref_metadata_2025_split huggingface dataset:
Towards personalized induction therapy for esophageal adenocarcinoma: organoids derived from endoscopic biopsy recapitulate the pre-treatment tumor
Authors: Derouet Mathieu F. , Allen Jonathan , Wilson Gavin W. , Ng Christine , Radulovich Nikolina , Kalimuthu Sangeetha , Tsao Ming-Sound , Darling Gail E. , Yeung Jonathan C. 
Published: September 2020

AbstractEsophageal adenocarcinoma has few known recurrent mutations and therefore robust, reliable and reproducible patient-specific models are needed for personalized treatment. Patient-derived organoid culture is a strategy that may allow for the personalized study of esophageal adenocarcinoma and the development of personalized induction therapy. We therefore developed a protocol to establish EAC organoids from endoscopic biopsies of naïve esophageal adenocarcinomas. Histologic characterization and molecular characterization of organoids by whole exome sequencing demonstrated recapitulation of the tumors’ histology and genomic (~ 60% SNV overlap) characteristics. Drug testing using clinically appropriate chemotherapeutics and targeted therapeutics showed an overlap between the patient’s tumor response and the corresponding organoids’ response. Furthermore, we identified Barrett’s esophagus epithelium as a potential source of organoid culture contamination. In conclusion, organoids can be robustly cultured from endoscopic biopsies of esophageal adenocarcinoma and recapitulate the originating tumor. This model demonstrates promise as a tool to better personalize therapy for esophageal adenocarcinoma patients.
Proposal for an electrostrictive logic device with the epitaxial oxide heterostructure
Authors: Anam Md. Khirul , Gopalakrishnan Pratheek , Sebastian Ann , Ahn Ethan C. 
Published: September 2020

AbstractThe possible use of electrostrictive materials for information processing devices has been widely discussed because it could allow low-power logic operation by overcoming the fundamental limit of subthreshold swing greater than 60 mV/decade in conventional MOSFETs. However, existing proposals for electrostrictive FET applications typically adopt approaches that are entirely theoretical and simulative, thus lacking practical insights into how an electrostrictive material can be best interfaced with a channel material. Here we propose an electrostrictive FET device, involving the epitaxial oxide heterostructure as an ideal material platform for maximum strain transfer. The ON/OFF switching occurs due to a stress-induced concentration change of oxygen vacancies in the memristive oxide channel layer. Based on finite-element simulations, we show that the application of a minimal gate voltage bias can induce stress in the channel layer as high as 108 N/m2 owing to the epitaxial interface between the electrostrictive and memristive oxide layers. Conductive AFM experiments further support the feasibility of the proposed device by demonstrating the stress-induced conductivity modulation of a perovskite oxide thin film, SrTiO3, that is well known to serve as the substrate for epitaxial growth of other functional oxide layers.
Using proteomics to identify host cell interaction partners for VgrG and IglJ
Authors: Proksova Magdalena , Rehulkova Helena , Rehulka Pavel , Lays Claire , Lenco Juraj , Stulik Jiri 
Published: September 2020

AbstractFrancisella tularensis is a highly virulent intracellular bacterium and the causative agent of tularemia. The disease is characterized by the suboptimal innate immune response and consequently by the impaired adaptive immunity. The virulence of this pathogen depends on proteins encoded by a genomic island termed the Francisella Pathogenicity Island (FPI). However, the precise biological roles of most of the FPI-encoded proteins remain to be clarified. In this study, we employed stable isotope labeling by amino acids in cell culture (SILAC) in combination with affinity protein purification coupled with liquid chromatography–mass spectrometry to identify potential protein-effector binding pairs for two FPI virulence effectors IglJ and VgrG. Our results may indicate that while the IglJ protein interactions primarily affect mitochondria, the VgrG interactions affect phagosome and/or autophagosome biogenesis via targeting components of the host’s exocyst complex.
A CRISPR activation and interference toolkit for industrial Saccharomyces cerevisiae strain KE6-12
Authors: Cámara Elena , Lenitz Ibai , Nygård Yvonne 
Published: September 2020

AbstractRecent advances in CRISPR/Cas9 based genome editing have considerably advanced genetic engineering of industrial yeast strains. In this study, we report the construction and characterization of a toolkit for CRISPR activation and interference (CRISPRa/i) for a polyploid industrial yeast strain. In the CRISPRa/i plasmids that are available in high and low copy variants, dCas9 is expressed alone, or as a fusion with an activation or repression domain; VP64, VPR or Mxi1. The sgRNA is introduced to the CRISPRa/i plasmids from a double stranded oligonucleotide by in vivo homology-directed repair, allowing rapid transcriptional modulation of new target genes without cloning. The CRISPRa/i toolkit was characterized by alteration of expression of fluorescent protein-encoding genes under two different promoters allowing expression alterations up to ~ 2.5-fold. Furthermore, we demonstrated the usability of the CRISPRa/i toolkit by improving the tolerance towards wheat straw hydrolysate of our industrial production strain. We anticipate that our CRISPRa/i toolkit can be widely used to assess novel targets for strain improvement and thus accelerate the design-build-test cycle for developing various industrial production strains.
Semi-automated identification of biological control agent using artificial intelligence
Authors: Liao Jhih-Rong , Lee Hsiao-Chin , Chiu Ming-Chih , Ko Chiun-Cheng 
Published: September 2020

AbstractThe accurate identification of biological control agents is necessary for monitoring and preventing contamination in integrated pest management (IPM); however, this is difficult for non-taxonomists to achieve in the field. Many machine learning techniques have been developed for multiple applications (e.g., identification of biological organisms). Some phytoseiids are biological control agents for small pests, such asNeoseiulus barkeriHughes. To identify a precise biological control agent, a boosting machine learning classification, namely eXtreme Gradient Boosting (XGBoost), was introduced in this study for the semi-automated identification of phytoseiid mites. XGBoost analyses were based on 22 quantitative morphological features among 512 specimens ofN. barkeriand related phytoseiid species. These features were extracted manually from photomicrograph of mites and included dorsal and ventrianal shield lengths, setal lengths, and length and width of spermatheca. The results revealed 100% accuracy rating, and setaj4achieved significant discrimination among specimens. The present study provides a path through which skills and experiences can be transferred between experts and non-experts. This can serve as a foundation for future studies on the automated identification of biological control agents for IPM.
Constraint on precipitation response to climate change by combination of atmospheric energy and water budgets
Authors: Dagan Guy , Stier Philip 
Published: September 2020

AbstractGlobal mean precipitation is expected to increase with increasing temperatures, a process which is fairly well understood. In contrast, local precipitation changes, which are key for society and ecosystems, demonstrate a large spread in predictions by climate models, can be of both signs and have much larger magnitude than the global mean change. Previously, two top-down approaches to constrain precipitation changes were proposed, using either the atmospheric water or energy budget. Here, using an ensemble of 27 climate models, we study the relative importance of these two budgetary constraints and present analysis of the spatial scales at which they hold. We show that specific geographical locations are more constrained by either one of the budgets and that the combination of water and energy budgets provides a significantly stronger constraint on the spatial scale of precipitation changes under anthropogenic climate change (on average about 3000 km, above which changes in precipitation approach the global mean change). These results could also provide an objective way to define the scale of ‘regional’ climate change.
BaSrTiO3 ceramic‐polymer composite material lens antennas at 220–330 GHz telecommunication applications
Authors: Myllymäki S. , Teirikangas M. , Kokkonen M. 
Published: September 2020

Ceramic (Ba0.55 Sr0.45 Ti1.01 O3 ) – polypropylene polymer ER182 composites‐based materials were applied for sub‐THz range antenna lens application in telecommunications. Typical plano‐convex ‐shaped lenses were simulated and measured with a standard rectangular waveguide at 220–330 GHz frequency band and applied on 150 mm on‐air distance. The lens fabricated with ER182 polymer material increased the signal strength by 15 dB, ER182/7 vol% BST by 6 dB and ER182/30 vol% BST by −23 dB. Material loss tangent values were 0.008 for ER182, 0.034 for ER182/7%BST and 0.081 for ER182/30%BST. The directivity of ER182 material lens and WR3 waveguide combination was 26 dBi at 300 GHz.
Impact of Patient Alignment on Image Quality in C-Arm Computed Tomography – Evaluation Using an ACR Phantom
Authors: Alikhani Babak , Renne Julius , Maschke Sabine , Hinrichs Jan B. , Wacker Frank K. , Werncke Thomas 
Published: September 2020

Purpose To evaluate the influence of patient alignment and thereby heel effect on the image quality (IQ) of C-arm flat-panel detector computed tomography (CACT).
Materials and Methods An ACR phantom placed in opposite directions along the z-axis (setup A and B) on the patient support was imaged using CACT. Image acquisition was performed with three different image acquisition protocols. The images were reconstructed with four convolution kernels. IQ was assessed in terms of high contrast using the modulation transfer function (MTF) and low contrast by assessing the image noise, signal-to-noise ratio (SNR) and contrast-to-noise ratios (CNR) as well as the reliability of density measurements. Furthermore, the dose intensity profiles were measured free-in-air.
Results The MTF in setup B is higher than the MTF measured in setup A (p < 0.01). The image noises measured in setup A for the air and bone inserts were higher compared to those measured in setup B (p > 0.05). Opposite behavior has been observed for the polyethylene, water-equivalent and acrylic inserts. The SNR for all inserts is inversely related to the image noise. A systematically increasing or decreasing trend of CNR could not be observed (p > 0.05). The intensity profile measured by the detector system free-in-air showed that the anode heel effect is perpendicular to the z-axis.
Conclusion The patient alignment has a minor influence on the IQ of CACT. This effect is not based on the X-ray anode heel effect but is caused mainly by the non-symmetrical rotation of CACT.
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Citation Format
Metabolic and Endocrine Challenges
Authors: Martucci Gennaro , Bonicolini Eleonora , Parekh Dhruv , Thein Onn Shaun , Scherkl Mario , Amrein Karin 
Published: September 2020

AbstractThis review aims to provide an overview of metabolic and endocrine challenges in the setting of intensive care medicine. These are a group of heterogeneous clinical conditions with a high degree of overlap, as well as nonspecific signs and symptoms. Several diseases involve multiple organ systems, potentially causing catastrophic dysfunction and death. In the majority of cases, endocrine challenges accompany other organ failures or manifest as a complication of prolonged intensive care unit stay and malnutrition. However, when endocrine disorders present as an isolated syndrome, they are a rare and extreme manifestation. As they are uncommon, these can typically challenge both with diagnosis and management. Acute exacerbations may be elicited by triggers such as infections, trauma, surgery, and hemorrhage. In this complex scenario, early diagnosis and prompt treatment require knowledge of the specific endocrine syndrome. Here, we review diabetic coma, hyponatremia, hypercalcemia, thyroid emergencies, pituitary insufficiency, adrenal crisis, and vitamin D deficiency, highlighting diagnostic tools and tricks, and management pathways through defining common clinical presentations.
Graphs
Authors: Swartz Clifford E. 
Published: September 2020

There are some general conventions about drawing graphs, most of them sensible. These are illustrated in the following pages. Adherence to the conventions is easy and is guaranteed to save time.
Data should usually be graphed as soon as they are obtained. Gross mistakes are not always apparent when the data are entered in tabular form. If, however, a graph of the data is being plotted while it is coming in, a point that is radically out of line is immediately obvious.
Properties of protein unfolded states suggest broad selection for expanded conformational ensembles
Authors: Bowman Micayla A. , Riback Joshua A. , Rodriguez Anabel , Guo Hongyu , Li Jun , Sosnick Tobin R. , Clark Patricia L. 
Published: September 2020

Significance
Amino acid sequences are known to be crucial for specifying the folded structure of a protein. Here we show that sequences also play an important role in specifying the properties of a protein’s unfolded ensemble. For an autotransporter protein, rearranging the order of only a few percent of amino acid residues can lead to more collapsed unfolded ensembles which have enhanced aggregation in vitro and degradation in vivo. Sequences that remain expanded, however, are more compatible with proper function. Most significantly, we show that the well-mixed sequence patterns that lead to expanded ensembles are broadly conserved amongst foldable, water-soluble proteins, suggesting expanded disordered states are under selection.
Stable unmethylated DNA demarcates expressed genes and their cis-regulatory space in plant genomes
Authors: Crisp Peter A. , Marand Alexandre P. , Noshay Jaclyn M. , Zhou Peng , Lu Zefu , Schmitz Robert J. , Springer Nathan M. 
Published: September 2020

Significance
Crop genomes can be very large, with many repetitive elements and pseudogenes. Distilling a genome down to the relatively small fraction of regions that are functionally valuable for trait variation can be like looking for needles in a haystack. The location of these regions is often not obvious, and current detection technologies are impractically expensive and intensive for many research projects. The unmethylated regions in a genome are highly stable during vegetative development and can reveal the locations of potentially expressed genes or cis-regulatory elements. This approach provides a framework toward complete annotation of genes and discovery of cis-regulatory elements using methylation profiles from only a single tissue.
Facilitating hydrogen atom migration via a dense phase on palladium islands to a surrounding silver surface
Authors: O’Connor Christopher R. , Duanmu Kaining , Patel Dipna A. , Muramoto Eri , van Spronsen Matthijs A. , Stacchiola Dario , Sykes E. Charles H. , Sautet Philippe , Madix Robert J. , Friend Cynthia M. 
Published: September 2020

SignificanceThe energy efficiency of catalytic processes hinges on achieving high selectivity and activity; bimetallic catalysts have potential to increase both by exploiting different chemical properties of the components. Transport of intermediates between the two metals, for example, transport of hydrogen atoms for selective hydrogenation, is required to capitalize on this bifunctionality. A mechanism for the migration of hydrogen atoms to silver from palladium is demonstrated here. Dihydrogen first dissociates on palladium, then forms a dense hydrogen phase on the palladium island. The dense phase includes weakly bound hydrogen atoms that are nearly isoenergetic with hydrogen on silver, rendering migration nearly energy neutral. The efficiency for hydrogen migration across the palladium−silver is maximized for small ensembles of palladium atoms.
A rapid technique to integrate micro-components on released MEMS dies using SU-8
Authors: Gour Amit , Nabki Frederic , Ménard Michaël 
Published: September 2020

Abstract
This technical note reports a rapid technique to post-process and assemble micro-components onto dies including released movable microstructures. The method is applied to microelectromechanical systems (MEMS) chips that were fabricated using a commercial process, PolyMUMPs from MEMSCAP. It allows the assembly of a micro-polyhedron over released micromotors and ensures that the micromotors remain fully functional. The micro-polyhedrons are fabricated using laser ablation and are spin coated with a thin layer of SU-8, acting as a bonding layer. Then, they are bonded to chips that are placed on a 3D integration platform with a navigating mask, which protects the released structure during the subsequent assembly steps. The resulting micro-polyhedron-integrated-micromotors were tested and found to rotate similarly to devices without micro-polyhedrons, demonstrating that the developed procedure can be applied for post-release 3D integration of MEMS without significantly affecting the mechanical performance of the devices.
Between a rock and a hard place: State-led territorial stigmatization, informal care practices and the interstitiality of local community workers in Denmark
Authors: Birk Rasmus H , Arp Fallov Mia 
Published: September 2020

AbstractThe purpose of this paper is to explore the relation between territorial stigmatization and community work in Denmark. In the paper, we firstly explore territorial stigmatization, relating it to the Danish context. We show how territorial stigmatization in Denmark happens via a complex amalgamation of bureaucratic practices which identify particular areas as problematic ‘ghettos’, and how this leads to top–down interventions upon many local residential areas, including local community work. Following this, we draw on participant observations in practices of local community work, and interviews with local community workers, to explore how they practically negotiate these particular political constructions of their work. We argue that local community workers come to take on interstitial roles—that is, they come to be in-between the state and authorities and the local communities themselves. This complex double role is what we call an interstitial position, meant to signify how Danish local community workers are both part of territorial stigmatization and simultaneously trying to escape from and undo this very role.
Epic Victories and Failures: Homer and Vergil in Russia
Authors: Kalb Judith E. , Torlone Zara M. 
Published: September 2020

Abstract
This article focuses on selected complete Russian verse translations of Homer’s Iliad and Odyssey and of Vergil’s Aeneid produced over a period of nearly two centuries. By focusing on translation approach and goals, historical and cultural circumstances, and the literary talent of the translators, the authors explore the reasons for a particular translation’s success or failure. Further, they address the question of how Russian translators achieved canonical, or generally accepted, translations of the Homeric epics, while translations of Vergil’s epic found no such success.
Pleiotropic actions of factor Xa inhibition in cardiovascular prevention: mechanistic insights and implications for anti-thrombotic treatment
Authors: ten Cate Hugo , Guzik Tomasz J , Eikelboom John , Spronk Henri M H 
Published: September 2020

AbstractAtherosclerosis is a chronic inflammatory disease in which atherothrombotic complications lead to cardiovascular morbidity and mortality. At advanced stages, myocardial infarction, ischaemic stroke, and peripheral artery disease, including major adverse limb events, are caused either by acute occlusive atherothrombosis or by thromboembolism. Endothelial dysfunction, vascular smooth muscle cell activation, and vascular inflammation are essential in the development of acute cardiovascular events. Effects of the coagulation system on vascular biology extend beyond thrombosis. Under physiological conditions, coagulation proteases in blood are pivotal in maintaining haemostasis and vascular integrity. Under pathological conditions, including atherosclerosis, the same coagulation proteases (including factor Xa, factor VIIa, and thrombin) become drivers of atherothrombosis, working in concert with platelets and vessel wall components. While initially atherothrombosis was attributed primarily to platelets, recent advances indicate the critical role of fibrin clot and plasma coagulation factors. Mechanisms of atherothrombosis and hypercoagulability vary depending on plaque erosion or plaque rupture. In addition to contributing to thrombus formation, factor Xa and thrombin can affect endothelial dysfunction, oxidative stress, vascular smooth muscle cell function as well as immune cell activation and vascular inflammation. By these mechanisms, they promote atherosclerosis and contribute to plaque instability. In this review, we first discuss the postulated vasoprotective mechanisms of protease-activated receptor signalling induced by coagulation enzymes under physiological conditions. Next, we discuss preclinical studies linking coagulation with endothelial cell dysfunction, thromboinflammation, and atherogenesis. Understanding these mechanisms is pivotal for the introduction of novel strategies in cardiovascular prevention and therapy. We therefore translate these findings to clinical studies of direct oral anticoagulant drugs and discuss the potential relevance of dual pathway inhibition for atherothrombosis prevention and vascular protection.