bluuebunny/crossref_metadata_2025_split huggingface dataset:
Eigenvector models for solving the seismic inverse problem for the Helmholtz equation
Authors: Faucher Florian , Scherzer Otmar , Barucq Hélène 
Published: January 2020

SUMMARY
We study the seismic inverse problem for the recovery of subsurface properties in acoustic media. In order to reduce the ill-posedness of the problem, the heterogeneous wave speed parameter is represented using a limited number of coefficients associated with a basis of eigenvectors of a diffusion equation, following the regularization by discretization approach. We compare several choices for the diffusion coefficient in the partial differential equations, which are extracted from the field of image processing. We first investigate their efficiency for image decomposition (accuracy of the representation with respect to the number of variables). Next, we implement the method in the quantitative reconstruction procedure for seismic imaging, following the full waveform inversion method, where the difficulty resides in that the basis is defined from an initial model where none of the actual structures is known. In particular, we demonstrate that the method may be relevant for the reconstruction of media with salt-domes. We use the method in 2-D and 3-D experiments, and show that the eigenvector representation compensates for the lack of low-frequency information, it eventually serves us to extract guidelines for the implementation of the method.
Effects of flanking sequences and cellular context on subcellular behavior and pathology of mutant HTT
Authors: Chongtham Anjalika , Bornemann Douglas J , Barbaro Brett A , Lukacsovich Tamas , Agrawal Namita , Syed Adeela , Worthge Shane , Purcell Judith , Burke John , Chin Theodore M , Marsh J Lawrence 
Published: January 2020

AbstractHuntington’s disease (HD) is caused by an expansion of a poly glutamine (polyQ) stretch in the huntingtin protein (HTT) that is necessary to cause pathology and formation of HTT aggregates. Here we ask whether expanded polyQ is sufficient to cause pathology and aggregate formation. By addressing the sufficiency question, one can identify cellular processes and structural parameters that influence HD pathology and HTT subcellular behavior (i.e. aggregation state and subcellular location). Using Drosophila, we compare the effects of expressing mutant full-length human HTT (fl-mHTT) to the effects of mutant human HTTexon1 and to two commonly used synthetic fragments, HTT171 and shortstop (HTT118). Expanded polyQ alone is not sufficient to cause inclusion formation since full-length HTT and HTTex1 with expanded polyQ are both toxic although full-length HTT remains diffuse while HTTex1 forms inclusions. Further, inclusions are not sufficient to cause pathology since HTT171-120Q forms inclusions but is benign and co-expression of HTT171-120Q with non-aggregating pathogenic fl-mHTT recruits fl-mHTT to aggregates and rescues its pathogenicity. Additionally, the influence of sequences outside the expanded polyQ domain is revealed by finding that small modifications to the HTT118 or HTT171 fragments can dramatically alter their subcellular behavior and pathogenicity. Finally, mutant HTT subcellular behavior is strongly modified by different cell and tissue environments (e.g. fl-mHTT appears as diffuse nuclear in one tissue and diffuse cytoplasmic in another but toxic in both). These observations underscore the importance of cellular and structural context for the interpretation and comparison of experiments using different fragments and tissues to report the effects of expanded polyQ.
The Effects of Gamma Irradiation on Chemical Biomarker Recovery from Mixed Chemical/Biological Threat Exposure Specimens
Authors: Isenberg Samantha L , Carter Melissa D , Moon Jonathan L , Laughlin Sarah , Petway Marla , Mojica Mike A , Rood Julia E , Gursky Alexis K , Sheppard Cody I , Bagarozzi Dennis A , Pirkle James L , Johnson Rudolph C 
Published: January 2020

AbstractBackgroundIrradiative sterilization of clinical specimens prior to chemical laboratory testing provides a way to not only sterilize pathogens and ensure laboratorian safety but also preserve sample volume and maintain compatibility with quantitative chemical diagnostic protocols. Since the compatibility of clinical biomarkers with gamma irradiation is not well characterized, a subset of diagnostic biomarkers ranging in molecular size, concentration, and clinical matrix was analyzed to determine recovery following gamma irradiation.MethodsSample irradiation of previously characterized quality control materials (QCs) at 5 Mrad was carried out at the Gamma Cell Irradiation Facility at the Centers for Disease Control and Prevention (CDC) in Atlanta, GA. Following irradiation, the QCs were analyzed alongside non-irradiated QCs to determine analyte recovery between dosed and control samples.ResultsBiomarkers for exposure to abrin, ricin, and organophosphorus nerve agents (OPNAs) were analyzed for their stability following gamma irradiation. The diagnostic biomarkers included adducts to butyrylcholinesterase, abrine, and ricinine, respectively, and were recovered at over 90% of their initial concentration.ConclusionsThe results from this pilot study support the implementation of an irradiative sterilization protocol for possible mixed-exposure samples containing both chemical and biological threat agents (mixed CBTs). Furthermore, irradiative sterilization significantly reduces a laboratorian’s risk of infection from exposure to an infectious agent without compromising chemical diagnostic testing integrity, particularly for diagnostic assays in which the chemical analyte has been shown to be fully conserved following a 5 Mrad irradiative dose.
CompactDry “Nissui” ETC for Enumeration of Enterococci in a Variety of Foods: AOAC Performance Tested MethodSM 111902
Authors: Mizuochi Shingo 
Published: January 2020

Abstract

Background
The CompactDry “Nissui” ETC is a ready-to-use dry media sheet using a chromogenic medium with selective agents for the detection and enumeration of Enterococcus spp. After a 20–24 h incubation at 37 ± 1°C, Enterococcus colonies appear blue.

Objective
The performance of the CompactDry “Nissui” ETC was compared to that of the Nordic Committee on Food Analysis (NMKL) reference method 68, Enterococcus, Determination in Foods and Feeds, for 10 matrixes including cream, custard, lettuce, parsley, pasta salad, frozen ground beef patties, fresh cooked prawns, sandwiches, raw beef, and tuna pate.

Methods
Performance indicators included repeatability, difference of means (DOM), robustness and inclusivity/exclusivity.

Results
For all 30 materials (10 matrixes each inoculated at three levels), the relative standard deviation of repeatability (RSDr) was &lt;10% for both methods. Most materials yielded RSDr &lt;5%, with five materials between 5 and 10% for the CompactDry “Nissui” ETC method and ten materials between 5 and 10% for the NMKL 68 method. The DOM ranged from –0.240 (95% CI–0.363, –0.118) to 0.228 (95% CI 0.041, 0.415) log10 CFU/g, well within the –0.5 to 0.5 log10 CFU/g range generally accepted as microbiologically insignificant. Both the reference method and this method have limitations of the species detected.

Conclusions
The CompactDry “Nissui” ETC was validated for the enumeration of Enterococcus species in cream, custard, lettuce, parsley, pasta salad, frozen ground beef patties, fresh cooked prawns, sandwiches, raw beef, and tuna pate.
Facultative Viviparity in a Flesh Fly (Diptera: Sarcophagidae): Forensic Implications of High Variability in Rates of Oviparity in Blaesoxipha plinthopyga (Diptera: Sarcophagidae)
Authors: Lesne Pierre , Srivastav Satyam P , El-Hefnawy Ahmed , Parrott Jonathan J , Sanford Michelle R , Tarone Aaron M 
Published: January 2020

Abstract
Flesh flies are major primary consumers of carrion and are commonly found on human remains. Due to this latter feeding habit, their development rates can be used to provide temporal information in forensic investigations. This is usually done by referencing published flesh fly development datasets. Flesh flies are typically assumed to be strictly viviparous and datasets reporting their development rates therefore start at the first larval instar. However, an increasing number of studies has identified oviposition by flesh flies, including the forensically relevant species Blaesoxipha plinthopyga Wiedemann. To assess the impact of egg-laying behavior on casework, oviparity rates and time before larval hatching were assessed under controlled laboratory conditions that reflect common casework conditions in Harris County, Texas. We demonstrated systematic deposition of viable eggs but at a very variable rate between samples. Similarly, the duration between oviposition and larval hatching was highly variable, with some eggs taking more than a day to hatch after deposition. These results highlight the need to account for embryonic development in forensic investigations including B. plinthopyga and advocates for the re-evaluation of the assumed strict viviparity of the Sarcophagidae.
Groupthink Bias in International Adjudication
Authors: Günther Philipp 
Published: January 2020

Abstract
One of the most common assumptions about decision-making is that groups usually enhance the quality of the outcomes of deliberative processes. The research on groupthink behaviour challenges this belief by hypothesizing that certain group constellations excessively seek concurrence and thereby increase the probability of faulty decision-making. Since the decision-making process in international adjudication almost always involves group choices, it is crucial to consider the group environment of collegial court decision-making. This article utilizes the General Group Problem Solving model (GGPS) to ascertain how strong the different group conformity antecedents are pronounced in five international courts (the ICJ, the ITLOS, the WTO AB, the ECtHR and the ICC). The results of the GGPS analysis indicate that the WTO AB and the ICC are most likely susceptible to groupthink effects while the other courts are relatively resilient.
Modal logics with hard diamond-free fragments
Authors: Achilleos Antonis 
Published: January 2020

AbstractWe investigate the complexity of modal satisfiability for a family of multi-modal logics with interdependencies among the modalities. In particular, we examine four characteristic multi-modal logics with dependencies and demonstrate that, even if we restrict the formulae to be diamond-free and to have only one propositional variable, these logics still have a high complexity. This result identifies and isolates two sources of complexity: the presence of axiom $D$ for some of the modalities and certain modal interdependencies. We then further investigate and characterize the complexity of the diamond-free, 1-variable fragments of multi-modal logics in a general setting.
Exploiting morphological data from Pulsar Wind Nebulae via a spatiotemporal leptonic transport code
Authors: van Rensburg C , Venter C , Seyffert A S , Harding Alice K 
Published: January 2020

ABSTRACT
The next era of ground-based Cherenkov telescope development will see a great increase in both quantity and quality of γ-ray morphological data. This initiated the development of a spatiotemporal leptonic transport code to model pulsar wind nebulae. We present results from this code that predicts the evolution of the leptonic particle spectrum and radiation at different radii in a spherically symmetric source. We simultaneously fit the overall broad-band spectral energy distribution, the surface brightness profile, and the X-ray photon index versus radius for PWN 3C 58, PWN G21.5 − 0.9, and PWN G0.9 + 0.1. Such concurrent fitting of disparate data sets is non-trivial and we thus investigate the utility of different goodness-of-fit statistics, specifically the traditional χ2 test statistic and a newly developed scaled-flux-normalized test statistic to obtain best-fitting parameters. We find reasonable fits to the spatial and spectral data of all three sources, but note some remaining degeneracies that will have to be broken by future observations.
First demonstration of OH suppression in a high-efficiency near-infrared spectrograph
Authors: Ellis S C , Bland-Hawthorn J , Lawrence J S , Horton A J , Content R , Roth M M , Pai N , Zhelem R , Case S , Hernandez E , Leon-Saval S G , Haynes R , Min S S , Giannone D , Madhav K , Rahman A , Betters C , Haynes D , Couch W , Kewley L J , McDermid R , Spitler L , Sharp R G , Veilleux S 
Published: January 2020

ABSTRACT
Ground-based near-infrared (NIR) astronomy is severely hampered by the forest of atmospheric emission lines resulting from the rovibrational decay of OH molecules in the upper atmosphere. The extreme brightness of these lines, as well as their spatial and temporal variability, makes accurate sky subtraction difficult. Selectively filtering these lines with OH suppression instruments has been a long standing goal for NIR spectroscopy. We have shown previously the efficacy of fibre Bragg gratings (FBGs) combined with photonic lanterns for achieving OH suppression. Here we report on PRAXIS, a unique NIR spectrograph that is optimized for OH suppression with FBGs. We show for the first time that OH suppression (of any kind) is possible with high overall throughput (18 per cent end-to-end), and provide examples of the relative benefits of OH suppression.
A blinding solution for inference from astronomical data
Authors: Sellentin Elena 
Published: January 2020

ABSTRACT
This paper presents a joint blinding and deblinding strategy for inference of physical laws from astronomical data. The strategy allows for up to three blinding stages, where the data may be blinded, the computations of theoretical physics may be blinded, and –assuming Gaussianly distributed data – the covariance matrix may be blinded. We found covariance blinding to be particularly effective, as it enables the blinder to determine close to exactly where the blinded posterior will peak. Accordingly, we present an algorithm which induces posterior shifts in predetermined directions by hiding untraceable biases in a covariance matrix. The associated deblinding takes the form of a numerically lightweight post-processing step, where the blinded posterior is multiplied with deblinding weights. We illustrate the blinding strategy for cosmic shear from KiDS-450, and show that even though there is no direct evidence of the KiDS-450 covariance matrix being biased, the famous cosmic shear tension with Planck could easily be induced by a mischaracterization of correlations between ξ− at the highest redshift and all lower redshifts. The blinding algorithm illustrates the increasing importance of accurate uncertainty assessment in astronomical inferences, as otherwise involuntary blinding through biases occurs.
Deep Imaging Analysis in VISUAL Reveals the Role of YABBY Genes in Vascular Stem Cell Fate Determination
Authors: Nurani Alif Meem , Ozawa Yasuko , Furuya Tomoyuki , Sakamoto Yuki , Ebine Kazuo , Matsunaga Sachihiro , Ueda Takashi , Fukuda Hiroo , Kondo Yuki 
Published: January 2020

AbstractStem cells undergo cell division and differentiation to ensure organized tissue development. Because plant cells are immobile, plant stem cells ought to decide their cell fate prior to differentiation, to locate specialized cells in the correct position. In this study, based on a chemical screen, we isolated a novel secondary cell wall indicator BF-170, which binds to lignin and can be used to image in vitro and in situ xylem development. Use of BF-170 to observe the vascular differentiation pattern in the in vitro vascular cell induction system, VISUAL, revealed that adaxial mesophyll cells of cotyledons predominantly generate ectopic xylem cells. Moreover, phloem cells are abundantly produced on the abaxial layer, suggesting the involvement of leaf adaxial–abaxial polarity in determining vascular cell fate. Analysis of abaxial polarity mutants highlighted the role of YAB3, an abaxial cell fate regulator, in suppressing xylem and promoting phloem differentiation on the abaxial domains in VISUAL. Furthermore, YABBY family genes affected in vivo vascular development during the secondary growth. Our results denoted the possibility that such mediators of spatial information contribute to correctly determine the cell fate of vascular stem cells, to conserve the vascular pattern of land plants.
The Impact of an Experimental Guaranteed Income on Crime and Violence
Authors: Calnitsky David , Gonalons-Pons Pilar 
Published: January 2020

AbstractWould unconditional cash payments reduce crime and violence? This paper examines data on crime and violence in the context of an understudied social experiment from the late 1970s called the Manitoba Basic Annual Income Experiment, or Mincome. We combine town-level crime statistics for all medium-sized Canadian Prairie towns with town-level socio-demographic data from the census to study how an experimental guaranteed income affected both violent crime and total crime. We find a significant negative relationship between Mincome and both outcomes. We also decompose total crime and analyze its main components, property crime and “other” crime, and find a significant negative relationship between Mincome and property crime. While the impact on property crime is theoretically straightforward, we close by speculating on the mechanisms that might link the availability of guaranteed annual income payments to a decline in violence, focusing on the mechanisms that shape patterns of inter-partner violence.
Single-cell analysis of human embryos reveals diverse patterns of aneuploidy and mosaicism
Authors: Starostik Margaret R. , Sosina Olukayode A. , McCoy Rajiv C. 
Published: January 2020

AbstractLess than half of human zygotes survive to live birth, primarily due to aneuploidies of meiotic or mitotic origin. Mitotic errors lead to chromosomal mosaicism, defined by multiple cell lineages with distinct chromosome complements. The incidence and fitness consequences of chromosomal mosaicism in human embryos remain controversial, with most previous studies based on bulk DNA assays or comparisons of multiple biopsies of a few embryonic cells. Single-cell genomic data provide an opportunity to quantify mosaicism on an embryo-wide scale. To this end, we extended an approach to infer aneuploidies based on chromosome dosage-associated changes in gene expression by integrating signatures of allelic imbalance. We applied this method to published single-cell RNA sequencing data from 74 disaggregated human embryos, spanning the morula to blastocyst stages. Our analysis revealed widespread mosaic aneuploidies across preimplantation development, with 59 of 74 (80%) embryos harboring at least one aneuploid cell (1% FDR). By clustering copy number calls, we reconstructed histories of chromosome mis-segregation, distinguishing meiotic and early mitotic errors from those occurring after lineage differentiation. We observed no significant enrichment of aneuploid cells in the trophectoderm compared to the inner cell mass, though we do detect such an enrichment in published data from later post-implantation stages. Finally, we observed that aneuploid cells exhibit upregulation of immune response genes, as well as downregulation of genes involved in proliferation, metabolism, and protein processing, consistent with stress responses previously documented in other stages and systems. Together, our work provides a high-resolution view of aneuploidy in preimplantation embryos and supports the conclusion that low-level mosaicism is a common feature of early human development.
Tiled Reconstruction Improves Structured Illumination Microscopy
Authors: Hoffman David P. , Betzig Eric 
Published: January 2020

AbstractStructured illumination microscopy (SIM) is widely used for fast, long-term, live-cell super-resolution imaging. However, SIM images can contain substantial artifacts if the sample does not conform to the underlying assumptions of the reconstruction algorithm. Here we describe a simple, easy to implement, process that can be combined with any reconstruction algorithm to alleviate many common SIM reconstruction artifacts and briefly discuss possible extensions.
Ecological Relationships in the Serengeti National Park
Authors: Brownstein Kole 
Published: January 2020

AbstractThe use of camera traps in animal ecology has transformed the field by allowing a greater quantity of detailed observations with limited human interference. One of largest camera trap studies published to date is from the Serengeti National Park (SNP) in Tanzania, East Africa which deployed 225 camera traps and obtained over 1.2 million pictures. This paper will focus primarily on the top predator of the Serengeti, the lion, and how it affects and is affected by prey, subordinate predators and the dramatic shift in the seasons. I asked the following three questions to better understand species relationships in the SNP: 1) Do the seasons in the SNP have an effect on the RAB of lions? 2) Does the presence or absence of lions have an effect on the RAB of hyenas in the wet season? 3) Does the presence/absence of Thompson gazelles (Eudorcas thomsonii) and impalas (Aepyceros melampus) in the wet season have an effect on the RAB of lions? During the dry and wet season of 2012 in the SNP there did not appear to be a change in the relative abundance of lions (Fig. 1), nor did lion relative abundance affect hyenas. The lions might possibly alter their diet during the dry seasons to include non-migratory species and choose not to change their territory on a season to season basis. Based on these findings research should focus on how the lions adapt to the changes in prey abundance during the wet and dry season. This preliminary analysis of the ecological dynamics of lions and associated species in the SNP is intriguing and yet raises significantly more questions than it has answered. Additional research surrounding the effects of yearly migration on the lions home territory, diet, and species interactions should be investigated more thoroughly, to greater understand the ecological relationships in the SNP.
Protein Sequence Design with a Learned Potential
Authors: Anand-Achim Namrata , Eguchi Raphael R. , Mathews Irimpan I. , Perez Carla P. , Derry Alexander , Altman Russ B. , Huang Po-Ssu 
Published: January 2020

AbstractThe task of protein sequence design is central to nearly all rational protein engineering problems, and enormous effort has gone into the development of energy functions to guide design. We investigate the capability of a deep neural network model to automate design of sequences onto protein backbones, having learned directly from crystal structure data and without any human-specified priors. The model generalizes to native topologies not seen during training, producing experimentally stable designs. We evaluate the generalizability of our method to a de novo TIM-barrel scaffold. The model produces novel sequences, and high-resolution crystal structures of two designs show excellent agreement with the in silico models. Our findings demonstrate the tractability of an entirely learned method for protein sequence design.