bluuebunny/crossref_metadata_2025_split huggingface dataset:
Affine registration of multispectral images of historical documents for optimized feature recovery
Authors: Jones Cerys , Christens-Barry William A , Terras Melissa , Toth Michael B , Gibson Adam 
Published: July 2019

Abstract
Multispectral (MSI) imaging of historical documents can recover lost features, such as text or drawings. This technique involves capturing multiple images of a document illuminated using different wavelengths of light. The images created must be registered in order to ensure optimal results are produced from any subsequent image processing techniques. However, the images may be misaligned due to the presence of optical elements such as filters, or because they were acquired at different times or because the images were captured from different copies of the documents . There is little prior work or information available about which image registration techniques are most appropriate. Image registration of multispectral images is challenging as the illumination changes for each image and the features visible in images captured at different wavelengths may not appear consistently throughout the image sequence. Here, we compare three image registration techniques: two based on similarity measures and a method based on phase correlation. These methods are characterized by applying them to realistic surrogate images and then assessed on three different sets of real multispectral images. Mutual information is recommended as a measure for affine image registration when working with multispectral images of documentary material as it was proven to be more robust than the other techniques tested.
Exploring a new definition of the green valley and its implications
Authors: Angthopo James , Ferreras Ignacio , Silk Joseph 
Published: July 2019

ABSTRACT
The distribution of galaxies on a colour–magnitude diagram reveals a bimodality, featuring a passively evolving red sequence and a star-forming blue cloud. The region between these two, the green valley (GV), represents a fundamental transition where quenching processes operate. We exploit an alternative definition of the GV using the 4000 Å break strength, an indicator that is more resilient than colour to dust attenuation. We compare and contrast our GV definition with the traditional one, based on dust-corrected colour, making use of data from the Sloan Digital Sky Survey. Our GV selection – that does not need a dust correction and thus does not carry the inherent systematics – reveals very similar trends regarding nebular activity (star formation, AGN, quiescence) to the standard dust-corrected 0.1(g − r). By use of high-SNR stacked spectra of the quiescent GV subsample, we derive the simple stellar population (SSP) age difference across the GV, a rough proxy of the quenching time-scale (Δt). We obtain an increasing trend with velocity dispersion (σ), from Δt ∼ 1.5 Gyr at σ = 100 km s−1, up to 3.5 Gyr at σ = 200 km s−1, followed by a rapid decrease in the most massive GV galaxies (Δt ∼ 1 Gyr at σ = 250 km s−1), suggesting two different modes of quenching, or the presence of an additional channel (rejuvenation).
Aging amorphous/crystalline heterophase PdCu nanosheets for catalytic reactions
Authors: Cheng Hongfei , Yang Nailiang , Liu Xiaozhi , Yun Qinbai , Goh Min Hao , Chen Bo , Qi Xiaoying , Lu Qipeng , Chen Xiaoping , Liu Wen , Gu Lin , Zhang Hua 
Published: July 2019

ABSTRACT
Phase engineering is arising as an attractive strategy to tune the properties and functionalities of nanomaterials. In particular, amorphous/crystalline heterophase nanostructures have exhibited some intriguing properties. Herein, the one-pot wet-chemical synthesis of two types of amorphous/crystalline heterophase PdCu nanosheets is reported, in which one is amorphous phase-dominant and the other one is crystalline phase-dominant. Then the aging process of the synthesized PdCu nanosheets is studied, during which their crystallinity increases, accompanied by changes in some physicochemical properties. As a proof-of-concept application, their aging effect on catalytic hydrogenation of 4-nitrostyrene is investigated. As a result, the amorphous phase-dominant nanosheets initially show excellent chemoselectivity. After aging for 14 days, their catalytic activity is higher than that of crystalline phase-dominant nanosheets. This work demonstrates the intriguing properties of heterophase nanostructures, providing a new platform for future studies on the regulation of functionalities and applications of nanomaterials by phase engineering.
Defining and Measuring Abstinence in Clinical Trials of Smoking Cessation Interventions: An Updated Review
Authors: Piper Megan E , Bullen Christopher , Krishnan-Sarin Suchitra , Rigotti Nancy A , Steinberg Marc L , Streck Joanna M , Joseph Anne M 
Published: July 2019

AbstractBackgroundChanges in tobacco products, use patterns, and assessment technology in the last 15 years led the Society for Research on Nicotine and Tobacco (SRNT) Treatment Research Network to call for an update to the 2003 SRNT recommendations for assessing abstinence in clinical trials of smoking cessation interventions.MethodsThe SRNT Treatment Research Network convened a group of investigators with decades of experience in conducting tobacco treatment clinical trials. To arrive at the updated recommendations, the authors reviewed the recommendations of the prior SRNT Workgroup as well as current literature. Ten additional experts in the field provided feedback on this paper and these recommendations.ResultsWith respect to defining abstinence, the authors recommend: (1) continuing to use the definition of no use of combustible tobacco products (regardless of use of noncombustible tobacco products [e.g., snus] and alternative products [e.g., e-cigarettes]) and collecting additional data to permit alternate abstinence definitions; (2) no use of combustible or smokeless tobacco products; and (3) no use of combustible or smokeless tobacco products or alternative products, as appropriate for the research question being addressed. The authors also recommend reporting point prevalence and prolonged abstinence at multiple timepoints (end of treatment, ≥3 months after the end of treatment, and ≥6 months postquit or posttreatment initiation).ConclusionsDefining abstinence requires specification of which products a user must abstain from using, the type of abstinence (i.e., point prevalence or continuous), and the duration of abstinence. These recommendations are intended to serve as guidelines for investigators as they collect the necessary data to accurately describe participants’ abstinence during smoking cessation clinical trials.ImplicationsThis paper provides updated recommendations for defining abstinence in the context of smoking cessation treatment clinical trials.
Retrospective Study Demonstrating High Rates of Sustained Virologic Response After Treatment With Direct-Acting Antivirals Among American Indian/Alaskan Natives
Authors: Mera Jorge , Joshi Kartik , Thornton Karla , Box Terry , Scott John , Sedillo Miranda , Deming Paulina , David Crystal , Essex Whitney , Manch Richard , Kohli Anita 
Published: July 2019

Abstract

Background
Treatment for chronic hepatitis C virus (HCV) has rapidly evolved to simple, well-tolerated, all-oral regimens of direct-acting antivirals (DAAs). There are few data on the epidemiology of HCV in American Indians/Alaska Natives (AI/ANs), a population disproportionately affected by HCV.

Methods
In this retrospective cohort study, all HCV-infected AI/AN patients treated with DAA therapies between January 1, 2014, and February 24, 2016, in specialty clinics or by primary care clinicians participating in Extension for Community Healthcare Outcomes (ECHO) were included. Demographic, clinical, and virologic data on all patients treated for HCV from pretreatment through sustained virologic response at 12 weeks (SVR12) were collected.

Results
Two hundred eighty patients were included; 71.1% of patients (n = 199) were infected with genotype 1 (GT1), 18.2% (n = 51) with GT2, and 10.7% with (n = 30) GT3. At baseline, 26.1% (n = 73) patients had cirrhosis and 22.6% (n = 56) had active substance use disorder; eighty-eight percent (n = 232) of patients achieved SVR12. Among the 165 GT1 patients treated with sofosbuvir (SOF)/ledipasvir for 8, 12, and 24 weeks, SVR12 was achieved by 91.5% (n = 54), 92.2% (n = 71), and 100% (n = 13), respectively. Among GT2 patients, 87.2% (n = 34) and 71.4% (n = 5) treated with 12 and 16 weeks of SOF/ribavirin (RBV) achieved SVR12, respectively. Among GT3 patients, 100% (n = 2) and 83.3% (n = 20) treated with 12 and 24 weeks of SOF/RBV achieved SVR12, respectively. SVR12 rates remained high among patients with active substance use disorder.

Conclusions
DAA therapies are highly efficacious in HCV-infected AI/ANs. SVR12 rates remained high among patients with active substance use disorder. More steps must be taken to increase access to treatment for this underserved, vulnerable population.
Syphilis Reactivates Latent Epstein-Barr Virus Reservoir via Toll-Like Receptor 2 and B-Cell Receptor Activation
Authors: Hirsiger Julia R , Fuchs Philipp S , Häusermann Peter , Müller-Durovic Bojana , Daikeler Thomas , Recher Mike , Hirsch Hans H , Terracciano Luigi , Berger Christoph T 
Published: July 2019

Abstract
Latent Epstein-Barr virus (EBV) infection can clinically reactivate in immunosuppressed individuals causing lymphoproliferative disease and rarely hepatitis. In this study, we provide in vivo and in vitro evidence that Treponema pallidum infection can cause EBV reactivation with hepatitis in an immunocompetent patient. We report the diagnostic challenges and immunological findings of coinciding syphilis and EBV-associated hepatitis. Using an in vitro EBV-reactivation assay, we demonstrate that T pallidum reactivates latent EBV in a Toll-like receptor (TLR)2/B-cell receptor signaling-dependent manner. Epstein-Barr virus-associated reactivation or lymphoproliferation should be considered in infections with pathogens that activate TLR2.
Kinetic trapping in protein folding
Authors: Varela Angela E , England Kevin A , Cavagnero Silvia 
Published: July 2019

AbstractThe founding principles of protein folding introduced by Christian Anfinsen, together with the numerous mechanistic investigations that followed, assume that protein folding is a thermodynamically controlled process. On the other hand, this review underscores the fact that thermodynamic control is far from being the norm in protein folding, as long as one considers an extended chemical-potential landscape encompassing aggregates, in addition to native, unfolded and intermediate states. Here, we highlight the key role of kinetic trapping of the protein native state relative to unfolded, intermediate and, most importantly, aggregated states. We propose that kinetic trapping serves an important role in biology by protecting the bioactive states of a large number of proteins from deleterious aggregation. In the event that undesired aggregates were somehow formed, specialized intracellular disaggregation machines have evolved to convert any aberrant populations back to the native state, thus restoring a fully bioactive and aggregation-protected protein cohort.
Affinity versus specificity in coupled binding and folding reactions
Authors: Gianni Stefano , Jemth Per 
Published: July 2019

Abstract
Intrinsically disordered protein regions may fold upon binding to an interaction partner. It is often argued that such coupled binding and folding enables the combination of high specificity with low affinity. The basic tenet is that an unfavorable folding equilibrium will make the overall binding weaker while maintaining the interaction interface. While theoretically solid, we argue that this concept may be misleading for intrinsically disordered proteins. In fact, experimental evidence suggests that interactions of disordered regions usually involve extended conformations. In such cases, the disordered region is exceptionally unlikely to fold into a bound conformation in the absence of its binding partner. Instead, these disordered regions can bind to their partners in multiple different conformations and then fold into the native bound complex, thus, if anything, increasing the affinity through folding. We concede that (de)stabilization of native structural elements such as helices will modulate affinity, but this could work both ways, decreasing or increasing the stability of the complex. Moreover, experimental data show that intrinsically disordered binding regions display a range of affinities and specificities dictated by the particular side chains and length of the disordered region and not necessarily by the fact that they are disordered. We find it more likely that intrinsically disordered regions are common in protein–protein interactions because they increase the repertoire of binding partners, providing an accessible route to evolve interactions rather than providing a stability–affinity trade-off.
DETERMINATION OF THE TOTAL EFFECTIVE DOSE OF EXTERNAL AND INTERNAL EXPOSURE BY DIFFERENT IONIZING RADIATION SOURCES
Authors: Kudryashev V A , Kim D S 
Published: July 2019

Abstract
The purpose of the research is to develop an integrated technique for determining the effective dose (E) of external and internal exposure by different sources of ionizing radiation. The proposing technique for determining the total effective dose is based on three methods of calculation. The first one is multiplying the value of the individual dose equivalent $H_{p}(10)$ by the factor of 0.642 to account for radiation shielding by various organs and tissues and its backscattering. The second method is multiplying $H_{p}(10)$ by the conversion factor of air kerma in free air in a plate phantom, depending on the photon energy. The third method is multiplying $H_{p}(10)$ by the sum of the radiosensitivity coefficients of various organs and tissues. As a result of research, a complex method was developed for determining the total effective dose, composed of doses of cosmic radiation, external gamma-, beta- and neutron radiation, internal exposure from radionuclides, including CDP of radon and thoron, entering the body through the organs of digestion and respiration. The proposed technique for determining the total effective dose allows one to take into account the comprehensive effect of ionizing radiation sources on a person and to obtain a more accurate measure of radiation risk than the existing methods provide.
Aerobic capacity predicts skeletal but not cardiac muscle damage after a full distance Ironman triathlon - the Iron(wo)man-study
Authors: Danielsson Tom , Carlsson Jörg , Siethoff Lasse Ten , Ahnesjö Jonas , Bergman Patrick 
Published: July 2019

AbstractPurposeThis study examines the association between aerobic capacity and biomarkers of skeletal- and cardiac muscle damage among amateur triathletes after a full distance Ironman.MethodsMen and women (N=55) were recruited from local sport clubs. One month before an Iron-man triathlon, they conducted a 20m shuttle run test to determine aerobic capacity. Blood samples were taken immediately after finishing the triathlon, and analyzed for biomarkers of cardiac- and skeletal muscle damage. Regression models examining the association between aerobic capacity expressed in both relative terms (mLO2*kg-1*min-1) and absolute terms (LO2*min-1) controlled for weight and were fitted.ResultA total of 39 subjects (26% females) had complete data and were included in the analysis. No association between aerobic capacity and cardiac muscle damage but a significant negative association between aerobic capacity and skeletal muscle damage was observed. This association was independent of how aerobic capacity was expressed, although the model with aerobic capacity expressed in absolute terms and controlled for weight resulted in slightly higher r2 values, than when aerobic capacity was expressed in relative terms.ConclusionA negative association between aerobic capacity and skeletal muscle damage was seen but despite the well-known cardio-protective health effect of high aerobic fitness no such association could be observed in this study.
Mechanistic diversification of XIST regulatory network in mammals
Authors: Rosspopoff Olga , Huret Christophe , Collier Amanda J. , Casanova Miguel , Rugg-Gunn Peter J. , Ouimette Jean-François , Rougeulle Claire 
Published: July 2019

SUMMARYX chromosome inactivation (XCI) is a developmental regulatory process that initiates with remarkable diversity in various mammalian species. Here we addressed the contribution of XCI regulators, most of which are lncRNA genes characterized in the mouse, to this mechanistic diversity. By combining analysis of single-cell RNA-seq data from early human embryogenesis with various functional assays in naïve and primed pluripotent stem cells and in differentiated cells, we demonstrate that JPX is a major regulator of XIST expression in human and in mouse. However, the underlying mechanisms differ radically between species and require Jpx RNA in the mouse and the act of transcription of JPX locus in the human. Moreover, biogenesis of XIST is affected at different regulatory steps between these species. This study illustrates how diversification of LRGs modes of action during evolution provide opportunities for innovations within constrained gene regulatory networks.Graphical abstract
Model-based decoupling of evoked and spontaneous neural activity in calcium imaging data
Authors: Triplett Marcus A. , Pujic Zac , Sun Biao , Avitan Lilach , Goodhill Geoffrey J. 
Published: July 2019

AbstractThe pattern of neural activity evoked by a stimulus can be substantially affected by ongoing spontaneous activity. Separating these two types of activity is particularly important for calcium imaging data given the slow temporal dynamics of calcium indicators. Here we present a statistical model that decouples stimulus-driven activity from low dimensional spontaneous activity in this case. The model identifies hidden factors giving rise to spontaneous activity while jointly estimating stimulus tuning properties that account for the confounding effects that these factors introduce. By applying our model to data from zebrafish optic tectum and mouse visual cortex, we obtain quantitative measurements of the extent that neurons in each case are driven by evoked activity, spontaneous activity, and their interaction. This broadly applicable model brings new insight into population-level neural activity in single trials without averaging away potentially important information encoded in spontaneous activity.
Distinct patterns of selective sweep and polygenic adaptation
Authors: Barghi Neda , Schlötterer Christian 
Published: July 2019

AbstractThe central paradigm of molecular population genetics is selective sweeps, where targets of selection have independent effects on the phenotype and quickly rise to fixation. In quantitative genetics, many loci contribute epistatically to adaptation and subtle frequency changes occur at many loci. Since both paradigms could result in a sweep-like genomic signature, additional criteria are needed to distinguish them. Using the framework of experimental evolution, we performed computer simulations to study the pattern of selected alleles under both paradigms. We identify several distinct patterns of selective sweeps and polygenic adaptation in populations of different sizes. These features could provide the foundation for development of quantitative approaches to differentiate the two paradigms.Author’s summaryThe selective sweep model assumes an independent frequency increase of favorable alleles and has been the basis of many tests for selection. While, polygenic adaptation is typically modelled by small frequency shifts in many loci. Recently, some theoretical and empirical work demonstrated that polygenic adaptation, similar to sweep, could also results in pronounced allele frequency changes. These results suggest that other distinct features need to be identified. Using computer simulations, we identified distinctive features for each paradigm that can be used to differentiate the sweep model from polygenic adaptation. Features such as allele frequency trajectories, time-series fitness, distribution of selected alleles on haplotypes, and parallelism among replicates can be used for development of suitable tests to distinguish between different adaptive architectures. These features provide the basis for theoretical modeling, design of selection experiments and data analysis.
DNA end-resection in highly accessible chromatin produces a toxic break
Authors: van den Berg Jeroen , Joosten Stacey E.P. , Kim YongSoo , Manjón Anna G. , Krenning Lenno , Koob Lisa , Feringa Femke M. , Klompmaker Rob , van den Broek Bram , Jalink Kees , Zwart Wilbert , Medema René H. 
Published: July 2019

The authors have withdrawn their manuscript whilst they perform additional experiments to test some of their conclusions further.Despite repetitive attempts to reproduce the data shown in figure 2I, we have failed to obtain convincing evidence that chemical inhibition of Mre11 can improve the fitness of cells exposed to the so-called “halt” breaks. Upon re-analysis of the raw data used to compose figure 2I, we noted inconsistencies in the inclusion of datapoints, for which a satisfactory motivation was not apparent.In order to reproduce the experiments with the DNA-PK inhibitor, we ordered new batches of this compound, but noticed that the IC50 was significantly lower than that of the earlier batch (as determined in suppl. fig.1). While this might be due to a difference in batches, the IC50 of the newer batches was more comparable to the IC50 of this compound described for other cell lines. This sheds doubts on the quality of the batch used for the experiments shown in our manuscript, and we no longer wish to draw any conclusions based on these experiments.The authors hope that future experiments can resolve if open chromatin does indeed produce a potentially more toxic DNA break. The authors do not wish this work to be cited as reference for the project. If you have any questions, please contact the corresponding author.
Genome sequencing of Musa acuminata Dwarf Cavendish reveals a duplication of a large segment of chromosome 2
Authors: Busche Mareike , Pucker Boas , Viehöver Prisca , Weisshaar Bernd , Stracke Ralf 
Published: July 2019

AbstractDifferent Musa species, subspecies, and cultivars are currently investigated to reveal their genomic diversity. Here, we compare the genome sequence of one of the commercially most important cultivars, Musa acuminata Dwarf Cavendish, against the Pahang reference genome assembly. Numerous small sequence variants were detected and the ploidy of the cultivar presented here was determined as triploid based on sequence variant frequencies. Illumina sequence data also revealed a duplication of a large segment on the long arm of chromosome 2 in the Dwarf Cavendish genome. Comparison against previously sequenced cultivars provided evidence that this duplication is unique to Dwarf Cavendish. Although no functional relevance of this duplication was identified, this example shows the potential of plants to tolerate such aneuploidies.