bluuebunny/crossref_metadata_2025_split huggingface dataset:
Variability in the Distribution of Histological Disease Activity in the Colon of Patients with Ulcerative Colitis
Authors: Bossuyt Peter , Bisschops Raf , Vermeire Séverine , De Hertogh Gert 
Published: October 2020

Abstract

Background and Aims
Histological activity scores have been developed and validated. However, data on the distribution of histological inflammation within one segment in patients with ulcerative colitis [UC] are lacking. This impacts on the reliability of histological activity scores. The aim of this study was to assess the variability in histological activity within one endoscopic segment in patients with UC.

Methods
Biopsies were taken in sequential patients with UC in three adjacent contiguous regions within a macroscopically homogeneous colonic segment. Biopsies were scored for Geboes score [GS], Robarts histological index [RHI] and Nancy histological index [NHI]. Variability was assessed by Kappa statistics for categorical outcomes and intraclass correlation coefficient [ICC] for continuous outcomes.

Results
A total of 161 biopsy sets from 55 endoscopic segments of 21 patients were analysed. Endoscopically active disease was present in 45% of segments. The continuous histological scores showed excellent agreement between the different regions. The ICC for RHI in all segments was 0.974 (95% confidence interval [CI] 0.958–0.984; p &lt; 0.0001) and 0.98 [95% CI: 0.968–0.988; p &lt; 0.0001] for the numerically converted GS. The categorical NHI showed higher variability: κ = 0.574 [95% CI: 0.571–0.577; p &lt; 0.0001]. In all segments the highest variability was seen in samples with NHI = 2. When dichotomizing based on histological remission, substantial agreement was seen for all scores, with κ &gt; 0.734 for all cut-offs. The homogeneity in the distribution of histological disease activity was comparable between colonic segments.

Conclusion
The distribution of histological disease activity in UC follows a homogeneous pattern in different locations of one segment.
Disease Activity Patterns, Mortality, and Colorectal Cancer Risk in Microscopic Colitis: A Danish Nationwide Cohort Study, 2001 to 2016
Authors: Weimers Petra , Vedel Ankersen Dorit , Lophaven Søren , Bonderup Ole Kristian , Münch Andreas , Løkkegaard Ellen Christine Leth , Munkholm Pia , Burisch Johan 
Published: October 2020

Abstract

Background and Aims
The disease course of microscopic colitis [MC], encompassing collagenous colitis [CC] and lymphocytic colitis [LC], is not well known. In a Danish nationwide cohort, we evaluated the disease activity patterns as well as the risk of colorectal cancer [CRC] and mortality based on disease severity.

Methods
All incident MC patients [n = 14 302] with a recorded diagnosis of CC [n = 8437] or LC [n = 5865] in the Danish Pathology Register, entered between 2001 and 2016, were matched to 10 reference individuals [n = 142 481]. Incident cases of CRC after the index date were captured from the Danish Cancer Registry. Mortality data were ascertained from the Danish Registry of Causes of Death, and information about treatment was obtained from the Danish National Prescription Registry. The risk of CRC and mortality analyses were investigated by Cox regression and Kaplan-Meier estimates.

Results
We identified a self-limiting or transient disease course in 70.6% of LC patients and in 59.9% of CC patients, p &lt;0.001. Less than 5% of MC patients experienced a budesonide-refractory disease course and were treated with immunomodulators or biologic treatment. A total of 2926 [20.5%] MC patients and 24 632 [17.3%] reference individuals died during the study period. MC patients with a severe disease had a relative risk [RR] of mortality of 1.41 (95% confidence interval [CI]: 1.32–1.50) compared with reference individuals. Only 90 MC patients were diagnosed with CRC during follow-up, corresponding to an RR of 0.48 [95% CI: 0.39–0.60].

Conclusions
A majority of MC patients experience an indolent disease course with a lower risk of developing CRC compared with the background population.
Inequalities and risk factors related to non-participation in colorectal cancer screening programmes: a systematic review
Authors: Unanue-Arza Saloa , Solís-Ibinagagoitia Maite , Díaz-Seoane Marta , Mosquera-Metcalfe Isabel , Idigoras Isabel , Bilbao Isabel , Portillo Isabel 
Published: October 2020

Abstract

Background
Colorectal cancer (CRC) screening programmes require high levels of participation in order to reduce mortality. To improve participation rates, it is necessary to identify the health risk factors and social inequalities associated with non-participation.

Methods
A systematic review was conducted between June and September of 2019 in six databases: CINHAL, Medline, Scopus, Social Sciences Citation Index, Embase and PsycINFO. Studies assessing the relationship between health risk factors, participation in preventive activities and participation in CRC screening were included. Methodological assessment was carried out according to the Quality Assessment Tools of the National Heart, Lung and Blood Institute.

Results
A total of nine studies that analyze participation in both organized and opportunistic screening programmes using any type of screening method were finally selected. Data were mainly self-reported although in two studies medical records were also studied. We identified several variables: gender, body mass index, consultation with a doctor or a specialist, educational level, employment, health insurance, residence, ethnicity, age, marital status, income, other preventive activities, obesity, physical activity, smoking, family history of CRC and general health status.

Conclusion
The scarcity of studies linking risk factors, social inequalities and participation in preventive activities for participation in screening in the same study makes it difficult to reach definitive patterns related to non-participation in CRC screening programmes. Nevertheless, being under 60, obese, smoker and sedentary have shown an association with non-participation as well as not visiting a doctor.
The inverse elastic scattering by an impenetrable obstacle and a crack
Authors: Xiang Jianli , Yan Guozheng 
Published: October 2020

Abstract
This paper is concerned with the inverse scattering problem of time-harmonic elastic waves by a mixed-type scatterer, which is given as the union of an impenetrable obstacle and a crack. We develop the modified factorization method to determine the shape of the mixed-type scatterer from the far field data. However, the factorization of the far field operator $F$ is related to the boundary integral matrix operator $A$, which is obtained in the study of the direct scattering problem. So, in the first part, we show the well posedness of the direct scattering problem by the boundary integral equation method. Some numerical examples are presented at the end of the paper to demonstrate the feasibility and effectiveness of the inverse algorithm.
Energy-based fluid–structure model of the vocal folds
Authors: Mora Luis A , Ramirez Hector , Yuz Juan I , Le Gorec Yann , Zañartu Matías 
Published: October 2020

AbstractLumped elements models of vocal folds are relevant research tools that can enhance the understanding of the pathophysiology of many voice disorders. In this paper, we use the port-Hamiltonian framework to obtain an energy-based model for the fluid–structure interactions between the vocal folds and the airflow in the glottis. The vocal fold behavior is represented by a three-mass model and the airflow is described as a fluid with irrotational flow. The proposed approach allows to go beyond the usual quasi-steady one-dimensional flow assumption in lumped mass models. The simulation results show that the proposed energy-based model successfully reproduces the oscillations of the vocal folds, including the collision phenomena, and it is useful to analyze the energy exchange between the airflow and the vocal folds.
Multiplex TaqMan Real-Time PCR Assay for Sensitive Detection of Two Weevil Species (Coleoptera: Curculionidae)
Authors: Aguirre Carlos , Sánchez Evelyn , Olivares Natalia , Hinrichsen Patricio 
Published: October 2020

Abstract
Rapid and cost-efficient identification of Naupactus species is becoming a key process for the exportation of citrus fruit from Chile and other countries, considering the quarantine regulations for some species of the cosmopolitan genus Naupactus. This study deals with the development of a fast and sensitive detection protocol for Naupactus cervinus (Coleoptera: Curculionidae) (Boheman) and Naupactus xanthographus (Coleoptera: Curculionidae) (Germar) based on multiplex TaqMan Real-time polymerase chain reaction. Both N. cervinus and N. xanthographus primer and probe sets achieved species-specific detection in a linear range from 1 pg/μl to 1 × 10-6 pg/μl, allowing detection of as few as 160 copies of template DNA. Non-target amplifications were not detected and a panel composed of 480 test samples had 100% coincidence with the respective morphological identification.
Social consequences of mass quarantine during epidemics: a systematic review with implications for the COVID-19 response
Authors: Chu Isaac Yen-Hao , Alam Prima , Larson Heidi J , Lin Leesa 
Published: October 2020

Abstract
Four billion people worldwide have experienced coronavirus disease 2019 (COVID-19) confinement. Such unprecedented extent of mobility restriction to curb the COVID-19 pandemic may have profound impacts on how individuals live, travel and retain well-being. This systematic review aims to identify (i) the social consequences of mass quarantine—community-wide movement restrictions—during previous and current infectious disease outbreaks and (ii) recommended strategies to mitigate the negative social implications of COVID-19 lockdowns. Considering social determinants of health, we conducted a systematic review by searching five databases (Ovid-MEDLINE, EMBASE, PsycINFO, China National Knowledge Infrastructure and the World Health Organization COVID-19 database) for publications from inception to 9 April 2020. No limitation was set on language, location or study type. Studies that (i) contained peer-reviewed original empirical evidence and (ii) focussed on non-epidemiological implications of mass quarantine were included. We thematically synthesized and reported data due to heterogeneous disease and country context. Of 3067 publications found, 15 original peer-reviewed articles were selected for full-text extraction. Psychological distress, heightened communication inequalities, food insecurity, economic challenges, diminished access to health care, alternative delivery of education and gender-based violence were identified as negative social consequences of community-based quarantine in six infectious disease epidemics, including the current COVID-19 pandemic. In contrast, altruistic attitudes were identified as a positive consequence during previous quarantines. Diverse psychological and social consequences of mass quarantine in previous and current epidemics were evident, but individual country policies had been highly varied in how well they addressed the needs of affected individuals, especially those who are socially marginalized. Policymakers should balance the pros and cons of movement restrictions, facilitate multisectoral action to tackle social inequalities, provide clear and coherent guidance to the public and undertake time-bound policy evaluations to mitigate the negative impact of COVID-19 lockdowns and to establish preparedness strategies for future epidemics.
Post-Newtonian Kozai–Lidov mechanism and its effect on cumulative shift of periastron time of binary pulsar
Authors: Suzuki Haruka , Gupta Priti , Okawa Hirotada , Maeda Kei-ichi 
Published: October 2020

ABSTRACT
We study the Kozai–Lidov mechanism in a hierarchical triple system in detail by the direct integration of the first-order post-Newtonian equations of motion. We analyse a variety of models with a pulsar to evaluate the cumulative shift of the periastron time of a binary pulsar caused by the gravitational wave emission in a hierarchical triple system with Kozai–Lidov mechanism. We compare our results with those by the double-averaging method. The deviation in the eccentricity, even if small, is important in the evaluation of the emission of the gravitational waves. We also calculate the cumulative shift of the periastron time by using obtained osculating orbital elements. If Kozai–Lidov oscillations occur, the cumulative shift curve will bend differently from that of the isolated binary. If such a bending is detected through the radio observation, it will be the first indirect observation of gravitational waves from a triple system.
Interpreting the X-ray afterglows of gamma-ray bursts with radiative losses and millisecond magnetars
Authors: Sarin Nikhil , Lasky Paul D , Ashton Gregory 
Published: October 2020

ABSTRACT
The spin-down energy of millisecond magnetars has been invoked to explain X-ray afterglow observations of a significant fraction of short and long gamma-ray bursts. Here, we extend models previously introduced in the literature, incorporating radiative losses with the spin-down of a magnetar central engine through an arbitrary braking index. Combining this with a model for the tail of the prompt emission, we show that our model can better explain the data than millisecond-magnetar models without radiative losses or those that invoke spin-down solely through vacuum dipole radiation. We find that our model predicts a subset of X-ray flares seen in some gamma-ray bursts. We can further explain the diversity of X-ray plateaus by altering the radiative efficiency and measure the braking index of newly born millisecond magnetars. We measure the braking index of GRB061121 as $n=4.85^{+0.11}_{-0.15}$ suggesting the millisecond-magnetar born in this gamma-ray burst spins down predominantly through gravitational-wave emission.
Machine learning for transient recognition in difference imaging with minimum sampling effort
Authors: Mong Y-L , Ackley K , Galloway D K , Killestein T , Lyman J , Steeghs D , Dhillon V , O’Brien P T , Ramsay G , Poshyachinda S , Kotak R , Nuttall L , Pallé E , Pollacco D , Thrane E , Dyer M J , Ulaczyk K , Cutter R , McCormac J , Chote P , Levan A J , Marsh T , Stanway E , Gompertz B , Wiersema K , Chrimes A , Obradovic A , Mullaney J , Daw E , Littlefair S , Maund J , Makrygianni L , Burhanudin U , Starling R L C , Eyles-Ferris R A J , Tooke S , Duffy C , Aukkaravittayapun S , Sawangwit U , Awiphan S , Mkrtichian D , Irawati P , Mattila S , Heikkilä T , Breton R , Kennedy M , Mata Sánchez D , Rol E 
Published: October 2020

ABSTRACT
The amount of observational data produced by time-domain astronomy is exponentially increasing. Human inspection alone is not an effective way to identify genuine transients from the data. An automatic real-bogus classifier is needed and machine learning techniques are commonly used to achieve this goal. Building a training set with a sufficiently large number of verified transients is challenging, due to the requirement of human verification. We present an approach for creating a training set by using all detections in the science images to be the sample of real detections and all detections in the difference images, which are generated by the process of difference imaging to detect transients, to be the samples of bogus detections. This strategy effectively minimizes the labour involved in the data labelling for supervised machine learning methods. We demonstrate the utility of the training set by using it to train several classifiers utilizing as the feature representation the normalized pixel values in 21 × 21 pixel stamps centred at the detection position, observed with the Gravitational-wave Optical Transient Observer (GOTO) prototype. The real-bogus classifier trained with this strategy can provide up to $95{{\ \rm per\ cent}}$ prediction accuracy on the real detections at a false alarm rate of $1{{\ \rm per\ cent}}$.
The origin of (47171) Lempo-like Kuiper belt triple systems during binary–binary interactions
Authors: Brunini Adrián , López María Cristina 
Published: October 2020

ABSTRACT
The trans-Neptunian triple Lempo–Paha–Hiisi is composed of a tight inner binary with components of similar size and an outer companion about half their size orbiting 10 times further away. Large trans-Neptunian objects like Pluto also have multiple small moons, but Lempo’s structure is unique in the Solar system, and the place and timing of its origin is still a subject of debate. We propose a new formation mechanism able to form a large number of systems like Lempo–Paha–Hiisi, which involves binary–binary close encounters in the primordial planetesimal disc at 30–40 au. Some of these systems were then implanted in different populations of the trans-Neptunian region during Neptune’s outward migration. Our results strongly support that the 4:7 resonant multiple object Manwë–Thorondor was once a triple system similar to Lempo–Paha–Hiisi, but the orbit of the inner binary evolved by tides, becoming a contact binary. As with Lempo–Paha–Hiisi, it should have originated in the planetesimal disc below 30–40 au. Triple systems like Lempo–Paha–Hiisi or Manwë–Thorondor could not have formed in situ and the existence of this kind of system is not expected in the cold classical Kuiper belt.
Multiharmonic Hamiltonian models with applications to first-order resonances
Authors: Lei Hanlun , Li Jian 
Published: October 2020

ABSTRACT
In this work, two multiharmonic Hamiltonian models for mean motion resonances are formulated and their applications to first-order resonances are discussed. For the kp:k resonance, the usual critical argument φ = kλ − kpλp + (kp − k)ϖ is taken as the resonant angle in the first model, while the second model is characterized by a new critical argument σ = φ/kp. Based on canonical transformations, the resonant Hamiltonians associated with these two models are formulated. It is found that the second Hamiltonian model holds two advantages in comparison with the first model: (i) providing a direct correspondence between phase portraits and Poincaré sections, and (ii) presenting new phase-space structures where the zero-eccentricity point is a visible saddle point. Then, the second Hamiltonian model is applied to the first-order inner and outer resonances, including the 2:1, 3:2, 4:3, 2:3, and 3:4 resonances. The phase-space structures of these first-order resonances are discussed in detail and then the libration centres and associated resonant widths are identified analytically. Simulation results show that there are pericentric and apocentric libration zones where the libration centres diverge away from the nominal resonance location as the eccentricity approaches zero and, in particular, the resonance separatrices do not vanish at arbitrary eccentricities for both the inner and outer (first-order) resonances.
Density weighted angular redshift fluctuations: a new cosmological observable
Authors: Hernández–Monteagudo Carlos , Chaves-Montero Jonás , Angulo Raúl E 
Published: October 2020

ABSTRACT
We propose the use of angular fluctuations in the galaxy redshift field as a new way to extract cosmological information in the Universe. This new probe $\delta z (\hat{\mathbf {n}})$ consists of the statistics of sky maps built by projecting redshifts under a Gaussian window of width σz centred upon a redshift zobs, and weighted by the galaxy density field. We compute the angular power spectrum of the $\delta z (\hat{\mathbf {n}})$ field in both numerical simulations and in linear perturbation theory. From these, we find that the $\delta z (\hat{\mathbf {n}})$ field (i) is sensitive to the underlying density and peculiar velocity fields; (ii) is highly correlated, at the $\gtrsim 60\, {{\ \rm per\ cent}}$ level, to the line-of-sight projected peculiar velocity field; (iii) for narrow windows (σz &lt; 0.03), it is almost completely uncorrelated to the projected galaxy angular density field under the same redshift window; and (iv) it is largely unaffected by multiplicative and additive systematic errors on the observed number of galaxies that are redshift-independent over ∼σz. We conclude that $\delta z (\hat{\mathbf {n}})$ is a simple and robust tomographic measure of the cosmic density and velocity fields, complementary to angular clustering, that will contribute to more complete exploitations of current and upcoming galaxy redshift surveys.
FlyRNAi.org—the database of the Drosophila RNAi screening center and transgenic RNAi project: 2021 update
Authors: Hu Yanhui , Comjean Aram , Rodiger Jonathan , Liu Yifang , Gao Yue , Chung Verena , Zirin Jonathan , Perrimon Norbert , Mohr Stephanie E 
Published: October 2020

AbstractThe FlyRNAi database at the Drosophila RNAi Screening Center and Transgenic RNAi Project (DRSC/TRiP) provides a suite of online resources that facilitate functional genomics studies with a special emphasis on Drosophila melanogaster. Currently, the database provides: gene-centric resources that facilitate ortholog mapping and mining of information about orthologs in common genetic model species; reagent-centric resources that help researchers identify RNAi and CRISPR sgRNA reagents or designs; and data-centric resources that facilitate visualization and mining of transcriptomics data, protein modification data, protein interactions, and more. Here, we discuss updated and new features that help biological and biomedical researchers efficiently identify, visualize, analyze, and integrate information and data for Drosophila and other species. Together, these resources facilitate multiple steps in functional genomics workflows, from building gene and reagent lists to management, analysis, and integration of data.
HeRA: an atlas of enhancer RNAs across human tissues
Authors: Zhang Zhao , Hong Wei , Ruan Hang , Jing Ying , Li Shengli , Liu Yaoming , Wang Jun , Li Wenbo , Diao Lixia , Han Leng 
Published: October 2020

Abstract
Enhancer RNA (eRNA) is a type of long non-coding RNA transcribed from DNA enhancer regions. Despite critical roles of eRNA in gene regulation, the expression landscape of eRNAs in normal human tissue remains unexplored. Using numerous samples from the Genotype-Tissue Expression project, we characterized 45 411 detectable eRNAs and identified tens of thousands of associations between eRNAs and traits, including gender, race, and age. We constructed a co-expression network to identify millions of putative eRNA regulators and target genes across different tissues. We further constructed a user-friendly data portal, Human enhancer RNA Atlas (HeRA, https://hanlab.uth.edu/HeRA/). In HeRA, users can search, browse, and download the eRNA expression profile, trait-related eRNAs, and eRNA co-expression network by searching the eRNA ID, gene symbol, and genomic region in one or multiple tissues. HeRA is the first data portal to characterize eRNAs from 9577 samples across 54 human tissues and facilitates functional and mechanistic investigations of eRNAs.