bluuebunny/crossref_metadata_2025_split huggingface dataset:
Performance evaluation of transcriptomics data normalization for survival risk prediction
Authors: Ni Ai , Qin Li-Xuan 
Published: June 2021

Abstract
One pivotal feature of transcriptomics data is the unwanted variations caused by disparate experimental handling, known as handling effects. Various data normalization methods were developed to alleviate the adverse impact of handling effects in the setting of differential expression analysis. However, little research has been done to evaluate their performance in the setting of survival outcome prediction, an important analysis goal for transcriptomics data in biomedical research. Leveraging a unique pair of datasets for the same set of tumor samples—one with handling effects and the other without, we developed a benchmarking tool for conducting such an evaluation in microRNA microarrays. We applied this tool to evaluate the performance of three popular normalization methods—quantile normalization, median normalization and variance stabilizing normalization—in survival prediction using various approaches for model building and designs for sample assignment. We showed that handling effects can have a strong impact on survival prediction and that quantile normalization, a most popular method in current practice, tends to underperform median normalization and variance stabilizing normalization. We demonstrated with a small example the reason for quantile normalization’s poor performance in this setting. Our finding highlights the importance of putting normalization evaluation in the context of the downstream analysis setting and the potential of improving the development of survival predictors by applying median normalization. We make available our benchmarking tool for performing such evaluation on additional normalization methods in connection with prediction modeling approaches.
Importance of Telomere Shortening in the Pathogenesis of Ulcerative Colitis: A New Treatment From the Aspect of Telomeres in Intestinal Epithelial Cells
Authors: Watanabe Sho , Hibiya Shuji , Katsukura Nobuhiro , Kitagawa Sayuki , Sato Ayako , Okamoto Ryuichi , Watanabe Mamoru , Tsuchiya Kiichiro 
Published: June 2021

Abstract

Background and Aims
Ulcerative colitis [UC] is a chronic inflammatory disease of the colon with frequent relapses. Telomere shortening in intestinal epithelial cells has been reported in severe or longstanding cases. However, its influence on UC pathogenesis remains unelucidated. To this end, we evaluated telomere shortening using a long-term organoid inflammation model that we had originally established.

Methods
A UC model using human colon organoids was established to assess telomere changes chronologically. MST-312 was used for the telomerase inhibition assay. The potential of telomerase activators as a novel UC treatment was evaluated with an in vitro model, including microarray analysis, and histological changes were assessed using xenotransplantation into mouse colonic mucosa.

Results
Our UC model reproduced telomere shortening in vitro, which was induced by the continuous suppression of telomerase activity via P53. MST-312-based analysis revealed that telomere shortening was involved in the pathogenesis of UC. Madecassoside [MD] improved the telomere length of the UC model and UC patient-derived organoids, which further promoted cell proliferation in vitro and improved the graft take-rate of xenotransplantation. Moreover, histological analysis revealed that MD induced normal crypt structure with abundant goblet cells.

Conclusions
This study is the first to reveal the mechanism and importance of telomere shortening in the pathogenesis of UC. MD could be a novel candidate for UC treatment beyond endoscopic mucosal healing.
Long-term prognostic value of right ventricular dysfunction on cardiovascular magnetic resonance imaging in anthracycline-treated cancer survivors
Authors: Chhikara Sanya , Hooks Matthew , Athwal Pal Satyajit Singh , Hughes Andrew , Ismail Mohamed F , Joppa Stephanie , Velangi Pratik S , Nijjar Prabhjot S , Blaes Anne H , Shenoy Chetan 
Published: June 2021

Abstract

Aims
We aimed to determine the prevalence of right ventricular (RV) systolic dysfunction on cardiovascular magnetic resonance imaging (CMR) and its impact on long-term adverse outcomes in a large cohort of cancer survivors treated with anthracycline-based chemotherapy.

Methods and results
Consecutive cancer survivors treated with anthracyclines who underwent clinical CMR for suspected anthracycline-related cardiomyopathy were studied. The primary endpoint was a composite of all-cause death or major adverse cardiac events (MACE): heart failure hospitalization, heart transplantation, ventricular assist device implantation, resuscitated cardiac arrest, or life-threatening ventricular arrhythmia. The secondary endpoints were all-cause death, and cardiac death or MACE. Among 249 survivors who underwent CMR at a median of 2.9 years after cancer treatment, RV systolic dysfunction was present in 54 (21.7%). Of these, 50 (92.6%) had an abnormal left ventricular ejection fraction (LVEF). At a median follow-up time after the CMR of 2.7 years, 105 survivors experienced the primary endpoint. On Kaplan–Meier analyses, the cumulative incidence of the primary endpoint was significantly higher in survivors with abnormal RVEF compared with those with normal RVEF (P = 0.002). However, on Cox multivariable analyses, RVEF was not associated with the primary endpoint (HR 1.04 per 5% decrease; 95% CI 0.93–1.17; P = 0.46) after adjustment for non-imaging variables and LVEF. RVEF was also not associated with the secondary endpoints.

Conclusion
Among anthracycline-treated cancer survivors undergoing CMR for suspected cardiotoxicity, RV systolic dysfunction was present in one in five cases, accompanied by LV systolic dysfunction in nearly all cases, and was not independently associated with long-term outcomes.
Reliability and Minimal Detectable Change Values for Performance-Based Measures of Physical Functioning in the Canadian Longitudinal Study on Aging
Authors: Beauchamp Marla K , Hao Qiukui , Kuspinar Ayse , D’Amore Cassandra , Scime Giulia , Ma Jinhui , Mayhew Alexandra , Bassim Carol , Wolfson Christina , Kirkland Susan , Griffith Lauren , Raina Parminder 
Published: June 2021

Abstract

Background
The aim of this study was to determine the relative and absolute reliabilities of 5 key performance-based measures of physical function in the Canadian Longitudinal Study on Aging (CLSA).

Methods
An age-stratified subsample of 147 participants from the CLSA who were undergoing their 3-year data collection visit participated in 2 repeat visits (within 1 week). Participants underwent tests of grip strength, 4-m gait speed, Timed Up and Go (TUG), chair rise, and single-leg stance (left, right, mean, maximum). Intraclass correlation coefficients (ICCs), standard error of measurement, and minimal detectable change (MDC) values were calculated.

Results
The relative reliability for grip strength was excellent (ICC = 0.95); the TUG and single-leg stance tests had good reliability (ICC = 0.80 or 0.78–0.82, respectively); gait speed and the chair-rise test had moderate reliability (ICC = 0.64 for both) for participants overall. For participants between 50 and 64 years, TUG and gait speed had poor reliabilities (ICC = 0.38 or 0.33, respectively). For participants aged 75 years and older, the single-leg stance had poor reliability (ICC = 0.30–0.39). The MDC90 was about 6 kg for grip strength, 2.3 seconds for TUG, 0.2 m/second for gait speed, 5.2 seconds for chair rise, and ranged from 22.8 to 26.2 seconds for the single-leg stance.

Conclusions
Among community-dwelling Canadians older than 50 years, the reliabilities of the CLSA measures were moderate to excellent. The TUG and gait speed in the youngest age group, and the single-leg stance in the oldest age group, showed poor reliability. MDC values can be used to interpret changes over time.
The revised direct stiffness matrix method for seismogram synthesis due to dislocations: from crustal to geotechnical scale
Authors: Ba Zhenning , Sang Qiaozhi , Wu Mengtao , Liang Jianwen 
Published: June 2021

SUMMARYThe seismograms for the multiscale crustal model due to dislocations are synthesized by a revised direct stiffness matrix method. By extracting the exponential growth terms related to wavenumber and layer thickness, the fast and accurate wavefield modelling can be achieved for the multiscale system with superficial fine layers (the layer thickness and velocity vary from metre level in the near-surface to kilometre level in deep crustal zones). This method allows relatively high-frequency cases of engineering interest (about 10 Hz) to be tackled without extra computations, linking the geophysics to the geotechnical earthquake engineering. The simulations considering superficial fine layers (5–50  m) show that the horizontal peak ground velocities can be amplified twice with superficial velocity decreasing from 0.4 to 0.15 km s–1. A case study using a realistic fine model in Tokyo metropolis elucidates that the displacements are localized within the epicentre distance about 5 km, predicting the displacement responses by factors up to 6.7, 1.1 and 6.7 for radial, tangential and vertical directions in comparison to the simplified model without superficial fine structures.
Glycowork: A Python package for glycan data science and machine learning
Authors: Thomès Luc , Burkholz Rebekka , Bojar Daniel 
Published: June 2021

Abstract
While glycans are crucial for biological processes, existing analysis modalities make it difficult for researchers with limited computational background to include these diverse carbohydrates into workflows. Here, we present glycowork, an open-source Python package designed for glycan-related data science and machine learning by end users. Glycowork includes functions to, for instance, automatically annotate glycan motifs and analyze their distributions via heatmaps and statistical enrichment. We also provide visualization methods, routines to interact with stored databases, trained machine learning models and learned glycan representations. We envision that glycowork can extract further insights from glycan datasets and demonstrate this with workflows that analyze glycan motifs in various biological contexts. Glycowork can be freely accessed at https://github.com/BojarLab/glycowork/.
Validation of the Clear Safety Listeria Method for Detection of Listeria Species in Hot Dogs and on Environmental Surface Matrixes: AOAC Performance Tested MethodSM 091901
Authors: Pollard Stephanie , Singh Atul K , Lin Andrew , Maloney James , Campos Anay , Khaksar Ramin , Bastin Benjamin , Thompson Wesley , Benzinger M Joseph , Agin James 
Published: June 2021

Abstract

Background
The Clear Safety Listeria method utilizes polymerase chain reaction (PCR) amplification and targeted next-generation sequencing technology to detect Listeria species (L. monocytogenes, L. innocua, L. ivanovii, L. marthii, L. grayi, L. welshimeri, and L. seeligeri) in hot dogs and on selected environmental surfaces.

Objective
The aim was to validate the candidate method according to current AOAC guidelines.

Method
The candidate method was compared to the reference method for hot dogs and the environmental surfaces. The method was also evaluated for inclusivity and exclusivity using 50 inclusivity strains and 30 exclusivity strains for each reported target. Product consistency and stability was tested and robustness was evaluated with changes in enrichment temperature, volume of sample treatment, and aliquot volume for PCR.

Results
The candidate method demonstrated no statistically significant differences using the probability of detection model between candidate and reference methods or between presumptive and confirmed results for all environmental surfaces and hot dogs. Additionally, the candidate method detected all inclusivity organisms and excluded all exclusivity organisms for each reported target. Product lots were shown to be consistent and data supported the kit’s shelf life. Finally, the robustness study demonstrated no statistical differences when the volume of sample or the aliquot volume for PCR was altered. Increasing the incubation temperature to 37 ± 1 °C resulted in greater recovery of L. monocytogenes as compared to 35 ± 1 °C and 30 ± 1 °C.

Conclusions
The Clear Safety Listeria method is statistically equivalent to the reference methods for the detection of L. monocytogenes and Listeria spp. in hot dogs and on selected environmental surfaces.

Highlights
The Clear Safety Listeria method is an automated, highthroughput NGS-based method capable of detecting Listeria species in the hot dog and environmental samples within 28h.
Cosmology with the Roman Space Telescope – multiprobe strategies
Authors: Eifler Tim , Miyatake Hironao , Krause Elisabeth , Heinrich Chen , Miranda Vivian , Hirata Christopher , Xu Jiachuan , Hemmati Shoubaneh , Simet Melanie , Capak Peter , Choi Ami , Doré Olivier , Doux Cyrille , Fang Xiao , Hounsell Rebekah , Huff Eric , Huang Hung-Jin , Jarvis Mike , Kruk Jeffrey , Masters Dan , Rozo Eduardo , Scolnic Dan , Spergel David N , Troxel Michael , von der Linden Anja , Wang Yun , Weinberg David H , Wenzl Lukas , Wu Hao-Yi 
Published: June 2021

ABSTRACT
We simulate the scientific performance of the Nancy Grace Roman Space Telescope High Latitude Survey (HLS) on dark energy and modified gravity. The 1.6-yr HLS Reference survey is currently envisioned to image 2000 deg2 in multiple bands to a depth of ∼26.5 in Y, J, H and to cover the same area with slit-less spectroscopy beyond z = 3. The combination of deep, multiband photometry and deep spectroscopy will allow scientists to measure the growth and geometry of the Universe through a variety of cosmological probes (e.g. weak lensing, galaxy clusters, galaxy clustering, BAO, Type Ia supernova) and, equally, it will allow an exquisite control of observational and astrophysical systematic effects. In this paper, we explore multiprobe strategies that can be implemented, given the telescope’s instrument capabilities. We model cosmological probes individually and jointly and account for correlated systematics and statistical uncertainties due to the higher order moments of the density field. We explore different levels of observational systematics for the HLS survey (photo-z and shear calibration) and ultimately run a joint likelihood analysis in N-dim parameter space. We find that the HLS reference survey alone can achieve a standard dark energy FoM of &gt;300 when including all probes. This assumes no information from external data sets, we assume a flat universe however, and includes realistic assumptions for systematics. Our study of the HLS reference survey should be seen as part of a future community-driven effort to simulate and optimize the science return of the Roman Space Telescope.
Line-depth ratios as indicators of effective temperature and surface gravity
Authors: Matsunaga Noriyuki , Jian Mingjie , Taniguchi Daisuke , Elgueta Scarlet S 
Published: June 2021

ABSTRACTThe analysis of stellar spectra depends on the effective temperature (Teff) and the surface gravity (log g). However, the estimation of log g with high accuracy is challenging. A classical approach is to search for log g that satisfies the ionization balance, i.e. the abundances from neutral and ionized metallic lines being in agreement. We propose a method of using empirical relations between Teff, log g, and line-depth ratios, for which we meticulously select pairs of Fe i and Fe ii lines and pairs of Ca i and Ca ii lines. Based on YJ-band (0.97–1.32 $\mu$m) high-resolution spectra of 42 FGK stars (dwarfs to supergiants), we selected 5 Fe i–Fe ii and 4 Ca i–Ca ii line pairs together with 13 Fe i–Fe i pairs (for estimating Teff), and derived the empirical relations. Using such relations does not require complex numerical models and tools for estimating chemical abundances. The relations we present allow one to derive Teff and log g with a precision of around 50 K and 0.2 dex, respectively, but the achievable accuracy depends on the accuracy of the calibrators’ stellar parameters. It is essential to revise the calibration by observing stars with accurate stellar parameters available, e.g. stars with asteroseismic log g and stars analysed with complete stellar models taking into account the effects of non-local thermodynamic equilibrium and convection. In addition, the calibrators we used have a limited metallicity range, −0.2 &lt; [Fe/H] &lt; +0.2 dex, and our relations need to be tested and re-calibrated based on a calibrating data set for a wider range of metallicities.
The galaxy H i–(sub)halo connection and the H i spatial clustering of local galaxies
Authors: Calette A R , Rodríguez-Puebla Aldo , Avila-Reese Vladimir , Lagos Claudia del P 
Published: June 2021

ABSTRACT
We extend the local stellar galaxy–(sub)halo connection to the atomic hydrogen (H i) component by seeding semi-empirically galaxies into a large N-body dark matter (DM) simulation. The main input to construct the mock galaxy catalogue are: our constrained stellar mass-to-(sub)halo circular velocity (M*–VDM) relation, assuming a scatter independent of any galaxy property, and the empirical $M_{\rm H\, \small {I}}$ conditional probability distributions given M* for central and satellite galaxies. We find that the $\langle \log \mbox{$M_{\rm H\, \small {I}}$}\rangle -\log \mbox{$M_{\rm DM}$}$ relation is not a monotonic increasing function. It increases with mass up to $\mbox{$M_{\rm DM}$}\sim 10^{12}$ M⊙, attaining a maximum of $\langle \log (\mbox{$M_{\rm H\, \small {I}}$}/\mbox{M$_{\odot }$})\rangle \sim 9.2$, and at higher (sub)halo masses, $\langle \log (\mbox{$M_{\rm H\, \small {I}}$})\rangle$ decreases slightly with MDM. The scatter around it is also large and mass dependent. The bivariate $M_{\rm H\, \small {I}}$ and MDM distribution is broad and bimodal, specially at $\mbox{$M_{\rm DM}$}\gtrsim 10^{12}$ M⊙, which is inherited from the input $M_{\rm H\, \small {I}}$ conditional distributions. We also report the total (central+satellites) H i gas mass within haloes, $M^{\rm tot}_{\rm H\, \small {I}}$, as a function of MDM. The mean $\mbox{$M^{\rm tot}_{\rm H\, \small {I}}$}$–$\mbox{$M_{\rm DM}$}$ relation is an increasing monotonic function. The galaxy spatial clustering increases weakly as the $M_{\rm H\, \small {I}}$ threshold increases. Our H i mock galaxies cluster more in comparison to the blind H i ALFALFA (Arecibo Fast Legacy ALFA) survey but we show that it is mainly due to the selection effects. We discuss the implications of our results in the light of predictions from semi-analytical models and hydrodynamics simulations of galaxy evolution.
Structure of the bacteriophage PhiKZ non-virion RNA polymerase
Authors: de Martín Garrido Natàlia , Orekhova Mariia , Lai Wan Loong Yuen Ting Emilie , Litvinova Anna , Ramlaul Kailash , Artamonova Tatyana , Melnikov Alexei S , Serdobintsev Pavel , Aylett Christopher H S , Yakunina Maria 
Published: June 2021

Abstract
Bacteriophage ΦKZ (PhiKZ) is the archetype of a family of massive bacterial viruses. It is considered to have therapeutic potential as its host, Pseudomonas aeruginosa, is an opportunistic, intrinsically antibiotic resistant, pathogen that kills tens of thousands worldwide each year. ΦKZ is an incredibly interesting virus, expressing many systems that the host already possesses. On infection, it forms a ‘nucleus’, erecting a barrier around its genome to exclude host endonucleases and CRISPR-Cas systems. ΦKZ infection is independent of the host transcriptional apparatus. It expresses two different multi-subunit RNA polymerases (RNAPs): the virion RNAP (vRNAP) is injected with the viral DNA during infection to transcribe early genes, including those encoding the non-virion RNAP (nvRNAP), which transcribes all further genes. ΦKZ nvRNAP is formed by four polypeptides thought to represent homologues of the eubacterial β/β′ subunits, and a fifth with unclear homology, but essential for transcription. We have resolved the structure of ΦKZ nvRNAP to better than 3.0 Å, shedding light on its assembly, homology, and the biological role of the fifth subunit: it is an embedded, integral member of the complex, the position, structural homology and biochemical role of which imply that it has evolved from an ancestral homologue to σ-factor.
Heterogeneous gains from countercyclical fiscal policy: new evidence from international industry-level data
Authors: Choi Sangyup , Furceri Davide , Jalles João Tovar 
Published: June 2021

AbstractEmpirical evidence to date suggests a positive relationship between fiscal policy countercyclicality and growth. But do all industries gain equally from countercyclical fiscal policy? What are the channels through which countercyclical fiscal policy affects industry-level growth? We answer these questions by applying a difference-in-difference approach to an unbalanced panel of 22 manufacturing industries for 55 countries—including both advanced and developing economies—during the period 1970–2014. Among the various industry characteristics guided by different theoretical channels, we find that the credit constraints channel identifies the best transmission mechanism through which countercyclical fiscal policy enhances growth. This channel becomes stronger during periods of weak economic activity when credit constraints are more likely to bind and periods of effective lower bound on the monetary policy rate.
Tourism, shamanism and the pandemic
Authors: Rivas Virgilio A 
Published: June 2021

Abstract
There can be no doubt that tourism has contributed to the popular understanding of folk Christianity, including shamanistic practices that, since colonial times, have formed part of the dominant Filipino faith. However, faced with the pandemic, the island’s co-existence with tourism risks losing vital economic lifeblood through commerce-driven spaces for cultural exchange and the psycho-noetic conditions that sustain the spiritual structure of folkloric practices threatened by the existential risks of Covid-19.
Transformative outcomes: assessing and reorienting experimentation with transformative innovation policy
Authors: Ghosh Bipashyee , Kivimaa Paula , Ramirez Matias , Schot Johan , Torrens Jonas 
Published: June 2021

AbstractThe impending climate emergency, the Paris agreement and Sustainable Development Goals demand significant transformations in economies and societies. Science funders, innovation agencies, and scholars have explored new rationales and processes for policymaking, such as transformative innovation policy (TIP). Here, we address the question of how to orient the efforts of science, technology, and innovation policy actors to enable transformations. We build on sustainability transitions research and a 4-year co-creation journey of the TIP Consortium to present twelve transformative outcomes that can guide public policy agencies in evaluating and reformulating their projects, programmes, and policies. We illustrate the transformative outcomes in two empirical cases: transitions towards mobility-as-a-service in the Finnish transport system and the emergence of speciality coffee in Colombia. We argue that the twelve transformative outcomes can guide public policy agents to fundamentally transform their ways of thinking and operation in advancing transformative change.