bluuebunny/crossref_metadata_2025_split huggingface dataset:
Long-term outcomes in extensive disease small cell lung cancer patients treated without immune checkpoint inhibitors
Authors: Wakuda Kazushige , Yabe Michitoshi , Kodama Hiroaki , Nishioka Naoya , Miyawaki Taichi , Miyawaki Eriko , Mamesaya Nobuaki , Kobayashi Haruki , Omori Shota , Ono Akira , Kenmotsu Hirotsugu , Naito Tateaki , Murakami Haruyasu , Shimizu Tetsuo , Gon Yasuhiro , Takahashi Toshiaki 
Published: October 2021

Abstract

Objective
Immune checkpoint inhibitors (ICIs) combined with chemotherapy have been approved as first-line treatment for patients with untreated extensive disease-small cell lung cancer (ED-SCLC). However, there are few reports about the long-term outcomes in patients with ED-SCLC treated without ICIs. Thus, we analyzed the long-term outcomes in patients with ED-SCLC.

Methods
We retrospectively examined the medical records of patients with SCLC who were treated at our hospital between September 2002 and September 2019. The main inclusion criteria were as follows: (i) histological or cytological confirmation of SCLC, (ii) diagnosed with ED-SCLC and (iii) received chemotherapy, not including ICIs, as the first-line treatment. To assess the trends of treatment outcomes, we compared the survival outcomes between 2002–2010 (early) and 2011–2019 (late) groups.

Results
A total of 314 patients were included in this study. Patient characteristics at the time of first-line treatment were as follows: median age was 69 years; 82% of the patients were male and 70% had a performance status of 0 or 1. The median follow-up time of overall survival (OS) was 7.4 years, and 89% of the patients died. The median progression-free survival and survival time were 4.9 and 12.1 months, respectively. Five-year survival rate was 2%. There was no significant difference in survival between the early and late groups.

Conclusions
We found that the long-term outcomes in ED-SCLC patients treated without ICIs were poor. Prior to the approval of ICI treatment for ED-SCLC, there was no improvement in the OS for ~20 years.
Withdrawn as duplicate: Social Ties and the Influence of Public Policies on Individual Opinions: The Case of Same-Sex Marriage Laws
Authors: Blasco Sylvie , Moreno Galbis Eva , Tanguy Jeremy 
Published: October 2021

Abstract
This article has been withdrawn due to a publisher error that caused the article to be duplicated. The definitive version of this article is published under DOI https://doi.org/10.1093/jleo/ewab001.
Satisfaction among patients and caregivers receiving value-added services during the COVID-19 pandemic outbreak in a tertiary hospital in the Perak state of Malaysia
Authors: Chew Lan-Sim , Yeo Yee-Ling , Chang Chee-Tao , Chew Chii-Chii , George Doris , Rajan Philip 
Published: October 2021

Abstract

Objectives
Patient satisfaction was used as an indicator of service quality in the public hospitals. The pharmacy value-added services (VAS) were intensified after the COVID-19 outbreak, and evaluation of user’s satisfaction was important for service improvement.

Methods
This was a single-centre, cross-sectional, web-based study in the outpatient pharmacy in a tertiary hospital in the Perak state of Malaysia. Patients and caregivers aged 18 years and above, received at least one prescription refill using the pharmacy VAS from April to September 2020, were included. The questionnaire was adapted from a validated tool, underwent face and content validation before dissemination. The link was disseminated to the targeted population through short messages service (SMS).

Key findings
Out of 1200 invited people, 303 agreed to participate. Majority of the respondents were male (160, 52.8%), Chinese (156, 51.5%), with tertiary education (201, 66.3%) and retiree (112, 37.0%). Out of a maximum score of 5, the overall mean satisfaction score was 4.42 (SD: 0.55). The respondents were most agreeable to time-saving benefits of the pharmacy VAS (4.56 ± 0.63). Majority of the respondents felt that pharmacy VAS had made their life easier (290, 95.7%) and planned to recommend the pharmacy VAS to others (292, 96.4%) Respondents aged more than 60 (versus age 18–35, β = 2.375, P &lt; 0.001) and those who used drive-through service (versus SPUB, β = 2.272, P = 0.001) reported higher satisfaction scores. Several suggestions were made for service improvement, including longer operating hours (18, 6.0%), upgraded communication system (9, 3.0%), smoother registration process (9, 3.0%), more polite staff (9, 3.0%), selection of preferred postage delivery time (6, 2.0%) and promotion of VAS (4, 1.3%)

Conclusions
Majority of the respondents were highly satisfied towards the pharmacy VAS. Future studies should compare the satisfaction of VAS with traditional counter service to compare the level and factors that contributed to the users’ satisfaction.
Anticancer agent α-sulfoquinovosyl-acylpropanediol enhances the radiosensitivity of human malignant mesothelioma in nude mouse models
Authors: Inamasu Eiko , Tsuchiya Tomoshi , Yamauchi Motohiro , Nishi Kodai , Matsuda Katsuya , Sugawara Fumio , Sakaguchi Kengo , Mori Ryoichi , Matsumoto Keitaro , Miyazaki Takuro , Hatachi Go , Doi Ryoichiro , Watanabe Hironosuke , Tomoshige Koichi , Matsuda Naoki , Higami Yoshikazu , Shimokawa Isao , Nakashima Masahiro , Nagayasu Takeshi 
Published: October 2021

Abstract
Malignant pleural mesothelioma (MPM) is a highly malignant disease that develops after asbestos exposure. Although the number of MPM cases is predicted to increase, no effective standard therapies have been established. The novel radiosensitizer α-sulfoquinovosyl-acylpropanediol (SQAP) enhances the effects of γ-radiation in human lung and prostate cancer cell lines and in animal models. In this study, we explored the radiosensitizing effect of SQAP and its mechanisms in MPM. The human MPM cell lines MSTO-211H and MESO-4 were implanted subcutaneously into the backs and thoracic cavities of immunodeficient KSN/Slc mice, then 2 mg/kg SQAP was intravenously administered with or without irradiation with a total body dose of 8 Gy. In both the orthotopic and ectopic xenograft murine models, the combination of irradiation plus SQAP delayed the implanted human MSTO-211H tumor growth. The analysis of the changes in the relative tumor volume of the MSTO-211H indicated a statistically significant difference after 8 Gy total body combined with 2 mg/kg SQAP, compared to both the untreated control (P = 0.0127) and the radiation treatment alone (P = 0.0171). After the treatment in each case, immunostaining of the harvested tumors revealed decreased cell proliferation, increased apoptosis and normalization of tumor blood vessels in the SQAP- and irradiation-treated group. Furthermore, hypoxia-inducible factor (HIF) 1 mRNA and protein expression were decreased, indicating reoxygenation in this group. In conclusion, SQAP improved hypoxic conditions in tumor tissue and may elicit a radiosensitizing effect in malignant mesothelioma models.
Quantitative analysis of the intra-beam respiratory motion with baseline drift for respiratory-gating lung stereotactic body radiation therapy
Authors: Yasue Kenji , Fuse Hiraku , Oyama Satoshi , Hanada Koichi , Shinoda Kazuya , Ikoma Hideaki , Fujisaki Tatsuya , Tamaki Yoshio 
Published: October 2021

Abstract
This study aimed to quantitatively clarify the baseline drift for each respiratory cycle in two respiratory-gating methods using the intra-beam respiratory motion data of lung cancer patients. The residual motion and dose distribution were calculated based on intra-beam respiratory motion data with the baseline drift. To quantify the baseline drift $\Delta$ during irradiation, it was defined as the inclination between the detected expiration point and the expiration point in the next cycle in the anterior–posterior (AP), cranial–caudal (CC) and left–right (LR) directions obtained using an in-house programme. The baseline drift value reached up to 0.74 mm/s in the CC direction as per the respiratory motion data of 10 patients. The homogeneity index (HI) of the phase-gating method tended to increase because the target was irradiated even when the amplitude position of the target differed from period to period. In contrast, the amplitude-gating method enabled irradiation considering the amplitude position of the target because the gating window was set considering the amplitude position of the respiratory motion. The respiratory-gating methods and respiratory phase in respiratory-gating lung stereotactic body radiation therapy (SBRT) must be determined based on the respiratory motion of the patients.
SARS-CoV-2 infection rates in air passengers arriving in Qatar
Authors: Butt Adeel A , Al-Halabi Anas M , Ghazouani Hafedh , Rhouma Mohamed Ben Haj , Ayoub Houssein H , Masoodi Naseer A , Borham Abdelsalam M , Hommos Ahmed A , Bertollini Roberto , Chemaitelly Hiam , Abu Raddad Laith J , Abou-Samra Abdul-Badi 
Published: October 2021

Among 352 174 airline travellers entering Qatar, 8236 (2.34%) tested positive on or within the first 7 days of arrival, with 3789 (1.08%) testing positive at the time of arrival and the remaining 4447 (1.26%) testing negative at arrival but positive 1 week later.
Pit and tracheid anatomy explain hydraulic safety but not hydraulic efficiency of 28 conifer species
Authors: Song Yanjun , Poorter Lourens , Horsting Angelina , Delzon Sylvain , Sterck Frank 
Published: October 2021

AbstractConifers face increased drought mortality risks because of drought-induced embolism in their vascular system. Variation in embolism resistance may result from species differences in pit structure and function, as pits control the air seeding between water-transporting conduits. This study quantifies variation in embolism resistance and hydraulic conductivity for 28 conifer species grown in a 50-year-old common garden experiment and assesses the underlying mechanisms. Conifer species with a small pit aperture, high pit aperture resistance, and large valve effect were more resistant to embolism, as they all may reduce air seeding. Surprisingly, hydraulic conductivity was only negatively correlated with tracheid cell wall thickness. Embolism resistance and its underlying pit traits related to pit size and sealing were more strongly phylogenetically controlled than hydraulic conductivity and anatomical tracheid traits. Conifers differed in hydraulic safety and hydraulic efficiency, but there was no trade-off between safety and efficiency because they are driven by different xylem anatomical traits that are under different phylogenetic control.
Luminosity functions of globular clusters in five nearby spiral galaxies using HST/ACS images
Authors: Lomelí-Núñez Luis , Mayya Y D , Rodríguez-Merino L H , Ovando P A , Rosa-González D 
Published: October 2021

ABSTRACT
We here present the luminosity function (LF) of globular clusters (GCs) in five nearby spiral galaxies using the samples of GC candidates selected in Hubble Space Telescope mosaic images in F435W, F555W, and F814W filters. Our search, which surpasses the fractional area covered by all previous searches in these galaxies, has resulted in the detection of 158 GC candidates in M81, 1123 in M101, 226 in NGC 4258, 293 in M51, and 173 in NGC 628. The LFs constructed from this data set, after correcting for relatively small contamination from reddened young clusters, are lognormal in nature, which was hitherto established only for the Milky Way (MW) and Andromeda among spiral galaxies. The magnitude at the turn-over (TO) corresponds to MV0(TO) = −7.41 ± 0.14 in four of the galaxies with Hubble types Sc or earlier, in excellent agreement with MV(TO) = −7.40 ± 0.10 for the MW. The TO magnitude is equivalent to a mass of ∼3 × 105 M⊙ for an old, metal-poor population. MV0(TO) is fainter by ∼1.16 magnitude for the fifth galaxy, M 101, which is of Hubble type Scd. The TO dependence on Hubble type implies that the GCs in early-type spirals are classical GCs, which have a universal TO, whereas the GC population in late-type galaxies is dominated by old disc clusters, which are in general less massive. The radial density distribution of GCs in our sample galaxies follows the Sérsic function with exponential power-law indices, and effective radii of 4.0–9.5 kpc. GCs in the sample galaxies have a mean specific frequency of 1.10 ± 0.24, after correcting for magnitude and radial incompleteness factors.
Action-based distribution function modelling for constraining the shape of the Galactic dark matter halo
Authors: Hattori Kohei , Valluri Monica , Vasiliev Eugene 
Published: October 2021

ABSTRACT
We estimate the 3D density profile of the Galactic dark matter (DM) halo within r ≲ 30 kpc from the Galactic centre by using the astrometric data for halo RR Lyrae stars from Gaia DR2. We model both the stellar halo distribution function and the Galactic potential, fully taking into account the survey selection function, the observational errors, and the missing line-of-sight velocity data for RR Lyrae stars. With a Bayesian method, we infer the model parameters, including the density flattening of the DM halo q, which is assumed to be constant as a function of radius. We find that 99 per cent of the posterior distribution of q is located at q &gt; 0.963, which strongly disfavours a flattened DM halo. We cannot draw any conclusions as to whether the Galactic DM halo at $r \lesssim 30 \, \mathrm{kpc}$ is prolate, because we restrict ourselves to axisymmetric oblate halo models with q ≤ 1. Our DM density profile might be biased especially in the inner few kpc, due to the uncertainty in the baryonic distribution. Our result is in tension with predictions from cosmological hydrodynamical simulations that advocate more oblate (〈q〉 ∼ 0.8 ± 0.15) DM haloes within ${\sim}15{{\ \rm per\ cent}}$ of the virial radius for Milky-Way-sized galaxies. An alternative possibility, based on our validation tests with a cosmological simulation, is that the true value q of the Galactic halo could be consistent with cosmological simulations but that disequilibrium in the Milky Way potential is inflating our measurement of q by 0.1–0.2. As a by-product, our model constrains the DM density in the Solar neighbourhood to be $\rho _{\mathrm{DM},\odot } = (9.01^{+0.18}_{-0.20})\times 10^{-3}{\,\rm M_\odot} \mathrm{pc}^{-3} = 0.342^{+0.007}_{-0.007}$ GeVcm−3, consistent with other recent measurements.
The impact of void environment on AGN
Authors: Ceccarelli Laura , Duplancic Fernanda , Garcia Lambas Diego 
Published: October 2021

ABSTRACT
We study the population of active galaxies in void environment in the Sloan Digital Sky Survey. We use optical spectroscopic information to analyse characteristics of the emission lines of galaxies, accomplished by WHAN and BPT diagrams. Also, we study Wide-field Infrared Survey Explorer(WISE) mid-IR colours to assess active galactic nucleus (AGN) activity. We investigate these different AGN classification schemes, both optical and mid-IR, and their dependence on the spatial location with respect to the void centres. To this end, we define three regions: void, the spherical region defined by voidcentric distance relative to void radius (distance/rvoid) smaller than 0.8, comprising overdensities lesser than −0.9, an intermediate/transition shell region (namely, void-wall) 0.8 &lt; distance/rvoid &lt; 1.2, and a region sufficiently distant from voids, the field: distance/rvoid &gt; 2. We find statistical evidence for a larger fraction of AGN and star-forming galaxies in the void region, regardless of the classification scheme addressed (either BPT, WHAN, or WISE). Moreover, we obtain a significantly stronger nuclear activity in voids compared to the field. We find an unusually large fraction of the most massive black holes undergoing strong accretion when their host galaxies reside in voids. Our results suggest a strong influence of the void environment on AGN mechanisms associated with galaxy evolution.
Bar-driven leading spiral arms in a counter-rotating dark matter halo
Authors: Lieb Emma , Collier Angela , Madigan Ann-Marie 
Published: October 2021

ABSTRACT
An overwhelming majority of galactic spiral arms trail with respect to the rotation of the galaxy, though a small sample of leading spiral arms has been observed. The formation of these leading spirals is not well understood. Here we show, using collisionless N-body simulations, that a barred disc galaxy in a retrograde dark matter halo can produce long-lived (∼3 Gyr) leading spiral arms. Due to the strong resonant coupling of the disc to the halo, the bar slows rapidly and spiral perturbations are forced ahead of the bar. We predict that such a system, if observed, will also host a dark matter wake oriented perpendicular to the stellar bar. More generally, we propose that any mechanism that rapidly decelerates the stellar bar will allow leading spiral arms to flourish.
Radii of young star clusters in nearby galaxies
Authors: Brown Gillen , Gnedin Oleg Y 
Published: October 2021

ABSTRACT
We measure the projected half-light radii of young star clusters in 31 galaxies from the Legacy Extragalactic UV Survey (LEGUS). We implement a custom pipeline specifically designed to be robust against contamination, which allows us to measure radii for 6097 clusters. This is the largest sample of young star cluster radii currently available. We find that most (but not all) galaxies share a common cluster radius distribution, with the peak at around 3 pc. We find a clear mass–radius relation of the form Reff ∝ M0.24. This relation is present at all cluster ages younger than 1 Gyr, but with a shallower slope for clusters younger than 10 Myr. We present simple toy models to interpret these age trends, finding that high-mass clusters are more likely to be not tidally limited and expand. We also find that most clusters in LEGUS are gravitationally bound, especially at older ages or higher masses. Lastly, we present the cluster density and surface density distributions, finding a large scatter that appears to decrease with cluster age. The youngest clusters have a typical surface density of 100$\, \mathrm{ M}_\odot \, \mathrm{pc}^{-2}$.
Detecting Selection in Multiple Populations by Modeling Ancestral Admixture Components
Authors: Cheng Jade Yu , Stern Aaron J , Racimo Fernando , Nielsen Rasmus 
Published: October 2021

Abstract
One of the most powerful and commonly used approaches for detecting local adaptation in the genome is the identification of extreme allele frequency differences between populations. In this article, we present a new maximum likelihood method for finding regions under positive selection. It is based on a Gaussian approximation to allele frequency changes and it incorporates admixture between populations. The method can analyze multiple populations simultaneously and retains power to detect selection signatures specific to ancestry components that are not representative of any extant populations. Using simulated data, we compare our method to related approaches, and show that it is orders of magnitude faster than the state-of-the-art, while retaining similar or higher power for most simulation scenarios. We also apply it to human genomic data and identify loci with extreme genetic differentiation between major geographic groups. Many of the genes identified are previously known selected loci relating to hair pigmentation and morphology, skin, and eye pigmentation. We also identify new candidate regions, including various selected loci in the Native American component of admixed Mexican-Americans. These involve diverse biological functions, such as immunity, fat distribution, food intake, vision, and hair development.
ViroidDB: a database of viroids and viroid-like circular RNAs
Authors: Lee Benjamin D , Neri Uri , Oh Caleb J , Simmonds Peter , Koonin Eugene V 
Published: October 2021

Abstract
We introduce ViroidDB, a value-added database that attempts to collect all known viroid and viroid-like circular RNA sequences into a single resource. Spanning about 10 000 unique sequences, ViroidDB includes viroids, retroviroid-like elements, small circular satellite RNAs, ribozyviruses, and retrozymes. Each sequence's secondary structure, ribozyme content, and cluster membership are predicted via a custom pipeline optimized for handling circular RNAs. The data can be explored via a purpose-built user interface that features visualizations, multiple sequence alignments, and a portal for downloading bulk data. Users can browse the data by sequence type, taxon, or typo-tolerant search of metadata fields. The database is freely accessible at https://viroids.org.
CompoDynamics: a comprehensive database for characterizing sequence composition dynamics
Authors: Jiang Shuai , Du Qiang , Feng Changrui , Ma Lina , Zhang Zhang 
Published: October 2021

Abstract
Sequence compositions of nucleic acids and proteins have significant impact on gene expression, RNA stability, translation efficiency, RNA/protein structure and molecular function, and are associated with genome evolution and adaptation across all kingdoms of life. Therefore, a devoted resource of sequence compositions and associated features is fundamentally crucial for a wide range of biological research. Here, we present CompoDynamics (https://ngdc.cncb.ac.cn/compodynamics/), a comprehensive database of sequence compositions of coding sequences (CDSs) and genomes for all kinds of species. Taking advantage of the exponential growth of RefSeq data, CompoDynamics presents a wealth of sequence compositions (nucleotide content, codon usage, amino acid usage) and derived features (coding potential, physicochemical property and phase separation) for 118 689 747 high-quality CDSs and 34 562 genomes across 24 995 species. Additionally, interactive analytical tools are provided to enable comparative analyses of sequence compositions and molecular features across different species and gene groups. Collectively, CompoDynamics bears the great potential to better understand the underlying roles of sequence composition dynamics across genes and genomes, providing a fundamental resource in support of a broad spectrum of biological studies.
Association of the chronic kidney disease urinary proteomic predictor CKD273 with clinical risk factors of graft failure in kidney allograft recipients
Authors: Rambabova-Bushljetik Irena , Metzger Jochen , Siwy Justyna , Dohcev Saso , Bushljetikj Oliver , Filipce Venko , Trajceska Lada , Mischak Harald , Spasovski Goce 
Published: October 2021

ABSTRACTBackgroundKidney transplantation is the best treatment option for end-stage kidney disease but is still associated with long-term graft failure. In this study, we evaluated the application of urinary proteomics to identify grafts with high failure risk before initial decline of estimated glomerular filtration rate (eGFR) with irreversible graft changes.MethodsFifty-two living donor kidney transplant recipients (KTR) with 8-year follow-up were enrolled. All patients underwent clinical examination and had a routine laboratory screening at 3, 6, 12, 24, 36, 48 and 96 months post-transplantation, including creatinine, urea, albumin and 24-h proteinuria. Graft function was estimated according to Nankivell. Urine samples at Month 24 were analysed by capillary electrophoresis coupled mass spectrometry followed by classification with the chronic kidney disease classifier CKD273.ResultsCKD273 showed significant correlation with serum creatinine at every time point and moderate inverse correlation for the slope in glomerular filtration rates by Nankivell (r = −0.29, P = 0.05). Receiver operating characteristics analysis for graft loss and death within the next 6 years after proteomic analysis resulted in an area under curve value of 0.89 for CKD273 being superior to 0.67 for Nankivell eGFR. Stratification into CKD273-positive and -negative patient groups revealed a hazard ratio of 16.5 for prevalence of graft loss in case of CKD273 positivity.ConclusionsUsing a representative KTR cohort with 8-year follow-up, we could demonstrate significant value of CKD273 for risk stratification of graft loss. This study provides the conceptual basis for further evaluation of CKD273 as a prognostic tool for long-term graft function risk stratification by large prospective clinical trials.