bluuebunny/crossref_metadata_2025_split huggingface dataset:
Current status and perspectives of immune checkpoint inhibitors for colorectal cancer
Authors: Hirano Hidekazu , Takashima Atsuo , Hamaguchi Tetsuya , Shida Dai , Kanemitsu Yukihide ,   the Colorectal Cancer Study Group (CCSG) of the Japan Clinical Oncology Group (JCOG)
Published: October 2020

AbstractImmunotherapy, especially immune checkpoint inhibitors, has revolutionized the standard-of-care of multiple types of tumors. For colorectal cancer, the clinical development of immune checkpoint inhibitors is mainly separated according to the status of microsatellite instability or mismatch repair in a tumor. High-level microsatellite instability/deficient mismatch repair metastatic colorectal cancer generally has a tumor microenvironment with infiltration of T cells, associated with a favorable response to immune checkpoint inhibitors. Immune checkpoint inhibitors, including pembrolizumab (anti-PD-1 inhibitor) and nivolumab (anti-PD-1 inhibitor) with or without ipilimumab (anti-CTLA-4 inhibitor), have been integrated into the standard-of-care for high-level microsatellite instability/deficient mismatch repair metastatic colorectal cancer. Conversely, limited T-cell infiltration in the tumor microenvironment of microsatellite stable/proficient mismatch repair metastatic colorectal cancer, which constitutes the majority of metastatic colorectal cancer, is assumed to be a major resistant mechanism to immune checkpoint inhibitors. Currently, clinical trials to improve the clinical activity of immune checkpoint inhibitors by immunomodulation are ongoing for metastatic colorectal cancer. Furthermore, immune checkpoint inhibitors are under development in neoadjuvant and/or adjuvant setting. Here, we review the existing clinical data with ongoing trials and discuss the future perspectives with a focus on the immunotherapy of colorectal cancer.
Subcapsular double-J stent following ureteroscopy: unique complication
Authors: Aljuhayman Ahmed , Balaraj Faisal , Ghazwani Yahya , Hamri Saeed Bin 
Published: October 2020

Abstract
Double-J (DJ) ureteral stent is a standard procedure in daily urological practice performed to relive ureteral obstruction or as a part of other endourological procedures. Although it is a common procedure, the widespread use of ureteral stents has corresponded to the increase in possible complication. We report a unique complication for a patient who presented with a renal subcapsular complete misplacement of DJ stent postureteroscopy for a distal ureteric stone. This challenging complication of ureteral stents is rare and organ threatening.
Chromosomal introgressions fromOryza meridionalisinto domesticated riceOryza sativaresult in iron tolerance
Authors: Wairich Andriele , de Oliveira Ben Hur Neves , Wu Lin-Bo , Murugaiyan Varunseelan , Margis-Pinheiro Marcia , Fett Janette Palma , Ricachenevsky Felipe Klein , Frei Michael 
Published: October 2020

AbstractIron (Fe) toxicity is one of the most common mineral disorders affecting rice (Oryza sativa) production in flooded lowland fields. Oryza meridionalis is indigenous to northern Australia and grows in regions with Fe-rich soils, making it a candidate for use in adaptive breeding. With the aim of understanding tolerance mechanisms in rice, we screened a population of interspecific introgression lines from a cross between O. sativa and O. meridionalis for the identification of quantitative trait loci (QTLs) contributing to Fe-toxicity tolerance. Six putative QTLs were identified. A line carrying one introgression from O. meridionalis on chromosome 9 associated with one QTL was highly tolerant despite very high shoot Fe concentrations. Physiological, biochemical, ionomic, and transcriptomic analyses showed that the tolerance of the introgression lines could partly be explained by higher relative Fe retention in the leaf sheath and culm. We constructed the interspecific hybrid genome in silico for transcriptomic analysis and identified differentially regulated introgressed genes from O. meridionalis that could be involved in shoot-based Fe tolerance, such as metallothioneins, glutathione S-transferases, and transporters from the ABC and MFS families. This work demonstrates that introgressions of O. meridionalis into the O. sativa genome can confer increased tolerance to excess Fe.
Analytical model for the local vertical structure of thin accretion discs
Authors: Fukue J 
Published: October 2020

ABSTRACT
We derive several analytical relations and approximate solutions for the local vertical structure of viscous thin accretion discs. Under the alpha prescription, when the viscous heating is proportional to the gas pressure p, we derive the analytical relation between the radiative flux F and the radiation pressure P: (F/F0)2 = [1 − (P/Pc)5/4]/[1 − (P0/Pc)5/4], where the subscript 0 means the value at the surface and the subscript c is the value at the disc centre. Both F and P are approximately integrated to yield the well-known uniform heating model. In this case, furthermore, the height z and density ρ are approximately fitted as a function of the optical depth τ. When the viscous heating is proportional to the radiation pressure P and the disc is almost isothermal, the flux F is proportional to z as F = (3/2)αΩPz, where α and Ω are the alpha parameter and angular speed, respectively. In this case, moreover, the height and density are analytically solved and expressed as $z=(\sqrt{2}c_{\rm T}/\Omega) {\rm erf}^{-1}(1-\tau /\tau _{\rm c})$ and ρ = ρcexp { − [erf−1(1 − τ/τc)]2}, cT being the isothermal sound speed, and erf−1 the inverse of the error function.
Seismic analysis of the double-mode radial pulsator SX Phoenicis
Authors: Daszyńska-Daszkiewicz J , Pamyatnykh A A , Walczak P , Szewczuk W 
Published: October 2020

ABSTRACT
We present the results of complex seismic analysis of the prototype star SX Phoenicis. This analysis consists of a simultaneous fitting of the two radial-mode frequencies, the corresponding values of the bolometric flux amplitude (the parameter f) and of the intrinsic mode amplitude ε. The effects of various parameters as well as the opacity data are examined. With each opacity table it is possible to find seismic models that reproduce the two observed frequencies with masses allowed by evolutionary models appropriate for the observed values of the effective temperature and luminosity. All seismic models are in the post-main sequence phase. The OPAL and OP seismic models are in hydrogen shell-burning phase and the OPLIB seismic model has just finished an overall contraction and starts to burn hydrogen in a shell. The OP and OPLIB models are less likely due to the requirement of high initial hydrogen abundance (X0 = 0.75) and too high metallicity (Z ≈ 0.004) as for a Population II star. The fitting of the parameter f, whose empirical values are derived from multicolour photometric observations, provides constraints on the efficiency of convective transport in the outer layers of the star and on the microturbulent velocity in the atmosphere. Our complex seismic analysis with each opacity data indicates low to moderately efficient convection in the star’s envelope, described by the mixing length parameter of αMLT ∈ (0.0, 0.7), and the microturbulent velocity in the atmosphere of about ξt ∈ (4, 8) km s−1.
G133.50+9.01: a likely cloud–cloud collision complex triggering the formation of filaments, cores, and a stellar cluster
Authors: Issac Namitha , Tej Anandmayee , Liu Tie , Wu Yuefang 
Published: October 2020

ABSTRACT
We present compelling observational evidence of G133.50+9.01 being a bona fide cloud–cloud collision candidate with signatures of induced filament, core, and cluster formation. The CO molecular line observations reveal that the G133.50+9.01 complex is made of two colliding molecular clouds with systemic velocities, $\rm -16.9$ and $\rm -14.1\, km\, s^{-1}$. The intersection of the clouds is characterized by broad bridging features characteristic of collision. The morphology of the shocked layer at the interaction front resembles an arc-like structure with enhanced excitation temperature and H2 column density. A complex network of filaments is detected in the Submillimeter Common-User Bolometer Array 2 850 $\rm \mu m$ image with 14 embedded dense cores, all well correlated spatially with the shocked layer. A stellar cluster revealed through an overdensity of identified Classes I and II young stellar objects is found located along the arc in the intersection region corroborating with a likely collision induced origin.
Clustering of the resonant triads induced by vertical-shear instability in astrophysical discs
Authors: Shtemler Yuri , Mond Michael 
Published: October 2020

ABSTRACT
Clustering of resonant triads that are induced by vertical-shear instability (VSI), driven by the combined effect of the vertical speed shear and small temperature gradients, is studied for vertically isothermal thin unmagnetized Keplerian discs. The authors’ recent study of isolated VSI resonant triads is extended to illustrate their clustering. The coupling conditions for two VSI resonant triads with one common mode are derived and generalized to higher dimension clustering. The clustering of two, three, and four triads connected via one common mode is numerically simulated. The numerical simulations demonstrate the chaotization of non-linear oscillations about the prototypes of the linearly stable modes with a growing cluster’s dimension that is accompanied by a decrease of the characteristic time of chaotization and an increase of the characteristic frequency of perturbations. The chaos associated with the VSI resonant clustering is believed to precede transition to sustainable turbulence in astrophysical discs.
Identification of a new ultraluminous X-ray source in NGC 1316
Authors: Allak S , Akyuz A , Aksaker N , Ozdogan Ela M , Avdan S , Soydugan F 
Published: October 2020

ABSTRACT
In this study, we report identification of a new ultraluminous X-ray source (ULX) named as X-7 in NGC 1316, with an unabsorbed luminosity of 2.1 × 1039 erg s−1 using the two recent Chandra archival observations. The X-7 was detected in the Chandra 2001 observation and was included in the source list of the NGC 1316 as CXOUJ032240.8−371224 with a luminosity of 5.7 × 1038 erg s−1. Present luminosity implies a luminosity increase of a factor of ∼4. The best-fitting spectral model parameters indicate that X-7 has a relatively hot disc and hard spectra. If explained by a disc blackbody model, the mass of compact object is estimated as ∼8 M⊙ which is in the range of a stellar-mass black hole. The X-7 shows a relatively long-term count rate variability while no short-term variability is observed. We also identified a unique optical candidate within 0.22 arcsec error circle at 95 per cent confidence level for X-7 using the archival HST/ACS (Hubble Space Telescope/Advanced Camera for Surveys) and HST/WFC3 (The Wide Field Camera 3) data. Absolute magnitude (MV) of this candidate is −7.8 mag. Its spectral energy distribution is adequately fitted a blackbody model with a temperature of 3100 K indicating an M type supergiant, assuming the donor star dominates the optical emission. In addition, we identified a transient ULX candidate (XT-1) located 6 arcsec away from X-7 has a (high) luminosity of ∼1039 erg s−1 with no visible optical candidate.
Long-Term m5C Methylome Dynamics Parallel Phenotypic Adaptation in the CyanobacteriumTrichodesmium
Authors: Walworth Nathan G , Lee Michael D , Dolzhenko Egor , Fu Fei-Xue , Smith Andrew D , Webb Eric A , Hutchins David A 
Published: October 2020

AbstractA major challenge in modern biology is understanding how the effects of short-term biological responses influence long-term evolutionary adaptation, defined as a genetically determined increase in fitness to novel environments. This is particularly important in globally important microbes experiencing rapid global change, due to their influence on food webs, biogeochemical cycles, and climate. Epigenetic modifications like methylation have been demonstrated to influence short-term plastic responses, which ultimately impact long-term adaptive responses to environmental change. However, there remains a paucity of empirical research examining long-term methylation dynamics during environmental adaptation in nonmodel, ecologically important microbes. Here, we show the first empirical evidence in a marine prokaryote for long-term m5C methylome modifications correlated with phenotypic adaptation to CO2, using a 7-year evolution experiment (1,000+ generations) with the biogeochemically important marine cyanobacterium Trichodesmium. We identify m5C methylated sites that rapidly changed in response to high (750 µatm) CO2 exposure and were maintained for at least 4.5 years of CO2 selection. After 7 years of CO2 selection, however, m5C methylation levels that initially responded to high-CO2 returned to ancestral, ambient CO2 levels. Concurrently, high-CO2 adapted growth and N2 fixation rates remained significantly higher than those of ambient CO2 adapted cell lines irrespective of CO2 concentration, a trend consistent with genetic assimilation theory. These data demonstrate the maintenance of CO2-responsive m5C methylation for 4.5 years alongside phenotypic adaptation before returning to ancestral methylation levels. These observations in a globally distributed marine prokaryote provide critical evolutionary insights into biogeochemically important traits under global change.
Tethering-facilitated DNA ‘opening’ and complementary roles of β-hairpin motifs in the Rad4/XPC DNA damage sensor protein
Authors: Paul Debamita , Mu Hong , Tavakoli Amirrasoul , Dai Qing , Chen Xuejing , Chakraborty Sagnik , He Chuan , Ansari Anjum , Broyde Suse , Min Jung-Hyun 
Published: October 2020

AbstractXPC/Rad4 initiates eukaryotic nucleotide excision repair on structurally diverse helix-destabilizing/distorting DNA lesions by selectively ‘opening’ these sites while rapidly diffusing along undamaged DNA. Previous structural studies showed that Rad4, when tethered to DNA, could also open undamaged DNA, suggesting a ‘kinetic gating’ mechanism whereby lesion discrimination relied on efficient opening versus diffusion. However, solution studies in support of such a mechanism were lacking and how ‘opening’ is brought about remained unclear. Here, we present crystal structures and fluorescence-based conformational analyses on tethered complexes, showing that Rad4 can indeed ‘open’ undamaged DNA in solution and that such ‘opening’ can largely occur without one or the other of the β-hairpin motifs in the BHD2 or BHD3 domains. Notably, the Rad4-bound ‘open’ DNA adopts multiple conformations in solution notwithstanding the DNA’s original structure or the β-hairpins. Molecular dynamics simulations reveal compensatory roles of the β-hairpins, which may render robustness in dealing with and opening diverse lesions. Our study showcases how fluorescence-based studies can be used to obtain information complementary to ensemble structural studies. The tethering-facilitated DNA ‘opening’ of undamaged sites and the dynamic nature of ‘open’ DNA may shed light on how the protein functions within and beyond nucleotide excision repair in cells.
The mouse Gene Expression Database (GXD): 2021 update
Authors: Baldarelli Richard M , Smith Constance M , Finger Jacqueline H , Hayamizu Terry F , McCright Ingeborg J , Xu Jingxia , Shaw David R , Beal Jonathan S , Blodgett Olin , Campbell Jeffrey , Corbani Lori E , Frost Pete J , Giannatto Sharon C , Miers Dave B , Kadin James A , Richardson Joel E , Ringwald Martin 
Published: October 2020

Abstract
The Gene Expression Database (GXD; www.informatics.jax.org/expression.shtml) is an extensive and well-curated community resource of mouse developmental gene expression information. For many years, GXD has collected and integrated data from RNA in situ hybridization, immunohistochemistry, RT-PCR, northern blot, and western blot experiments through curation of the scientific literature and by collaborations with large-scale expression projects. Since our last report in 2019, we have continued to acquire these classical types of expression data; developed a searchable index of RNA-Seq and microarray experiments that allows users to quickly and reliably find specific mouse expression studies in ArrayExpress (https://www.ebi.ac.uk/arrayexpress/) and GEO (https://www.ncbi.nlm.nih.gov/geo/); and expanded GXD to include RNA-Seq data. Uniformly processed RNA-Seq data are imported from the EBI Expression Atlas and then integrated with the other types of expression data in GXD, and with the genetic, functional, phenotypic and disease-related information in Mouse Genome Informatics (MGI). This integration has made the RNA-Seq data accessible via GXD’s enhanced searching and filtering capabilities. Further, we have embedded the Morpheus heat map utility into the GXD user interface to provide additional tools for display and analysis of RNA-Seq data, including heat map visualization, sorting, filtering, hierarchical clustering, nearest neighbors analysis and visual enrichment.
MolluscDB: an integrated functional and evolutionary genomics database for the hyper-diverse animal phylum Mollusca
Authors: Liu Fuyun , Li Yuli , Yu Hongwei , Zhang Lingling , Hu Jingjie , Bao Zhenmin , Wang Shi 
Published: October 2020

AbstractMollusca represents the second largest animal phylum but remains poorly explored from a genomic perspective. While the recent increase in genomic resources holds great promise for a deep understanding of molluscan biology and evolution, access and utilization of these resources still pose a challenge. Here, we present the first comprehensive molluscan genomics database, MolluscDB (http://mgbase.qnlm.ac), which compiles and integrates current molluscan genomic/transcriptomic resources and provides convenient tools for multi-level integrative and comparative genomic analyses. MolluscDB enables a systematic view of genomic information from various aspects, such as genome assembly statistics, genome phylogenies, fossil records, gene information, expression profiles, gene families, transcription factors, transposable elements and mitogenome organization information. Moreover, MolluscDB offers valuable customized datasets or resources, such as gene coexpression networks across various developmental stages and adult tissues/organs, core gene repertoires inferred for major molluscan lineages, and macrosynteny analysis for chromosomal evolution. MolluscDB presents an integrative and comprehensive genomics platform that will allow the molluscan community to cope with ever-growing genomic resources and will expedite new scientific discoveries for understanding molluscan biology and evolution.
Genetic diversity, phylogeography, and evolutionary dynamics of highly pathogenic avian influenza A (H5N6) viruses
Authors: Zhang Jiahao , Chen Yiqun , Shan Nan , Wang Xiaomin , Lin Shuxia , Ma Kaixiong , Li Bo , Li Huanan , Liao Ming , Qi Wenbao 
Published: October 2020

Abstract
From 2013 onwards, the spread of novel H5N6 highly pathogenic avian influenza (HPAI) viruses in China has posed great threats to not only poultry industry but also human health. Since late-2016 in particular, frequent outbreaks of clade 2.3.4.4 H5N6 HPAI viruses among wild birds have promoted viral dissemination in South Korea, Japan, and European countries. In response to those trends, we conducted molecular genetic analysis of global clade 2.3.4.4 H5N6 viruses in order to characterize spatio-temporal patterns of viral diffusion and genetic diversity among wild birds and poultry. The clade 2.3.4.4 H5N6 viruses were classified into three groups (Group B, C, and D). During the cocirculation of Group C/D H5N6 viruses from 2013 to 2017, viral movements occurred between close or adjacent regions of China, Vietnam, South Korea, and Japan. In addition, viral migration rates from Guangdong and Hunan to multiple adjacent provinces seemed to have been highly supported by transmission routes (Bayes factors &gt;100), suggesting that southern China was an epicenter for the spread of H5N6 viruses in poultry during that period. Since the introduction of H5N6 viruses originating in wild birds in late-2016, evolving H5N6 viruses have lost most previous genotypes (e.g. G1, G2, and G1.2), whereas some prevailing genotypes (e.g. G1.1, G1.1.b, and G3) in aquatic birds have been dominated, and in particular, the effective population size of H5N6 originating in wild birds dramatically increased; however, the population size of poultry-origin H5N6 viruses declined during the same period, indicating that wild bird migration might accelerate the genetic diversity of H5N6 viruses. Phylogeographic approaches revealed that two independent paths of H5N6 viruses into South Korea and Japan from 2016 to 2018 and provided evidence of Group B and Group C H5N6 viruses were originated from Europe and China, respectively, as regions located in the East Asia–Australian migration flyway, which accelerated the genetic variability and dissemination. Altogether, our study provides insights to examine time of origin, evolutionary rate, diversification patterns, and phylogeographical approach of global clade 2.3.4.4 H5N6 HPAI viruses for assessing their evolutionary process and dissemination pathways.
“Babywearing” in the NICU
Authors: Williams Lela Rankin , Gebler-Wolfe Molly , Grisham Lisa M. , Bader M. Y. 
Published: October 2020

Background:
The US opioid epidemic has resulted in an increase of infants at risk for developing neonatal abstinence syndrome (NAS). Traditionally, treatment has consisted of pharmacological interventions to reduce symptoms of withdrawal. However, nonpharmacological interventions (eg, skin-to-skin contact, holding) can also be effective in managing the distress associated with NAS.

Purpose:
The purpose of this study was to examine whether infant carrying or “babywearing” (ie, holding an infant on one's body using cloth) can reduce distress associated with NAS among infants and caregivers.

Methods:
Heart rate was measured in infants and adults (parents vs other adults) in a neonatal intensive care unit (NICU) pre- (no touching), mid- (20 minutes into being worn in a carrier), and post-babywearing (5 minutes later).

Results:
Using a 3-level hierarchical linear model at 3 time points (pre, mid, and post), we found that babywearing decreased infant and caregiver heart rates. Across a 30-minute period, heart rates of infants worn by parents decreased by 15 beats per minute (bpm) compared with 5.5 bpm for infants worn by an unfamiliar adult, and those of adults decreased by 7 bpm (parents) and nearly 3 bpm (unfamiliar adult).

Implications for Practice:
Results from this study suggest that babywearing is a noninvasive and accessible intervention that can provide comfort for infants diagnosed with NAS. Babywearing can be inexpensive, support parenting, and be done by nonparent caregivers (eg, nurses, volunteers).

Implications for Research:
Close physical contact, by way of babywearing, may improve outcomes in infants with NAS in NICUs and possibly reduce the need for pharmacological treatment.
See the video abstract for a digital summary of the study.

Video Abstract Available at:

https://journals.lww.com/advancesinneonatalcare/Pages/videogallery.aspx?autoPlay=false&videoId=38