bluuebunny/crossref_metadata_2025_split huggingface dataset:
The molecular mechanisms of MLKL-dependent and MLKL-independent necrosis
Authors: Li Lu , Tong An , Zhang Qiangsheng , Wei Yuquan , Wei Xiawei 
Published: October 2020

AbstractNecrosis, a type of unwanted and passive cell demise, usually occurs under the excessive external stress and is considered to be unregulated. However, under some special conditions such as caspase inhibition, necrosis is regulable in a well-orchestrated way. The term ‘regulated necrosis’ has been proposed to describe such programed necrosis. Recently, several forms of necrosis, including necroptosis, pyroptosis, ferroptosis, parthanatos, oxytosis, NETosis, and Na+/K+-ATPase-mediated necrosis, have been identified, and some crucial regulators governing regulated necrosis have also been discovered. Mixed lineage kinase domain-like pseudokinase (MLKL), a core regulator in necroptosis, acts as an executioner in response to ligands of death receptor family. Its activation requires the receptor-interacting protein kinases, RIP1 and RIP3. However, MLKL is only involved in necroptosis, i.e. MLKL is dispensable for necrosis. Therefore, this review is aimed at summarizing the molecular mechanisms of MLKL-dependent and MLKL-independent necrosis.
Duodenal perforation in the pediatric population: two rare cases at a small community hospital
Authors: Hattingh Genevieve , Salas-Parra Ruben D , Nuzhad Afrin , Salvador Joselyn , Farkas Daniel T 
Published: October 2020

Abstract
Duodenal ulcer perforation is very uncommon in the pediatric population; hence, it is usually not considered in the differential diagnosis of acute abdomen in this age group. In our small community hospital, we had two rare cases of perforated peptic ulcer in the pediatric population within a short span of time. A 14-year-old male and a 13-year-old female child presented to the emergency room with acute abdominal pain. No other symptoms were reported and neither had any history of peptic ulcer disease. Abdominal CT showed pneumoperitoneum consistent with perforated hollow viscus. Subsequent exploratory laparotomy indicated perforated duodenal ulcer in both children. These cases illustrate that perforated peptic ulcers should be considered in children presenting with acute abdomen.
A case of an asymptomatic sacrococcygeal teratoma diagnosed in adulthood
Authors: Mourad Ali P , De Robles Marie Shella , O’Toole Sandra , Paver Elizabeth , Winn Robert D 
Published: October 2020

Abstract
Sacrococcygeal teratomas are rare congenital tumours that are even more uncommon when present in adulthood. They are derived from residual stem cells in the presacral space that differentiate into clusters of somatic cell. We present the diagnosis, management and post-operative follow-up in a 37-year-old gentleman referred to our department with an incidental finding of a lobulated presacral cystic mass on computed tomography imaging. Magnetic resonance imaging and fluorodeoxyglucose (FDG)-positron emission tomography (PET) scans were performed to further characterize the lesion. The decision was then made for surgical excision and the specimen along with the coccyx was retrieved en-bloc via a trans-sacral surgical approach. Histopathology of the mass uncovered the presence of squamous, respiratory and prostatic epithelium consistent with the diagnosis of a sacrococcygeal teratoma.
Genome-wide analyses reveal footprints of divergent selection and popping-related traits in CIMMYT’s maize inbred lines
Authors: Li Jing , Li Delin , Espinosa Cristian Zavala , Pastor Viridiana Trejo , Rasheed Awais , Rojas Natalia Palacios , Wang Jiankang , Varela Amalio Santacruz , Carolina de Almeida Silva Natália , Schnable Patrick S , Costich Denise E , Li Huihui 
Published: October 2020

Abstract
Popcorn (Zea mays L. var. Everta) is the most ancient type of cultivated maize. However, there is little known about the genetics of popping-related traits based on genotyping-by-sequencing (GBS) technology. Here, we characterized the phenotypic variation for seven popping-related traits in maize kernels among 526 CIMMYT inbred lines (CMLs). In total, 155 083 high-quality single nucleotide polymorphism (SNP) markers were identified by a GBS approach. Several trait-associated loci were detected by genome-wide association study for color, popping expansion volume, shape, pericarp, flotation index, floury/vitreous, and protein content, explaining a majority of the observed phenotypic variance, and these were validated by a diverse panel comprising 764 tropical landrace accessions. Sixty two of the identified loci were recognized to have undergone selection. On average, there was a 55.27% frequency for alleles that promote popping in CMLs. Our work not only pinpoints previously unknown loci for popping-related traits, but also reveals that many of these loci have undergone selection. Beyond establishing a new benchmark for the genetics of popcorn, our study provides a foundation for gene discovery and breeding. It also presents evidence to investigate the role of a gradual loss of popping ability as a by-product of diversification of culinary uses throughout the evolution of teosinte–to–modern maize.
Endogenous indole-3-acetamide levels contribute to the crosstalk between auxin and abscisic acid, and trigger plant stress responses in Arabidopsis
Authors: Pérez-Alonso Marta-Marina , Ortiz-García Paloma , Moya-Cuevas José , Lehmann Thomas , Sánchez-Parra Beatriz , Björk Robert G , Karim Sazzad , Amirjani Mohammad R , Aronsson Henrik , Wilkinson Mark D , Pollmann Stephan 
Published: October 2020

AbstractThe evolutionary success of plants relies to a large extent on their extraordinary ability to adapt to changes in their environment. These adaptations require that plants balance their growth with their stress responses. Plant hormones are crucial mediators orchestrating the underlying adaptive processes. However, whether and how the growth-related hormone auxin and the stress-related hormones jasmonic acid, salicylic acid, and abscisic acid (ABA) are coordinated remains largely elusive. Here, we analyse the physiological role of AMIDASE 1 (AMI1) in Arabidopsis plant growth and its possible connection to plant adaptations to abiotic stresses. AMI1 contributes to cellular auxin homeostasis by catalysing the conversion of indole-acetamide into the major plant auxin indole-3-acetic acid. Functional impairment of AMI1 increases the plant’s stress status rendering mutant plants more susceptible to abiotic stresses. Transcriptomic analysis of ami1 mutants disclosed the reprogramming of a considerable number of stress-related genes, including jasmonic acid and ABA biosynthesis genes. The ami1 mutants exhibit only moderately repressed growth but an enhanced ABA accumulation, which suggests a role for AMI1 in the crosstalk between auxin and ABA. Altogether, our results suggest that AMI1 is involved in coordinating the trade-off between plant growth and stress responses, balancing auxin and ABA homeostasis.
The dependence of Type Ia Supernovae salt2 light-curve parameters on host galaxy morphology
Authors: Pruzhinskaya M V , Novinskaya A K , Pauna N , Rosnet P 
Published: October 2020

ABSTRACT
Type Ia Supernovae (SNe Ia) are widely used to measure distances in the Universe. Despite the recent progress achieved in SN Ia standardization, the Hubble diagram still shows some remaining intrinsic dispersion. The remaining scatter in supernova luminosity could be due to the environmental effects that are accounted for as mass step correction in the current cosmological analyses. In this work, we compare the local and global colour (U − V), the local star formation rate, and the host stellar mass to the host galaxy morphology. The observed trends suggest that the host galaxy morphology is a relevant parameter to characterize the SN Ia environment. Therefore, we study the influence of host galaxy morphology on light-curve parameters of SNe Ia from the pantheon cosmological supernova sample. We determine the Hubble morphological type of host galaxies for a subsample of 330 SNe Ia. We confirm that the salt2 stretch parameter x1 depends on the host morphology with the p-value ∼10−14. The supernovae with lower stretch value are hosted mainly by elliptical and lenticular galaxies. No correlation for the salt2 colour parameter c is found. We also examine Hubble diagram residuals for supernovae hosted by ‘early-type’ and ‘late-type’ morphological groups of galaxies. The analysis reveals that the mean distance modulus residual in early-type galaxies is smaller than the one in late-type galaxies, which means that early-type galaxies contain brighter supernovae after stretch and colour corrections. However, we do not observe any difference in the residual dispersion for these two morphological groups. The obtained results are in the line with other analyses showing environmental dependence of SN Ia light-curve parameters and luminosity. We confirm the importance of including a host galaxy parameter into the standardization procedure of SNe Ia for further cosmological studies.
Network of thermal cracks in meteorites due to temperature variations: new experimental evidence and implications for asteroid surfaces
Authors: Libourel Guy , Ganino Clément , Delbo Marco , Niezgoda Mathieu , Remy Benjamin , Aranda Lionel , Michel Patrick 
Published: October 2020

ABSTRACT
In recent years, several studies have shown the importance of thermal fracturing of rocks due to temperature variations, on The Earth and Mars. Rock thermal cracking might also be a process at play on the lunar surface. These temperature variations as well as change rates can reach important amplitude on bodies without an atmosphere, in particular on those that reach small perihelion distances such as near-Earth asteroids. On the other hand, the formation, geometry, and extension of cracks on these bodies have not been fully investigated yet. Here, we show results of thermal cracking laboratory experiments on chondrite meteorites, which develop networks of cracks when subjected to rapid temperature cycles with amplitudes similar to those experienced by asteroids with low perihelion distances. The depth of the cracks can reach a few hundred of microns in some hundreds of temperature cycles, in agreement with theoretical studies. We find that dehydration of hydrous minerals enhances the cracking process. The formation of crack networks increases the porosity both at the surface and in the sub-surface of our specimens. We propose that this process could help explaining the recent finding of the very highly porous surfaces of most of the boulders on the asteroids Ryugu and Bennu.
Characteristic scale of star formation – I. Clump formation efficiency on local scales
Authors: Eden D J , Moore T J T , Plume R , Rigby A J , Urquhart J S , Marsh K A , Peñaloza C H , Clark P C , Smith M W L , Tahani K , Ragan S E , Thompson M A , Johnstone D , Parsons H , Rani R 
Published: October 2020

ABSTRACT
We have used the ratio of column densities derived independently from the 850-μm continuum James Clerk Maxwell Telescope Plane Survey and the 13CO/C18O (J = 3 → 2) Heterodyne Inner Milky Way Plane Survey to produce maps of the dense-gas mass fraction (DGMF) in two slices of the Galactic plane centred at ℓ = 30° and 40°. The observed DGMF is a metric for the instantaneous clump formation efficiency (CFE) in the molecular gas. We split the two fields into velocity components corresponding to the spiral arms that cross them, and a two-dimensional power-spectrum analysis of the spiral-arm DGMF maps reveals a break in slope at the approximate size scale of molecular clouds. We interpret this as the characteristic scale of the amplitude of variations in the CFE and a constraint on the dominant mechanism regulating the CFE and, hence, the star formation efficiency in CO-traced clouds.
Line-drag damping of Alfvén waves in radiatively driven winds of magnetic massive stars
Authors: Driessen F A , Kee N D , Sundqvist J O , Owocki S P 
Published: October 2020

ABSTRACT
Line-driven stellar winds from massive (OB) stars are subject to a strong line-deshadowing instability. Recently, spectropolarimetric surveys have collected ample evidence that a subset of Galactic massive stars hosts strong surface magnetic fields. We investigate here the propagation and stability of magnetoradiative waves in such a magnetized, line-driven wind. Our analytic, linear stability analysis includes line-scattering from the stellar radiation, and accounts for both radial and non-radial perturbations. We establish a bridging law for arbitrary perturbation wavelength after which we analyse separately the long- and short-wavelength limits. While long-wavelength radiative and magnetic waves are found to be completely decoupled, a key result is that short-wavelength, radially propagating Alfvén waves couple to the scattered radiation field and are strongly damped due to the line-drag effect. This damping of magnetic waves in a scattering-line-driven flow could have important effects on regulating the non-linear wind dynamics, and so might also have strong influence on observational diagnostics of the wind structure and clumping of magnetic line-driven winds.
magritte, a modern software library for 3D radiative transfer – II. Adaptive ray-tracing, mesh construction, and reduction
Authors: De Ceuster Frederik , Bolte Jan , Homan Ward , Maes Silke , Malfait Jolien , Decin Leen , Yates Jeremy , Boyle Peter , Hetherington James 
Published: October 2020

ABSTRACT
Radiative transfer is a notoriously difficult and computationally demanding problem. Yet, it is an indispensable ingredient in nearly all astrophysical and cosmological simulations. Choosing an appropriate discretization scheme is a crucial part of the simulation, since it not only determines the direct memory cost of the model but also largely determines the computational cost and the achievable accuracy. In this paper, we show how an appropriate choice of directional discretization scheme as well as spatial model mesh can help alleviate the computational cost, while largely retaining the accuracy. First, we discuss the adaptive ray-tracing scheme implemented in our 3D radiative transfer library magritte, that adapts the rays to the spatial mesh and uses a hierarchical directional discretization based on healpix. Second, we demonstrate how the free and open-source software library gmsh can be used to generate high-quality meshes that can be easily tailored for magritte. In particular, we show how the local element size distribution of the mesh can be used to optimize the sampling of both analytically and numerically defined models. Furthermore, we show that when using the output of hydrodynamics simulations as input for a radiative transfer simulation, the number of elements in the input model can often be reduced by an order of magnitude, without significant loss of accuracy in the radiation field. We demonstrate this for two models based on a hierarchical octree mesh resulting from adaptive mesh refinement, as well as two models based on smoothed particle hydrodynamics data.
Using commensurabilities and orbit structure to understand barred galaxy evolution
Authors: Petersen Michael S , Weinberg Martin D , Katz Neal 
Published: October 2020

ABSTRACTWe interpret simulations of secularly evolving disc galaxies through orbit morphology. Using a new algorithm that measures the volume of orbits in real space using a tessellation, we rapidly isolate commensurate (resonant) orbits. We identify phase-space regions occupied by different orbital families. Compared to spectral methods, the tessellation algorithm can identify resonant orbits within a few dynamical periods, crucial for understanding an evolving galaxy model. The flexible methodology accepts arbitrary potentials, enabling detailed descriptions of the orbital families. We apply the machinery to four different potential models, including two barred models, and fully characterize the orbital membership. We identify key differences in the content of orbit families, emphasizing the presence of orbit families indicative of the bar evolutionary state and the shape of the dark matter halo. We use the characterization of orbits to investigate the shortcomings of analytic and self-consistent studies, comparing our findings to the evolutionary epochs in self-consistent barred galaxy simulations. Using insight from our orbit analysis, we present a new observational metric that uses spatial and kinematic information from integral field spectrometers that may reveal signatures of commensurabilities and allow for a differentiation between models.
The TFIIH subunits p44/p62 act as a damage sensor during nucleotide excision repair
Authors: Barnett Jamie T , Kuper Jochen , Koelmel Wolfgang , Kisker Caroline , Kad Neil M 
Published: October 2020

AbstractNucleotide excision repair (NER) in eukaryotes is orchestrated by the core form of the general transcription factor TFIIH, containing the helicases XPB, XPD and five ‘structural’ subunits, p62, p44, p34, p52 and p8. Recent cryo-EM structures show that p62 makes extensive contacts with p44 and in part occupies XPD’s DNA binding site. While p44 is known to regulate the helicase activity of XPD during NER, p62 is thought to be purely structural. Here, using helicase and adenosine triphosphatase assays we show that a complex containing p44 and p62 enhances XPD’s affinity for dsDNA 3-fold over p44 alone. Remarkably, the relative affinity is further increased to 60-fold by dsDNA damage. Direct binding studies show this preference derives from p44/p62’s high affinity (20 nM) for damaged ssDNA. Single molecule imaging of p44/p62 complexes without XPD reveals they bind to and randomly diffuse on DNA, however, in the presence of UV-induced DNA lesions these complexes stall. Combined with the analysis of a recent cryo-EM structure, we suggest that p44/p62 acts as a novel DNA-binding entity that enhances damage recognition in TFIIH. This revises our understanding of TFIIH and prompts investigation into the core subunits for an active role during DNA repair and/or transcription.
Novel ribonucleotide discrimination in the RNA polymerase-like two-barrel catalytic core of Family D DNA polymerases
Authors: Zatopek Kelly M , Alpaslan Ece , Evans Thomas C , Sauguet Ludovic , Gardner Andrew F 
Published: October 2020

AbstractFamily D DNA polymerase (PolD) is the essential replicative DNA polymerase for duplication of most archaeal genomes. PolD contains a unique two-barrel catalytic core absent from all other DNA polymerase families but found in RNA polymerases (RNAPs). While PolD has an ancestral RNA polymerase catalytic core, its active site has evolved the ability to discriminate against ribonucleotides. Until now, the mechanism evolved by PolD to prevent ribonucleotide incorporation was unknown. In all other DNA polymerase families, an active site steric gate residue prevents ribonucleotide incorporation. In this work, we identify two consensus active site acidic (a) and basic (b) motifs shared across the entire two-barrel nucleotide polymerase superfamily, and a nucleotide selectivity (s) motif specific to PolD versus RNAPs. A novel steric gate histidine residue (H931 in Thermococcus sp. 9°N PolD) in the PolD s-motif both prevents ribonucleotide incorporation and promotes efficient dNTP incorporation. Further, a PolD H931A steric gate mutant abolishes ribonucleotide discrimination and readily incorporates a variety of 2′ modified nucleotides. Taken together, we construct the first putative nucleotide bound PolD active site model and provide structural and functional evidence for the emergence of DNA replication through the evolution of an ancestral RNAP two-barrel catalytic core.
GRNdb: decoding the gene regulatory networks in diverse human and mouse conditions
Authors: Fang Li , Li Yunjin , Ma Lu , Xu Qiyue , Tan Fei , Chen Geng 
Published: October 2020

Abstract
Gene regulatory networks (GRNs) formed by transcription factors (TFs) and their downstream target genes play essential roles in gene expression regulation. Moreover, GRNs can be dynamic changing across different conditions, which are crucial for understanding the underlying mechanisms of disease pathogenesis. However, no existing database provides comprehensive GRN information for various human and mouse normal tissues and diseases at the single-cell level. Based on the known TF-target relationships and the large-scale single-cell RNA-seq data collected from public databases as well as the bulk data of The Cancer Genome Atlas and the Genotype-Tissue Expression project, we systematically predicted the GRNs of 184 different physiological and pathological conditions of human and mouse involving &gt;633 000 cells and &gt;27 700 bulk samples. We further developed GRNdb, a freely accessible and user-friendly database (http://www.grndb.com/) for searching, comparing, browsing, visualizing, and downloading the predicted information of 77 746 GRNs, 19 687 841 TF-target pairs, and related binding motifs at single-cell/bulk resolution. GRNdb also allows users to explore the gene expression profile, correlations, and the associations between expression levels and the patient survival of diverse cancers. Overall, GRNdb provides a valuable and timely resource to the scientific community to elucidate the functions and mechanisms of gene expression regulation in various conditions.
Sexually dimorphic radiogenomic models identify distinct imaging and biological pathways that are prognostic of overall survival in glioblastoma
Authors: Beig Niha , Singh Salendra , Bera Kaustav , Prasanna Prateek , Singh Gagandeep , Chen Jonathan , Saeed Bamashmos Anas , Barnett Addison , Hunter Kyle , Statsevych Volodymyr , Hill Virginia B , Varadan Vinay , Madabhushi Anant , Ahluwalia Manmeet S , Tiwari Pallavi 
Published: October 2020

AbstractBackgroundRecent epidemiological studies have suggested that sexual dimorphism influences treatment response and prognostic outcome in glioblastoma (GBM). To this end, we sought to (i) identify distinct sex-specific radiomic phenotypes—from tumor subcompartments (peritumoral edema, enhancing tumor, and necrotic core) using pretreatment MRI scans—that are prognostic of overall survival (OS) in GBMs, and (ii) investigate radiogenomic associations of the MRI-based phenotypes with corresponding transcriptomic data, to identify the signaling pathways that drive sex-specific tumor biology and treatment response in GBM.MethodsIn a retrospective setting, 313 GBM patients (male = 196, female = 117) were curated from multiple institutions for radiomic analysis, where 130 were used for training and independently validated on a cohort of 183 patients. For the radiogenomic analysis, 147 GBM patients (male = 94, female = 53) were used, with 125 patients in training and 22 cases for independent validation.ResultsCox regression models of radiomic features from gadolinium T1-weighted MRI allowed for developing more precise prognostic models, when trained separately on male and female cohorts. Our radiogenomic analysis revealed higher expression of Laws energy features that capture spots and ripple-like patterns (representative of increased heterogeneity) from the enhancing tumor region, as well as aggressive biological processes of cell adhesion and angiogenesis to be more enriched in the “high-risk” group of poor OS in the male population. In contrast, higher expressions of Laws energy features (which detect levels and edges) from the necrotic core with significant involvement of immune related signaling pathways was observed in the “low-risk” group of the female population.ConclusionsSexually dimorphic radiogenomic models could help risk-stratify GBM patients for personalized treatment decisions.