bluuebunny/crossref_metadata_2025_split huggingface dataset:
Limits on the presence of planets in systems with debris discs: HD 92945 and HD 107146
Authors: Mesa D , Marino S , Bonavita M , Lazzoni C , Fontanive C , Pérez S , D’Orazi V , Desidera S , Gratton R , Engler N , Henning T , Janson M , Kral Q , Langlois M , Messina S , Milli J , Pawellek N , Perrot C , Rigliaco E , Rickman E , Squicciarini V , Vigan A , Wahhaj Z , Zurlo A , Boccaletti A , Bonnefoy M , Chauvin G , De Caprio V , Feldt M , Gluck L , Hagelberg J , Keppler M , Lagrange A-M , Launhardt R , Maire A-L , Meyer M , Moeller-Nilsson O , Pavlov A , Samland M , Schmidt T , Weber L 
Published: February 2021

ABSTRACT
Recent observations of resolved cold debris discs at tens of au have revealed that gaps could be a common feature in these Kuiper-belt analogues. Such gaps could be evidence for the presence of planets within the gaps or closer in near the edges of the disc. We present SPHERE observations of HD 92945 and HD 107146, two systems with detected gaps. We constrained the mass of possible companions responsible for the gap to 1–2 MJup for planets located inside the gap and to less than 5 MJup for separations down to 20 au from the host star. These limits allow us to exclude some of the possible configurations of the planetary systems proposed to explain the shape of the discs around these two stars. In order to put tighter limits on the mass at very short separations from the star, where direct-imaging data are less effective, we also combined our data with astrometric measurements from Hipparcos and Gaia and radial-velocity measurements. We were able to limit the separation and the mass of the companion potentially responsible for the proper-motion anomaly of HD 107146 to values of 2–7 au and 2–5 MJup, respectively.
The Impact of Purifying and Background Selection on the Inference of Population History: Problems and Prospects
Authors: Johri Parul , Riall Kellen , Becher Hannes , Excoffier Laurent , Charlesworth Brian , Jensen Jeffrey D. 
Published: February 2021

Abstract
Current procedures for inferring population history generally assume complete neutrality—that is, they neglect both direct selection and the effects of selection on linked sites. We here examine how the presence of direct purifying selection and background selection may bias demographic inference by evaluating two commonly-used methods (MSMC and fastsimcoal2), specifically studying how the underlying shape of the distribution of fitness effects and the fraction of directly selected sites interact with demographic parameter estimation. The results show that, even after masking functional genomic regions, background selection may cause the mis-inference of population growth under models of both constant population size and decline. This effect is amplified as the strength of purifying selection and the density of directly selected sites increases, as indicated by the distortion of the site frequency spectrum and levels of nucleotide diversity at linked neutral sites. We also show how simulated changes in background selection effects caused by population size changes can be predicted analytically. We propose a potential method for correcting for the mis-inference of population growth caused by selection. By treating the distribution of fitness effect as a nuisance parameter and averaging across all potential realizations, we demonstrate that even directly selected sites can be used to infer demographic histories with reasonable accuracy.
Pulmonary findings on high-resolution computed tomography in Takayasu arteritis
Authors: Kong Xiufang , Zhang Jing , Lin Jiang , Lv Peng , Chen Huiyong , Ji Zongfei , Dai Xiaomin , Jin Xuejuan , Ma Lili , Jiang Lindi 
Published: February 2021

Abstract

Objective
This study aimed to describe pulmonary high-resolution CT (HRCT) findings in Takayasu arteritis (TA) and to determine possible causes.

Methods
A total of 243 TA patients were enrolled from a prospective cohort after excluding patients with other pulmonary disorders or incomplete data. Patients were divided into two groups: those with normal lung HRCT and those with abnormal lung HRCT. Clinical characteristics were compared between groups and binary logistic regression analysis was applied to identify possible causes of the lung lesions. Follow-up HRCT (obtained in 64 patients) was analysed to study changes in pulmonary lesions after treatment.

Results
Of the 243 patients, 107 (44.0%) had normal lung HRCT while 136 (56.0%) had abnormal lung HRCT, including stripe opacity (60.3%), nodules (44.9%), patchy opacity (25.0%), pleural thickening (15.4%), pleural effusion (10.3%), ground-glass opacity (8.1%), pulmonary infarction (6.6%), mosaic attenuation (4.4%), bronchiectasis (3.7%) and pulmonary oedema (2.2%). Patients with abnormal HRCT were significantly more likely to have type II arterial involvement (25% vs 12.2%, P = 0.04), pulmonary arterial involvement (PAI; 21.3% vs 5.6%, P &lt; 0.001), pulmonary hypertension (20.6% vs 8.4%, P = 0.01) and abnormal heart function (27.9% vs 7.6%, P &lt; 0.001). Logistic regression analysis demonstrated that PAI, worsened heart function and age were associated with presence of pulmonary lesions. Pulmonary infarction, pleural effusion and patchy opacities improved partially after treatment.

Conclusion
Pulmonary lesions are not rare in patients with TA. Age, PAI and worsened heart function are potential risk factors for presence of pulmonary lesions in TA.
CO2 refixation is higher in leaves of woody species with high mesophyll and stomatal resistances to CO2 diffusion
Authors: Eckert Diana , Martens Helle Juel , Gu Lianhong , Jensen Anna Monrad 
Published: February 2021

Abstract
The percentage of respiratory and photorespiratory CO2 refixed in leaves (Pr) represents part of the CO2 used in photosynthesis. The importance of Pr as well as differences between species and functional types are still not well investigated. In this study, we examine how Pr differs between six temperate and boreal woody species: Betula pendula, Quercus robur, Larix decidua, Pinus sylvestris, Picea abies and Vaccinium vitis-idaea. The study covers early and late successional species, deciduous broadleaves, deciduous conifers, evergreen conifers and evergreen broadleaves. We investigated whether some species or functional types had higher refixation percentages than others, whether leaf traits could predict higher Pr and whether these traits and their impact on Pr changed during growing seasons. Photosynthesis CO2 response (A/Ci)-curves, measured early, mid and late season, were used to estimate and compare Pr, mesophyll resistance (rm) and stomatal resistance (rs) to CO2 diffusion. Additionally, light images and transmission electron microscope images were used to approximate the fraction of intercellular airspace and cell wall thickness. We found that evergreens, especially late successional species, refixed a significantly higher amount of CO2 than the other species throughout the entire growing season. In addition, rm, rs and leaf mass per area, traits that typically are higher in evergreen species, were also significantly, positively correlated with Pr. We suggest that this is due to higher rm decreasing diffusion of (photo) respiratory CO2 out of the leaf. Cell wall thickness had a positive effect on Pr and rm, while the fraction of intercellular airspace had no effect. Both were significantly different between evergreen conifers and other types. Our findings suggest that species with a higher rm use a greater fraction of mitochondria-derived CO2, especially when stomatal conductance is low. This should be taken into account when modeling the overall CO2 fertilization effect for terrestrial ecosystems dominated by high rm species.
Effect of ozone exposure on Amyotrophic Lateral Sclerosis (ALS) pathology using a mice model of TDP-43 proteinopathy
Authors: Rodriguez Ana , Ferrer-Donato Agueda , Cabrera-Pinto Marta , Seseña Susana , Fernández Paloma , Aranda Alfonso , Fernandez-Martos Carmen M. 
Published: February 2021

AbstractBackgroundOzone (O3), one of the main photochemical pollutants in the atmosphere today, is a serious health risk factor. Although the effects of O3exposure have been documented on many diseases, they have not yet been examined on Amyotrophic Lateral Sclerosis (ALS)- a fatal progressive and neurodegenerative disease.ObjectivesTo investigate the effect of the O3exposure in a mice model of TDP-43 proteinopathy, exploring a possible association between the O3exposure and the ALS pathogenesis.MethodsTDP-43A315Tand wild-type (WT) mice were exposed to O3(0.25 ppm) or filtered air (FA) for 15 days (4 hours/day). We assessed (1) weight loss (2) motor performance (3) plasma glucose content and (4) metabolic markers from plasma samples of the animals.ResultsThroughout the experiment, we observed a progressive decline in body weight and the motor coordination in TDP-43A315Tmice compared to WT controls. Although there was a trend, there were no significant differences in the decline of body weight of TDP-43A315Tmice when exposed to either FA or O3. In O3-TDP-43A315Tmice, the disease duration lasted longer. In addition, O3-TDP-43A315Tmice showed improvements in motor performance as well TDP-43A315Tmice were hypoglycemic compared to WT mice. However, FA-TDP-43A315Tmice showed lower plasma glucose levels at the disease end-stage. We found altered levels of adipokines and metabolic proteins in TDP-43A315Tmice compared to WT controls. A positive correlation was found among GIP and glucagon compared to insulin concentrations in control mice. Interestingly, resistin, Gastric Inhibitory Peptide (GIP), Glucagon Like Peptide 1 (GIP-1) and insulin levels were higher in O3-TDP-43A315Tmice.DiscussionWe provide new evidence about a mechanistic link between O3exposure and the improvement of the metabolic disturbances present in TDP-43A315Tmice. Further studies are needed to corroborate the obtained results as they warrant to understanding the underlying mechanisms.
DLAB - Deep learning methods for structure-based virtual screening of antibodies
Authors: Schneider Constantin , Buchanan Andrew , Taddese Bruck , Deane Charlotte M. 
Published: February 2021

AbstractAntibodies are one of the most important classes of pharmaceuticals, with over 80 approved molecules currently in use against a wide variety of diseases. The drug discovery process for antibody therapeutic candidates however is time-and cost-intensive and heavily reliant onin-vivoandin-vitrohigh throughput screens. Here, we introduce a framework for structure-based deep learning for antibodies (DLAB) which can virtually screen putative binding antibodies against antigen targets of interest. DLAB is built to be able to predict antibody-antigen binding for antigens with no known antibody binders.We demonstrate that DLAB can be used both to improve antibody-antigen docking and structure-based virtual screening of antibody drug candidates. DLAB enables improved pose ranking for antibody docking experiments as well as selection of antibody-antigen pairings for which accurate poses are generated and correctly ranked. We also show that DLAB can identify binding antibodies against specific antigens in a case study. Our results demonstrate the promise of deep learning methods for structure-based virtual screening of antibodies.
Integument transcriptome profile of the European sea cucumberHolothuria forskali (Holothuroidea, Echinodermata)
Authors: Delroisse Jérôme , Bonneel Marie , Demeuldre Mélanie , Eeckhaut Igor , Flammang Patrick 
Published: February 2021

AbstractIn non-model organisms, Next Generation Sequencing (NGS) technology improve our ability to analyze gene expression and identify new genes or transcripts of interest. In this research, paired-end Illumina HiSeq sequencing has been used to describe a composite transcriptome based on two libraries generated from dorsal and ventral integuments of the European sea cucumberHolothuria forskali (Holothuroidea, Echinodermata). A total of 43,044,977 million HQ reads were initially generated. Afterde novoassembly, a total of 111,194 unigenes were predicted. On all predicted unigenes, 32,569 show significant matches with genes/proteins present in the reference databases. Around 50% of annotated unigenes were significantly similar to sequences from the purple sea urchinStrongylocentrotus purpuratusgenome. Annotation analyses were performed on predicted unigenes using public reference databases. These RNA-seq data provide an interesting resource for researchers with a broad interest in sea cucumber biology.
Penalized Logistic Regression Analysis for Genetic Association Studies of Binary Phenotypes
Authors: Yu Ying , Chen Siyuan , Jones Samantha J. , Hoque Rawnak , Vishnyakova Olga , Brooks-Wilson Angela , McNeney Brad 
Published: February 2021

ABSTRACTIntroductionIncreasingly, logistic regression methods for genetic association studies of binary phenotypes must be able to accommodate data sparsity, which arises from unbalanced case-control ratios and/or rare genetic variants. Sparseness leads to maximum likelihood estimators (MLEs) of log-OR parameters that are biased away from their null value of zero and tests with inflated type 1 errors. Different penalized-likelihood methods have been developed to mitigate sparse-data bias. We study penalized logistic regression using a class of log-Fpriors indexed by a shrinkage parametermto shrink the biased MLE towards zero.MethodsWe propose a two-step approach to the analysis of a genetic association study: first, a set of variants that show evidence of association with the trait is used to estimatem; and second, the estimatedmis used for log-F-penalized logistic regression analyses of all variants using data augmentation with standard software. Our estimate ofmis the maximizer of a marginal likelihood obtained by integrating the latent log-ORs out of the joint distribution of the parameters and observed data. We consider two approximate approaches to maximizing the marginal likelihood: (i) a Monte Carlo EM algorithm (MCEM) and (ii) a Laplace approximation (LA) to each integral, followed by derivative-free optimization of the approximation.ResultsWe evaluate the statistical properties of our proposed two-step method and compared its performance to other shrinkage methods by a simulation study. Our simulation studies suggest that the proposed log-F-penalized approach has lower bias and mean squared error than other methods considered. We also illustrate the approach on data from a study of genetic associations with “super senior” cases and middle aged controls.Discussion/ConclusionWe have proposed a method for single rare variant analysis with binary phenotypes by logistic regression penalized by log-Fpriors. Our method has the advantage of being easily extended to correct for confounding due to population structure and genetic relatedness through a data augmentation approach.
Epigenetic modulation in the pathogenesis and treatment of inherited aortic aneurysm conditions
Authors: Kang Benjamin E. , Bagirzadeh Rustam , Bedja Djahida , Doyle Jefferson J. , MacFarlane Elena G. , Dietz Harry C. 
Published: February 2021

AbstractShprintzen-Goldberg syndrome (SGS) is a rare systemic connective tissue disorder characterized by craniofacial, skeletal, neurodevelopmental, cutaneous, and cardiovascular manifestations, including aortic root aneurysm. It has significant phenotypic overlap with both Marfan syndrome (MFS) and Loeys-Dietz syndrome (LDS). We previously reported that SGS is caused by heterozygous mutations in the Sloan-Kettering Institute proto-oncogene (SKI), which encodes a potent suppressor of transforming growth factor beta (TGFβ) target gene expression. Herein, we show that mouse lines harboring orthologous amino acid substitutions inSkirecapitulate multiple human SGS phenotypic manifestations, including skin collagen deposition, skeletal kyphosis, behavioral hypoactivity, and aortic root aneurysm. Furthermore, aortic root aneurysm in SGS mice is associated with both increased acetylation of histone H3 at lysine-27 (H3K27) and TGFβ target gene expression, all of which can be ameliorated by pharmacological CBP/P300 inhibition in vivo; similar findings were seen in cultured dermal fibroblast from SGS patients. Aortic root growth is also abrogated in a mouse model of MFS by selective CBP/P300 inhibition in association with blunted expression of TGFβ target genes. These data document excessive H3K27 acetylation and hence TGFβ target gene expression in the pathogenesis of inherited presentations of aortic root aneurysm and the therapeutic potential of pharmacological epigenetic modulation.
Hydrogels Containing Gradients in Vascular Density Reveal Dose-Dependent Role of Angiocrine Cues on Stem Cell Behavior
Authors: Ngo Mai T. , Barnhouse Victoria R. , Gilchrist Aidan E. , Hunter Christine J. , Hensold Joy N. , Harley Brendan A.C. 
Published: February 2021

AbstractBiomaterials that replicate patterns of microenvironmental signals from the stem cell niche offer the potential to refine platforms to regulate stem cell behavior. While significant emphasis has been placed on understanding the effects of biophysical and biochemical cues on stem cell fate, vascular-derived or angiocrine cues offer an important alternative signaling axis for biomaterial-based stem cell platforms. Elucidating dose-dependent relationships between angiocrine cues and stem cell fate are largely intractable in animal models and two-dimensional cell culture. In this study, we leverage microfluidic mixing devices to generate three-dimensional hydrogels containing lateral gradients in vascular density alongside murine hematopoietic stem cells (HSCs). Regional differences in vascular density can be generated via embossed gradients in cell, matrix, or growth factor density. HSCs co-cultured alongside vascular gradients reveal spatial patterns of HSC phenotype in response to angiocrine signals. Notably, decreased Akt signaling in high vessel density regions led to increased expansion of lineage-positive hematopoietic cells. This approach offers a combinatorial tool to rapidly screen a continuum of microenvironments with varying vascular, biophysical, and biochemical cues to reveal the influence of local angiocrine signals on HSC fate.
CompMap: an allele-specific expression read-counter based on competitive mapping
Authors: Sánchez-Ramírez S. , Cutter A. D. 
Published: February 2021

ABSTRACTSummaryChanges to regulatory sequences account for important phenotypic differences between species and populations. In heterozygote individuals, regulatory polymorphism typically manifests as allele-specific expression (ASE) of transcripts. ASE data from inter-species and inter-population hybrids, in conjunction with expression data from the parents, can be used to infer regulatory changes incisandtransthroughout the genome. Improper data handling, however, can create problems of mapping bias and excessive loss of information, which are prone to arise unintentionally from the cumbersome pipelines with multiple dependencies that are common among current methods. Here, we introduce a new, selfcontained method implemented in Python that generates allele-specific expression counts from genotype-specific map alignments. Rather than assessing individual SNPs, our approach sorts and counts reads within a given homologous region by comparing individual read-mapping statistics from each parental alignment. Reads that are aligned ambiguously to both references are resolved proportionally to the allele-specific matching read counts or statistically using a binomial distribution. Using simulations, we showCompMaphas low error rates in assessing regulatory divergence.AvailabilityThe Python code with examples and installation instructions is available on the GitHub repositoryhttps://github.com/santiagosnchez/CompMapContactsantiago.snchez@gmail.comSupplementary information
Tooth chipping patterns inParanthropusdo not support regular hard food mastication
Authors: Towle Ian , Irish Joel D. , Loch Carolina 
Published: February 2021

AbstractThe paranthropines, includingParanthropus boiseiandParanthropus robustus, have often been considered hard-food specialists. The large post-canine teeth, thick enamel, and robust craniofacial features are often suggested to have evolved to cope with habitual mastication of hard foods. Yet, direct evidence for Paranthropus feeding behaviour often challenges these morphological interpretations. The main exception being antemortem tooth chipping which is still regularly used as evidence of habitual mastication of hard foods in this genus. In this study, data were compiled from the literature for six hominin species (includingP. boiseiandP. robustus) and 17 extant primate species, to analyse Paranthropus chipping patterns in a broad comparative framework. Severity of fractures, position on the dentition, and overall prevalence were compared among species. The results indicate that both Paranthropus species had a lower prevalence of tooth fractures compared to other fossil hominin species (P. boisei: 4%;P. robustus: 11%;Homo naledi: 37%;Australopithecus africanus: 17%;Homo neanderthalensis: 45%; EpipalaeolithicHomo sapiens: 29%); instead, their frequencies are similar to apes that masticate hard items in a non-regular frequency, including chimpanzees, gibbons, and gorillas (4%, 7% and 9% respectively). The prevalence is several times lower than in extant primates known to habitually consume hard items, such as sakis, mandrills, and sooty mangabeys (ranging from 28% to 48%). Comparative chipping analysis suggests that both Paranthropus species were unlikely habitual hard object eaters, at least compared to living durophage analogues.
Pulsed broad-spectrum UV light effectively inactivates SARS-CoV-2 on multiple surfaces
Authors: Jureka Alexander S. , Williams Caroline G. , Basler Christopher F. 
Published: February 2021

AbstractThe ongoing SARS-CoV-2 pandemic has resulted in an increased need for technologies capable of efficiently disinfecting public spaces as well as personal protective equipment. UV light disinfection is a well-established method for inactivating respiratory viruses. Here, we have determined that broad-spectrum, pulsed UV light is effective at inactivating SARS-CoV-2 on multiple surfaces. For hard, non-porous surfaces we observed that SARS-CoV-2 was inactivated to undetectable levels on plastic and glass with a UV dose of 34.9 mJ/cm2and stainless steel with a dose of 52.5 mJ/cm2. We also observed that broad-spectrum, pulsed UV light is effective at reducing SARS-CoV-2 on N95 respirator material to undetectable levels with a dose of 103 mJ/cm2. We included UV dosimeter cards that provide a colorimetric readout of UV dose and demonstrated their utility as a means to confirm desired levels of exposure were reached. Together, the results present here demonstrate that broad-spectrum, pulsed UV light is an effective technology for the inactivation of SARS-CoV-2 on multiple surfaces.
VisVariant: A java program to visualise genetic variants in next-generation sequencing data
Authors: Lau King Wai , Kleeman Michelle , Reuter Caroline , Lorincz Attila 
Published: February 2021

AbstractSummaryExtremely large datasets are impossible or very difficult for humans to comprehend by standard mental approaches. Intuitive visualization of genetic variants in genomic sequencing data could help in the review and confirmation process of variants called by automated variant calling programs. To help facilitate interpretation of genetic variant next-generation sequencing (NGS) data we developed VisVariant, a customizable visualization tool that creates a figure showing the overlapping sequence information of thousands of individual reads including the variant and flanking regions.Availability and implementationDetailed information on how to download, install and run VisVariant together with an example is available on our github website [https://github.com/hugging-biorxiv/visvariant].