bluuebunny/crossref_metadata_2025_split huggingface dataset:
Negative thermal expansion in α-Zr2SP2O12 based on phase transition- and framework-type mechanisms
Authors: Isobe Toshihiro , Hayakawa Yuko , Adachi Yuri , Uehara Ryosuke , Matsushita Sachiko , Nakajima Akira 
Published: December 2020

AbstractMaterials with negative coefficients of thermal expansion (CTEs) can be used to prepare composites with specific CTE values. Negative thermal expansion behavior can be primarily attributed to two types of mechanisms: phase transition- and framework-type mechanisms. This paper reports Zr2SP2O12, which has unique negative thermal expansion behavior involving both mechanisms. Zr2SP2O12 undergoes a framework-type mechanism at temperatures <393 K or >453 K and an isosymmetric phase transition at 393–453 K. The volumetric CTE of α-Zr2SP2O12 is ~−70 p.p.m./K during the isosymmetric phase transition, and this value can be decreased by decreasing the proportion of sulfur. The minimum volumetric CTE of α-Zr2S0.9P2O12-δ is ~−108 p.p.m./K in the temperature range of 393–453 K. Between 303 and 773 K, the volume of α-Zr2S0.9P2O12 − δ is reduced by ~1.3%. Finally, this paper presents methods for the hydrothermal synthesis of α-Zr2SP2O12 and for controlling the sulfur content.
Genomic signatures of recombination in a natural population of the bdelloid rotifer Adineta vaga
Authors: Vakhrusheva Olga A. , Mnatsakanova Elena A. , Galimov Yan R. , Neretina Tatiana V. , Gerasimov Evgeny S. , Naumenko Sergey A. , Ozerova Svetlana G. , Zalevsky Arthur O. , Yushenova Irina A. , Rodriguez Fernando , Arkhipova Irina R. , Penin Aleksey A. , Logacheva Maria D. , Bazykin Georgii A. , Kondrashov Alexey S. 
Published: December 2020

AbstractSexual reproduction is almost ubiquitous among extant eukaryotes. As most asexual lineages are short-lived, abandoning sex is commonly regarded as an evolutionary dead end. Still, putative anciently asexual lineages challenge this view. One of the most striking examples are bdelloid rotifers, microscopic freshwater invertebrates believed to have completely abandoned sexual reproduction tens of Myr ago. Here, we compare whole genomes of 11 wild-caught individuals of the bdelloid rotifer Adineta vaga and present evidence that some patterns in its genetic variation are incompatible with strict clonality and lack of genetic exchange. These patterns include genotype proportions close to Hardy-Weinberg expectations within loci, lack of linkage disequilibrium between distant loci, incongruent haplotype phylogenies across the genome, and evidence for hybridization between divergent lineages. Analysis of triallelic sites independently corroborates these findings. Our results provide evidence for interindividual genetic exchange and recombination in A. vaga, a species previously thought to be anciently asexual.
Linear and nonlinear optical responses in the chiral multifold semimetal RhSi
Authors: Ni Zhuoliang , Xu B. , Sánchez-Martínez M.-Á. , Zhang Y. , Manna K. , Bernhard C. , Venderbos J. W. F. , de Juan F. , Felser C. , Grushin A. G. , Wu Liang 
Published: December 2020

AbstractChiral topological semimetals are materials that break both inversion and mirror symmetries. They host interesting phenomena such as the quantized circular photogalvanic effect (CPGE) and the chiral magnetic effect. In this work, we report a comprehensive theoretical and experimental analysis of the linear and nonlinear optical responses of the chiral topological semimetal RhSi, which is known to host multifold fermions. We show that the characteristic features of the optical conductivity, which display two distinct quasi-linear regimes above and below 0.4 eV, can be linked to excitations of different kinds of multifold fermions. The characteristic features of the CPGE, which displays a sign change at 0.4 eV and a large non-quantized response peak of around 160 μA/V2 at 0.7 eV, are explained by assuming that the chemical potential crosses a flat hole band at the Brillouin zone center. Our theory predicts that, in order to observe a quantized CPGE in RhSi, it is necessary to increase the chemical potential as well as the quasiparticle lifetime. More broadly, our methodology, especially the development of the broadband terahertz emission spectroscopy, could be widely applied to study photogalvanic effects in noncentrosymmetric materials and in topological insulators in a contact-less way and accelerate the technological development of efficient infrared detectors based on topological semimetals.
Assessment of skin barrier function using skin images with topological data analysis
Authors: Koseki Keita , Kawasaki Hiroshi , Atsugi Toru , Nakanishi Miki , Mizuno Makoto , Naru Eiji , Ebihara Tamotsu , Amagai Masayuki , Kawakami Eiryo 
Published: December 2020

AbstractRecent developments of molecular biology have revealed diverse mechanisms of skin diseases, and precision medicine considering these mechanisms requires the frequent objective evaluation of skin phenotypes. Transepidermal water loss (TEWL) is commonly used for evaluating skin barrier function; however, direct measurement of TEWL is time-consuming and is not convenient for daily clinical practice. Here, we propose a new skin barrier assessment method using skin images with topological data analysis (TDA). TDA enabled efficient identification of structural features from a skin image taken by a microscope. These features reflected the regularity of the skin texture. We found a significant correlation between the topological features and TEWL. Moreover, using the features as input, we trained machine-learning models to predict TEWL and obtained good accuracy (R2 = 0.524). Our results suggest that assessment of skin barrier function by topological image analysis is promising.
Obstacles to the reuse of study metadata in ClinicalTrials.gov
Authors: Miron Laura , Gonçalves Rafael S. , Musen Mark A. 
Published: December 2020

AbstractMetadata that are structured using principled schemas and that use terms from ontologies are essential to making biomedical data findable and reusable for downstream analyses. The largest source of metadata that describes the experimental protocol, funding, and scientific leadership of clinical studies is ClinicalTrials.gov. We evaluated whether values in 302,091 trial records adhere to expected data types and use terms from biomedical ontologies, whether records contain fields required by government regulations, and whether structured elements could replace free-text elements. Contact information, outcome measures, and study design are frequently missing or underspecified. Important fields for search, such as condition and intervention, are not restricted to ontologies, and almost half of the conditions are not denoted by MeSH terms, as recommended. Eligibility criteria are stored as semi-structured free text. Enforcing the presence of all required elements, requiring values for certain fields to be drawn from ontologies, and creating a structured eligibility criteria element would improve the reusability of data from ClinicalTrials.gov in systematic reviews, metanalyses, and matching of eligible patients to trials.
Multi-task learning for the simultaneous reconstruction of the human and mouse gene regulatory networks
Authors: Mignone Paolo , Pio Gianvito , Džeroski Sašo , Ceci Michelangelo 
Published: December 2020

AbstractThe reconstruction of Gene Regulatory Networks (GRNs) from gene expression data, supported by machine learning approaches, has received increasing attention in recent years. The task at hand is to identify regulatory links between genes in a network. However, existing methods often suffer when the number of labeled examples is low or when no negative examples are available. In this paper we propose a multi-task method that is able to simultaneously reconstruct the human and the mouse GRNs using the similarities between the two. This is done by exploiting, in a transfer learning approach, possible dependencies that may exist among them. Simultaneously, we solve the issues arising from the limited availability of examples of links by relying on a novel clustering-based approach, able to estimate the degree of certainty of unlabeled examples of links, so that they can be exploited during the training together with the labeled examples. Our experiments show that the proposed method can reconstruct both the human and the mouse GRNs more effectively compared to reconstructing each network separately. Moreover, it significantly outperforms three state-of-the-art transfer learning approaches that, analogously to our method, can exploit the knowledge coming from both organisms. Finally, a specific robustness analysis reveals that, even when the number of labeled examples is very low with respect to the number of unlabeled examples, the proposed method is almost always able to outperform its single-task counterpart.
Methylation of estrogen receptor 2 (ESR2) in deep paravertebral muscles and its association with idiopathic scoliosis
Authors: Chmielewska Małgorzata , Janusz Piotr , Andrusiewicz Mirosław , Kotwicki Tomasz , Kotwicka Małgorzata 
Published: December 2020

AbstractIdiopathic scoliosis (IS) is one of the most common spinal disorders in adolescents. Despite many studies, the etiopathogenesis of IS is still poorly understood. In recent years, the role of epigenetic factors in the etiopathogenesis of IS has been increasingly investigated. It has also been postulated that the development and progression of the disease is related to gender and puberty, and could be associated with estrogen action. Estrogen hormones act via estrogen receptor 1 (ESR1) and estrogen receptor 2 (ESR2). It has been suggested that ESR2 expression is dependent on methylation within its gene promoter. So far, no studies have evaluated local, tissue-specific DNA methylation in patients with IS. Thus, our study aimed to analyze the methylation and expression level of ESR2 in the paraspinal muscles of the convex and concave side of the IS curvature. The methylation level within ESR2 promoter 0N, but not exon 0N, was significantly higher on the concave side of the curvature compared to the convex side. There was no significant correlation between ESR2 expression and methylation level in the promoter 0N on the convexity of thoracic scoliosis, whereas, on the concave side of the curvature, we observed a moderate negative correlation. There was no difference in the methylation levels of the ESR2 promoter and exon 0N between groups of patients with Cobb angle ≤ 70° and > 70° on the concave and convex side of the curvature. We also found no statistically significant correlation between the Cobb angle value and the mean methylation level in either the ESR2 promoter or exon 0N on the convex or concave side of the curvature. Our findings demonstrate that DNA methylation at the ESR2 promoter in deep paravertebral muscle tissue is associated with the occurrence but not with the severity of idiopathic scoliosis.
K63-linked ubiquitylation induces global sequestration of mitochondria
Authors: Richard Thibaud J. C. , Herzog Laura K. , Vornberger Julia , Rahmanto Aldwin Suryo , Sangfelt Olle , Salomons Florian A. , Dantuma Nico P. 
Published: December 2020

AbstractEven though K63-linked polyubiquitin chains do not target proteins for proteasomal degradation, they play nevertheless a complementary protective role in maintaining protein homeostasis by directing malfunctioning proteins and organelles to inclusion bodies or autophagosomes. A paradigm for this process is the sequestration and autophagic degradation of dysfunctional mitochondria. Although studies have shown that K63-ubiquitylation of mitochondrial proteins by the ubiquitin ligase Parkin is important in this process, it is presently not clear if this modification also suffices to initiate this cascade of events. To address this question, we have engineered the ubiquitin ligase ProxE3, which in an inducible manner synthesizes K63-linked ubiquitin chains on the surface of mitochondria. We found that the presence of K63-linked ubiquitin chains on mitochondria resulted in the recruitment of the ubiquitin adaptor p62 and induced a dramatic redistribution of mitochondria, which was reminiscent to the Parkin-facilitated sequestration in response to mitochondrial uncoupler. However, ProxE3 did not induce autophagic degradation of mitochondria. Our data show that K63-linked ubiquitin chains at the mitochondrial membrane are sufficient for the induction of mitochondrial sequestration, but not mitophagy, without the need of extrinsically inflicting mitochondrial dysfunction.
Dynamic data-driven meta-analysis for prioritisation of host genes implicated in COVID-19
Authors: Parkinson Nicholas , Rodgers Natasha , Head Fourman Max , Wang Bo , Zechner Marie , Swets Maaike C. , Millar Jonathan E. , Law Andy , Russell Clark D. , Baillie J. Kenneth , Clohisey Sara 
Published: December 2020

AbstractThe increasing body of literature describing the role of host factors in COVID-19 pathogenesis demonstrates the need to combine diverse, multi-omic data to evaluate and substantiate the most robust evidence and inform development of therapies. Here we present a dynamic ranking of host genes implicated in human betacoronavirus infection (SARS-CoV-2, SARS-CoV, MERS-CoV, seasonal coronaviruses). We conducted an extensive systematic review of experiments identifying potential host factors. Gene lists from diverse sources were integrated using Meta-Analysis by Information Content (MAIC). This previously described algorithm uses data-driven gene list weightings to produce a comprehensive ranked list of implicated host genes. From 32 datasets, the top ranked gene was PPIA, encoding cyclophilin A, a druggable target using cyclosporine. Other highly-ranked genes included proposed prognostic factors (CXCL10, CD4, CD3E) and investigational therapeutic targets (IL1A) for COVID-19. Gene rankings also inform the interpretation of COVID-19 GWAS results, implicating FYCO1 over other nearby genes in a disease-associated locus on chromosome 3. Researchers can search and review the gene rankings and the contribution of different experimental methods to gene rank at https://baillielab.net/maic/covid19. As new data are published we will regularly update the list of genes as a resource to inform and prioritise future studies.
Identification and functional characterization of the first molluscan neuromedin U receptor in the slug, Deroceras reticulatum
Authors: Ahn Seung-Joon , Mc Donnell Rory J. , Corcoran Jacob A. , Martin Ruth C. , Choi Man-Yeon 
Published: December 2020

AbstractNeuromedin U (NmU) is a neuropeptide regulating diverse physiological processes. The insect homologs of vertebrate NmU are categorized as PRXamide family peptides due to their conserved C-terminal end. However, NmU homologs have been elusive in Mollusca, the second largest phylum in the animal kingdom. Here we report the first molluscan NmU/PRXamide receptor from the slug, Deroceras reticulatum. Two splicing variants of the receptor gene were functionally expressed and tested for binding with ten endogenous peptides from the slug and some insect PRXamide and vertebrate NmU peptides. Three heptapeptides (QPPLPRYa, QPPVPRYa and AVPRPRIa) triggered significant activation of the receptors, suggesting that they are true ligands for the NmU/PRXamide receptor in the slug. Synthetic peptides with structural modifications at different amino acid positions provided important insights on the core moiety of the active peptides. One receptor variant always exhibited higher binding activity than the other variant. The NmU-encoding genes were highly expressed in the slug brain, while the receptor gene was expressed at lower levels in general with relatively higher expression levels in both the brain and foot. Injection of the bioactive peptides into slugs triggered defensive behavior such as copious mucus secretion and a range of other anomalous behaviors including immobilization, suggesting their role in important physiological functions.
Skin microbiome correlates with bioclimate and Batrachochytrium dendrobatidis infection intensity in Brazil’s Atlantic Forest treefrogs
Authors: Ruthsatz Katharina , Lyra Mariana L. , Lambertini Carolina , Belasen Anat M. , Jenkinson Thomas S. , da Silva Leite Domingos , Becker C. Guilherme , Haddad Célio F. B. , James Timothy Y. , Zamudio Kelly R. , Toledo Luís Felipe , Vences Miguel 
Published: December 2020

AbstractIn Brazil’s Atlantic Forest (AF) biodiversity conservation is of key importance since the fungal pathogenBatrachochytrium dendrobatidis(Bd) has led to the rapid loss of amphibian populations here and worldwide. The impact of Bd on amphibians is determined by the host's immune system, of which the skin microbiome is a critical component. The richness and diversity of such cutaneous bacterial communities are known to be shaped by abiotic factors which thus may indirectly modulate host susceptibility to Bd.This study aimed to contribute to understanding the environment-host–pathogen interaction determining skin bacterial communities in 819 treefrogs (Anura: Hylidae and Phyllomedusidae) from 71 species sampled across the AF. We investigated whether abiotic factors influence the bacterial community richness and structure on the amphibian skin. We further tested for an association between skin bacterial community structure and Bd co-occurrence. Our data revealed that temperature, precipitation, and elevation consistently correlate with richness and diversity of the skin microbiome and also predict Bd infection status. Surprisingly, our data suggest a weak but significant positive correlation of Bd infection intensity and bacterial richness. We highlight the prospect of future experimental studies on the impact of changing environmental conditions associated with global change on environment-host–pathogen interactions in the AF.
Lipid metabolism in Calanus finmarchicus is sensitive to variations in predation risk and food availability
Authors: Skottene Elise , Tarrant Ann M. , Altin Dag , Olsen Rolf Erik , Choquet Marvin , Kvile Kristina Ø. 
Published: December 2020

AbstractLate developmental stages of the marine copepods in the genusCalanuscan spend extended periods in a dormant stage (diapause) that is preceded by the accumulation of large lipid stores. We assessed how lipid metabolism during development from the C4 stage to adult is altered in response to predation risk and varying food availability, to ultimately understand more of the metabolic processes during development inCalanuscopepods. We used RNA sequencing to assess if perceived predation risk in combination with varied food availability affects expression of genes associated with lipid metabolism and diapause preparation inC. finmarchicus. The lipid metabolism response to predation risk differed depending on food availability, time and life stage. Predation risk caused upregulation of lipid catabolism with high food, and downregulation with low food. Under low food conditions, predation risk disrupted lipid accumulation. The copepods showed no clear signs of diapause preparation, supporting earlier observations of the importance of multiple environmental cues in inducing diapause inC. finmarchicus. This study demonstrates that lipid metabolism is a sensitive endpoint for the interacting environmental effects of predation pressure and food availability. As diapause may be controlled by lipid accumulation, our findings may contribute towards understanding processes that can ultimately influence diapause timing.
The diagnostic accuracy of isothermal nucleic acid point-of-care tests for human coronaviruses: A systematic review and meta-analysis
Authors: Subsoontorn Pakpoom , Lohitnavy Manupat , Kongkaew Chuenjid 
Published: December 2020

AbstractMany recent studies reported coronavirus point-of-care tests (POCTs) based on isothermal amplification. However, the performances of these tests have not been systematically evaluated. Cochrane Handbook for Systematic Reviews of Diagnostic Test Accuracy was used as a guideline for conducting this systematic review. We searched peer-reviewed and preprint articles in PubMed, BioRxiv and MedRxiv up to 28 September 2020 to identify studies that provide data to calculate sensitivity, specificity and diagnostic odds ratio (DOR). Quality Assessment of Diagnostic Accuracy Studies 2 (QUADAS-2) was applied for assessing quality of included studies and Preferred Reporting Items for a Systematic Review and Meta-analysis of Diagnostic Test Accuracy Studies (PRISMA-DTA) was followed for reporting. We included 81 studies from 65 research articles on POCTs of SARS, MERS and COVID-19. Most studies had high risk of patient selection and index test bias but low risk in other domains. Diagnostic specificities were high (> 0.95) for included studies while sensitivities varied depending on type of assays and sample used. Most studies (n = 51) used reverse transcription loop-mediated isothermal amplification (RT-LAMP) to diagnose coronaviruses. RT-LAMP of RNA purified from COVID-19 patient samples had pooled sensitivity at 0.94 (95% CI: 0.90–0.96). RT-LAMP of crude samples had substantially lower sensitivity at 0.78 (95% CI: 0.65–0.87). Abbott ID Now performance was similar to RT-LAMP of crude samples. Diagnostic performances by CRISPR and RT-LAMP on purified RNA were similar. Other diagnostic platforms including RT- recombinase assisted amplification (RT-RAA) and SAMBA-II also offered high sensitivity (> 0.95). Future studies should focus on the use of un-bias patient cohorts, double-blinded index test and detection assays that do not require RNA extraction.
Metabotropic glutamate receptor 1 is associated with unfavorable prognosis in ER-negative and triple-negative breast cancer
Authors: Bastiaansen Anna E. M. , Timmermans A. Mieke , Smid Marcel , van Deurzen Carolien H. M. , Hulsenboom Esther S. P. , Prager-van der Smissen Wendy J. C. , Foekens Renée , Trapman-Jansen Anita M. A. C. , Sillevis Smitt Peter A. E. , Luider Theo M. , Martens John W. M. , vanDuijn Martijn M. 
Published: December 2020

AbstractNew therapies are an urgent medical need in all breast cancer subgroups. Metabotropic glutamate receptor 1 (mGluR1) is suggested as a potential new molecular target. We examined the prevalence mGluR1 expression in different clinically relevant breast cancer subgroups and determined its association with prognosis. In this retrospective cohort, 394 consecutive primary breast cancer tissues were incorporated into a tissue microarray and immunohistochemically stained for mGluR1. The prevalence of mGluR1 protein expression in different breast cancer subgroups was evaluated and correlated with metastasis-free survival (MFS) and overall survival (OS). In total, 56% (n = 219) breast cancer tissues had mGluR1 expression. In estrogen receptor (ER)-negative tumors, 31% (n = 18/58) had mGluR1 expression that was significantly associated with MFS (HR 5.00, 95% CI 1.03–24.35, p = 0.046) in multivariate analysis, independently from other prognostic factors. Of the 44 triple-negative breast cancer (TNBC), 25% (n = 11) expressed mGluR1. mGluR1 expression in TNBC was significantly associated with shorter MFS (HR 8.60, 95% CI 1.06–20.39, p = 0.044) and with poor OS (HR 16.07, 95% CI 1.16–223.10, p = 0.039). In conclusion, mGluR1 is frequently expressed in breast cancer. In ER-negative breast cancer and in TNBC mGluR1 protein expression is an unfavorable prognostic marker. This study provides rationale to explore mGluR1 as a novel target for breast cancer treatment, especially for the more aggressive TNBC.