bluuebunny/crossref_metadata_2025_split huggingface dataset:
The cytosine methylation landscape of spring barley revealed by a new reduced representation bisulfite sequencing pipeline, WellMeth
Authors: Malinowska Marta , Nagy Istvan , Wagemaker Cornelis A. M. , Ruud Anja K. , Svane Simon F. , Thorup‐Kristensen Kristian , Jensen Christian S. , Eriksen Birger , Krusell Lene , Jahoor Ahmed , Jensen Jens , Eriksen Lars Bonde , Asp Torben 
Published: November 2020

AbstractPatterns and level of cytosine methylation vary widely among plant species and are associated with genome size as well as the proportion of transposons and other repetitive elements in the genome. We explored epigenetic patterns and diversity in a representative proportion of the spring barley (Hordeum vulgare L.) genome across several commercial and historical cultivars. This study adapted a genotyping‐by‐sequencing (GBS) approach for the detection of methylated cytosines in genomic DNA. To analyze the data, we developed WellMeth, a complete pipeline for analysis of reduced representation bisulfite sequencing. WellMeth enabled quantification of context‐specific DNA methylation at the single‐base resolution as well as identification of differentially methylated sites (DMCs) and regions (DMRs). On average, DNA methylation levels were significantly higher than what is commonly observed in many plants species, reaching over 10‐fold higher levels than those in Arabidopsis thaliana (L.) Heynh. in the CHH methylation. Preferential methylation was observed within and at the edges of long‐terminal repeats (LTR) retrotransposons Gypsy and Copia. From a pairwise comparison of cultivars, numerous DMRs could be identified of which more than 5,000 were conserved within the analyzed set of barley cultivars. The subset of regions overlapping with genes showed enrichment in gene ontology (GO) categories associated with chromatin and cellular structure and organization. A significant correlation between genetic and epigenetic distances suggests that a considerable portion of methylated regions is under strict genetic control in barley. The data presented herein represents the first step in efforts toward a better understanding of genome‐level structural and functional aspects of methylation in barley.
Engineering spatiotemporal organization and dynamics in synthetic cells
Authors: Groaz Alessandro , Moghimianavval Hossein , Tavella Franco , Giessen Tobias W. , Vecchiarelli Anthony G. , Yang Qiong , Liu Allen P. 
Published: November 2020

AbstractConstructing synthetic cells has recently become an appealing area of research. Decades of research in biochemistry and cell biology have amassed detailed part lists of components involved in various cellular processes. Nevertheless, recreating any cellular process in vitro in cell‐sized compartments remains ambitious and challenging. Two broad features or principles are key to the development of synthetic cells—compartmentalization and self‐organization/spatiotemporal dynamics. In this review article, we discuss the current state of the art and research trends in the engineering of synthetic cell membranes, development of internal compartmentalization, reconstitution of self‐organizing dynamics, and integration of activities across scales of space and time. We also identify some research areas that could play a major role in advancing the impact and utility of engineered synthetic cells.This article is categorized under:
Biology‐Inspired Nanomaterials > Lipid‐Based Structures
Biology‐Inspired Nanomaterials > Protein and Virus‐Based Structures
Yet another lesson on the stability conditions in multi-Higgs potentials
Authors: Ivanov Igor P. , Vazão Francisco 
Published: November 2020

Abstract
We discuss a rather common but often unnoticed pitfall which arises when deriving the bounded-from-below (BFB) conditions in multi-Higgs models with softly broken global symmetries. Namely, necessary and sufficient BFB conditions derived for the case with an exact symmetry can be ruined by introducing soft symmetry breaking terms. Using S4 and A4-symmetric three-Higgs-doublet models as an example, we argue that all published necessary and sufficient BFB conditions, even those which are correct for the exactly symmetric case, are no longer sufficient if soft symmetry breaking is added. Using the geometric formalism, we derive the exact necessary and sufficient BFB conditions for the 3HDM with the symmetry group S4, either exact or softly broken, and review the situation for the A4-symmetric case.
Post-Minkowskian effective field theory for conservative binary dynamics
Authors: Kälin Gregor , Porto Rafael A. 
Published: November 2020

Abstract
We develop an Effective Field Theory (EFT) formalism to solve for the conservative dynamics of binary systems in gravity via Post-Minkowskian (PM) scattering data. Our framework combines a systematic EFT approach to compute the deflection angle in the PM expansion, together with the ‘Boundary-to-Bound’ (B2B) dictionary introduced in [1, 2]. Due to the nature of scattering processes, a remarkable reduction of complexity occurs both in the number of Feynman diagrams and type of integrals, compared to a direct EFT computation of the potential in a PM scheme. We provide two illustrative examples. Firstly, we compute all the conservative gravitational observables for bound orbits to 2PM, which follow from only one topology beyond leading order. The results agree with those in [1, 2], obtained through the ‘impetus formula’ applied to the classical limit of the one loop amplitude in Cheung et al. [3]. For the sake of comparison we reconstruct the conservative Hamiltonian to 2PM order, which is equivalent to the one derived in [3] from a matching calculation. Secondly, we compute the scattering angle due to tidal effects from the electric- and magnetic-type Love numbers at leading PM order. Using the B2B dictionary we then obtain the tidal contribution to the periastron advance. We also construct a Hamiltonian including tidal effects at leading PM order. Although relying on (relativistic) Feynman diagrams, the EFT formalism developed here does not involve taking the classical limit of a quantum amplitude, neither integrals with internal massive fields, nor additional matching calculations, nor spurious (‘super-classical’) infrared singularities. By construction, the EFT approach can be automatized to all PM orders.
Random boundary geometry and gravity dual of $$ T\overline{T} $$ deformation
Authors: Hirano Shinji , Shigemori Masaki 
Published: November 2020

Abstract
We study the random geometry approach to the $$ T\overline{T} $$
T

T
¯

deformation of 2d conformal field theory developed by Cardy and discuss its realization in a gravity dual. In this representation, the gravity dual of the $$ T\overline{T} $$
T

T
¯

deformation becomes a straightforward translation of the field theory language. Namely, the dual geometry is an ensemble of AdS3 spaces or BTZ black holes, without a finite cutoff, but instead with randomly fluctuating boundary diffeomorphisms. This reflects an increase in degrees of freedom in the renormalization group flow to the UV by the irrelevant $$ T\overline{T} $$
T

T
¯

operator. We streamline the method of computation and calculate the energy spectrum and the thermal free energy in a manner that can be directly translated into the gravity dual language. We further generalize this approach to correlation functions and reproduce the all-order result with universal logarithmic corrections computed by Cardy in a different method. In contrast to earlier proposals, this version of the gravity dual of the $$ T\overline{T} $$
T

T
¯

deformation works not only for the energy spectrum and the thermal free energy but also for correlation functions.
Induction of Cyp450 enzymes by 4-thiazolidinone-based derivatives in 3T3-L1 cells in vitro
Authors: Szychowski Konrad A. , Skóra Bartosz , Kryshchyshyn-Dylevych Anna , Kaminskyy Danylo , Rybczyńska-Tkaczyk Kamila , Lesyk Roman , Gmiński Jan 
Published: November 2020

Abstract4-Thiazolidinones and related derivatives are regarded as privileged structures in medicinal chemistry and a source of new drug-like compounds. To date it is known that thiazolidinones are able to induce CYP1A1 activity in 3T3-L1 cells. Therefore, to extend the knowledge of the mechanism of thiazolidinones in the cell, four chemically synthesized heterocycles were tested on 3T3-L1 cells. The 3T3-L1 cells were exposed to Les-2194, Les-3640, Les-5935, and Les-6166. Our study showed that 1 μM βNF, Les-2194, and Les-6166 decreased the expression of Ahr mRNA. In turn, βNF, Les-2194, and Les-3640 increased the Cyp1a1 mRNA expression at the same time interval. On the other hand, Les-5935 was found to decrease the Cyp1a1 mRNA expression. Interestingly, the expression of Cyp1a2 mRNA was activated only by βNF and Les-2194. The expression of Cyp1b1 mRNA in the 3T3 cell line increased after the βNF and Les-2194 treatment but declined after the exposure to Les-5935 and Les-6166. Moreover, the Les-2194 and Les-5935 compounds were shown to increase the activity of EROD, MROD, and PROD. Les-3640 increased the activity of EROD and decreased the activity of PROD. In turn, the treatment with Les-6166 resulted in an increase in the activity of EROD and a decrease in the activity of MROD and PROD in the 3T3-L1 cells.
Comparison of DAFH and FALDI-like approaches
Authors: Cooper David L. , de Lange Jurgens H. , Ponec Robert 
Published: November 2020

AbstractTwo complementary methodologies for extracting useful insights into electronic structure and bonding from contemporary wavefunctions are compared. The first of these, known as the analysis of domain-averaged Fermi holes (DAFH), mostly provides visually appealing descriptions of the role and the extent of electron sharing in chemical bonding. The second one, known as the fragment, atom, localized, delocalized and interatomic (FALDI) charge density decomposition scheme, uses the partitioning of certain localization and delocalization indices to focus on highly visual contributions associated with individual domains and with pairs of domains, respectively. Four variants of a FALDI-like approach are investigated here in some detail, mostly to establish which of them are the most reliable and the most informative. In addition to ‘full’ calculations that use the correlated pair density, the consequences for the DAFH and FALDI-like procedures of using instead a popular one-electron approximation are explored. Additionally, the geometry dependence of the degree of acceptability of the errors that this introduces for delocalization indices is assessed for different formal bond multiplicities. The familiar molecular test systems employed for these various linked investigations are the breaking of the bonds in H2and in N2, as well as the nature of the bonding in B2H6, as a simple example of multicenter bonding. One of the key outcomes of this study is a clear understanding of how DAFH analysis and a particular variant of FALDI-like analysis could be most profitably deployed to extract complementary insights into more complex and/or controversial bonding situations.
Study on Maternal SNPs of MTHFR Gene and HCY Level Related to Congenital Heart Diseases
Authors: Shi Hui , Yang Shiwei , Lin Ning , Huang Peng , Yu Rongbin , Chen Mei , Wang Lijuan , Jiang Zhixin , Sun Xiaoru 
Published: November 2020

AbstractThe aim of this study is to evaluate the relationship between maternal single nucleotide polymorphisms (SNPs) of methylenetetrahydrofolate reductase (MTHFR) gene with plasma homocysteine (HCY) level and offspring congenital heart diseases (CHDs). 338 mothers with offspring CHDs as case group and 306 mothers of normal children as control group were recruited. Their pregnant histories were interviewed by questionnaire and the MTHFR rsl801133 and rsl801131 were genotyped. The case–control analysis was used to find out the relationship between maternal SNPs of MTHFR gene and offspring CHDs. And the plasma HCY concentration of the mothers of CHDs children was detected. This case–case study was intended to find out the relevance between maternal HCY level and SNPs of MTHFR gene. There were significant differences in the gender of children, occupation of mothers, family history with CHDs, history of abortion, history of adverse pregnancy, early pregnancy health, fetus during pregnancy, pesticide exposure and drug exposure in CHDs group and control group (P < 0.05). MTHFR rs1801133 was significantly associated with their offspring CHDs in mothers. The polymorphism of maternal MTHFR rs1801133 increased plasma HCY level, especially the homozygous mutation. Besides the environmental factors, our results suggested that the maternal MTHFR rs1801133 polymorphism might be a risk factor of their offspring CHDs, which may be due to the hyperhomocysteinemia by abnormal metabolism of HCY.
Predicting tumor response and outcome of second-look surgery with 18F-FDG PET/CT: insights from the GINECO CHIVA phase II trial of neoadjuvant chemotherapy plus nintedanib in stage IIIc-IV FIGO ovarian cancer
Authors: Aide Nicolas , Fauchille Pauline , Coquan Elodie , Ferron Gwenael , Combe Pierre , Meunier Jérome , Alexandre Jerôme , Berton Dominique , Leary Alexandra , De Rauglaudre Gaétan , Bonichon Nathalie , Pujade Lauraine Eric , Joly Florence 
Published: November 2020

Abstract
Background
This ancillary study aimed to evaluate 18F-FDG PET parameter changes after one cycle of treatment compared to baseline in patients receiving first-line neoadjuvant anti-angiogenic nintedanib combined to paclitaxel-carboplatin chemotherapy or chemotherapy plus placebo and to evaluate the ability of 18F-FDG PET parameters to predict progression-free survival (PFS), overall survival (OS), and success of second-look surgery.

Materials and methods
Central review was performed by two readers blinded to the received treatment and to the patients’ outcome, in consensus, by computing percentage change in PET metrics within a volume of interest encompassing the entire tumor burden. EORTC and PERCIST criteria were applied to classify patients as responders (partial metabolic response and complete metabolic response) or non-responders (stable metabolic disease and progressive metabolic disease). Also analyzed was the percentage change in metabolic active tumor volume (MATV) and total lesion glycolysis (TLG).

Results
Twenty-four patients were included in this ancillary study: 10 received chemotherapy + placebo and 14 chemotherapy + nintedanib. PERCIST and EORTC criteria showed similar discriminative power in predicting PSF and OS. Variation in MATV/TLG did not predict PFS or OS, and no optimal threshold could be found for MATV/TLG for predicting survival. Complete cytoreductive surgery (no residual disease versus residual disease < 0.25 cm/0.25–2.5 cm/> 2.5 cm) was more frequent in responders versus non-responders (P = 0.002 for PERCIST and P = 0.02 for EORTC criteria). No correlation was observed between the variation of PET data and the variation of CA-125 blood level between baseline sample and that performed contemporary to the interim PET, but a statistically significant correlation was observed between ΔSULpeak and ΔCA-125 between baseline sample and that performed after the second cycle.

Conclusion
18F-FDG PET using EORTC or PERCIST criteria appeared to be a useful tool in ovarian cancer trials to analyze early tumor response, and predict second-look surgery outcome and survival. An advantage of PERCIST is the correlation of ΔSULpeak and ΔCA-125, PET response preceding tumor markers response by 1 month. Neither MATV nor TLG was useful in predicting survival.

Trial registration
NCT01583322 ARCAGY/ GINECO GROUP GINECO-OV119, 24 April 2012
Heterogeneity in populations of enterohaemorrhagic Escherichia coli undergoing d-serine adaptation
Authors: O’Boyle Nicky , Roe Andrew J. 
Published: November 2020

AbstractPhenotypic and genetic heterogeneities are conserved features of prokaryotic populations. During periods of stress, this programmed diversity increases the likelihood that variants within the population will survive the adverse conditions, allowing for proliferation. Phenotypic heterogeneity can have a mutational or indeed a non-mutational basis as observed in bet-hedging strategies adopted by antibiotic-tolerant persister cells. Genetic variants can arise by phase variation (slip-strand mispairing, promoter inversions etc.), nucleotide polymorphisms resulting from replication errors or larger rearrangements such as deletions and insertions. In the face of selective pressures, these alterations may be neutral, beneficial or deleterious.We recently described the genetic basis of tolerance to a normally toxic metabolite, d-serine (d-ser) in enterohaemorrhagic E. coli (EHEC). Here we summarize our work in the context of population dynamics, provide further discussion on the distinction between these tolerance mechanisms and the importance of heterogeneity for maximising adaptive potential.
Datasets for the CMIP6 Scenario Model Intercomparison Project (ScenarioMIP) Simulations with the Coupled Model CAS FGOALS-f3-L
Authors: Zhao Shuwen , Yu Yongqiang , Lin Pengfei , Liu Hailong , He Bian , Bao Qing , Guo Yuyang , Hua Lijuan , Chen Kangjun , Wang Xiaowei 
Published: November 2020

AbstractThe datasets for the tier-1 Scenario Model Intercomparison Project (ScenarioMIP) experiments from the Chinese Academy of Sciences (CAS) Flexible Global Ocean-Atmosphere-Land System model, finite-volume version 3 (CAS FGOALS-f3-L) are described in this study. ScenarioMIP is one of the core MIP experiments in phase 6 of the Coupled Model Intercomparison Project (CMIP6). Considering future CO2, CH4, N2O and other gases’ concentrations, as well as land use, the design of ScenarioMIP involves eight pathways, including two tiers (tier-1 and tier-2) of priority. Tier-1 includes four combined Shared Socioeconomic Pathways (SSPs) with radiative forcing, i.e., SSP1-2.6, SSP2-4.5, SSP3-7.0 and SSP5-8.5, in which the globally averaged radiative forcing at the top of the atmosphere around the year 2100 is approximately 2.6, 4.5, 7.0 and 8.5 W m−2, respectively. This study provides an introduction to the ScenarioMIP datasets of this model, such as their storage location, sizes, variables, etc. Preliminary analysis indicates that surface air temperatures will increase by about 1.89°C, 3.07°C, 4.06°C and 5.17°C by around 2100 under these four scenarios, respectively. Meanwhile, some other key climate variables, such as sea-ice extension, precipitation, heat content, and sea level rise, also show significant long-term trends associated with the radiative forcing increases. These datasets will help us understand how the climate will change under different anthropogenic and radiative forcings.
Early changes in laboratory parameters are predictors of mortality and ICU admission in patients with COVID-19: a systematic review and meta-analysis
Authors: Kiss Szabolcs , Gede Noémi , Hegyi Péter , Németh Dávid , Földi Mária , Dembrovszky Fanni , Nagy Bettina , Juhász Márk Félix , Ocskay Klementina , Zádori Noémi , Molnár Zsolt , Párniczky Andrea , Hegyi Péter Jenő , Szakács Zsolt , Pár Gabriella , Erőss Bálint , Alizadeh Hussain 
Published: November 2020

Abstract
Despite the growing knowledge of the clinicopathological features of COVID-19, the correlation between early changes in the laboratory parameters and the clinical outcomes of patients is not entirely understood. In this study, we aimed to assess the prognostic value of early laboratory parameters in COVID-19. We conducted a systematic review and meta-analysis based on the available literature in five databases. The last search was on July 26, 2020, with key terms related to COVID-19. Eligible studies contained original data of at least ten infected patients and reported on baseline laboratory parameters of patients. We calculated weighted mean differences (WMDs) for continuous outcomes and odds ratios (ORs) with 95% confidence intervals. 93 and 78 studies were included in quantitative and qualitative syntheses, respectively. Higher baseline total white blood cell count (WBC), C-reactive protein (CRP), lactate-dehydrogenase (LDH), creatine kinase (CK), D-dimer and lower absolute lymphocyte count (ALC) (WMDALC = − 0.35 × 109/L [CI − 0.43, − 0.27], p < 0.001, I2 = 94.2%; < 0.8 × 109/L, ORALC = 3.74 [CI 1.77, 7.92], p = 0.001, I2 = 65.5%) were all associated with higher mortality rate. On admission WBC, ALC, D-dimer, CRP, LDH, and CK changes could serve as alarming prognostic factors. The correct interpretation of laboratory abnormalities can guide therapeutic decisions, especially in early identification of potentially critical cases. This meta-analysis should help to allocate resources and save lives by enabling timely intervention.
Patterns of care and follow-up care of patients with uveal melanoma in German-speaking countries: a multinational survey of the German Dermatologic Cooperative Oncology Group (DeCOG)
Authors:   the German Dermatologic Cooperative Oncology Group (DeCOG, committee ocular melanoma), Steeb Theresa , Wessely Anja , Alter Mareike , Bayerl Christiane , Bender Armin , Bruning Guido , Dabrowski Evelyn , Debus Dirk , Devereux Nina , Dippel Edgar , Drexler Konstantin , Dücker Pia , Dummer Reinhard , Emmert Steffen , Elsner Peter , Enk Alexander , Gebhardt Christoffer , Gesierich Anja , Goebeler Matthias , Goerdt Sergij , Goetze Steven , Gutzmer Ralf , Haferkamp Sebastian , Hansel Gesina , Hassel Jessica C. , Heinzerling Lucie , Kähler Katharina C. , Kaume Kjell M. , Krapf Wolfgang , Kreuzberg Nicole , Lehmann Percy , Livingstone Elisabeth , Löffler Harald , Loquai Carmen , Mauch Cornelia , Mangana Johanna , Meier Friedegund , Meissner Markus , Moritz Rose K. C. , Maul Lara Valeska , Müller Verena , Mohr Peter , Navarini Alexander , Van Nguyen Ahn , Pfeiffer Christiane , Pföhler Claudia , Posch Christian , Richtig Erika , Rompel Rainer , Sachse Michael M. , Sauder Stefanie , Schadendorf Dirk , Schatton Kerstin , Schulze Hans-Joachim , Schultz Erwin , Schilling Bastian , Schmuth Matthias , Simon Jan. C. , Streit Markus , Terheyden Patrick , Thiem Alexander , Tüting Thomas , Welzel Julia , Weyandt Gerhard , Wesselmann Ulrich , Wollina Uwe , Ziemer Mirjana , Zimmer Lisa , Zutt Markus , Berking Carola , Schlaak Max , Heppt Markus V. 
Published: November 2020

Abstract
Purpose
Uveal melanoma (UM) is an orphan cancer of high unmet medical need. Current patterns of care and surveillance remain unclear as they are situated in an interdisciplinary setting.

Methods
A questionnaire addressing the patterns of care and surveillance in the management of patients with uveal melanoma was distributed to 70 skin cancer centers in Austria, Germany and Switzerland. Frequency distributions of responses for each item of the questionnaire were calculated.

Results
44 of 70 (62.9%) skin cancer centers completed the questionnaire. Thirty-nine hospitals were located in Germany (88.6%), three in Switzerland (6.8%) and two in Austria (4.5%). The majority (68.2%) represented university hospitals. Most patients with metastatic disease were treated in certified skin cancer centers (70.7%, 29/41). Besides, the majority of patients with UM were referred to the respective skin cancer center by ophthalmologists (87.2%, 34/39). Treatment and organization of follow-up of patients varied across the different centers. 35.1% (14/37) of the centers stated to not perform any screening measures.

Conclusion
Treatment patterns of patients with uveal melanoma in Germany, Austria and Switzerland remain extremely heterogeneous. A guideline for the treatment and surveillance is urgently needed.