bluuebunny/crossref_metadata_2025_split huggingface dataset:
Draft genome of a novel methanotrophic Methylobacter sp. from the volcanic soils of Pantelleria Island
Authors: Hogendoorn Carmen , Picone Nunzia , van Hout Femke , Vijverberg Sophie , Poghosyan Lianna , van Alen Theo A. , Frank Jeroen , Pol Arjan , Gagliano Antonia L. , Jetten Mike S. M. , D’Alessandro Walter , Quatrini Paola , Op den Camp Huub J. M. 
Published: February 2021

AbstractThe genus Methylobacter is considered an important and often dominant group of aerobic methane-oxidizing bacteria in many oxic ecosystems, where members of this genus contribute to the reduction of CH4 emissions. Metagenomic studies of the upper oxic layers of geothermal soils of the Favara Grande, Pantelleria, Italy, revealed the presence of various methane-oxidizing bacteria, and resulted in a near complete metagenome assembled genome (MAG) of an aerobic methanotroph, which was classified as a Methylobacter species. In this study, the Methylobacter sp. B2 MAG was used to investigate its metabolic potential and phylogenetic affiliation. The MAG has a size of 4,086,539 bp, consists of 134 contigs and 3955 genes were found, of which 3902 were protein coding genes. All genes for CH4 oxidation to CO2 were detected, including pmoCAB encoding particulate methane monooxygenase (pMMO) and xoxF encoding a methanol dehydrogenase. No gene encoding a formaldehyde dehydrogenase was present and the formaldehyde to formate conversion follows the tetrahydromethanopterin (H4MPT) pathway. “Ca. Methylobacter favarea” B2 uses the Ribulose-Mono-Phosphate (RuMP) pathway for carbon fixation. Analysis of the MAG indicates that Na+/H+ antiporters and the urease system might be important in the maintenance of pH homeostasis of this strain to cope with acidic conditions. So far, thermoacidophilic Methylobacter species have not been isolated, however this study indicates that members of the genus Methylobacter can be found in distinct ecosystems and their presence is not restricted to freshwater or marine sediments.
Regional myocardial function at preclinical disease stage of hypertrophic cardiomyopathy in female gene variant carriers
Authors: Parbhudayal Rahana Y. , Seegers Celine , Croisille Pierre , Clarysse Patrick , van Rossum Albert C. , Germans Tjeerd , van der Velden Jolanda 
Published: February 2021

AbstractWe recently showed more severe diastolic dysfunction at the time of myectomy in female compared to male patients with obstructive hypertrophic cardiomyopathy. Early recognition of aberrant cardiac contracility using cardiovascular magnetic resonance (CMR) imaging may identify women at risk of cardiac dysfunction. To define myocardial function at an early disease stage, we studied regional cardiac function using CMR imaging with tissue tagging in asymptomatic female gene variant carriers. CMR imaging with tissue tagging was done in 13 MYBPC3, 11 MYH7 and 6 TNNT2 gene carriers and 16 age-matched controls. Regional peak circumferential strain was derived from tissue tagging images of the basal and midventricular segments of the septum and lateral wall. Left ventricular wall thickness and global function were comparable between MYBPC3, MYH7, TNNT2 carriers and controls. MYH7 gene variant carriers showed a different strain pattern as compared to the other groups, with higher septal peak circumferential strain at the basal segments compared to the lateral wall, whereas MYBPC3, TNNT2 carriers and controls showed higher strain at the lateral wall compared to the septum. Only subtle gene-specific changes in strain pattern occur in the myocardium preceding development of cardiac hypertrophy. Overall, our study shows that there are no major contractile deficits in asymptomatic females carrying a pathogenic gene variant, which would justify the use of CMR imaging for earlier diagnosis.
Extremely low-resource neural machine translation for Asian languages
Authors: Rubino Raphael , Marie Benjamin , Dabre Raj , Fujita Atushi , Utiyama Masao , Sumita Eiichiro 
Published: February 2021

AbstractThis paper presents a set of effective approaches to handle extremely low-resource language pairs for self-attention based neural machine translation (NMT) focusing on English and four Asian languages. Starting from an initial set of parallel sentences used to train bilingual baseline models, we introduce additional monolingual corpora and data processing techniques to improve translation quality. We describe a series of best practices and empirically validate the methods through an evaluation conducted on eight translation directions, based on state-of-the-art NMT approaches such as hyper-parameter search, data augmentation with forward and backward translation in combination with tags and noise, as well as joint multilingual training. Experiments show that the commonly used default architecture of self-attention NMT models does not reach the best results, validating previous work on the importance of hyper-parameter tuning. Additionally, empirical results indicate the amount of synthetic data required to efficiently increase the parameters of the models leading to the best translation quality measured by automatic metrics. We show that the best NMT models trained on large amount of tagged back-translations outperform three other synthetic data generation approaches. Finally, comparison with statistical machine translation (SMT) indicates that extremely low-resource NMT requires a large amount of synthetic parallel data obtained with back-translation in order to close the performance gap with the preceding SMT approach.
Genomic and pedigree‐based predictive ability for quality traits in tea (Camellia sinensis (L.) O. Kuntze)
Authors: Lubanga Nelson , Massawe Festo , Mayes Sean 
Published: February 2021

AbstractGenetic improvement of quality traits in tea (Camellia sinensis(L.) O. Kuntze) through conventional breeding methods has been limited, because tea quality is a difficult and expensive trait to measure. Genomic selection (GS) is suitable for predicting such complex traits, as it uses genome wide markers to estimate the genetic values of individuals. We compared the prediction accuracies of six genomic prediction models including Bayesian ridge regression (BRR), genomic best linear unbiased prediction (GBLUP), BayesA, BayesB, BayesC and reproducing kernel Hilbert spaces models incorporating the pedigree relationship namely; RKHS-pedigree, RKHS-markers and RKHS markers and pedigree (RKHS-MP) to determine the breeding values for 12 tea quality traits. One hundred and three tea genotypes were genotyped using genotyping-by-sequencing and phenotyped using nuclear magnetic resonance spectroscopy in replicated trials. We also compared the effect of trait heritability and training population size on prediction accuracies. The traits with the highest prediction accuracies were; theogallin (0.59), epicatechin gallate (ECG) (0.56) and theobromine (0.61), while the traits with the lowest prediction accuracies were theanine (0.32) and caffeine (0.39). The performance of all the GS models were almost the same, with BRR (0.53), BayesA (0.52), GBLUP (0.50) and RKHS-MP (0.50) performing slightly better than the others. Heritability estimates were moderate to high (0.35–0.92). Prediction accuracies increased with increasing training population size and trait heritability. We conclude that the moderate to high prediction accuracies observed suggests GS is a promising approach in tea improvement and could be implemented in breeding programmes.
Theoretical and Experimental Results from Laboratory Tests by ILCM
Authors: Cardu M. , Rispoli A. , Iabichino G. , Oreste P. , Vagnon F. 
Published: February 2021

AbstractThe intermediate linear cutting machine (ILCM) is a machine designed to work on an intermediate scale between the full- and the small-scale. The reduced scale involves several advantages compared to full-scale tests, especially in terms of sample supplying and transportation. On the other hand, it has an impact on the testing conditions, resulting in a limitation of the cutting penetration and spacing during the test, as well as in a smaller disc cutter. This affects most of the results, which cannot be directly used for the on-site machine performance prediction. However, some experimental results provided in the literature show that the optimal spacing/penetration ratio is not significantly affected by the changes involved. On this basis, the results obtained from ILCM tests should provide reliable information about the optimal cutting conditions of a tunnel boring machine in massive rock mass. The work performed included the development of some improvements of the testing rig, as well as a modified ILCM testing procedure, according to the one typically used in standard LCM tests. The results provide information about the attitude of the tested lithotypes to mechanical excavation by means of disc tools, including the optimal cutting conditions. Additional work was developed in terms of detailed characterisation of the rock samples involved and assessment of the size distribution of the debris produced during the ILCM tests. Nevertheless, further tests are necessary, in order to assess the consistency of the experimental procedure employed and to investigate the scale effect.
Tackling Lateral Variability Using Surface Waves: A Tomography-Like Approach
Authors: Barone Ilaria , Boaga Jacopo , Carrera Alberto , Flores-Orozco Adrian , Cassiani Giorgio 
Published: February 2021

AbstractLateral velocity variations in the near-surface reflect the presence of buried geological or anthropic structures, and their identification is of interest for many fields of application. Surface wave tomography (SWT) is a powerful technique for detecting both smooth and sharp lateral velocity variations at very different scales. A surface-wave inversion scheme derived from SWT is here applied to a 2-D active seismic dataset to characterize the shape of an urban waste deposit in an old landfill, located 15 km South of Vienna (Austria). First, the tomography-derived inverse problem for the 2-D case is defined: under the assumption of straight rays at the surface connecting sources and receivers, the forward problem for one frequency reduces to a linear relationship between observed phase differences at adjacent receivers and wavenumbers (from which phase velocities are straightforwardly derived). A norm damping regularization constraint is applied to ensure a smooth solution in space: the choice of the damping parameter is made through a minimization process, by which only phase variations of the order of the average wavelength are modelled. The inverse problem is solved for each frequency with a weighted least-squares approach, to take into account the data error variances. An independent multi-offset phase analysis (MOPA) is performed using the same dataset, for comparison: pseudo-sections from the tomography-derived linear inversion and MOPA are very consistent, with the former giving a more continuous result both in space and frequency and less artefacts. Local dispersion curves are finally depth inverted and a quasi-2-D shear wave velocity section is retrieved: we identify a well-defined low velocity zone and interpret it as the urban waste deposit body. Results are consistent with both electrical and electromagnetic measurements acquired on the same line.
Effect of substrate particle size on burrowing of the juvenile freshwater pearl mussel Margaritifera margaritifera
Authors: Hyvärinen Heini , Saarinen-Valta Mari , Mäenpää Eero , Taskinen Jouni 
Published: February 2021

AbstractJuveniles of the endangered freshwater pearl mussel (FPM,Margaritifera margaritifera) live burrowed in stream substrate for the first years of their life. Fine sediments block water exchange within substrate and may cause juvenile mortality and recruitment failure. To better understand the connection between success of juvenile FPM and substrate particle size, it would be important to understand behavioural responses of FPM to varying substrate sizes at this critical life stage. We placed newly detached FPM juveniles in a 7-mm layer of sieved sand sorted into five sizes (< 120, 120–200, 200–250, 250–500 and 500–650 µm) each with 10 replicate dishes, 10 juveniles per dish, with burrowing status monitored for 96 h. Mean dish-specific proportion burrowed (PB) was significantly affected by substrate size, increasing from 52% in the finest sand to 98% in the coarsest sand. Furthermore, the significant substrate × time interaction was observed due to dropped PB (30-34%) in finest sand at 2–4 h time points. Thus, results suggest a clear behavioural response by juvenile FPM to substrate size, with fine sediments triggering surfacing behaviour. Surfacing may indicate stress, can increase predation risk, and expose to drift and/or enable drift of juveniles.
The Association Between β-Dystroglycan in Airway Smooth Muscle and Eosinophils in Allergic Asthma
Authors: Shareef Suhayla H. , Amin Kawa , Janson Christer 
Published: February 2021

Abstract
Allergic asthma (AA) is a complex disorder with heterogeneous features of airway hyperresponsiveness, inflammation, and remodeling. The increase of airway smooth muscle (ASM) mass is a fundamental component of bronchial remodeling in AA, yet the pathophysiological mechanisms and clinical outcomes associated with ASM modulation are still elusive. The objective of this study is to compare the expression level of β-dystroglycan (β-DG) in ASM in AA subjects and a healthy control group and to investigate the relationship between eosinophils and β-DG in ASM in patients with AA. Thirteen AA patients and seven control subjects were analyzed for the ASM area and eosinophil cells. Bronchial biopsies were stained by β-DG and eosinophil cationic protein (ECP) using immunohistochemistry. The proportion of ASM with β-DG staining was greater in those with AA than in the healthy control group (mean (95% CI) (28.3% (23.8–32.7%) vs. 16.4% (14.1–18.5%), P < 0.0001). The number of ECP positive cells was higher in patients with AA than in the control group (4056 (3819–4296) vs. 466 (395–537) cells/mm2P < 0.0001). In AA, the number of ECP positive cells was significantly correlated to the β-DG expression in ASM (r = 0.77, P = 0.002). There is an increased β-DG expression in ASM and a higher number of ECP positive cells in the bronchial biopsy of those with AA than those in the control group. The increased expression of β-DG in ASM in AA subjects correlates with the number of eosinophils, suggesting a role for this cell in airway remodeling in AA.
Cones from quantum groups to tropical flag varieties
Authors: Fang Xin , Fourier Ghislain , Reineke Markus 
Published: February 2021

AbstractWe relate quantum degree cones, parametrizing PBW degenerations of quantized enveloping algebras, to (negative tight monomial) cones introduced by Lusztig in the study of monomials in canonical bases, toK-theoretic cones for quiver representations, and to some maximal prime cones in tropical flag varieties.
Insect diversity across an afro-tropical forest biodiversity hotspot
Authors: Habel Jan Christian , Koc Elisabeth , Gerstmeier Roland , Gruppe Axel , Seibold Sebastian , Ulrich Werner 
Published: February 2021

Abstract
Tropical forests host a remarkable proportion of global arthropod diversity. Yet, arthropod communities living in tropical forests are still poorly studied, particularly for dry forests of Eastern Africa. The aim of this study was to analyse community structures, species richness and relative abundances of insects across a heterogeneous forest consisting of various forest types. We collected insects in the lower canopies with light traps across the Arabuko Sokoke forest, part of the East African coastal forest biodiversity hotspot in southeast Kenya. Sampling was conducted across three forest types and along the forest edge. In total we collected > 250,000 individuals. We grouped these individuals into orders, and beetles into (sub)families. Representatives of the taxonomically well-known beetle families Cerambycidae, Tenebrionidae and Scolytinae were further determined to species level. We subsequently classified these groups into guilds according to their ecological requirements and life-histories. Relative abundances of arthropods strongly differed among taxonomic groups and forest types. Evenness was highest in the heterogeneous natural Brachystegia forest type. The mixed forest type and the forest edges showed intermediate degrees of evenness, while the structurally homogenous Cynometra forest showed comparatively low degrees of evenness.

Implications for insect conservation
We found that taxonomic and guild compositions strongly differed among the forest types. Our findings reveal that structural heterogeneity of a forest is the major driver of insect diversity, community composition, and relative abundance. Our study underlines that the preservation of all three forest types is crucial to maintain the complete diversity of arthropods across all taxonomic groups.
Why understanding-why is contrastive
Authors: Egler Miguel 
Published: February 2021

AbstractContrastivism about interrogative understanding is the view that ‘S understands why p’ posits a three-place epistemic relation between a subject S, a fact p, and an alternative to p, q. This thesis stands in stark opposition to the natural idea that a subject S can be said to understand why psimpliciter. I argue that contrastivism offers the best explanation for the fact that evaluations of the form ‘S understands why p’ vary depending on the alternatives to p under consideration. I also show that contrastivism offers valuable resources with which to explain the gradability of interrogative understanding attributions, as well as the sensitivity of these attributions to the perceived degree of epistemic demandingness of different contexts.
A shift from anaerobic digestion to dark fermentation in glycol ethylene fermentation
Authors: Sołowski Gaweł , Ziminski Tadeusz , Cenian Adam 
Published: February 2021

AbstractAnaerobic digestion of aqueous glycol ethylene was tested. The process lasted two cycles of 7 days, but after the second cycle, high hydrogen production occurred shift to dark fermentation. The biogas production lasted 14 days, obtaining peak values of hydrogen, and then rapidly stopped. In investigations, the following were checked: dependence of hydrogen, methane and hydrogen sulphide in the process. Mixtures of water with glycol ethylene mass ratio from 0.6 to 0.85 were substrates in experiments. The highest methane production was for water ethylene 0.7 ratio 2.85 L of methane with a yield of 178 mL of methane/g VSS (volatile suspended solids) of glycol ethylene. The optimal ratio of water and glycol ethylene was 0.85 25.5 mL of hydrogen (giving yield 1.71 mL of hydrogen/g VSS of glycol ethylene) and 1.71 mL of hydrogen sulphide emission for a 0.6 ratio. Popular polymer industry wastes, glycol ethylene, can be utilised by anaerobic digestion.
Efficient, high-resolution topology optimization method based on convolutional neural networks
Authors: Xue Liang , Liu Jie , Wen Guilin , Wang Hongxin 
Published: February 2021

AbstractTopology optimization is a pioneer design method that can provide various candidates with high mechanical properties. However, high resolution is desired for optimum structures, but it normally leads to a computationally intractable puzzle, especially for the solid isotropic material with penalization (SIMP) method. In this study, an efficient, high-resolution topology optimization method is developed based on the superresolution convolutional neural network (SRCNN) technique in the framework of SIMP. SRCNN involves four processes, namely, refinement, path extraction and representation, nonlinear mapping, and image reconstruction. High computational efficiency is achieved with a pooling strategy that can balance the number of finite element analyses and the output mesh in the optimization process. A combined treatment method that uses 2D SRCNN is built as another speed-up strategy to reduce the high computational cost and memory requirements for 3D topology optimization problems. Typical examples show that the high-resolution topology optimization method using SRCNN demonstrates excellent applicability and high efficiency when used for 2D and 3D problems with arbitrary boundary conditions, any design domain shape, and varied load.
Distribution of tumor-infiltrating-T-lymphocytes and possible tumor-escape mechanisms avoiding immune cell attack in locally advanced adenocarcinomas of the esophagus
Authors: Schoemmel M. , Loeser H. , Kraemer M. , Wagener-Ryczek S. , Hillmer A. , Bruns C. , Thelen M. , Schröder W. , Zander T. , Lechner A. , Buettner R. , Schlösser H. , Gebauer F. , Quaas A. ,   Gastrointestinal Cancer Group Cologne (GCGC), Loeser H. , Zander T. , Gebauer F. , Quaas A. 
Published: February 2021

Abstract
Introduction
The inflammatory microenvironment has emerged as one of the focuses of cancer research. Little is known about the immune environment in esophageal adenocarcinoma (EAC) and possible tumor-escape mechanisms to avoid immune cell attack.

Patients and methods
We measured T cell inflammation (CD3, CD8) in the microenvironment using a standardized software-based evaluation algorithm considering different predefined tumor areas as well as expression of MHC class 1 and PD-L1 on 75 analyzable primarily resected and locally advanced (≥ pT2) EACs. We correlated these findings statistically with clinical data.

Results
Patients with high amounts of T cell infiltration in their tumor center showed a significant survival benefit of 41.4 months compared to 16.3 months in T cell poor tumors (p = 0.025), although CD3 fails to serve as an independent prognostic marker in multivariate analysis. For the invasion zone, a correlation between number of T-cells and overall survival was not detectable. Loss of MHC1 protein expression on tumor cells was seen in 32% and PD-L1 expression using the combined positive score (CPS) in 21.2%. Most likely due to small numbers of cases, both markers are not prognostically relevant, even though PD-L1 expression correlates with advanced tumor stages.

Discussion
Our analyses reveal an outstanding, though not statistically independent, prognostic relevance of T-cell-rich inflammation in our group of EACs, in particular driven by the tumor center. For the first time, we describe that the inner part of the invasion zone in EACs shows significantly fewer T-cells than other tumor segments and is prognostically irrelevant. We also demonstrate that the loss of antigen presenting ability via MHC1 downregulation by the carcinoma cells is a common escape mechanism in EACs. Future work will need to show whether tumors with MHC class 1 loss respond less well to immunotherapy.
MILP formulations for highway petrol station replenishment in initiative distribution mode
Authors: Wei Xin-Tong , Liao Qi , Zhang Hao-Ran , Liang Yong-Tu , Wang Bo-Hong , Xu Ning , Yuan Meng 
Published: February 2021

AbstractTo investigate highway petrol station replenishment in initiative distribution mode, this paper develops a mixed-integer linear programming (MILP) model with minimal operational costs that includes loading costs, unloading costs, transport costs and the costs caused by unpunctual distribution. Based on discrete representation, the working day is divided into equal time intervals, and the truck distribution process is decomposed into a pair of tasks including driving, standby, rest, loading and unloading. Each truck must execute one task during a single interval, and the currently executing task is closely related to the preceding and subsequent tasks. By accounting for predictive time-varying sales at petrol stations, real-time road congestion and a series of operational constraints, the proposed model produces the optimal truck dispatch, namely, a detailed task assignment for all trucks during each time interval. The model is tested on a real-world case of a replenishment system comprising eight highway petrol stations, one depot, one garage and eight trucks to demonstrate its applicability and accuracy.