bluuebunny/crossref_metadata_2025_split huggingface dataset:
Electrodeposited WS2 monolayers on patterned graphene
Authors: Noori Y J , Thomas S , Ramadan S , Greenacre V K , Abdelazim N M , Han Y , Zhang J , Beanland R , Hector A L , Klein N , Reid G , Bartlett P N , de Groot C H 
Published: November 2021

Abstract
The development of scalable techniques to make two-dimensional (2D) material heterostructures is a major obstacle that needs to be overcome before these materials can be implemented in device technologies. Electrodeposition is an industrially compatible deposition technique that offers unique advantages in scaling 2D heterostructures. In this work, we demonstrate the electrodeposition of atomic layers of WS2 over graphene electrodes using a single source precursor. Using conventional microfabrication techniques, graphene was patterned to create micro-electrodes where WS2 was site-selectively deposited to form 2D heterostructures. We used various characterization techniques, including atomic force microscopy, transmission electron microscopy, Raman spectroscopy and x-ray photoelectron spectroscopy to show that our electrodeposited WS2 layers are highly uniform and can be grown over graphene at a controllable deposition rate. This technique to selectively deposit transition metal dichalcogenides over microfabricated graphene electrodes paves the way towards wafer-scale production of 2D material heterostructures for nanodevice applications.
Deeptime: a Python library for machine learning dynamical models from time series data
Authors: Hoffmann Moritz , Scherer Martin , Hempel Tim , Mardt Andreas , de Silva Brian , Husic Brooke E , Klus Stefan , Wu Hao , Kutz Nathan , Brunton Steven L , Noé Frank 
Published: November 2021

Abstract
Generation and analysis of time-series data is relevant to many quantitative fields ranging from economics to fluid mechanics. In the physical sciences, structures such as metastable and coherent sets, slow relaxation processes, collective variables, dominant transition pathways or manifolds and channels of probability flow can be of great importance for understanding and characterizing the kinetic, thermodynamic and mechanistic properties of the system. Deeptime is a general purpose Python library offering various tools to estimate dynamical models based on time-series data including conventional linear learning methods, such as Markov state models (MSMs), Hidden Markov Models and Koopman models, as well as kernel and deep learning approaches such as VAMPnets and deep MSMs. The library is largely compatible with scikit-learn, having a range of Estimator classes for these different models, but in contrast to scikit-learn also provides deep Model classes, e.g. in the case of an MSM, which provide a multitude of analysis methods to compute interesting thermodynamic, kinetic and dynamical quantities, such as free energies, relaxation times and transition paths. The library is designed for ease of use but also easily maintainable and extensible code. In this paper we introduce the main features and structure of the deeptime software. Deeptime can be found under https://deeptime-ml.github.io/.
Theoretical evidence that root penetration ability interacts with soil compaction regimes to affect nitrate capture
Authors: Strock Christopher F , Rangarajan Harini , Black Christopher K , Schäfer Ernst D , Lynch Jonathan P 
Published: November 2021

Abstract

Background and Aims
Although root penetration of strong soils has been intensively studied at the scale of individual root axes, interactions between soil physical properties and soil foraging by whole plants are less clear. Here we investigate how variation in the penetration ability of distinct root classes and bulk density profiles common to real-world soils interact to affect soil foraging strategies.

Methods
We utilize the functional–structural plant model ‘OpenSimRoot’ to simulate the growth of maize (Zea mays) root systems with variable penetration ability of axial and lateral roots in soils with (1) uniform bulk density, (2) plow pans and (3) increasing bulk density with depth. We also modify the availability and leaching of nitrate to uncover reciprocal interactions between these factors and the capture of mobile resources.

Key Results
Soils with plow pans and bulk density gradients affected overall size, distribution and carbon costs of the root system. Soils with high bulk density at depth impeded rooting depth and reduced leaching of nitrate, thereby improving the coincidence of nitrogen and root length. While increasing penetration ability of either axial or lateral root classes produced root systems of comparable net length, improved penetration of axial roots increased allocation of root length in deeper soil, thereby amplifying N acquisition and shoot biomass. Although enhanced penetration ability of both root classes was associated with greater root system carbon costs, the benefit to plant fitness from improved soil exploration and resource capture offset these.

Conclusions
While lateral roots comprise the bulk of root length, axial roots function as a scaffold determining the distribution of these laterals. In soils with high soil strength and leaching, root systems with enhanced penetration ability of axial roots have greater distribution of root length at depth, thereby improving capture of mobile resources.
Genomic style: yet another deep-learning approach to characterize bacterial genome sequences
Authors: Yoshimura Yuka , Hamada Akifumi , Augey Yohann , Akiyama Manato , Sakakibara Yasubumi 
Published: November 2021

Abstract

Motivation
Biological sequence classification is the most fundamental task in bioinformatics analysis. For example, in metagenome analysis, binning is a typical type of DNA sequence classification. In order to classify sequences, it is necessary to define sequence features. The k-mer frequency, base composition and alignment-based metrics are commonly used. On the other hand, in the field of image recognition using machine learning, image classification is broadly divided into those based on shape and those based on style. A style matrix was introduced as a method of expressing the style of an image (e.g. color usage and texture).

Results
We propose a novel sequence feature, called genomic style, inspired by image classification approaches, for classifying and clustering DNA sequences. As with the style of images, the DNA sequence is considered to have a genomic style unique to the bacterial species, and the style matrix concept is applied to the DNA sequence. Our main aim is to introduce the genomics style as yet another basic sequence feature for metagenome binning problem in replace of the most commonly used sequence feature k-mer frequency. Performance evaluations showed that our method using a style matrix has the potential for accurate binning when compared with state-of-the-art binning tools based on k-mer frequency.

Availability and implementation
The source code for the implementation of this genomic style method, along with the dataset for the performance evaluation, is available from https://github.com/friendflower94/binning-style.

Supplementary information
Supplementary data are available at Bioinformatics Advances online.
Geodispersal of the Typical Neotropical cenocron from South America to the Mexican Transition Zone: a cladistic biogeographical test
Authors: López-García Margarita M , Morrone Juan J 
Published: November 2021

AbstractAnalysis of the biotic assembly of the Mexican Transition Zone (MTZ) is challenging because of the convergence of taxa with different origins and biogeographical histories. The typical Neotropical cenocron corresponds to genera widespread in South America that might have dispersed to the MTZ in the Pliocene–Holocene. It has been exemplified with distributional patterns of several plant and animal taxa; however, their historical congruence has not been tested. We examined the historical relationships among the areas of endemism where Typical Neotropical taxa are found through a cladistic biogeographical analysis to determine whether they have dispersed simultaneously, showing a geodispersal pattern. We searched for Neotropical clades that dispersed to the MTZ from the Pliocene to the present. The distribution of nine animal clades in seven areas of endemism was analysed by cladistic biogeography. Redundant areas and widespread taxa were treated with paralogy-free and transparent methods. Patterns of area relationships were searched using a parsimony analysis of paralogy-free subtrees. The parsimony analysis found a single resolved tree showing a general pattern of area relationships: (Chacoan ((South Brazilian (Boreal Brazilian + Lesser Antilles)), (South American Pacific (Mesoamerican-Central America + Western Mexico)))). Distributional and phylogenetic information on the groups analysed contrast with a previous cladistic biogeographical analysis that has shown different area relationships, thus supporting the general hypothesis of a geodispersal event of the Typical Neotropical cenocron in the MTZ. Additionally, the analysis provided evidence of vicariant events related to the lifting of the Northern Andes and climatic changes during the Pleistocene.
Phylogeny is a stronger predictor of activity than allometry in an African mammal community
Authors: Kasozi Herbert , Moll Remington J , Kityo Robert M , Montgomery Robert A 
Published: November 2021

AbstractIn promoting coexistence, sympatric species often partition shared resources along spatio-temporal domains. Similarly sized and phylogenetically close species, for instance, partition the times of day in which they are active to limit interference competition. Given that variation in species body mass has evolutionary underpinnings, species activity levels (time spent active in a 24-h daily cycle) within animal communities might be structured by phylogeny. However, few studies have tested this hypothesis across animal communities, and none among medium-sized to large mammals. We quantified the relative contributions of phylogeny and body mass in predicting activity levels in a community of 22 sympatric mammal species in Murchison Falls National Park, Uganda. We show that phylogeny is a stronger predictor of species activity levels than body mass. Our findings provide empirical evidence for the phylogenetic structuring of mammal activity in diverse communities. More broadly, our results suggest that evolutionary relationships mask allometry in predicting species traits in diverse animal communities.
Paediatric Ulcerative Colitis Is a Fibrotic Disease and Is Linked with Chronicity of Inflammation
Authors: Gordon Ilyssa O , Abushamma Suha , Kurowski Jacob A , Holubar Stefan D , Kou Lei , Lyu Ruishen , Rieder Florian 
Published: November 2021

Abstract

Background and Aims
Intestinal fibrosis has recently been characterised in adult ulcerative colitis and may affect motility, diarrhoea, and the symptom of urgency. We aimed to charactersze the presence of fibrosis in paediatric patients with ulcerative colitis, and its link to severity and chronicity of mucosal inflammation, as well as clinical factors of severity.

Methods
We performed a single-centre cross-sectional study in children ages 1–18 years with ulcerative colitis, undergoing colectomy or proctocolectomy. Tissue cross-sections were derived from proximal, mid, and distal colon and rectum, and inflammation and fibrosis were graded based on previously developed scores. Clinical data were collected prospectively.

Results
From 62 patients, 205 intestinal sections were evaluated. Median age at diagnosis was 13 years, 100% had extensive colitis, and all resections were done for refractory disease. The presence, chronicity, and degree of inflammation were linked with the presence of fibrosis. Thickness of the muscularis mucosa was also linked with presence and chronicity of inflammation. The overall submucosal fibrosis burden was associated with prior anti-tumour necrosis factor use.

Conclusions
Paediatric patients with ulcerative colitis exhibit colorectal submucosal fibrosis and muscularis mucosa thickening, which correlate with the presence, chronicity, and degree of mucosal inflammation. Fibrosis should be recognised as a complication of paediatric ulcerative colitis, and ulcerative colitis should be considered a progressive disease.
STAT3 as a target for sensitizing prostate cancer cells to irradiation
Authors: Zhang Qu , Zhou Xiao-Mei , Wei Shao-Zhong , Cui Dian-Sheng , Deng Kang-Li , Liang Gai , Luo Yan , Luo Bo , Liang Xin-Jun 
Published: November 2021

Abstract
Radioresistance of prostate cancer (PCa) is a major factor leading to local failure of radiotherapy. STAT3 is an oncogenic protein that was recently found to be activated in PCa tumors. This study aimed to investigate the radiosensitization effect of targeting STAT3 in PCa tumors. Here, the radiosensitization effect of STAT3 blockade was investigated by clonogenic assay, flow cytometry and western blot analysis in human PCa cells in vitro and in vivo. We demonstrated that STAT3 blockade with a STAT3 inhibitor or siRNA increased the radiosensitivity of PCa cells and that radiation together with STAT3 blockade induced more apoptosis and double-strand breaks (DSBs) than radiation alone in LNCaP cells. In addition, radiation induced STAT3 activation and survivin expression in PCa cells, which was inhibited by STAT3 blockade. Transfection with survivin cDNA attenuated the radiosensitization effect of STAT3 blockade. These effects were further confirmed by in vivo studies, which showed that the STAT3 inhibitor enhanced the treatment efficacy of radiation on LNCaP xenografts with decreased STAT3 activation and survivin expression.
These findings suggest that STAT3 blockade radiosensitizes PCa cells through regulation of survivin. Thus, our study has revealed STAT3 as a potential sensitizer for irradiation in PCa cells. Its clinical application as an adjuvant in radiotherapy of PCa should be explored in the future.
Hybrid simulations of the ring-beam instabilities driven by the pickup ions in the outer heliosheath
Authors: Mousavi Ameneh , Liu Kaijun , Sadeghzadeh Sina 
Published: November 2021

ABSTRACT
One-dimensional hybrid simulations are performed to investigate the plasma instabilities driven by the pickup ions in the outer heliosheath, which are believed to have a ring-beam velocity distribution in general. The modes propagating parallel and antiparallel to the background magnetic field are studied for pickup ion ring-beam distributions of different pickup angles, following the linear kinetic instability analysis presented in our previous work. The simulation results first confirm the unstable modes predicted by the linear analysis and further reveal how the pickup ions are scattered by the excited waves. While the maximum growth rate of the low-frequency, left-helicity waves occurs at the pickup angle of 82° (consistent with the linear analysis results), the saturation level of the fluctuating magnetic field is the highest around 45° pickup angle. For the pickup ion parameters examined, the pitch-angle spread of the pickup ions at the end of the simulations decreases with increasing pickup angle. Our study goes beyond previous studies of the pickup-ion-driven instabilities in the outer heliosheath which mainly focused on ring-like distributions of around 90° pickup angle. With the caveats that the pickup ion parameters are in the Alfvén cyclotron stability gap and that the one-dimensional simulations only include parallel and antiparallel-propagating modes, our results show that the scattering of pickup ions at small pickup angles is limited to one hemisphere so they can drift away from the ribbon direction as required by the spatial retention scenario of the energetic neutral atom ribbon observed by the Interstellar Boundary EXplorer.
Super resolution microscopy reveals how elongating RNA polymerase II and nascent RNA interact with nucleosome clutches
Authors: Castells-Garcia Alvaro , Ed-daoui Ilyas , González-Almela Esther , Vicario Chiara , Ottestrom Jason , Lakadamyali Melike , Neguembor Maria Victoria , Cosma Maria Pia 
Published: November 2021

Abstract
Transcription and genome architecture are interdependent, but it is still unclear how nucleosomes in the chromatin fiber interact with nascent RNA, and which is the relative nuclear distribution of these RNAs and elongating RNA polymerase II (RNAP II). Using super-resolution (SR) microscopy, we visualized the nascent transcriptome, in both nucleoplasm and nucleolus, with nanoscale resolution. We found that nascent RNAs organize in structures we termed RNA nanodomains, whose characteristics are independent of the number of transcripts produced over time. Dual-color SR imaging of nascent RNAs, together with elongating RNAP II and H2B, shows the physical relation between nucleosome clutches, RNAP II, and RNA nanodomains. The distance between nucleosome clutches and RNA nanodomains is larger than the distance measured between elongating RNAP II and RNA nanodomains. Elongating RNAP II stands between nascent RNAs and the small, transcriptionally active, nucleosome clutches. Moreover, RNA factories are small and largely formed by few RNAP II. Finally, we describe a novel approach to quantify the transcriptional activity at an individual gene locus. By measuring local nascent RNA accumulation upon transcriptional activation at single alleles, we confirm the measurements made at the global nuclear level.
An epigenetic switch activates bacterial quorum sensing and horizontal transfer of an integrative and conjugative element
Authors: Ramsay Joshua P , Bastholm Tahlia R , Verdonk Callum J , Tambalo Dinah D , Sullivan John T , Harold Liam K , Panganiban Beatrice A , Colombi Elena , Perry Benjamin J , Jowsey William , Morris Calum , Hynes Michael F , Bond Charles S , Cameron Andrew D S , Yost Christopher K , Ronson Clive W 
Published: November 2021

AbstractHorizontal transfer of the integrative and conjugative element ICEMlSymR7A converts non-symbiotic Mesorhizobium spp. into nitrogen-fixing legume symbionts. Here, we discover subpopulations of Mesorhizobium japonicum R7A become epigenetically primed for quorum-sensing (QS) and QS-activated horizontal transfer. Isolated populations in this state termed R7A* maintained these phenotypes in laboratory culture but did not transfer the R7A* state to recipients of ICEMlSymR7A following conjugation. We previously demonstrated ICEMlSymR7A transfer and QS are repressed by the antiactivator QseM in R7A populations and that the adjacently-coded DNA-binding protein QseC represses qseM transcription. Here RNA-sequencing revealed qseM expression was repressed in R7A* cells and that RNA antisense to qseC was abundant in R7A but not R7A*. Deletion of the antisense-qseC promoter converted cells into an R7A*-like state. An adjacently coded QseC2 protein bound two operator sites and repressed antisense-qseC transcription. Plasmid overexpression of QseC2 stimulated the R7A* state, which persisted following curing of this plasmid. The epigenetic maintenance of the R7A* state required ICEMlSymR7A-encoded copies of both qseC and qseC2. Therefore, QseC and QseC2, together with their DNA-binding sites and overlapping promoters, form a stable epigenetic switch that establishes binary control over qseM transcription and primes a subpopulation of R7A cells for QS and horizontal transfer.
Tubular phosphate handling: references from child to adulthood in the era of standardized serum creatinine
Authors: Derain Dubourg Laurence , Aurelle Manon , Chardon Laurence , Flammier Sacha , Lemoine Sandrine , Bacchetta Justine 
Published: November 2021

ABSTRACT

Background
The assessment of phosphate homeostasis in clinical practice relies not only on circulating phosphate levels but also on phosphate tubular reabsorption, ideally assessed using the tubular maximum phosphate reabsorption per glomerular filtration rate (TmP/GFR). TmP/GFR reference values were established before the onset of isotope-dilution mass spectrometry-standardized (IDMS) creatinine assays and thus need to be updated. Our objective is to provide reference values for TmP/GFR from childhood to adulthood, using the gold-standard of GFR assessment and IDMS-standardized creatinine values.

Methods
We retrospectively analysed all the inulin and iohexol clearances [measured glomerular filtration rate (mGFR)] performed in children and in adults screened for a living-donation in our unit since the beginning of IDMS-creatinine assays. TmP/GFR was calculated on a fasting sample, using the conventional formula without correction for tubular reabsorption of phosphate (TRP) in subjects below 19 years of age.

Results
A total of 2051 subjects (1711 children, 340 adults), aged from 1.9 to 73.4 years with normal GFR, normal phosphate and normal calcium levels, were included for TmP/GFR analysis. As expected, there was a progressive decrease along puberty in both genders of plasma phosphate and TmP/GFR, the decrease occurring earlier in girls. After the age of 19 years, there was a stabilization of plasma phosphate and TmP/GFR levels until the age of 55 years, phosphate levels and TmP/GFR being slightly lower in men than in women.

Conclusion
We present the largest cohort describing TmP/GFR reference values in the era of IDMS-standardized creatinine assays. We believe that these data will help physicians to better diagnose and manage patients with abnormal phosphate metabolism in daily clinical routine.
COVID-19 vaccination uptake amongst ethnic minority communities in England: a linked study exploring the drivers of differential vaccination rates
Authors: Gaughan Charlotte Hannah , Razieh Cameron , Khunti Kamlesh , Banerjee Amitava , Chudasama Yogini V , Davies Melanie J , Dolby Ted , Gillies Clare L , Lawson Claire , Mirkes Evgeny M , Morgan Jasper , Tingay Karen , Zaccardi Francesco , Yates Thomas , Nafilyan Vahe 
Published: November 2021

AbstractBackgroundDespite generally high coronavirus disease 2019 (COVID-19) vaccination rates in the UK, vaccination hesitancy and lower take-up rates have been reported in certain ethnic minority communities.MethodsWe used vaccination data from the National Immunisation Management System (NIMS) linked to the 2011 Census and individual health records for subjects aged ≥40 years (n = 24 094 186). We estimated age-standardized vaccination rates, stratified by ethnic group and key sociodemographic characteristics, such as religious affiliation, deprivation, educational attainment, geography, living conditions, country of birth, language skills and health status. To understand the association of ethnicity with lower vaccination rates, we conducted a logistic regression model adjusting for differences in geographic, sociodemographic and health characteristics. ResultsAll ethnic groups had lower age-standardized rates of vaccination compared with the white British population, whose vaccination rate of at least one dose was 94% (95% CI: 94%–94%). Black communities had the lowest rates, with 75% (74–75%) of black African and 66% (66–67%) of black Caribbean individuals having received at least one dose. The drivers of these lower rates were partly explained by accounting for sociodemographic differences. However, modelled estimates showed significant differences remained for all minority ethnic groups, compared with white British individuals.ConclusionsLower COVID-19 vaccination rates are consistently observed amongst all ethnic minorities.