bluuebunny/crossref_metadata_2025_split huggingface dataset:
Emerging nanotechnological strategies to reshape tumor microenvironment for enhanced therapeutic outcomes of cancer immunotherapy
Authors: Lin Xinyi , Wang Xiaoyan , Gu Qing , Lei Dongqin , Liu Xiaolong , Yao Cuiping 
Published: February 2021

AbstractImmunotherapy has emerged as a novel cancer treatment over the last decade, however, efficacious responses to mono-immunotherapy have only been achieved in a relatively small portion of patients whereas combinational immunotherapies often lead to concurrent side effects. It has been proved that the tumor microenvironment (TME) is responsible for tumor immune escape and the ultimate treatment failure. Recently, there has been remarkable progress in both the understanding of the TME and the applications of nanotechnological strategies, and reviewing the emerging immune-regulatory nanosystems may provide valuable information for specifically modulating the TME at different immune stages. In this review, we focus on comprehending the recently-proposed T-cell-based tumor classification and identifying the most promising targets for different tumor phenotypes, and then summarizing the nanotechnological strategies to best target corresponding immune-related factors. For future precise personalized immunotherapy, tailor-made TME modulation strategies conducted by well-designed nanosystems to alleviate the suppressive TME and then promote anti-tumor immune responses will significantly benefit the clinical outcomes of cancer patients.
Nanozyme-based medicine for enzymatic therapy: progress and challenges
Authors: Wang Qian , Jiang Jing , Gao Lizeng 
Published: February 2021

Abstract
Nanozymes are nanomaterials with enzyme-like characteristics. As a new generation of artificial enzymes, nanozymes have the advantages of low cost, good stability, simple preparation, and easy storage, allowing them to overcome many of the limitations of natural enzymes in enzymatic therapy. Currently, most reported nanozymes exhibit oxidoreductase-like activities and can regulate redox balance in cells. Nanozymes with superoxide dismutase and catalase activity can be used to scavenge reactive oxygen species (ROS) for cell protection, while those with peroxidase and oxidase activity can generate ROS to kill harmful cells, such as tumor cells and bacteria. In this review, we summarize recent progress in nanozyme-based medicine for enzymatic therapy and highlight the opportunities and challenges in this field for future study.
Assessing local CO2 contamination revealed by two near-by high altitude records at Jungfraujoch, Switzerland
Authors: Affolter Stéphane , Schibig Michael , Berhanu Tesfaye , Bukowiecki Nicolas , Steinbacher Martin , Nyfeler Peter , Hervo Maxime , Lauper Jürg , Leuenberger Markus 
Published: February 2021

Abstract
Remote research stations are guarantor of high-quality atmospheric measurements as they are essentially exposed to pristine air masses. However, in a context of increasing touristic pressure for certain sites, attention should be paid to the local anthropogenic emission related to the infrastructure itself. Among emissions, carbon dioxide (CO2) is the most important anthropogenic greenhouse gas and a major contributor to the current global warming. Here, we compared two years of CO2 dry air mole fraction records from Jungfraujoch (Swiss Alps) measured at the Sphinx Laboratory (3580 m a.s.l.; JFJ) and the East Ridge facility (3705 m a.s.l.; JER; horizontal distance of ∼1 km), respectively. Both stations show an overall increase of the annual mean CO2 mole fraction in line with current global trends. On a daily basis, values during the night (00h00–06h00) show robust coherence with variability ranging within the measurement uncertainties matching the WMO compatibility goal of 0.1 ppm, which we considered to be background air CO2 mole fraction for Central and Western Europe. However, JFJ record shows superimposed short-term variability with diurnal CO2 spikes centered around noon. Whereas the variability occurring during time intervals ranging from days to weeks seem to be driven by inputs of air masses from the planetary boundary layer, we suppose that the super-imposed diurnal CO2 spikes occurring essentially in summer are explained by local emission sources related to the infrastructure (visitors, tourism, etc). Nevertheless, we cannot point to a single triggering cause for those spikes as it probably results from a combination of factors. In order to minimize these local emissions, smooth collaboration between all the involved stakeholders is required.
Global urban reforestation can be an important natural climate solution
Authors: Teo Hoong Chen , Zeng Yiwen , Sarira Tasya Vadya , Fung Tze Kwan , Zheng Qiming , Song Xiao Ping , Chong Kwek Yan , Koh Lian Pin 
Published: February 2021

Abstract
The climate mitigation potential of urban nature-based solutions (NBSs) is often perceived as insignificant and thus overlooked, as cities primarily pursue NBSs for local ecosystem services. Given the rising interest and capacities in cities for such projects, the potential of urban forests for climate mitigation needs to be better understood. We modelled the global potential and limits of urban reforestation worldwide, and find that 10.9 ± 2.8 Mha of land (17.6% of all city areas) are suitable for reforestation, which would offset 82.4 ± 25.7 MtCO2e yr−1 of carbon emissions. Among the cities analysed, 1189 are potentially able to offset >25% of their city carbon emissions through reforestation. Urban natural climate solutions should find a place on global and local agendas.
Environmental aspects of plant introduction in the context of global climate change
Authors: Glinushkin A P , Startsev V I , Startseva L V 
Published: February 2021

Abstract
The results of analytical and practical research on expanding the range of cultivated crops that are of strategic importance for the development of the crop industry forming feed production in the Moscow region of the Russian Federation on the basis of the introduction of highly productive crops, without the use of chemically synthesized fertilizers and plant protection products that pose a threat to indemic agrophytocenoses and soil microbiota are presented.
Retraction: Financial Information Security Using Modular Communication (IOP Conf. Series: Materials Science and Engineering
677 032091)
Authors: Wang Wenwen , Zhang Yanwei 
Published: February 2021

This article has been retracted by IOP Publishing on 17 February 2021 in light of clear evidence that it was computer generated. IOP Publishing is investigating why this was not identified during the submission and peer review process by the conference. As a member of the Committee for Publication Ethics (COPE) this has been investigated in accordance with COPE guidelines and it was agreed the article should be retracted.
Retraction published: 17 February 2021
Direct growth of monolayer 1T–2H MoS2 heterostructures using KCl-assisted CVD process
Authors: Arellano Arreola Victor M , Salazar Mario Flores , Zhang Tianyi , Wang Ke , Barajas Aguilar Aaron H , Chandra Sekhar Reddy K , Strupiechonski Elodie , Terrones Mauricio , De Luna Bugallo Andres 
Published: February 2021

Abstract
Accessing the metastable phases in a controlled fashion can further expand the applications of atomically thin transition metal dichalcogenides (TMDs). Although top-down approaches based on ion intercalation exfoliation have shown to be an effective route to transform 2H phase into 1T and/or 1T′ polytype phases, a bottom-up growth strategy could be more suitable for device integration. Herein, we show that by assisting the atmospheric pressure chemical vapor deposition (APCVD) growth with a specific alkali metal halide (AMH), it possible to induce the direct synthesis of 1T phase domains coexisting with 2H phase structure in micrometer-sized MoS2 monolayer flakes. The photoluminescence emission and structural properties of three different AMH (NaCl, KBr and KCl) MoS2 crystals are compared. Both NaCl and KBr assisted MoS2 monolayers displayed the semiconducting 2H-phase. On the other hand, we demonstrate that KCl promotes the formation of a 1T–2H phase mixture. X-ray photoemission spectroscopy and resonant Raman studies performed on KCl–MoS2 monolayers show the emergence of a second chemical state and 1T Raman bands compared to the rest of the samples. High-resolution scanning transmission electron microscope imaging revealed important changes in the atomic arrangement between 2H and 1T domains, providing clear evidence of the presence of the 1T metastable phase in the lattice. Moreover, the growth 1T domains can also be controlled by modifying the deposition temperature. Our experiments show that the introduction of KCl during the APCVD growth result in stable 1T-MoS2 domains, providing a simple and reproducible route towards the polymorphism phase engineering of layered TMDs using a direct bottom-up approach.
Growth kinetics and wear resistance of vanadium carbide on AISI D2 steel produced by TRD process
Authors: Zhou Lianpu , Zhu Chundong , Guo Lian , Wei Zihao 
Published: February 2021

Abstract
Vanadium carbide coating was obtained on the surface of AISI D2 steel by thermal reactive diffusion process using molten borax as based salt and vanadium pentoxide as vanadium donor. The process was performed at 900 °C, 940 °C, 980 °C and 1020 °C for 3 h, 4 h, 5 h and 6 h. The Optical Microscopy was used to observe the morphology of cross section of coating layer. Energy Dispersive Spectroscopy was used to analyse the element content of the matrix and the coating layer by spot scanning and line scanning. X-ray Diffraction was used to obtained the phase composition of the coating layer. Microhardness Tester was used to measure the Vickers hardness of the coating layer and matrix. Friction and wear tester were used to explore wear resistance of the coated and uncoated specimens. The results show that the thickness of vanadium carbide coating ranges from 7.54 μm to 19.1 μm under different treatment time and temperatures. The V8C7 and VC
x
are the main phases contained in the vanadium coating layer. A thickness of about 3 μm transition layer is between the matrix and coating layer and the transition layer has a block effect on the diffusion of iron. The growth rate constants of vanadium carbide coating layer at 900 °C, 940 °C, 980 °C and 1020 °C were obtained as (5.20 ± 0.116) ×10–11 cm2 s−1, (8.91 ± 0.253) ×10–11 cm2 s−1, (1.26 ± 0.020) ×10–10 cm2 s−1, and (1.70 ± 0.036) ×10–10 cm2 s−1 respectively. The activation energy for vanadium carbide layer is 123.3 ± 10.1 kJ mol−1 and the diffusion constant is (2.58 ± 1.96) ×10–5 cm2 s−1. The maximum hardness of vanadium carbide coating layer on the surface of AISI D2 steel can reach 2594HV. The wear rate of untreated and treated specimens was evaluated as 15.58 × 10–13 m3/(N·m), 5.63 × 10–13 m3/(N·m) respectively and the wear resistance of treated specimens by TRD process was about 3 times than untreated specimens.
A DFT study on physical properties of III–V compounds (AlN, GaN, AlP, and GaP) in the P3121 phase
Authors: Zhang Zheren , Chai Changchun , Song Yanxing , Kong Linchun , Yang Yintang 
Published: February 2021

Abstract
In this work, four III-V compounds in the P3121 phase are proposed. Based on density functional theory (DFT), their structures, stability, and mechanical, anisotropic, electronic and optical properties were investigated in detail. P3121-AlN/GaN/AlP/GaP are all proven to have dynamic and mechanical stability based on their elastic constants and phonon spectra. The calculated Vickers hardness shows that P3121-AlN and P3121-GaN possess high hardness values of 18.7 GPa and 18.1 GPa, respectively. The anisotropic properties reveal that all these materials exhibit obvious elastic anisotropy. In the P3121 phase, AlN, GaN, and GaP are direct semiconductor materials, whereas AlP is an indirect semiconductor material, with calculated energy bandgaps of 4.51 eV (P3121-AlN), 2.36 eV (P3121-GaN), 1.84 eV (P3121-GaP), and 2.01 eV (P3121-AlP). In addition, P3121-AlP has high photoelectron absorption. The calculated energy bandgaps and mechanical and optical properties suggest that P3121-AlN/GaN/AlP/GaP may possess great potential to become high-performance materials in the electronics manufacturing industry.
Unexpected False-Positive Rates in Pediatric SARS-CoV-2 Serology Using the EUROIMMUN Anti-SARS-CoV-2 ELISA IgG Assay
Authors: Geisler Daniel , Freeman Megan Culler , Rapsinski Glenn J , Wheeler Sarah E 
Published: February 2021

Abstract

Objectives
Serologic assay performance studies for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-​2) in pediatric populations are lacking, and few seroprevalence studies have routinely incorporated orthogonal testing to improve accuracy.

Methods
Remnant serum samples for routine bloodwork from 2,338 pediatric patients at UPMC Children’s Hospital of Pittsburgh were assessed using the EUROIMMUN Anti-SARS-CoV-2 ELISA IgG (EuroIGG) assay. Reactive cases with sufficient volume were also tested using 3 additional commercial assays.

Results
Eighty-five specimens were reactive according to the EuroIGG, yielding 3.64% (95% confidence interval [CI], 2.91%-4.48%) seropositivity, of which 73 specimens had sufficient remaining volume for confirmation by orthogonal testing. Overall, 19.18% (95% CI, 10.18%-28.18%) of samples were positive on a second and/or third orthogonal assay. This 80.82% false positivity rate is disproportionate to the expected false positivity rate of 50% given our pediatric population prevalence and assay performance.

Conclusions
In pediatric populations, false-positive SARS-CoV-2 serology may be more common than assay and prevalence parameters would predict, and further studies are needed to establish the performance of SARS-CoV-2 serology in children.
MicroRNA annotation in plants: current status and challenges
Authors: Zhao Yongxin , Kuang Zheng , Wang Ying , Li Lei , Yang Xiaozeng 
Published: February 2021

Abstract
Last two decades, the studies on microRNAs (miRNAs) and the numbers of annotated miRNAs in plants and animals have surged. Herein, we reviewed the current progress and challenges of miRNA annotation in plants. Via the comparison of plant and animal miRNAs, we pinpointed out the difficulties on plant miRNA annotation and proposed potential solutions. In terms of recalling the history of methods and criteria in plant miRNA annotation, we detailed how the major progresses made and evolved. By collecting and categorizing bioinformatics tools for plant miRNA annotation, we surveyed their advantages and disadvantages, especially for ones with the principle of mimicking the miRNA biogenesis pathway by parsing deeply sequenced small RNA (sRNA) libraries. In addition, we summarized all available databases hosting plant miRNAs, and posted the potential optimization solutions such as how to increase the signal-to-noise ratio (SNR) in these databases. Finally, we discussed the challenges and perspectives of plant miRNA annotations, and indicated the possibilities offered by an all-in-one tool and platform according to the integration of artificial intelligence.
Accurate deep learning off-target prediction with novel sgRNA-DNA sequence encoding in CRISPR-Cas9 gene editing
Authors: Charlier Jeremy , Nadon Robert , Makarenkov Vladimir 
Published: February 2021

Abstract

Motivation
Off-target predictions are crucial in gene editing research. Recently, significant progress has been made in the field of prediction of off-target mutations, particularly with CRISPR-Cas9 data, thanks to the use of deep learning. CRISPR-Cas9 is a gene editing technique which allows manipulation of DNA fragments. The sgRNA-DNA (single guide RNA-DNA) sequence encoding for deep neural networks, however, has a strong impact on the prediction accuracy. We propose a novel encoding of sgRNA-DNA sequences that aggregates sequence data with no loss of information.

Results
In our experiments, we compare the proposed sgRNA-DNA sequence encoding applied in a deep learning prediction framework with state-of-the-art encoding and prediction methods. We demonstrate the superior accuracy of our approach in a simulation study involving Feedforward Neural Networks (FNNs), Convolutional Neural Networks (CNNs) and Recurrent Neural Networks (RNNs) as well as the traditional Random Forest (RF), Naive Bayes (NB) and Logistic Regression (LR) classifiers. We highlight the quality of our results by building several FNNs, CNNs and RNNs with various layer depths and performing predictions on two popular gene editing datasets (CRISPOR and GUIDE-seq). In all our experiments, the new encoding led to more accurate off-target prediction results, providing an improvement of the area under the Receiver Operating Characteristic (ROC) curve up to 35%.

Availability and implementation
The code and data used in this study are available at: https://github.com/dagrate/dl-offtarget.

Supplementary information
Supplementary data are available at Bioinformatics online.
Inferring perturbation profiles of cancer samples
Authors: Pirkl Martin , Beerenwinkel Niko 
Published: February 2021

AbstractMotivationCancer is one of the most prevalent diseases in the world. Tumors arise due to important genes changing their activity, e.g. when inhibited or over-expressed. But these gene perturbations are difficult to observe directly. Molecular profiles of tumors can provide indirect evidence of gene perturbations. However, inferring perturbation profiles from molecular alterations is challenging due to error-prone molecular measurements and incomplete coverage of all possible molecular causes of gene perturbations.ResultsWe have developed a novel mathematical method to analyze cancer driver genes and their patient-specific perturbation profiles. We combine genetic aberrations with gene expression data in a causal network derived across patients to infer unobserved perturbations. We show that our method can predict perturbations in simulations, CRISPR perturbation screens and breast cancer samples from The Cancer Genome Atlas.Availability and implementationThe method is available as the R-package nempi at https://github.com/cbg-ethz/nempi and http://bioconductor.org/packages/nempi.Supplementary informationSupplementary data are available at Bioinformatics online.
Significant Declines in Juvenile-onset Recurrent Respiratory Papillomatosis Following Human Papillomavirus (HPV) Vaccine Introduction in the United States
Authors: Meites Elissa , Stone Laura , Amiling Raiza , Singh Vidisha , Unger Elizabeth R , Derkay Craig S , Markowitz Lauri E 
Published: February 2021

AbstractBackgroundJuvenile-onset recurrent respiratory papillomatosis (JORRP) is a rare and serious disease caused by human papillomavirus (HPV) presumably acquired during vaginal delivery. HPV vaccination of females through age 26 years, recommended in the United States since 2006, can prevent HPV transmission. We assessed trends in JORRP cases before and after HPV vaccine introduction in the United States.MethodsCase-patients were identified from 26 pediatric otolaryngology centers in 23 U.S. states. Demographics and clinical history were abstracted from medical records. Case-patients were grouped by year of birth, and birth-cohort incidences were calculated using number of births from either national or state-level natality data from the 23 states. We calculated incidence rate ratios (IRR) and 95% confidence intervals (CI) in 2-year intervals.ResultsWe identified 576 U.S. JORRP case-patients born in 2004–2013. Median age at diagnosis was 3.4 years (interquartile range: 1.9, 5.5). Number of identified JORRP case-patients declined from a baseline of 165 born in 2004–2005 to 36 born in 2012–2013. Incidence of JORRP per 100 000 births using national data declined from 2.0 cases in 2004–2005 to 0.5 cases in 2012–2013 (IRR = 0.2, 95% CI = .1–.4); incidence using state-level data declined from 2.9 cases in 2004–2005 to 0.7 cases in 2012–2013 (IRR = 0.2, 95% CI = .1–.4).ConclusionsOver a decade, numbers of JORRP case-patients and incidences declined significantly. Incidences calculated using national denominator data are likely underestimates; those calculated using state-level denominator data could be overestimates. These declines are most likely due to HPV vaccination. Increasing vaccination uptake could lead to elimination of this HPV-related disease.
Technical or political? The socialist economic calculation debate
Authors: Camarinha Lopes Tiago 
Published: February 2021

Abstract
The paper presents both the key arguments and the historical context of the socialist economic calculation debate. I argue that Oskar Lange presented the most developed strategy to deal with bourgeois economics, decisively helping to create the scientific consensus that rational economic calculation under socialism is possible. Lange’s arguments based on standard economic theory reveal that the most ardent defenders of capitalism cannot reject socialism on technical terms and that, as a consequence, the Austrian School was left with no choice but to diverge from mainstream economics in its search to develop a framework that could support its political position. This shows that Mises’ challenge from 1920 was solved and has been replaced by a political posture developed by Hayek and leading Austrians economists, who have been struggling since the 1980s to revise the standard interpretation of the socialist economic calculation debate. I argue that this revision should not be uncritically accepted and conclude that socialism cannot be scientifically rejected; it can only be politically rejected, by those whose economic interests it opposes.
Prospective study of surgical site infections post-open esophageal cancer surgery, and the impact of care bundles
Authors: Raftery Nicola B , Murphy Conor F , Donlon Noel E , Heneghan Helen , Donohoe Claire L , King Sinead , O’Connell Brian , Ravi Narayanasamy , Reynolds John V 
Published: February 2021

Summary
SSIs represent common infection-related morbidity following major surgery. Modern care bundles have been established as prophylactic measures aimed at preventing SSI occurring postoperatively. SSI incidence and data on common culprit pathogens post-esophagectomy for cancer have not been previously reported. Patients (2013–2018) treated with curative intent were studied. SSI was defined as per the Center for Disease Control (CDC) definition. A care bundle pathway following the National Institute for Clinical Excellence (NICE) guidelines for prevention of SSIs was introduced in 2013 and was audited quarterly. Risk factors and associations of SSIs were analyzed, as was the prevalence of isolated pathogens. Multivariable logistic regression examined independently predictive factors of SSIs and oncologic outcomes. Of 343 patients, 34 (9.9%) developed a postoperative SSI, with a median (range) of 8 (6–17). Quarterly audit carried out over 6 years showed no significant annual variance or trend. The most prevalent pathogen cultured was Methicillin-sensitive Staphylococcus aureus (MSSA) in nine patients (32%) followed by Candida albicans (29%), Escherichia coli (14%), and Enterococcus faecium (11%). SSI was significantly associated with pneumonia (P = 0.001), respiratory failure (P = 0.014), atrial fibrillation (P = 0.004), anastomotic leak (P &lt; 0.001), and in-hospital blood transfusions (P = 0.031). SSI did not impact the overall survival (P = 0.951). SSI rates can be maintained at less than 10% using strict care bundles and regular audit. The most common culprit pathogen is gram-positive MSSA representing 32% of cases. These data are novel and may represent a modern benchmark for SSI post-open esophagectomy for cancer. This study highlights the incidence and associations of SSI post-esophageal cancer surgery.