bluuebunny/crossref_metadata_2025_split huggingface dataset:
Conservation tillage regulates soil bacterial community assemblies, network structures and ecological functions in black soils
Authors: Liu Zhuxiu , Gu Haidong , Liang Aizhen , Li Lujun , Yao Qin , Xu Yanxia , Liu Junjie , Jin Jian , Liu Xiaobing , Wang Guanghua 
Published: June 2021

Abstract
Aims
Conventional tillage is a serious threat to the stability of soil ecosystems. Understanding the response mechanisms of soil microbial community assemblies to anthropogenic activities is a major topic of ecological research.
Methods
Here, we investigated the bacterial community structures and assemblies in bulk and rhizosphere soils of soybeans grown with conventional tillage (moldboard plow, MP) and with conservation tillage that involved no-tillage (NT) or ridge tillage (RT) using high-throughput sequencing methods.
Results
We found that soil bacterial community compositions, structures and assembly processes were primarily altered by tillage practices. Briefly, in comparison to MP, NT and RT increased the relative abundances of the nitrogen-fixing bacteria Mesorhizobium sp., Bradyrhizobium sp. and Burkholderia sp., but decreased the abundance of soil carbon-degrading bacteria, especially Blastococcus sp., Streptomyces sp. and Sphingomonas sp. In addition, in comparison to MP, NT and RT resulted in more stable bacterial networks and more lower the relative contribution of homogenizing dispersal. Soil pH was the primary soil factor regulating both the bacterial community structures and assembly processes under the three tillage practices.
Conclusions
The altered functional bacteria under conservation tillage was mostly affiliated with biomarkers and keystone taxa, inferring that conservation tillage might contribute to biological nitrogen fixation and soil carbon sequestration.
Severe COVID-19 pneumonia in an intensive care setting and comparisons with historic severe viral pneumonia due to other viruses
Authors: Dadhwal Kiran , Stonham Rosalind , Poole Stephen , Saeed Kordo , Dushianthan Ahilanandan 
Published: June 2021

Abstract
Purpose
Severe viral pneumonia is associated with significant morbidity and mortality. Recent COVID-19 pandemic continues to impose significant health burden worldwide and individual pandemic waves often leads to a large surge in the ICU admissions for respiratory support. Comparisons of severe SARS-CoV-2 pneumonia with other seasonal and non-seasonal severe viral infections are rarely studied in an intensive care setting.
Methods
A retrospective cohort study comparing patients admitted to ICU with COVID-19 between March-June 2020 and those with viral pneumonias between January-December 2019. We compared patient specific demographic variables, duration of illness, ICU organ supportive measures and outcomes between both groups.
Results
Analysis of 93 COVID-19 (group 1) and 52 other viral pneumonia patients (group 2) showed an increased proportion of obesity (42% vs 23%, p = 0.02), non-white ethnicities (41% vs 6%, p < 0.001) and diabetes mellitus (30% vs 13%, p = 0.03) in group 1, with lower prevalence of COPD/asthma (16% vs 34%, p = 0.02). In group 1, the neutrophil to lymphocyte ratio was much lower (6.7 vs 10, p = 0.006) and invasive mechanical ventilation (58% vs 26%, p < 0.001) was more common. Length of ICU (8 vs 4, p < 0.001) and hospital stay (22 vs 11, p < 0.001) was prolonged in group 1, with no significant difference in mortality. Influenza A and rhinovirus were the most common pathogens in group 2 (26% each).
Conclusions
Key differences were identified within demographics (obesity, ethnicity, age, ICU scores, co-morbidities) and organ support. Despite these variations, there was no significant differences in mortality between both groups. Further studies with larger sample sizes would allow for further assessment of clinical parameters in these patients.
Kernel-Based Fuzzy Local Information Clustering Algorithm Self-integrating Non-Local Information
Authors: Song Qiuyu , Wu Chengmao , Tian Xiaoping , Song Yue , Guo Xiaokang 
Published: June 2021

Abstract
The application of fuzzy clustering algorithms in image segmentation is a hot research topic nowadays. Existing fuzzy clustering algorithms have the following three problems: (1)The parameters of spatial information constraints can$'$t be selected adaptively; (2)The image corrupted by high noise can$'$t be segmented effectively; (3)It is difficult to achieve a balance between noise removal and detail preservation. In the fuzzy clustering based on the optimization model, the choice of distance metric is very important. Since the use of Euclidean distance will lead to sensitivity to outliers and noise, it is difficult to obtain satisfactory segmentation results, which will affect the clustering performance. This paper proposes an optimization algorithm based on the kernel-based fuzzy local information clustering integrating non-local information (KFLNLI). The algorithm adopts a self-integration method to introduce local and non-local information of images, which solves the common problems of current clustering algorithm. Firstly, the self-integration method solves the problem of selecting spatial constraint parameters. The algorithm uses continuous self-learning iteration to calculate the weight coefficients; Secondly, the distance metric uses Gaussian kernel function to induce the distance to further enhance the robustness against noise and the adaptivity of processing different images; Finally, both local and non-local information are introduced to achieve a segmentation effect that can eliminate most of the noise and retain the original details of the image. Experimental results show that the algorithm is superior to existing state-of-the-art fuzzy clustering-related algorithm in the presence of high noise.
Studying the Chemical Reactivity Properties of Cytosine and its Antiviral Analogues: Zebularine, 5-Aza-Cytosine And 5-Aza-5,6-Dihydro-Cytosine through Density Functional Theory
Authors: wang guixiu , Wu Yifang 
Published: June 2021

Abstract
Zebularine, 5-aza-cytosine and 5-aza-5,6-dihydro-cytosine are structurally similar to cytosine, but their biological functions are rather different. Cytosine can be methylated which is a gene lesion that can cause human disease. On the contrary, zebularine and 5-aza-cytosine are inhibitors of DNA methylation. 5-aza-5,6-dihydro-cytosine is specifically designed to induce lethal mutagenesis in HIV for its structurally variability. Here, theoretical research into their chemical properties through density functional theory is reported. Molecular hardness and molecular electronic surface potential were analysed. Compared to cytosine, the main reason for the inability of methyl addition of zebularine is the reduced nucleophilicity of C5 atom. The lack of a hydrogen atom at N5 atom in 5-aza-cytosine is responsible for the incomplete reaction of methyl transfer. Variability of 5-aza-5,6-dihydro-cytosine is responsible for the mutagenesis treatment by paring with guanine or adenine with its different tautomers. Aspect of these chemical reactivities can be accounted for the distinctive biological functions of these molecules.
Phase I Study of Weekly Nab-Paclitaxel Plus Carboplatin And Concurrent Thoracic Radiotherapy in Elderly Patients with Unresectable Locally Advanced Non-Small-Cell Lung Cancer
Authors: Omori Shota , Harada Hideyuki , Mori Keita , Hisamatsu Yasushi , Tsuboguchi Yuko , Yoshioka Hiroshige , Morinaga Ryotaro , Daga Haruko , Kurata Takayasu , Takahashi Toshiaki 
Published: June 2021

Abstract
Few clinical studies have been designed for elderly patients with locally advanced non-small cell lung cancer (NSCLC). We conducted a phase I study to evaluate the tolerability of carboplatin/nab-paclitaxel and concurrent thoracic radiotherapy in elderly patients with locally advanced NSCLC. The eligibility criteria were: unresectable stage III NSCLC, performance status 0 or 1, and age ≥75 years. Eligible patients received 6 weeks of weekly carboplatin/nab-paclitaxel and concurrent thoracic radiotherapy with a total dose of 64 Gy in 32 fractions. Carboplatin was fixed to an area under the plasma concentration time curve (AUC) of 2 mg/mL/min, and the recommended dose of nab-paclitaxel was evaluated using a dose-escalation study (30 or 40 mg/m2). Tolerability at the recommended dose was evaluated in an expansion study. Nineteen patients were enrolled at four institutions, all of whom were eligible and assessable. The recommended nab-paclitaxel dose was set at 30 mg/m2 because two patients experienced dose-limiting toxicity at 40 mg/m2. The treatment completion rate of the 17 patients analyzed at the recommended dose was 100% (80% confidence interval (CI), 83.8–100%). The overall response rate was 76.5%, and the median progression free survival was 13.4 months (95% CI, 4.2–21.4 months). Common grade 3 and 4 toxicities included leukopenia (23.5%), neutropenia (17.6%), anemia (5.9%), and infection (5.9%). One treatment-related death due to pneumonitis was observed six months after the end of the study. In conclusion, carboplatin/nab-paclitaxel and concurrent thoracic radiotherapy show good tolerability and exhibit promising efficacy in elderly patients with locally advanced NSCLC. This trial was registered with the Japan Registry of Clinical Trials on March 11, 2019 (trial no. jRCTs042180077).
SARS-CoV-2 virus masking of RBD epitopes; unmasking and cross-reactivity induced by mRNA vaccines
Authors: de Assis Rafael Ramiro , Jain Aarti , Nakajima Rie , Jasinskas Algis , Kahn Saahir , Palma Anton , Parker Daniel , Chau Anthony , Leung Amanda , Grabar Christina , Muqolli Fjolla , Khalil Ghali , Escobar Jessica , Ventura Jenny , Davies David , Albala Bruce , Boden-Albala Bernadette , Schubl Sebastian , Felgner Philip 
Published: June 2021

Abstract
We analyzed data from two ongoing COVID-19 longitudinal serological surveys in Orange County, CA., between April 2020 and March 2021. A total of 8,476 finger stick blood specimens were collected before and after an aggressive mRNA vaccination campaign. IgG levels were determined using a multiplex antigen microarray containing 10 SARS-CoV-2 antigens, 4 SARS, 3 MERS, 12 Common CoV, and 8 Influenza antigens. Twenty-six percent of 3,347 specimens from unvaccinated Orange County residents in December 2020 were SARS-CoV-2 seropositive. The Ab response was predominantly against nucleocapsid (NP), full length spike and the spike S2 domain. Anti-receptor binding domain (RBD) reactivity was low and there was no cross-reactivity against SARS S1 or SARS RBD. An aggressive mRNA vaccination campaign at the UCI Medical Center started on December 16, 2020 and 6,724 healthcare workers were vaccinated within 3 weeks. Seroprevalence increased from 13% in December to 79% in January, 93% in February and 99% in March. mRNA vaccination induced much higher Ab levels especially against the RBD domain and significant cross-reactivity against SARS RBD and S1 was also observed. Nucleocapsid protein Abs can be used to distinguish individuals in a population of vaccinees to classify those who have been previously infected and those who have not, because nucleocapsid is not in the vaccine. Previously infected individuals developed higher Ab titers to the vaccine than those who have not been previously exposed. These results indicate that mRNA vaccination rapidly induces a much stronger and broader Ab response than SARS-CoV-2 infection.
Altered Differentiation of Endometrial Mesenchymal Stromal Fibroblasts Is Associated With Endometriosis Susceptibility
Authors: McKinnon Brett , Lukowski Samuel , Mortlock Sally , Crawford Joanna , Johnston Rebecca , Nirgianankis Kostantinos , Mueller Michael , Montgomery Grant 
Published: June 2021

Abstract
Cellular development is tightly regulated as mature cells with aberrant functions may initiate pathogenic processes. The endometrium is a highly regenerative tissue, shedding and regenerating each month. Endometrial stromal fibroblasts are regenerated each cycle from mesenchymal stem cells and play a pivotal role in endometriosis, a disease characterised by endometrial cells that grow outside the uterus. Why the cells of some women are more capable of developing into endometriosis lesions is not clear. Using isolated, purified and cultured endometrial cells of mesenchymal origin from 19 women with (n = 10) and without (n = 9) endometriosis we analysed the transcriptome of 33,758 individual cells and compared these to clinical characteristics and in vitro growth profiles. We show purified mesenchymal cell cultures include a mix of mesenchymal stem cells and two endometrial stromal fibroblast subtypes with distinct transcriptomic signatures indicative of varied progression through the differentiation processes. The fibroblast subgroup characterised by incomplete differentiation was predominantly (81%) derived from women with endometriosis and exhibited an altered in vitro growth profile. These results uncover an inherent difference in endometrial cells of women with endometriosis and highlight the relevance of cellular differentiation and its potential to contribute to disease susceptibility.
First-In-Asian Double-Blind Randomized Trial To Assess The Efficacy And Safety Of Insulin Sensitizer In Nonalcoholic Steatohepatitis Patients
Authors: Huang Jee-Fu , Dai Chia-Yen , Huang Chung-Feng , Tsai Pei-Chien , Yeh Ming-Lun , Hsu Po-Yau , Huang Shiu-Feng , Bair Ming-Jong , Hou Nai-Jen , Huang Ching-I , Liang Po-Cheng , Lin Yi-Hung , Wang Chih-Wen , Hsieh Ming-Yen , Chen Shinn-Chern , Lin Zu-Yau , Yu Ming-Lung , Chuang Wan-Long 
Published: June 2021

Abstract
Background: The efficacy and safety of insulin sensitizer in Asians with non-alcoholic steatohepatitis (NASH) remain elusive. Aims: The double-blind, randomized, placebo-controlled trial was conducted aiming to investigate the efficacy and safety of pioglitazone in NASH patients. Methods: A total of 90 NASH patients (66 males, age= 44.1 ± 12.7 years) were prospectively randomized into oral pioglitazone 30 mg/day (Arm A) or placebo (Arm B) for 24 weeks. The primary endpoint was the efficacy of pioglitazone in reducing inflammation and liver fat at end-of-treatment (EOT). NASH resolution/improvement without fibrosis worsening were also evaluated.Results: At EOT, there was a significantly decline of alanine aminotransferase (86.9 ± 34.3 to 45.7 ± 35.8 IU/L, P=0.003) level in Arm A patients. In intention-to-treat analysis among 66 patients who completed paired biopsies, The NAFLD activity score (NAS) of 30 Arm A patients significantly decreased from 4.27 ± 1.14 at baseline to 2.53 ± 1.63 at EOT (P< 0.0001), whereas there was no significant change in patients of Arm B (3.94 ± 1.41 vs 3.94 ± 1.51, P= 1.0). NASH improvement without worsening of fibrosis was achieved in 46.7% (14/30) patients in Arm A, compared to 11.1% (4/36) patients in Arm B (P= 0.002). Liver fat content reduced (20.2 ± 9.0 to 14.3 ± 6.9%, P<0.0001) on MRI-PDFF in Arm A compared to their counterparts. No significant difference of adverse events occurred between groups. Conclusions: A 24-weeks pioglitazone treatment was well-tolerated and effective in improving liver histology and reducing liver steatosis in Asian NASH patients. (ClinicalTrials.gov number: NCT01068444)
Semaphorin3A Promotes the Development of Nickel Allergy
Authors: Liu Lipei , Watanabe Megumi , Minami Norikazu , Yunizar Mohammad , Ichikawa Tetsuo 
Published: June 2021

Abstract
Metal allergy is one of the typical immune disorders encountered during the application of dental/medical materials and has a highly complex pathogenic mechanism. Semaphorin 3A (Sema3A), a member of the semaphorin family, is reported to be involved in various immune disorders. However, its role in metal allergy has not been clarified yet. Herein, we show that Sema3A promoted nickel (Ni) allergy by mediating tumor necrosis factor-alpha (TNF-α) production and mitogen-activated protein kinase (MAPK) activation in keratinocytes. Sema3A was upregulated in NiCl2-stimulated mouse keratinocytes and in Ni allergy-induced mouse ear tissue. TNF-α production and MAPK activation were altered when Sema3A was suppressed in keratinocytes. The specific deletion of Sema3A in keratinocytes alleviated Ni allergy and regulated the macrophage polarization towards an anti-inflammatory direction. Our results demonstrate that Sema3A promotes the development of metal allergy and should be explored as a potential target for the prevention and treatment of metal allergy.
Fifth fundamental force and unification of fundamental forces
Authors: Singh Raghvendra 
Published: June 2021

Abstract
There are four known fundamental forces of nature and there is a need to combine them into a unified theory. Progress has been made toward this goal but gravity remains an issue. However, the four forces are body forces that act on points. They together do not make the universe a closed system. Here, I identify a surface force, which acts outward normal to the surface of the universe. Further, using water drop hanging in a vacuum as a model, I provide a formula to find the magnitude of this force. The fifth force is generated by surface tension, a property of dark energy. On the other hand, matter particles interact with each other through cohesive forces and with dark matter through adhesive forces. I give a range of functional forms of all cohesive and adhesive forces and present an equation that unifies all the forces of nature.
Institutional “Paris Agreement Compatible” Mitigation Scenarios Evaluated Against the Paris Agreement 1.5°C Goal
Authors: Brecha Robert , Ganti Gaurav , Lamboll Robin , Nicholls Zebedee , Hare William , Lewis Jared , Meinshausen Malte , Schaeffer Michiel , Gidden Matthew 
Published: June 2021

Abstract
Scientifically rigorous guidance to policy makers on mitigation options for meeting the Paris Agreement long-term temperature goal requires an evaluation of long-term global-warming implications of greenhouse gas emissions pathways. Here we employ a uniform and transparent methodology to evaluate Paris Agreement compatibility of influential “institutional” emission scenarios from the grey literature. We compare a selection of these scenarios analyzed with this methodology to the Integrated Assessment Model scenarios assessed by the Intergovernmental Panel on Climate Change. We harmonize emissions to a consistent base-year and account for all greenhouse gases and aerosol precursor emissions, ensuring a self-consistent comparison of climate variables. An evaluation of peak and end-of-century temperatures is made, with both being relevant to the Paris Agreement goal. We find that few published scenarios that claim to be compatible with the Paris Agreement are so, and investigate root causes based on the underlying energy system transformation.
JUMPER Enables Discontinuous Transcript Assembly in Coronaviruses
Authors: Sashittal Palash , Zhang Chuanyi , Peng Jian , El-Kebir Mohammed 
Published: June 2021

Abstract
Genes in SARS-CoV-2 and other viruses in the order of Nidovirales are expressed by a process of discontinuous transcription mediated by the viral RNA-dependent RNA polymerase. This process is distinct from alternative splicing in eukaryotes and produces subgenomic RNAs that express different viral genes. Here, we introduce the DISCONTINUOUS TRANSCRIPT ASSEMBLY problem of finding transcripts T and their abundances c given an alignment R of paired end short reads under a maximum likelihood model that accounts for varying transcript lengths. Underpinning our approach is the concept of a segment graph, a directed acyclic graph that, distinct from the splice graph used to characterize alternative splicing, has a unique Hamiltonian path. We provide a compact characterization of solutions as subsets of non-overlapping edges in this graph, enabling the formulation of an efficient progressive heuristic that uses mixed integer linear program. We show using simulations that our method, JUMPER, drastically outperforms existing methods for classical transcript assembly. On short-read data of SARS-CoV-1, SARS-CoV-2 and MERS-CoV samples, we find that JUMPER not only identifies canonical transcripts that are part of the reference transcriptome, but also predicts expression of non-canonical transcripts that are well supported by direct evidence from long-read data, presence in multiple, independent samples or a conserved core sequence. Moreover, application of JUMPER on samples with and without treatment reveals viral drug response at the transcript level. As such, JUMPER enables detailed analyses of Nidovirales transcriptomes under varying conditions.
Hydrogel tapes for fault-tolerant strong wet adhesion
Authors: Cao Yi , Xue Bin , Gu Jie , Yu Wenting , Li Lan , Qin Meng , Jiang Qing , Wang Wei 
Published: June 2021

Abstract
Fast and strong bio-adhesives are in high demand for many biomedical applications, including closing wounds in surgeries, fixing implantable devices, and haemostasis. However, most strong bio-adhesives rely on the instant formation of irreversible covalent crosslinks to provide strong surface binding. Repositioning misplaced adhesives during surgical operations may cause severe secondary damage to tissues. Here, we report hydrogel tapes that can form strong physical interactions with tissues in seconds and gradually form covalent bonds in hours. This timescale-dependent adhesion mechanism allows instant and robust wet adhesion to be combined with fault-tolerant convenient surgical operations. Specifically, inspired by the catechol chemistry discovered in mussel foot proteins, we develop an electrical oxidation approach to controllably oxidize catechol to catecholquinone, which reacts slowly with amino groups on the tissue surface. We demonstrate that the tapes show fast and reversible adhesion at the initial stage and ultrastrong adhesion after the formation of covalent linkages over hours for various tissues and electronic devices. Given that the hydrogel tapes are biocompatible, easy to use, and robust for bio-adhesion, we anticipate that they may find broad biomedical and clinical applications.
Wear and Friction Behavior of Gr/Sn Solid Lubricated Dual Reinforced AMCs
Authors: Singhal Varun , Pandey Om Prakash 
Published: June 2021

Abstract
The current work has been undertaken to see the effect of Gr/Sn as a solid lubricant for the development of hybrid aluminum metal matrix composite (HAMCs). HAMCs were fabricated by reinforcing 10 wt. % (sillimanite + ilmenite) minerals with or without 1 wt. % Sn/Gr/both solid via stir casting technique. Optical microscopy revealed a homogenous distribution of reinforced particles with the refinement of silicon. Vicker hardness of the HAMCs showed a good interfacial bonding of particles with the matrix. The wear rate and coefficient of friction of the HAMCs are reduced with a maximum of composite with tin and graphite as lubrication agents. The composite contained tin and graphite wear rate as lubrication agents were in tune with the cast-iron brake drum used in the automobile industries. Abrasive wear was dominant at low loads and adhesive wear at high load, as confirmed from SEM analysis.