bluuebunny/crossref_metadata_2025_split huggingface dataset:
SARS-CoV-2 infection induces inflammatory bone loss in golden Syrian hamsters
Authors: Qiao Wei , Lau Hui En , Xie Huizhi , Poon Vincent Kwok-Man , Chan Chris Chung-Sing , Chu Hin , Yuan Shuofeng , Yuen Terrence Tsz-Tai , Chik Kenn Ka-Heng , Tsang Jessica Oi-Ling , Chan Chris Chun-Yiu , Cai Jian-Piao , Luo Cuiting , Yuen Kwok-Yung , Cheung Kenneth Man-Chee , Chan Jasper Fuk-Woo , Yeung Kelvin Wai-Kwok 
Published: May 2022

AbstractExtrapulmonary complications of different organ systems have been increasingly recognized in patients with severe or chronic Coronavirus Disease 2019 (COVID-19). However, limited information on the skeletal complications of COVID-19 is known, even though inflammatory diseases of the respiratory tract have been known to perturb bone metabolism and cause pathological bone loss. In this study, we characterize the effects of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection on bone metabolism in an established golden Syrian hamster model for COVID-19. SARS-CoV-2 causes significant multifocal loss of bone trabeculae in the long bones and lumbar vertebrae of all infected hamsters. Moreover, we show that the bone loss is associated with SARS-CoV-2-induced cytokine dysregulation, as the circulating pro-inflammatory cytokines not only upregulate osteoclastic differentiation in bone tissues, but also trigger an amplified pro-inflammatory cascade in the skeletal tissues to augment their pro-osteoclastogenesis effect. Our findings suggest that pathological bone loss may be a neglected complication which warrants more extensive investigations during the long-term follow-up of COVID-19 patients. The benefits of potential prophylactic and therapeutic interventions against pathological bone loss should be further evaluated.
Gut microbiota regulates acute myeloid leukaemia via alteration of intestinal barrier function mediated by butyrate
Authors: Wang Ruiqing , Yang Xinyu , Liu Jinting , Zhong Fang , Zhang Chen , Chen Yuhong , Sun Tao , Ji Chunyan , Ma Daoxin 
Published: May 2022

AbstractThe gut microbiota has been linked to many cancers, yet its role in acute myeloid leukaemia (AML) progression remains unclear. Here, we show decreased diversity in the gut microbiota of AML patients or murine models. Gut microbiota dysbiosis induced by antibiotic treatment accelerates murine AML progression while faecal microbiota transplantation reverses this process. Butyrate produced by the gut microbiota (especially Faecalibacterium) significantly decreases in faeces of AML patients, while gavage with butyrate or Faecalibacterium postpones murine AML progression. Furthermore, we find the intestinal barrier is damaged in mice with AML, which accelerates lipopolysaccharide (LPS) leakage into the blood. The increased LPS exacerbates leukaemia progression in vitro and in vivo. Butyrate can repair intestinal barrier damage and inhibit LPS absorption in AML mice. Collectively, we demonstrate that the gut microbiota promotes AML progression in a metabolite-dependent manner and that targeting the gut microbiota might provide a therapeutic option for AML.
Molecular basis for cooperative binding and synergy of ATP-site and allosteric EGFR inhibitors
Authors: Beyett Tyler S. , To Ciric , Heppner David E. , Rana Jaimin K. , Schmoker Anna M. , Jang Jaebong , De Clercq Dries J. H. , Gomez Gabriel , Scott David A. , Gray Nathanael S. , Jänne Pasi A. , Eck Michael J. 
Published: May 2022

AbstractLung cancer is frequently caused by activating mutations in the epidermal growth factor receptor (EGFR). Allosteric EGFR inhibitors offer promise as the next generation of therapeutics, as they are unaffected by common ATP-site resistance mutations and synergize with the drug osimertinib. Here, we examine combinations of ATP-competitive and allosteric inhibitors to better understand the molecular basis for synergy. We identify a subset of irreversible EGFR inhibitors that display positive binding cooperativity and synergy with the allosteric inhibitor JBJ-04-125-02 in several EGFR variants. Structural analysis of these complexes reveals conformational changes occur mainly in the phosphate-binding loop (P-loop). Mutation of F723 in the P-loop reduces cooperative binding and synergy, supporting a mechanism in which F723-mediated contacts between the P-loop and the allosteric inhibitor are critical for synergy. These structural and mechanistic insights will aid in the identification and development of additional inhibitor combinations with potential clinical value.
The flying spider-monkey tree fern genome provides insights into fern evolution and arborescence
Authors: Huang Xiong , Wang Wenling , Gong Ting , Wickell David , Kuo Li-Yaung , Zhang Xingtan , Wen Jialong , Kim Hoon , Lu Fachuang , Zhao Hansheng , Chen Song , Li Hui , Wu Wenqi , Yu Changjiang , Chen Su , Fan Wei , Chen Shuai , Bao Xiuqi , Li Li , Zhang Dan , Jiang Longyu , Khadka Dipak , Yan Xiaojing , Liao Zhenyang , Zhou Gongke , Guo Yalong , Ralph John , Sederoff Ronald R. , Wei Hairong , Zhu Ping , Li Fay-Wei , Ming Ray , Li Quanzi 
Published: May 2022

AbstractTo date, little is known about the evolution of fern genomes, with only two small genomes published from the heterosporous Salviniales. Here we assembled the genome of Alsophila spinulosa, known as the flying spider-monkey tree fern, onto 69 pseudochromosomes. The remarkable preservation of synteny, despite resulting from an ancient whole-genome duplication over 100 million years ago, is unprecedented in plants and probably speaks to the uniqueness of tree ferns. Our detailed investigations into stem anatomy and lignin biosynthesis shed new light on the evolution of stem formation in tree ferns. We identified a phenolic compound, alsophilin, that is abundant in xylem, and we provided the molecular basis for its biosynthesis. Finally, analysis of demographic history revealed two genetic bottlenecks, resulting in rapid demographic declines of A. spinulosa. The A. spinulosa genome fills a crucial gap in the plant genomic landscape and helps elucidate many unique aspects of tree fern biology.
Association between inflammatory bowel disease and Parkinson’s disease: A Mendelian randomization study
Authors: Freuer D. , Meisinger C. 
Published: May 2022

AbstractEmerging evidence from observational studies suggests an increased risk of Parkinson’s disease (PD) in patients with inflammatory bowel disease (IBD). However, to date it is not clear whether a causal relationship exists. To investigate whether IBD is causally related to PD, a two-sample Mendelian randomization study was carried out. Independent genetic instruments from the largest available genome-wide association study (GWAS) for IBD (7045 cases, 456,327 controls) including European participants were used to investigate the association with PD (56,306 cases; 1.4 million controls). The results were validated by using a second IBD sample (12,882 cases; 21,770 controls) including the main subtypes ulcerative colitis (UC; 6968 cases; 20,464 controls) and Crohn’s disease (CD; 5956 cases; 14,927 controls). The radial inverse-variance weighted (IVW) approach was used in the primary analysis, and the robustness of the findings were confirmed in a number of sensitivity analyses. Finally, the recently proposed CAUSE approach was performed. There was no evidence of an association between IBD and PD (ORIVW = 0.98; 95% CI: [0.93; 1.04]; P = 0.48). This finding could be validated using a second sample of IBD cases (ORIVW = 0.98; 95% CI: [0.95; 1.02]; P = 0.36). Furthermore, MR analyses did not support a causal effect of CD (ORIVW = 1.00; 95% CI: [0.98; 1.03]; P = 0.96) or UC (ORIVW = 1.02; 95% CI: [0.98; 1.06]; P = 0.45) on PD. The present study suggests that neither IBD nor its subtypes CD and UC causally affect Parkinson’s disease in the European population. Further research is necessary to investigate whether intestinal inflammation impacts the development of PD.
A multiscale model of the regulation of aquaporin 2 recycling
Authors: Leberecht Christoph , Schroeder Michael , Labudde Dirk 
Published: May 2022

AbstractThe response of cells to their environment is driven by a variety of proteins and messenger molecules. In eukaryotes, their distribution and location in the cell are regulated by the vesicular transport system. The transport of aquaporin 2 between membrane and storage region is a crucial part of the water reabsorption in renal principal cells, and its malfunction can lead to Diabetes insipidus. To understand the regulation of this system, we aggregated pathways and mechanisms from literature and derived three models in a hypothesis-driven approach. Furthermore, we combined the models to a single system to gain insight into key regulatory mechanisms of Aquaporin 2 recycling. To achieve this, we developed a multiscale computational framework for the modeling and simulation of cellular systems. The analysis of the system rationalizes that the compartmentalization of cAMP in renal principal cells is a result of the protein kinase A signalosome and can only occur if specific cellular components are observed in conjunction. Endocytotic and exocytotic processes are inherently connected and can be regulated by the same protein kinase A signal.
Directional ballistic transport in the two-dimensional metal PdCoO2
Authors: Bachmann Maja D. , Sharpe Aaron L. , Baker Graham , Barnard Arthur W. , Putzke Carsten , Scaffidi Thomas , Nandi Nabhanila , McGuinness Philippa H. , Zhakina Elina , Moravec Michal , Khim Seunghyun , König Markus , Goldhaber-Gordon David , Bonn Douglas A. , Mackenzie Andrew P. , Moll Philip J. W. 
Published: May 2022

AbstractIn an idealized infinite crystal, the material properties are constrained by the symmetries of the unit cell. The point-group symmetry is broken by the sample shape of any finite crystal, but this is commonly unobservable in macroscopic metals. To sense the shape-induced symmetry lowering in such metals, long-lived bulk states originating from an anisotropic Fermi surface are needed. Here we show how a strongly facetted Fermi surface and the long quasiparticle mean free path present in microstructures of PdCoO2 yield an in-plane resistivity anisotropy that is forbidden by symmetry on an infinite hexagonal lattice. We fabricate bar-shaped transport devices narrower than the mean free path from single crystals using focused ion beam milling, such that the ballistic charge carriers at low temperatures frequently collide with both of the side walls that define the channel. Two symmetry-forbidden transport signatures appear: the in-plane resistivity anisotropy exceeds a factor of 2, and a transverse voltage appears in zero magnetic field. Using ballistic Monte Carlo simulations and a numerical solution of the Boltzmann equation, we identify the orientation of the narrow channel as the source of symmetry breaking.
Army liposome formulation containing QS-21 render human monocyte-derived macrophages less permissive to HIV-1 infection by upregulating APOBEC3A
Authors: Jobe Ousman , Kim Jiae , Pinto Daniel O. , Villar Zuzana , Hewitt Tiffany , Duncan Elizabeth H. , Anderson Alexander , Gohain Neelakshi , Gong Hua , Tucker Courtney , Alving Carl R. , Matyas Gary R. , Bergmann-Leitner Elke , Rao Mangala 
Published: May 2022

AbstractMonocyte-derived macrophages (MDM) are highly permissive to HIV-1 infection potentially due to the downregulation of innate factors during the differentiation process. The environmental milieu and innate anti-viral factors which are modulated during macrophage differentiation, have been associated with their increased permissiveness to HIV-1 infection. Here, we demonstrate that the Army Liposome Formulation containing MPLA, and QS-21 (ALFQ) activated MDM that are normally permissive to HIV-1 infection to generate a proinflammatory environment and upregulated anti-viral factors notably APOBEC3A. Induction of APOBEC3A by ALFQ decreased permissiveness to HIV-1 infection, while knockdown of APOBEC3A with APOBEC3AsiRNA resulted in a significant loss in the restriction of HIV-1 infectivity. The liposome formulation ALF55, with identical lipid composition but lacking QS-21 had no effect. Furthermore, the capacity of ALFQ to modulate MDM permissiveness to HIV-1 infection was predominantly mediated by large ALFQ liposomes. Our findings highlight a relationship between innate immune activation, proinflammatory milieu, and upregulation of anti-HIV proteins. Induction of these responses can switch the HIV-1 permissive MDM into a more refractory phenotype.
A randomised clinical trial to assess the adjuvant potential of methotrexate to corticosteroids in mucosal or limited mucocutaneous pemphigus vulgaris
Authors: Jain Khimit , Thakur Vishal , Handa Sanjeev , Thakur Neha , Shilpa  , Sachdeva Naresh , Mahajan Rahul , De Dipankar 
Published: May 2022

AbstractGlucocorticoids are the mainstay of treatment for pemphigus vulgaris (PV). However, the requirement of high doses for long durations often leads to serious adverse events. Methotrexate as an adjuvant has shown potential in retrospective studies but randomized trials are lacking. The objective of the study was to assess the adjuvant potential of methotrexate in mucosal/limited mucocutaneous PV. In this randomised prospective study, 44 patients with mucosal/limited mucocutaneous PV were randomised (1:1) to receive either prednisolone 1 mg/kg/day (later fixed at a maximum dose of 60 mg/day) alone or with methotrexate 0.3 mg/kg/week for 9-months study period. Prednisolone dose was tapered once there was an 80% reduction in Pemphigus Disease Activity Index. Outcome measures were total cumulative dose of prednisolone, the proportion of patients achieving disease control, time taken for disease control and remission on minimal treatment, and adverse effects. No significant difference in the total cumulative dose of prednisolone among the groups was observed (p = 0.68). Disease control was achieved in 95.5% and 86.4% of patients in the prednisolone alone group, and prednisolone and methotrexate group respectively (p = 0.61). No statistically significant difference was observed among the groups with respect to the proportion of patients achieving remission, time taken for disease control and remission, and the number of adverse events. Our study showed no additional benefit of methotrexate to prednisolone in the treatment of mucosal/limited mucocutaneous PV.Trial registration: CTRI/2018/07/015002; Registered on 23/07/2018]; Trial Registered Retrospectively. http://ctri.nic.in/Clinicaltrials/pdf_generate.php?trialid=24964&EncHid=&modid=&compid=%27,%2724964det%27.
An allometric model-based approach for estimating biomass in seven Indian bamboo species in western Himalayan foothills, India
Authors: Kaushal R. , Islam S. , Tewari Salil , Tomar J. M. S. , Thapliyal S. , Madhu M. , Trinh T. L. , Singh Tarun , Singh Avnindra , Durai J. 
Published: May 2022

AbstractThe rapid growth rate, high biomass production, and annual harvesting make bamboo a suitable species for commercial production. Allometric equations for many broadleaf and conifer tree species are available. However, knowledge of biomass production and allometric equations of bamboos is limited. This study aims to develop species- specific allometric models for predicting biomass and synthetic height values as a proxy variable for seven bamboo species in Himalayan foothills. Two power form-based allometric models were used to predict aboveground and culm biomass using diameter at breast height (D) alone and D combined with culm height (H) as an independent variable. This study also extended to establishing an H–D allometric model that can be used to generate synthetic H values as a proxy to missing H. In the seven bamboo species studied, among three major biomass components (culm, branch and foliage), culm is the most important component with the highest share (69.56–78.71%). The distribution of percentage (%) share of culm, branch and foliage to above-ground fresh weight varies significantly between different bamboo species. D. hamiltonii has the highest productivity for above-ground biomass components. Ratio of dry to fresh weight of seven bamboo species was estimated for culm, branch, foliage and above-ground biomass to convert fresh weight to dry weight.
Animal-vehicle collisions during the COVID-19 lockdown in early 2020 in the Krakow metropolitan region, Poland
Authors: Basak Sayantani M. , O’Mahony Declan T. , Lesiak Maciej , Basak Arpan Kumar , Ziółkowska Elżbieta , Kaim Dominik , Hossain Md Sarwar , Wierzbowska Izabela A. 
Published: May 2022

AbstractThe interrelations between human activity and animal populations are of increasing interest due to the emergence of the novel COVID-19 and the consequent pandemic across the world. Anthropogenic impacts of the pandemic on animals in urban-suburban environments are largely unknown. In this study, the temporal and spatial patterns of urban animal response to the COVID-19 lockdown were assessed using animal-vehicle collisions (AVC) data. We collected AVC data over two 6-month periods in 2019 and 2020 (January to June) from the largest metropolis in southern Poland, which included lockdown months. Furthermore, we used traffic data to understand the impact of lockdown on AVC in the urban area. Our analysis of 1063 AVC incidents revealed that COVID-19 related lockdown decreased AVC rates in suburban areas. However, in the urban area, even though traffic volume had significantly reduced, AVC did not decrease significantly, suggesting that lockdown did not influence the collision rates in the urban area. Our results suggest that there is a need to focus on understanding the effects of changes in traffic volume on both human behaviour and wildlife space use on the resulting impacts on AVC in the urban area.
Proton pump inhibitor therapy usage and associated hospitalization rates and critical care outcomes of COVID-19 patients
Authors: Shupp Brittney , Mehta Sagar V. , Chirayath Subin , Patel Nishit , Aiad Mina , Sapin Jared , Stoltzfus Jill , Schneider Yecheskel 
Published: May 2022

AbstractProton Pump Inhibitors (PPI) are one of the most prescribed medications in the United States. However, PPIs have been shown to increase the risk of enteric infections. Our study aims to evaluate the correlation between PPI and COVID-19 severity. We performed a retrospective cohort study on patients who tested positive for SARS-CoV-2 from March to August 2020. Patients were categorized based on PPI user status. Primary outcomes included need for hospital or ICU admission and 30-day mortality. Secondary outcomes looked to determine the severity of COVID-19 infection and effect of comorbid conditions. 2,594 patients were reviewed. The primary outcomes of our study found that neither active nor past PPI use was associated with increased hospital admission or 30-day mortality following completion of multivariate analysis. Additionally, there was no association between COVID-19 infection and the strength of PPI dosing (low, standard, high). However, the following covariates were independently and significantly associated with increased admission: age, male gender, diabetes, COPD, composite cardiovascular disease, kidney disease, and obesity. The following covariates were associated with increased mortality: age, male gender, COPD, and kidney disease. In conclusion, the high risk features and comorbidities of PPI users were found to have a stronger correlation to severe COVID-19 infection and poor outcomes as opposed to the use of PPI therapy.
High-efficiency dual-polarized broadband reflecting metasurface using continuous polarization conversion technique and element with multi degree of freedom
Authors: Karimipour Majid , Aryanian Iman 
Published: May 2022

AbstractIn this study, two effective approaches are combined which are implemented at the element design level and system design level to simultaneously improve the frequency bandwidth and aperture efficiency of a dual-polarized single-layer reflecting metasurface. At the element design level, a broadband behavior is realized by using the polarization conversion technique (PCT) which is a novel technique to enhance the bandwidth of the element. To this end, an anisotropic metasurface with the I-shaped metal patch is proposed for rotating the polarization of the wave emitted from a point source by 90$$^{\circ }$$

∘

and making a continuous phase shift in a full range of 360$$^{\circ }$$

∘

within 8-18 GHz. Therefore, a completely equiphase aperture is achieved leading to enhancing the metasurface performance such as directivity and aperture efficiency and reducing the sidelobe level compared to reflecting metasurface developed by 1-bit phase quantization technique. At the system design level, the three-frequency phase synthesis (TFPS) method, which is based on determining the best constant reference phase for the aperture, is used and the corresponding constant reference phases are optimized to minimize the phase error in the whole band. The combination of TFPS and PCT enhances the effectiveness of the TFPS method considerably. An 841 element reflecting metasurface with aperture dimensions of 290 cm $$\times $$
×
290 cm is designed, simulated, and fabricated in Ku-band to verify the concept. The measurement results show that the 1-dB gain bandwidth before and after combining PCT and TFPS techniques are 17.47% (14.1–16.8 GHz) and 30.3% (14–19 GHz), respectively. In addition, the maximum aperture efficiency of the proposed metasurface is 63.62% which occurs at 14.5 GHz.