bluuebunny/crossref_metadata_2025_split huggingface dataset:
SARS-CoV-2 quasi-species analysis from patients with persistent nasopharyngeal shedding
Authors: Dudouet Pierre , Colson Philippe , Aherfi Sarah , Levasseur Anthony , Beye Mamadou , Delerce Jeremy , Burel Emilie , Lavrard Philippe , Bader Wahiba , Lagier Jean-Christophe , Fournier Pierre-Edouard , La Scola Bernard , Raoult Didier 
Published: November 2022

AbstractAt the time of a new and unprecedented viral pandemic, many questions are being asked about the genomic evolution of SARS-CoV-2 and the emergence of different variants, leading to therapeutic and immune evasion and survival of this genetically highly labile RNA virus. The nasopharyngeal persistence of infectious virus beyond 17 days proves its constant interaction with the human immune system and increases the intra-individual mutational possibilities. We performed a prospective high-throughput sequencing study (ARTIC Nanopore) of SARS-CoV-2 from so-called "persistent" patients, comparing them with a non-persistent population, and analyzing the quasi-species present in a single sample at time t. Global intra-individual variability in persistent patients was found to be higher than in controls (mean 5.3%, Standard deviation 0.9 versus 4.6% SD 0.3, respectively, p < 0.001). In the detailed analysis, we found a greater difference between persistent and non-persistent patients with non-severe COVID 19, and between the two groups infected with clade 20A. Furthermore, we found minority N501Y and P681H mutation clouds in all patients, with no significant differences found both groups. The question of the SARS-CoV-2 viral variants’ genesis remains to be further investigated, with the need to prevent new viral propagations and their consequences, and quasi-species analysis could be an important key to watch out.
Genome-wide identification, phylogenetic, and expression analysis under abiotic stress conditions of Whirly (WHY) gene family in Medicago sativa L.
Authors: Ruan Qian , Wang Yizhen , Xu Haoyu , Wang Baoqiang , Zhu Xiaolin , Wei Bochuang , Wei Xiaohong 
Published: November 2022

AbstractThe WHY family is a group of plant-specific transcription factors, that can bind to single-stranded DNA molecules and play a variety of functions in plant nuclei and organelles, participating in the regulation of plant leaf senescence. It has been identified and analyzed in many species, however, the systematic identification and analysis of the WHY genes family have not yet been reported in alfalfa (Medicago sativa L.). Therefore, to explore the function of alfalfa the WHY genes, and 10 MsWHY genes were identified and further characterized their evolutionary relationship and expression patterns by analyzing the recently published genome of alfalfa. Comprehensive analysis of the chromosome location, physicochemical properties of the protein, evolutionary relationship, conserved motifs, and responses to abiotic stresses of the WHY gene family in alfalfa using bioinformatics methods. The results showed that 10 MsWHY genes were distributed on 10 chromosomes, and collinearity analysis showed that many MsWHYs might be derived from segmental duplications, and these genes are under purifying selection. Based on phylogenetic analyses, the WHY gene family of alfalfa can be divided into four subfamilies: I-IV subfamily, and approximately all the WHY genes within the same subfamily share similar gene structures. The 10 MsWHY gene family members contained 10 motifs, of which motif 2 and motif 4 are the conserved motifs shared by these genes. Furthermore, the analysis of cis-regulatory elements indicated that regulatory elements related to transcription, cell cycle, development, hormone, and stress response are abundant in the promoter sequence of the MsWHY genes. Real-time quantitative PCR demonstrated that MsWHYs gene expression is induced by drought, salt, and methyl jasmonate. The present study serves as a basic foundation for future functional studies on the alfalfa WHY family.
Ornamental roses for conservation of leafcutter bee pollinators
Authors: Sinu Palatty Allesh , Jamal Mubarak , Shaji Greeshma , Hariraveendra M. , Viswan Gopika , Abhiram Krishnan P. , Das Ankita , Aneha K. , Pooja A. R. , Salikity Spandana , Arathy V. 
Published: November 2022

AbstractPollinator conservation is a global priority. Efforts are taken to restore pollinators by improving flower resources, a crucial driver of pollinator diversity and population growth. It helped gardening and landscaping supply chains, which introduced lists of bee-friendly plants and bee hotels, yet, desirable results seem distant. One shortcoming of the present schemes is that they lack a cohesive planning for nesting opportunities and nesting provisions for wild solitary bees, the crucial pollinators of crop and wild plants. We tested whether the world’s popular ornamental plant, rose (Rosa chinensis Jacq.)—a hitherto unlisted bee-friendly plant—can aid in conserving leafcutter bees, which require fresh leaves for constructing nest cells. We surveyed 2360 rose plants in 136 sites in rural and urban places and lowlands and highlands of south (8°N–12°N) and northeastern India (26°N–27°N) for the characteristic notches the bees leave on foraged leaves. We reared brood constructed with rose and non-rose leaves to examine the brood success rate. About a quarter of all the roses surveyed had the notches of leafcutter bees on the leaves. However, the proportion of cut roses varied considerably among sites. Bees used roses much higher in urban areas and lowlands than in rural areas and highlands. The selection of plants was negatively associated with pesticide application. The brood success rate was 100% for the brood that was constructed by the leaves of rose and non-rose plants. Rose flowers do not support bees, but rose leaves indeed do. We recommend rose plants in leafcutter bee conservation and restoration schemes, particularly in urban environment.
Paeoniflorin drives the immunomodulatory effects of mesenchymal stem cells by regulating Th1/Th2 cytokines in oral lichen planus
Authors: Zhang Zhihui , Zhang Yan , Zhao Zhongfang , Li Pei , Chen Danyang , Wang Wei , Han Ying , Zou Shiqi , Jin Xin , Zhao Jianling , Liu Hongwei , Wang Xiao , Zhu Weili 
Published: November 2022

AbstractLichen planus (LP) is a chronic inflammatory disease. Oral lichen planus (OLP) mainly appears as oral mucosal reticular or ulcerative lesions with an unknown etiology. We aimed to explore the immunomodulatory effect of paeoniflorin (PF) in mesenchymal stem cells (MSCs) and the potential involvement of Th1/Th2 cytokines in OLP. The effects of paeoniflorin on the proliferation and migration of MSCs were detected by Cell Counting Kit-8 (CCK8) and Transwell assays. MSCs were subjected to osteogenic, adipogenic and neurogenic induction followed by Alizarin red, oil red O, real-time PCR and immunofluorescence assays. We found that paeoniflorin promoted the proliferation, migration and multilineage differentiation of MSCs from OLP lesions (OLP-MSCs) in vitro. Paeoniflorin pretreatment increased the inhibitory effect of OLP-MSCs on peripheral blood mononuclear cells. Furthermore, paeoniflorin-pretreated OLP-MSCs simultaneously decreased Th1 cytokine levels and increased Th2 cytokine levels in T lymphocyte cocultures. Finally, paeoniflorin-pretreated OLP-MSCs also promoted the Th1/Th2 balance both in vitro and in the serum of mice that received skin allografts. In conclusion, paeoniflorin enhanced MSC immunomodulation and changed the inflammatory microenvironment via T lymphocytes, suggesting that the improvement of OLP-MSCs is a promising therapeutic approach for OLP.
Characteristics and local risk factors of community-acquired and health-care-associated Staphylococcus aureus pneumonia
Authors: Lee Li-Na , Chou Wen-Ru , Wang Jann-Yuan , Kuo Yen-Liang , Chang Chi-Yueh , Lee Yi-Chien , Tung Shao-Hsien , Tsao Wen-Ching , Chao Ke-Yun , Liu Wei-Lun 
Published: November 2022

AbstractThis study aims at identifying characteristics, risk factors and mortality of community-acquired (CAP) and health-care-associated pneumonia (HCAP) by Staphylococcus aureus (S. aureus). We retrieved adults with S. aureus CAP or HCAP diagnosed by blood or pleural effusion culture in 2.6 years, and compared with those of Streptococcus pneumoniae (S. pneumoniae) CAP or HCAP diagnosed by blood or respiratory culture, or urine antigen. We found 18 patients with CAP and 9 HCAP due to S. aureus (female 33%, 66.6 ± 12.4 years-old), and 48 patients with CAP and 15 HCAP due to S pneumoniae (female 41%, 69.5 ± 17.5 years). Diabetes mellitus (52% vs. 24%, p = 0.019), hemodialysis (11% vs. 0%, p = 0.046), skin lesions (44% vs. 0%, p < 0.001), cavitary nodules (37% vs. 1.6%, p < 0.001) and pleural effusions (48% vs. 18%, p = 0.007) were more common in staphylococcal than pneumococcal group. Three patients with staphylococcal pneumonia had acute myocardial infarction. Pneumonia severity index (139 ± 52 vs. 109 ± 43, p = 0.005) and 30-day mortality (41% vs. 9.5%, p = 0.001) were higher in staphylococcal group. Multivariate analysis showed underlying disease (especially cancer and cirrhosis), risk class 4/5, altered mentality, shock and bilateral pneumonia were risk factors for 30-day mortality.
Element-specific visualization of dynamic magnetic coupling in a Co/Py bilayer microstructure
Authors: Feggeler Thomas , Meckenstock Ralf , Spoddig Detlef , Schöppner Christian , Zingsem Benjamin , Schaffers Taddäus , Ohldag Hendrik , Wende Heiko , Farle Michael , Ney Andreas , Ollefs Katharina 
Published: November 2022

AbstractWe present the element-specific and time resolved visualization of uniform ferromagnetic resonance excitations of a Permalloy (Py) disk–Cobalt (Co) stripe bilayer microstructure. The transverse high frequency component of the resonantly excited magnetization is sampled in the ps regime by a combination of ferromagnetic resonance (FMR) and scanning transmission X-ray microscopy (STXM-FMR) recording snapshots of the local magnetization precession of Py and Co with nanometer spatial resolution. The approach allows us to individually image the resonant dynamic response of each element, and we find that angular momentum is transferred from the Py disk to the Co stripe and vice versa at their respective resonances. The integral (cavity) FMR spectrum of our sample shows an unexpected additional third resonance. This resonance is observed in the STXM-FMR experiments as well. Our microscopic findings suggest that it is governed by magnetic exchange between Py and Co, showing for the Co stripe a difference in relative phase of the magnetization due to stray field influence.
Modulation of mouse laryngeal inflammatory and immune cell responses by low and high doses of mainstream cigarette smoke
Authors: Easwaran Meena , Martinez Joshua D. , Kim Juyong Brian , Erickson-DiRenzo Elizabeth 
Published: November 2022

AbstractCigarette smoking is a major risk factor for laryngeal diseases. Despite well-documented cigarette smoke (CS) induced laryngeal histopathological changes, the underlying immunopathological mechanisms remain largely unexplored. The goal of this study was to evaluate inflammatory and immune cell responses in a CS-exposed larynx. Specifically, we used a 4-week subacute whole-body CS inhalation mouse model to assess these responses in the laryngeal mucosa upon exposure to low (LD; 1 h/day) and high dose (HD; 4 h/day) CS. Laryngeal tissues were harvested and evaluated using a 254-plex NanoString inflammation panel and neutrophil/macrophage/T-cell immunohistochemistry (IHC). NanoString global and differential gene expression analysis revealed a unique expression profile only in the HD group, with 26 significant differentially expressed genes (DEGs). StringDB KEGG pathway enrichment analysis revealed the involvement of these DEGs with pro-inflammatory pathways including TNF/TNFα and IL-17. Furthermore, inflammatory responses remained inhibited in conjunction with predicted activated states of anti-inflammatory regulators like PPARγ and NFE2L2 upon Ingenuity Pathway Analysis (IPA). Subglottic T-cell levels remained significantly inhibited as corroborated by IPA predictions. Overall, our key findings are consistent with HD exposures being anti-inflammatory and immunosuppressive. Furthermore, the identification of important regulatory genes and enriched pathways may help improve clinical interventions for CS-induced laryngeal diseases.
Effect of the high voltage waveform on the ionic wind produced by a needle-to-plate dielectric barrier discharge
Authors: Moreau Eric , Defoort Etienne 
Published: November 2022

AbstractAlthough corona discharges are used in many industrial applications because of their ability to produce chemical species, the ionic wind they induce is less known and often ignored. Therefore, the present study aims at investigating the ionic wind produced by a corona discharge ignited between a high voltage needle and a grounded plate electrode covered by a dielectric material. More specifically, the work focuses on the influence of the high voltage waveform on the temporal behavior of the ionic wind. The results highlight that the high voltage waveform plays a key role on the dynamics of the flow produced inside the discharge. On the one hand, for the sine, triangle and sawtooth waveforms, there is a flow acceleration during both the positive and the negative half-cycles, the positive discharge being more effective in velocity production. On the other hand, for the square waveform, the increase in velocity occurs during the rises and falls of the voltage, because of the strengthening of the electric field due to the ions remaining from the previous half-cycle at the wall of the dielectric material.
Ultrafast inactivation of SARS-CoV-2 with 266 nm lasers
Authors: Sun Kexiong , Niu Gang , Zhang Yanfang , Yang Juan , Zhang Danna , Wu Han , Shao Xinyu , Ma Xiuquan 
Published: November 2022

AbstractDisinfection eliminates pathogenic microorganisms and ensures a biosafe environment for human beings. The rapid spread of COVID-19 is challenging traditional disinfection methods in terms of reducing harmful side effects and conducting faster processes. Spraying large-scale chemical disinfectants is harmful to individuals and the environment, while UV lamp and light-emitting diode (LED) disinfection still requires a long exposure time due to the low irradiance and highly divergent beam characteristics. Given that a laser maintains a high irradiance over a long distance, we studied the effectiveness of lasers as a new disinfection method, and the results show the capability for ultrafast inactivation of SARS-CoV-2 virus with a 266 nm laser. This work confirms UV lasers as a good candidate for disinfection.
Assessing the feasibility of mapping the tibialis anterior muscle with navigated transcranial magnetic stimulation in neuro-oncologic patients
Authors: Eibl Thomas , Schrey Michael , Weigel Jens , Liebert Adrian , Lange Rüdiger , Städt Michael , Eff Florian , Holtmannspötter Markus , Steiner Hans-Herbert 
Published: November 2022

AbstractMapping the lower extremity with navigated transcranial magnetic stimulation (nTMS) still remains challenging for the investigator. Clinical factors influencing leg mapping with nTMS have not been fully investigated yet. The aim of the study was to identify factors which influence the possibility of eliciting motor evoked potentials (MEPs) from the tibialis anterior muscle (TA). Patient records, imaging, nTMS examinations and tractography were retrospectively evaluated. 48 nTMS examinations were performed in 46 brain tumor patients. Reproducible MEPs were recorded in 20 patients (41.67%). Younger age (p = 0.044) and absence of perifocal edema (p = 0.035, Cramer’s V = 0.34, OR = 0.22, 95% CI = 0.06–0.81) facilitated mapping the TA muscle. Leg motor deficit (p = 0.49, Cramer’s V = 0.12, OR = 0.53, 95%CI = 0.12–2.36), tumor entity (p = 0.36, Cramer’s V = 0.22), tumor location (p = 0.52, Cramer’s V = 0.26) and stimulation intensity (p = 0.158) were no significant factors. The distance between the tumor and the pyramidal tract was higher (p = 0.005) in patients with successful mapping of the TA. The possibility to stimulate the leg motor area was associated with no postoperative aggravation of motor deficits in general (p = 0.005, Cramer’s V = 0.45, OR = 0.63, 95%CI = 0.46–0.85) but could not serve as a specific predictor of postoperative lower extremity function. In conclusion, successful mapping of the TA muscle for neurosurgical planning is influenced by young patient age, absence of edema and greater distance to the CST, whereas tumor entity and stimulation intensity were non-significant.
A mitophagy-related gene signature associated with prognosis and immune microenvironment in colorectal cancer
Authors: Zhang Cong , Zeng Cailing , Xiong Shaoquan , Zhao Zewei , Wu Guoyu 
Published: November 2022

AbstractColorectal cancer (CRC) is a heterogeneous disease and one of the most prevalent malignancies worldwide. Previous research has demonstrated that mitophagy is crucial to developing colorectal cancer. This study aims to examine the association between mitophagy-related genes and the prognosis of CRC patients. Gene expression profiles and clinical information of CRC patients were obtained from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) databases. Univariate Cox regression and the least absolute shrinkage and selection operator (LASSO) regression analysis were applied to establish a prognostic signature using mitophagy related genes. Kaplan–Meier and receiver operating characteristic (ROC) curves were used to analyze patient survival and predictive accuracy. Meanwhile, we also used the Genomics of Drug Sensitivity in Cancer (GDSC) database and Tumor Immune Dysfunction and Exclusion (TIDE) algorithm to estimate the sensitivity of chemotherapy, targeted therapy and immunotherapy. ATG14 overexpression plasmid was used to regulate the ATG14 expression level in HCT116 and SW480 cell lines, and cell counting kit-8, colony formation and transwell migration assay were performed to validate the function of ATG14 in CRC cells. A total of 22 mitophagy-driven genes connected with CRC survival were identified, and then a novel prognostic signature was established based on 10 of them (AMBRA1, ATG14, MAP1LC3A, MAP1LC3B, OPTN, VDAC1, ATG5, CSNK2A2, MFN1, TOMM22). Patients were divided into high-risk and low-risk groups based on the median risk score, and the survival of patients in the high-risk group was significantly shorter in both the training cohort and two independent cohorts. ROC curve showed that the area under the curves (AUC) of 1-, 3- and 5-year survival were 0.66, 0.66 and 0.64, respectively. Multivariate Cox regression analysis confirmed the independent prognostic value of the signature. Then we constructed a Nomogram combining the risk score, age and M stage, which had a concordance index of survival prediction of 0.77 (95% CI 0.71–0.83) and more robust predictive accuracy. Results showed that CD8+ T cells, regulatory T cells and activated NK cells were significantly more enriched in the high-risk group. Furthermore, patients in the high-risk group are more sensitive to targeted therapy or chemotherapy, including bosutinib, elesclomol, lenalidomide, midostaurin, pazopanib and sunitinib, while the low-risk group is more likely to benefit from immunotherapy. Finally, in vitro study confirmed the oncogenic significance of ATG14 in both HCT116 and SW480 cells, whose overexpression increased CRC cell proliferation, colony formation, and migration. In conclusion, we developed a novel mitophagy-related gene signature that can be utilized not only as an independent predictive biomarker but also as a tool for tailoring personalizing treatment for CRC patients, and we confirmed ATG14 as a novel oncogene in CRC.
Evolution of direct reciprocity in group-structured populations
Authors: Murase Yohsuke , Hilbe Christian , Baek Seung Ki 
Published: November 2022

AbstractPeople tend to have their social interactions with members of their own community. Such group-structured interactions can have a profound impact on the behaviors that evolve. Group structure affects the way people cooperate, and how they reciprocate each other’s cooperative actions. Past work has shown that population structure and reciprocity can both promote the evolution of cooperation. Yet the impact of these mechanisms has been typically studied in isolation. In this work, we study how the two mechanisms interact. Using a game-theoretic model, we explore how people engage in reciprocal cooperation in group-structured populations, compared to well-mixed populations of equal size. In this model, the population is subdivided into groups. Individuals engage in pairwise interactions within groups while they also have chances to imitate strategies outside the groups. To derive analytical results, we focus on two scenarios. In the first scenario, we assume a complete separation of time scales. Mutations are rare compared to between-group comparisons, which themselves are rare compared to within-group comparisons. In the second scenario, there is a partial separation of time scales, where mutations and between-group comparisons occur at a comparable rate. In both scenarios, we find that the effect of population structure depends on the benefit of cooperation. When this benefit is small, group-structured populations are more cooperative. But when the benefit is large, well-mixed populations result in more cooperation. Overall, our results reveal how group structure can sometimes enhance and sometimes suppress the evolution of cooperation.
Nutritional value and antioxidant capacity of organic and conventional vegetables of the genus Allium
Authors: Czech Anna , Szmigielski Marek , Sembratowicz Iwona 
Published: November 2022

AbstractThere are indications that organically grown plants are safer for health and have higher antioxidant content than conventional ones. Vegetables of the genus Allium L. are a valuable source of health-promoting substances, including compounds with antioxidant properties. The aim of the study was to compare the antioxidant potential and nutritional value of four species of Allium L. vegetables obtained from organic and conventional production: garlic, leek and red and yellow onion. Their proximate and mineral composition were determined, as well as the content of bioactive substances and antioxidant potential. The study showed that the cultivation method significantly influenced the parameters tested. Comparison of organic vegetables with conventional ones in terms of content of dry matter, crude protein and crude fibre revealed no general trend indicating the superiority of one method over the other. However, all organic vegetables analysed were more abundant in minerals (Ca, Mg, Fe, Zn, Cu and Mn) and bioactive compounds. They also exhibited higher antioxidant capacity as measured by the FRAP and DPPH. tests. Their consumption (especially organic garlic and leek) may therefore strengthen the body's natural antioxidant defences and is beneficial for health.