bluuebunny/crossref_metadata_2025_split huggingface dataset:
Osteosarcoma Multi-omics Landscape and Subtypes
Authors: Tang Shan , Roberts Ryan , Cheng Lijun , Li Lang 
Published: September 2022

Abstract
Background
Osteosarcoma is the most common primary bone malignancy exhibiting remarkable histologic diversity and genetic heterogeneity. The complex nature of osteosarcoma has confounded precise molecular categorization, prognosis and prediction for this disease. Despite intensive studies aimed at identifying genes or biomarkers involved in pathogeneses, linking clinical outcomes with omics profiles in osteosarcoma has far remained elusive.
Results
86 osteosarcoma tumors with matched profiles of somatic copy-number alteration, gene expression and methylation were categorized into three subgroups by similarity network fusion. The subgrouping criteria was validated on another cohort osteosarcoma tumors. Then the differences among these three subgroups were then investigated based on single-platform profiles.
Conclusions
The multiplatform analysis yields three molecularly distinct and clinically relevant subtypes for osteosarcoma. Previously unappreciated osteosarcoma-type-specific changes at genomic, transcriptomic and epigenetic level were revealed. Several novel factors, such as copy number in 17p13.1-17q11.2, expression of CDK6 or EGFR, and methylation status of Hippo signaling pathway, were found to be closely related to the diverse clinical outcomes in osteosarcoma patients. These findings provide a comprehensive genomic architecture for osteosarcoma and emphasize the need for data integration from different platforms.
Complete Genome Sequencing and Functional Property Analysis of Lactobacillus gasseri LM1065 for industrial application
Authors: Bae Won-Young , Lee Youngjin , Jung Woo-Hyun , Shin So Lim , Sohn Minn , Kim Tae-Rahk 
Published: September 2022

Abstract
Probiotics are defined as live organisms in the host that contribute to health benefits. Lactobacillus gasseri LM1065, isolated from human breast milk, was investigated for its probiotic properties based on its genome. Human breast milk was donated by a healthy woman. The isolated Lactobacillus strain was identified as L. gasseri and named LM1065. Complete genome sequencing and de novo assembly were performed using the PacBio RS II system and hierarchical genome assembly process (HGAP). Probiotic properties were determined by the resistance of the strain to gastric conditions, adherence ability, enzyme production, and safety assessment. The fungistatic effect and the ability to inhibit hyphae transition were studied using the cell-free supernatant (CFS) of L. gasseri LM1065. L. gasseri LM1065 showed high gastric pepsin tolerance and mild tolerance to bile salts. Auto-aggregation ability and hydrophobicity were measured to be 61.21% and 61.55%, respectively. These properties resulted in the adherence of the bacteria to the human intestinal epithelial cells (2.02%). In addition, antibiotic-resistance genes and putative virulence genes were not predicted in the complete genome sequence of L. gasseri LM1065, and antibiotic susceptibility was satisfied by the criteria of the European Food Safety Authority using a cut-off test. CFS showed a fungistatic effect and suppressed the tricarboxylic acid cycle in Candida albicans (29.02%). CFS also inhibited the transition to true hyphae and damaged the blastoconidia. This study demonstrates the essential properties of this novel probiotic, L. gasseri LM1065, and its potential to inhibit vaginal Candida albicans infection.
Comparisons of lymphocytes profiles and inflammatory cytokines levels in blood of patients with differed severity of infection by human adenovirus type 7 Running title: HAdV-7 infection and immune dysfunction
Authors: Sun Junping , Ma Xidong , Zhang Mingyue , Xie Mei , Zhang Xingang , Han Xinjie , Li Xinfu , Zhou Enlu , Wang Junyu , She Danyang , Wang Jianxin 
Published: September 2022

Abstract
Background
Human adenovirus (HAdV) infection outbreak causes community-acquired pneumonia. Cellular immune dysfunction and hypercytokinemia play important roles in the pathogenesis of adenovirus respiratory infection. Some soluble factors in peripheral blood can predict the virus-induced disease progression accurately. The expression levels of inflammatory cytokines differ among patients with different disease severity. However, whether and how HAdV-7 infection influences the composition of blood immune cells and serum cytokine levels in patients at different disease stages, as well as the diagnosis and prognosis values of these parameters, have rarely been intensively studied. We aimed to investigate lymphocytes profiles and cytokines levels in blood of patients at different disease stages upon human adenovirus type 7 (HAdV-7) infections, and explored the diagnosis and prognosis values of the investigated parameters.
Methods
Patients from two outbreaks of HAdV-7 in military of China were categorized into upper respiratory infection (URI) group, common pneumonia (CP) group and severe pneumonia (SP) group according to disease severity. Peripheral blood samples were subjected to routine laboratory tests, while flow cytometry and ELISA were used to measure the lymphocyte subsets and cytokines in blood, respectively. The receiver operating characteristic (ROC) curves were performed to examine the diagnostic and prognostic abilities of these blood parameters.
Results
Signs of imbalanced lymphocytes composition and hypercytokinemia were observed in HAdV-7-infected patients. The percentages of CD3+ T cells and NK cells were significantly decreased along with the aggravation of the disease, particularly for NK cells and CD4+ T cells. The neutrophil to lymphocyte ratio (NLR) increased significantly in patients with more severe disease. In addition, the levels of serum CXCL10, IL-2 and TNF-α were positively correlated with disease severity, while reduced levels of IFN-γ and IL-10 were found in SP patients. Furthermore, analysis of ROC showed that multiple parameters including the percentage of blood CD3+ cells and serum CXCL10 level could predict the progression of HAdV-7 infection.
Conclusions
Imbalance of immune state with hypercytokinemia occurred during HAdV-7 infection. The percentages of blood immune cells such as CD3+ T cells and the levels of serum cytokines such as CXCL10 showed potential diagnosis and prognosis values in HAdV-7 infection.
Sediment vibration characteristics based on accelerometer measurements
Authors: Wang Pingyi , Yuan Jun , Wang Meili , Wang Mi 
Published: September 2022

Abstract
The study of the vibration phenomenon of pebbles under turbulence is still a gap despite recent technological advancements in measurement capabilities. In this study, the vibration process of a fully exposed, isolated smart pebble on a rough bed was measured using a miniature inertial accelerometer and combined with simultaneous local measurements of the near-bed velocities. The paper conducts a series of experimental studies with different flow conditions. The test data match well with the manually observed phenomena, indicating the authenticity of the sediment vibration data collected by the measurement system. The test results show that the pebble motion (before entrainment) subjected to turbulence is a nonlinear vibration process, and its vibration types include in-situ vibration and ex-situ strong vibration. The probability distribution for the amplitude of vibration acceleration is well parameterized by the normal distribution. The vibration intensity tends to increase before approaching the threshold , but it weakens when approaching the point. The sediment vibration frequency is within 20~25 Hz, similar to the flow pulsation frequency and belongs to low-frequency vibration. The data indicate that the near-bed flow velocity is most directly related to the particle vibration events.
Hope, coping strategies, and their predictors in older prostate and breast cancer patients under radiotherapy: a cross sectional study
Authors: Yildizel Sema , Arayici Mehmet Emin , Umay Cenk , Sahin Sevnaz 
Published: September 2022

Abstract
Purpose: The aim of this paper was to evaluate the level of hope, coping methods, and the factors affecting them in patients aged 60 years and over who were diagnosed with breast and prostate cancer, who underwent surgery and/or chemotherapy according to the condition of the disease, and who were at the stage of radiotherapy (RT).
Method: A total of 66 patients, 37 breast cancer and 29 prostate cancer patients, were included in this cross-sectional study. RT and treatment information of the patients were collected by using the records in the hospital database. The personal information of the participants was also collected through the personal information form and scales [HHI (Heart Hope Index), COPE (Coping Attitudes Assessment Scale), VAS (Visual Analogue Scale)].
Results:The median age of the participants was 65 (min-max: 60-80) years. There was a decrease in the weight and waist circumference of the participants after RT (p<0.05). There was no significant change in the HHI and COPE total scores of the patients before and after RT (p>0.05). When only patients with prostate cancer were studied, the self-help sub-dimension of COPE was found to be lower (p=0.018).
Conclusions: It is recommended that patients with prostate cancer be evaluated more sensitively in terms of coping levels during and after radiotherapy. There is an increasing need for further studies in larger populations and cohorts related to this topic in the literature.
Implications for Cancer Survivors: Multidimensional evaluations and interventions may be required in terms of hope levels and coping attitudes of cancer patients receiving radiotherapy.
Bifidobacterium animalis sup F1-7 and Lactobacillus plantarum FWDG alleviate the malnutrition of mice via ghrelin-GHSR/PKC pathway
Authors: Lu Youyou , Wang Ruiqi , Wu Yeting , Cui Qingyu , Tian Xiaoying , Zhang Zhe , Yi Huaxi , Liu Tongjie , Gong Pimin , Zhang Lanwei 
Published: September 2022

Abstract
Purpose: Intestinal microecology was closely
related to malnutrition, but the related mechanism was still
unclear. This study aimed to reveal how microorganisms alleviated
malnutrition via ghrelin-GHSR/PKC-SCFAs
pathway.

Methods and results: Melanoma cells
B16F10-induced malnourished mice of lung cancer. Strains Bif.
animalis F1-7 and L. plantarum FWDG alleviated the
malnutrition of mice to some extent by increasing the dietary
intake level of mice, but the effect of Bif. animalis F1-7
was more prominent. This process was through increasing the
expression level of GHSR and PKC, reducing the expression level of
IP3, and finally regulating the secretion level of ghrelin and
improving the anorexia of mice. Meanwhile, Bif. animalis
F1-7 also reduced the expression levels of GLUT2, SGLT1 and PEPT1
genes and proteins, promoted the increase of acetic acid, butyric
acid, isovaleric acid and total acid levels, regulated the
nutritional transport process of intestinal energy, and finally
improved the nutritional status of tumor mice via
ghrelin-GHSR/PKC-SCFAs pathway.

Conclusion: Our study provided a data support
for the application of potentially beneficial microorganisms of
Bif.animalis F1-7 could acts as an auxiliary component to
alleviate malnutrition.
Analysis of communal Pathogenesis and Immune Infiltration Characteristics Between Psoriasis and Pulmonary Arterial Hypertension
Authors: xia qingyue , su wenxing , cheng yuxin , zeng ni , lu zhiyu , Su Wenxing , Luo Dan 
Published: September 2022

Abstract
Background
Increasingly evidence has shown pulmonary arterial hypertension (PAH) was predisposed to occur in psoriasis, however, the common mechanism of this phenomenon is still not fully clarified. This study aims to further explore the molecular mechanisms of this complication.
Methods
Four datasets were downloaded from the Gene Expression Omnibus (GEO) database based on the study inclusion/exclusion criteria. After screening the communal DEGs, modules, and hub genes of psoriasis and PAH, subsequent bioinformatic analyses, consisting of function annotation analysis, co-expression analysis, drug-gene interaction prediction, and mRNA–miRNA regulation network construction were conducted. Moreover, Immune cell infiltration analysis and correlation analysis were performed to further uncover the related immune pathogenesis in psoriasis and PAH.
Results
170 communal DEGs, 4 modules, and 6 hub genes were identified between GSE15197 and GSE30999, and the expression of hub genes was verified in the GSE41662 and GSE113439 respectively. The function annotation analysis of these genes mainly enriched in the Immune System and associated signal transduction, and the immune cell infiltration analysis highlighted the existence of the overlap in terms of mast cells between PAH and psoriasis.
Conclusions
The analysis of communal DEGs, modules, and hub genes underlined the potential role of the immune system and associated signal transduction in the common pathogenesis of psoriasis and PAH, and immune Infiltration analysis of two diseases provide us with new perspectives and exploring direction. Moreover, six hub genes (MYO5A, CDT1, ASPM, ACTR2, PTPN11, and SOST) may be used as biomarkers or therapeutic targets in psoriasis and PAH.
Comparison of clinical and radiological outcomes after three different surgical treatments for resistant calcifying tendinitis of the shoulder: a short-term randomized controlled trial.
Authors: Verstraelen Freek , Schotanus Martijn , Klemann-Harings Steffie , Heerspink Okke Lambers , Jansen Edwin 
Published: September 2022

Abstract
Background: A preferable surgical treatment for patients with conservative therapy resistant calcifying tendinitis of the shoulder is still a matter of debate. Therefore, the purpose of this study was to evaluate and compare short-term clinical and radiological results of three surgical treatment options for these patients.
Methods: A multicenter randomized trial was conducted. 69 patients were randomly assigned to receive 1. subacromial decompression (Group SAD), 2. debridement of calcifications (Group D), or 3. debridement of calcifications with SAD (Group D+SAD). Stringent inclusion and exclusion criteria were used. Primary outcome was improvement in VAS for pain (pVAS) six months postoperatively. Secondary outcomes were improvement in pVAS six weeks postoperatively, functional outcome (CMS, DASH, ASES), radiological outcome, side treatments and complications.
Results: The improvement in pVAS was significant in all groups (p<0.001) and did not differ between the groups after six months. Six weeks postoperatively, the improvement in pVAS was significantly (p=0.03) less in Group SAD compared to Group D+SAD (16.5mm, SD 19.3mm vs 33.1mm, SD 19.7mm, respectively). The mean size of calcifications decreased significantly in all groups (p<0.0001). In Group SAD the size of the calcifications decreased less (p=0.04) compared to Group D and group D+SAD after six weeks. Group SAD received more side treatments (p=0.003) compared to Group D+SAD (9 vs 1), which were mainly subacromial cortisone injections.
Conclusions: All patient groups showed significant pain relief and improvement of shoulder function six months after surgery. However, patients in group SAD showed inferior pain relief and improvement in DASH score after six weeks. Furthermore, this group required more postoperative side treatments. No significant differences in clinical and radiological outcomes were observed between patients in group D compared to group D+SAD. Therefore, an arthroscopic debridement without subacromial decompression seems to be advisable for patients with therapy resistant calcifying tendinitis of the shoulder.
Level of evidence: 2, Open Label Randomized Clinical Trial.
IRB: METC Zuyderland MC. Number: 14-T-112.
Registered at trialregister.nl: NL 4947
Discovery and significance of nanoparticles released by plants
Authors: Zhang Wanqin , Cao JianJin , Luo Xiaoen , Qiu Junwei , Qi Yonghao 
Published: September 2022

Abstract

As an important part of nature, the role of plants in the material cycle has been widely studied. Nanoparticles, as a common form of existence, have also been confirmed to be absorbed and retained by plants, but there are few studies on the environmental effects of exhaled nanoparticles from plants. In this paper, a sampling device is designed to sample the exhaled substances from plants in Fogang, Qingyuan, Guangdong province and Liushutang, Hunan Province, and analyzed by transmission electron microscopy. It is found that plants emit a large number of nanoparticles. The particle diameter is mostly between 50-300nm, usually sulfate and phosphate. The discovery of nanoparticles emitted by plants makes an important supplement to the respiration of plants. It is estimated that about 5.066×1019 nanoparticles are produced by plants every month. These particles have a similar effect to anthropogenic sulfate particles but have a smaller particle size and have an important impact on global cooling and rainfall.
The abnormal glucose metabolism due to endogenous serine synthesis for selenoprotein expression in vitro under high-Se
Authors: Wang Qin , Wang Jianrong , Zhan Shuo , Han Feng , Liu Yiqun , Huang Zhenwu 
Published: September 2022

Abstract
Objective: The purpose of this study is to observe whether the glycolysis bypass is activated under high-Se stress.
Method: Firstly, five different concentrations of selenomethionine (SeMet, 0.001, 0.01, 0.1, 1 and 10 mmol/L) were added into the three kinds of cell lines (L02, HepG2 and HCT-116) and incubated for 48 hours. The expressions of selenoproteins (GPX1 and SELENOP) and key enzymes for the de novo serine biosynthesis (PHGDH) or synthetic serine as the one carbon unit donor (SHMT1) were analyzed by ELISA and WB to screen the most sensitive cell line. Then, with more detailed levels of SeMet (0.001, 0.005, 0.01, 0.025, 0.05, 0.075, 0.1, 0.25, 0.5, 1, and 10 µmol/L) given, L02 cell was cultured for 48 hours to analyze the trends of selenoproteins and serine-related metabolic enzymes by WB. Finally, the impact of exogenous serine or glycine on the expressions of selenoproteins and metabolic enzymes were evaluated in L02 cell cultured in high-Se media.
Result: Unlike in HepG2 cell and HCT-116 cell, the expression trend of selenoproteins and key metabolic enzymes with increased SeMet concentration is similar in L02 cells, which is a parabola with slight differences at the top. The corresponding SeMet concentration for the inflection point of GPx1, SELENOP, PHGDH and SHMT1 is 0.075µmol/L, 0.05µmol/L, 0.05µmol/L and 0.05µmol/L respectively. Also in L02 cell cultured in high-Se media (added with 0.05µmol/L SeMet), there were dose-dependent feedback inhibition effects of exogenous serine or glycine on the expressions of PHGDH. Meanwhile there were promotional effects of exogenous serine or glycine on the expressions of GPx1 and SELENOP.
Conclusions: The L02 cell line is the most suitable for the studies of selenoprotein expression and regulation in vitro among the three kinds of cell lines. Under high-Se stress, the serine de novo synthetic pathway might be utilized to synthesize more endogenous serine and could be feedback inhibited by exogenous serine or glycine. Further research works need to be taken based on the well-tested high-Se induced IR animal models.
Risk of postpartum depressive symptoms is influenced by psychological burden related to the COVID-19 pandemic and dependent from individual stress coping
Authors: Meister Sarah , Dreyer Eva-Maria , Hahn Laura , Thomann Marilena , Keilmann Lucia , Beyer Susanne , Mayer Clarissa , Prins Gwendolin , Hasbargen Uwe , Mahner Sven , jeschke udo , Kolben Thomas , Burges Alexander 
Published: September 2022

Abstract
Purpose
There are different studies worldwide, which have shown a higher risk of mental disorders due to the COVID-19 pandemic. One aim of this study was to characterize factors influencing the psychological burden related to the COVID-19 pandemic and the impact on postpartum depressive symptoms. Further, the role of individual stress and coping strategies was analyzed in this context.
Material and Methods
131 women, who were in obstetric care at the LMU Clinic Munich, between March and October 2020, were questioned by different self-report questionnaires, before birth, one month, two months and 6 months after birth. A designed questionnaire to evaluate the psychological burden related to the COVID-19 pandemic, a modified version of the Stress and coping inventory (SCI) and the Edinburgh Postnatal Depression Scale (EPDS) were utilized
Results
We could show that the psychological burden related to the COVID-19 pandemic influenced the EPDS score one, two and 6 months after birth. In addition, the prenatal stress and individual coping strategies affected the EPDS and the burden related to the COVID-19 pandemic before and after birth significantly.
Conclusion
An association of the psychological burden related to the COVID-19 pandemic with the risk of developing postpartum depressive symptoms could be shown in this study. In this context, the separation of the partner and the family were recognized as important factors. Furthermore, the SCI was identified as effective screening instrument for mothers before delivery to possibly avoid the development of postpartum depression by early diagnosis and intervention.
Succinate promotes pulmonary fibrosis through GPR91 and predicts death in idiopathic pulmonary fibrosis
Authors: He Yijun , Han Yuanyuan , Zou Lijun , Yao Tingting , Zhang Yan , Lv Xin , Jiang Mao , Long Lingzhi , Li Mengyu , Cheng Xiaoyun , Jiang Guoliang , Peng Zhangzhe , Tao Lijian , Jie Meng 
Published: September 2022

Abstract

Background
IPF has been associated with a notable disruption of cellular metabolism. It is still unknown how cellular energy metabolism problems contribute to the onset of pulmonary fibrosis. In an effort to pinpoint the metabolic factors that contribute to pulmonary fibrosis, we investigated the serum metabolomic changes among IPF patients.
Methods
Metabolomics was performed on serum samples from IPF patients using liquid chromatography-mass spectrometry. Further evidence for the crucial metabolic difference came from an IPF cohort. Multivariate analysis and COX regression analysis confirmed its clinical utility in the diagnosis and prognosis of IPF. Our study explored the potential role of this metabolic molecule in pulmonary fibrosis in mice and cells.
Results
Through metabolomics research, it was discovered that the TCA cycle intermediates changed dramatically in IPF, with succinate being of particular concern. There was an accumulation of serum succinate in a prospective cohort of 55 patients with IPF compared to 19 healthy controls. A high serum succinate level was independently associated with higher rates of disease progression (OR = 13.087, 95% CI (2.819–60.761)) and mortality (HR = 3.418, 95% CI (1.308–8.927)). A succinate accumulation was also observed in mice with lung fibrosis induced by bleomycin (BLM). Exogenous succinate administration exacerbated the lung fibrosis caused by BLM, whereas lowering succinate accumulation lessened the fibrosis. Succinate-specific receptors (GPR91) were also elevated in lung tissues from patients with IPF. Furthermore, GPR91-/- mice were protected against lung fibrosis caused by BLM. Through GPR91, succinate promoted TGF-induced activation of normal human lung fibroblasts in vitro.
Conclusions
The findings demonstrate a previously unknown and highly novel association between energy metabolic reprogramming, succinate, fibroblast activation, and clinical prognosis in IPF.