bluuebunny/crossref_metadata_2025_split huggingface dataset:
Quantitative phosphoproteomic analysis reveals chemoresistance-related proteins and signaling pathways induced by rhIL-6 in human osteosarcoma cells
Authors: Zhang Rui , Wang Huan , Li Erliang , Wu Yonghong , Wen Yanhua , Li Chenyu , Liao Bo , Ma Qiong 
Published: October 2021

Abstract
Background
IL-6 plays a pivotal role in resistance to chemotherapeutics, including lobaplatin. However, the underlying mechanisms are still unclear. This study was to investigate the changes in phosphoproteins and their related signaling pathways in the process of IL-6-induced chemoresistance to lobaplain in osteosarcoma cells.

Methods
We performed a quantitative phosphoproteomic analysis of the response of SaOS-2 osteosarcoma cells to recombinant human IL-6 (rhIL-6) intervention prior to lobaplatin treatment. The cells were divided into the control group (Con), the lobaplatin group (Lob), and the rhIL-6-and-lobaplatin group (IL-6). Three biological replicates of each group were included. The differentially expressed phosphoproteins were subjected to Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses. Netphos 3.1 was used for the prediction of kinases, and STRING was used for the visualization of protein–protein interactions. The conserved motifs surrounding the phosphorylated residues were analyzed using the motif-x algorithm. Western blot analysis was performed to verify the differential expression of p-FLNC, its predicted kinase and the related signaling pathway. The results of the bioinformatic analysis were validated by immunohistochemical staining of clinical specimens.

Results
In total, 3373 proteins and 12,183 peptides, including 3232 phosphorylated proteins and 11,358 phosphorylated peptides, were identified and quantified. Twenty-three significantly differentially expressed phosphoproteins were identified in the comparison between the IL-6 and Lob groups, and p-FLNC ranked second among these phosphoproteins. GO and KEGG analyses revealed the pivotal role of mitogen-activated protein kinase signaling in drug resistance induced by rhIL-6. Four motifs, namely, -SPxxK-, -RxxSP-, -SP-, and -SPK-, demonstrated higher expression in the IL-6 group than in the Lob group. The western blot analysis results verified the higher expression of p-FLNC, AKT1, and p-ERK and the lower expression of p-JNK in the IL-6 group than in the Con and Lob groups. The immunohistochemical staining results showed that p-FLNC, AKT1 and p-ERK1/2 were highly expressed in platinum-resistant clinical specimens but weakly expressed in platinum-sensitive specimens, and platinum-resistant osteosarcoma specimens demonstrated weak expression of p-JNK.

Conclusions
This phosphoproteomic study is the first to reveal the signature associated with rhIL-6 intervention before lobaplatin treatment in human osteosarcoma cells. p-FLNC, AKT1, and MAPK signaling contributes to resistance to lobaplatin in osteosarcoma SaOS-2 cells and may represent molecular targets to overcome osteosarcoma chemoresistance.
Clinical M2 macrophages-related genes to aid therapy in pancreatic ductal adenocarcinoma
Authors: Xu Qianhui , Chen Shaohuai , Hu Yuanbo , Huang Wen 
Published: October 2021

Abstract
Background
Increasing evidence supports that infiltration M2 Macrophages act as pivotal player in tumor progression of pancreatic ductal adenocarcinoma (PDAC). Nonetheless, comprehensive analysis of M2 Macrophage infiltration and biological roles of hub genes (FAM53B) in clinical outcome and immunotherapy was lack.

Method
The multiomic data of PDAC samples were downloaded from distinct datasets. CIBERSORT algorithm was performed to uncover the landscape of TIME. Weighted gene co-expression network analysis (WGCNA) was performed to identify candidate module and significant genes associated with M2 Macrophages. Kaplan-Meier curve and receiver operating characteristic (ROC) curves were applied for prognosis value validation. Mutation data was analyzed by using “maftools” R package. Gene set variation analysis (GSVA) was employed to assign pathway activity estimates to individual sample. Immunophenoscore (IPS) was implemented to estimate immunotherapeutic significance of risk score. The half-maximal inhibitory concentration (IC50) of chemotherapeutic drugs was predicted by using the pRRophetic algorithm. Finally, quantitative real-time polymerase chain reaction was used to determine FAM53B mRNA expression and TIMER database was utilized to uncover its possible role in immune infiltration of PDAC.

Results
Herein, 17,932 genes in 234 samples (214 tumor and 20 normal) were extracted from three platforms. Taking advantage of WGCNA, significant module (royalblue) and 135 candidate genes were considered as M2 Macrophages-related genes. Subsequently, risk signature including 5 hub genes was developed by multiple analysis, which exhibited excellent prognostic performance. Besides, comprehensive prognostic nomogram was constructed to quantitatively estimate risk. Then, intrinsic link between risk score with tumor mutation burden (TMB) was explored. Additionally, risk score significantly correlated with diversity of tumor immune microenvironment (TIME). PDAC samples within different risk presented diverse signaling pathways activity and experienced significantly distinct sensitivity to administering chemotherapeutic or immunotherapeutic agents. Finally, the biological roles of FAM53B were revealed in PDAC.

Conclusions
Taken together, comprehensive analyses of M2 Macrophages profiling will facilitate prognostic prediction, delineating complexity of TIME, and contribute insight into precision therapy for PDAC.
Long noncoding RNA SNHG4: a novel target in human diseases
Authors: Chu Qingfei , Gu Xinyu , Zheng Qiuxian , Guo Zixuan , Shan Dandan , Wang Jing , Zhu Haihong 
Published: October 2021

AbstractRecently, long noncoding RNAs (lncRNAs) have attracted great attention from researchers. LncRNAs are non-protein-coding RNAs of more than 200 nucleotides in length. Multiple studies have been published on the relationship between lncRNA expression and the progression of human diseases. LncRNA small nucleolar RNA host gene 4 (SNHG4), a member of the lncRNA SNHG family, is abnormally expressed in a variety of human diseases, including gastric cancer, renal cell carcinoma, glioblastoma, neuroblastoma, prostate cancer, colorectal cancer, osteosarcoma, cervical cancer, liver cancer, lung cancer, non-small-cell lung cancer, neonatal pneumonia, diabetic retinopathy, neuropathic pain, acute cerebral infarction, acute myeloid leukaemia, and endometriosis. In this paper, the structure of SNHG4 is first introduced, and then studies in humans, animal models and cells are summarized to highlight the expression and function of SNHG4 in the above diseases. In addition, the specific mechanism of SNHG4 as a competing endogenous RNA (ceRNA) is discussed. The findings indicate that SNHG4 can be used as a biomarker for disease prognosis evaluation and as a potential target for disease diagnosis and treatment.
Rethinking the economic costs of hospitalization for malaria: accounting for the comorbidities of malaria patients in western Kenya
Authors: Watts Caroline , Atieli Harrysone , Alacapa Jason , Lee Ming-Chieh , Zhou Guofa , Githeko Andrew , Yan Guiyun , Wiseman Virginia 
Published: October 2021

AbstractBackgroundMalaria causes significant mortality and morbidity in sub-Saharan Africa, especially among children under five years of age and places a huge economic burden on individuals and health systems. While this burden has been assessed previously, few studies have explored how malaria comorbidities affect inpatient costs. This study in a malaria endemic area in Western Kenya, assessed the total treatment costs per malaria episode including comorbidities in children and adults.MethodsTotal economic costs of malaria hospitalizations were calculated from a health system and societal perspective. Patient-level data were collected from patients admitted with a malaria diagnosis to a county-level hospital between June 2016 and May 2017. All treatment documented in medical records were included as health system costs. Patient and household costs included direct medical and non-medical expenses, and indirect costs due to productivity losses.ResultsOf the 746 patients admitted with a malaria diagnosis, 64% were female and 36% were male. The mean age was 14 years (median 7 years). The mean length of stay was three days. The mean health system cost per patient was Kenyan Shilling (KSh) 4288 (USD 42.0) (95% confidence interval (CI) 95% CI KSh 4046–4531). The total household cost per patient was KSh 1676 (USD 16.4) (95% CI KSh 1488–1864) and consisted of: KSh 161 (USD1.6) medical costs; KSh 728 (USD 7.1) non-medical costs; and KSh 787 (USD 7.7) indirect costs. The total societal cost (health system and household costs) per patient was KSh 5964 (USD 58.4) (95% CI KSh 5534–6394). Almost a quarter of patients (24%) had a reported comorbidity. The most common malaria comorbidities were chest infections, diarrhoea, and anaemia. The inclusion of comorbidities compared to patients with-out comorbidities led to a 46% increase in societal costs (health system costs increased by 43% and patient and household costs increased by 54%).ConclusionsThe economic burden of malaria is increased by comorbidities which are associated with longer hospital stays and higher medical costs to patients and the health system. Understanding the full economic burden of malaria is critical if future malaria control interventions are to protect access to care, especially by the poor.
Opening the policy blackbox: unravelling the process for changing national diagnostic and treatment guidelines for vivax malaria in seven countries
Authors: Ruwanpura Varunika , Neukom Josselyn , Grietens Koen Peeters , Price Ric N. , Thriemer Kamala , Lynch Caroline A. 
Published: October 2021

Abstract
Background
The changing global health landscape has highlighted the need for more proactive, efficient and transparent health policy-making. After more than 60 years of limited development, novel tools for vivax malaria are finally available, but need to be integrated into national policies. This paper maps the malaria policy-making processes in seven endemic countries, to identify areas where it can be improved to align with best practices and optimal efficiency.

Methods
Data were collected during a workshop, convened by the Asia Pacific Malaria Elimination Network’s Vivax Working Group in 2019, and subsequent interviews with key stakeholders from Cambodia, Ethiopia, Indonesia, Pakistan, Papua New Guinea (PNG), Sri Lanka and Vietnam. Documentation of policy processes provided by respondents was reviewed. Data analysis was guided by an analytic framework focused on three a priori defined domains: “context,” “actors” and “processes”.

Results
The context of policy-making varied with available funding for malaria, population size, socio-economic status, and governance systems. There was limited documentation of the process itself or terms of reference for involved actors. In all countries, the NMP plays a critical role in initiating and informing policy change, but the involvement of other actors varied considerably. Available evidence was described as a key influencer of policy change; however, the importance of local evidence and the World Health Organization’s endorsement of new treatments and diagnostics varied. The policy process itself and its complexity varied but was mostly semi-siloed from other disease specific policy processes in the wider Ministry of Health. Time taken to change and introduce a new policy guideline previously varied from 3 months to 3 years.

Conclusions
In the medium to long term, a better alignment of anti-malarial policy-making processes with the overall health policy-making would strengthen health governance. In the immediate term, shortening the timelines for policy change will be pivotal to meet proposed malaria elimination milestones.
Limited Plasmodium sporozoite gliding motility in the absence of TRAP family adhesins
Authors: Beyer Konrad , Kracht Simon , Kehrer Jessica , Singer Mirko , Klug Dennis , Frischknecht Friedrich 
Published: October 2021

Abstract
Background
Plasmodium sporozoites are the highly motile forms of malaria-causing parasites that are transmitted by the mosquito to the vertebrate host. Sporozoites need to enter and cross several cellular and tissue barriers for which they employ a set of surface proteins. Three of these proteins are members of the thrombospondin related anonymous protein (TRAP) family. Here, potential additive, synergistic or antagonistic roles of these adhesion proteins were investigated.

Methods
Four transgenic Plasmodium berghei parasite lines that lacked two or all three of the TRAP family adhesins TRAP, TLP and TREP were generated using positive–negative selection. The parasite lines were investigated for their capacity to attach to and move on glass, their ability to egress from oocysts and their capacity to enter mosquito salivary glands. One strain was in addition interrogated for its capacity to infect mice.

Results
The major phenotype of the TRAP single gene deletion dominates additional gene deletion phenotypes. All parasite lines including the one lacking all three proteins were able to conduct some form of active, if unproductive movement.

Conclusions
The individual TRAP-family adhesins appear to play functionally distinct roles during motility and infection. Other proteins must contribute to substrate adhesion and gliding motility.

Graphical Abstract
Clinical characteristics of cardiovascular patients with extremely low levels of high-density lipoprotein cholesterol
Authors: Sun Lufan , Duan Lian , Jia Dalin 
Published: October 2021

Abstract
Background
Extremely low levels of high-density lipoprotein cholesterol (HDL-C) are related to high cardiovascular mortality. The underlying mechanism is not well known. This research aims to study the clinical characteristics of cardiovascular patients with extremely low levels of HDL-C.

Methods
All cardiovascular patients in a single Chinese cardiology center that were admitted from January to December 2019 were reviewed. The clinical characteristics of those with HDL-C<20 mg/dL were investigated.

Results
A total of 20,655 individuals were enrolled. Of these, 52.17 % were males, and the average age was 58.20 ± 12.98 years old. The prevalence of HDL-C<20 mg/dL was 0.47 % for all patients (N=98) and 1.05 % for inpatients. Of those with HDL-C<20 mg/dL, 88.8 % were inpatients, and 77.6 % were males. Their average age was 60.7 ± 15.1 years. Compared with matched patients with normal HDL-C, systemic inflammation (OR= 5.556, 95% CI 2.798–11.030), hypoalbuminemia (OR=5.714, 95% CI 2.702–12.085), hyperuricemia (OR=5.156, 95% CI 2.560–10.386), low T3 syndrome (OR=4.278, 95% CI 1.627–11.245), anemia (OR=3.577, 95% CI 1.680–7.617), diabetes (OR=3.534, 95% CI 1.693–7.376) and hypertriglyceridemia (OR=2.493, 95% CI 1.264–4.918) were identified as adverse concomitant factors of extremely low HDL-C. HDL-C levels were inversely correlated with the total risk scores in patients with HDL-C<20 mg/dL (r=-0.381, P<0.001) and more significantly correlated in patients with HDL-C<15 mg/dL (r=-0.511, P=0.004).

Conclusions
Extremely low levels of HDL-C tend to occur more frequently in males, older individuals and inpatients. For cardiovascular patients, extremely low levels of HDL-C are usually due to the presence of multiple adverse factors with relatively severe conditions. This could explain the high cardiovascular mortality of individuals with extremely low levels of HDL-C.
The use of direct oral anticoagulants for thromboprophylaxis or treatment of cancer-associated venous thromboembolism: a meta-analysis and review of the guidelines
Authors: Alsubaie Norah S. , Al Rammah Shahad M. , Alshouimi Reema A. , Alzahrani Mohammed Y. , Al Yami Majed S. , Almutairi Abdulaali R. , Alfayez Osamah M. , Korayem Ghazwa B. , Almohammed Omar A. 
Published: October 2021

Abstract
Background
Venous thromboembolism (VTE) is a common complication among patients with cancer and is one of the most common causes of increased morbidity and mortality. The use of direct oral anticoagulants (DOACs) for thromboprophylaxis and treatment of cancer-associated venous thromboembolism (CA-VTE) has been evaluated in several randomized clinical trials (RCTs). The aim of this meta-analysis was to assess efficacy and safety of using DOACs for thromboprophylaxis and treatment of CA-VTE and provide a summary for available guidelines’ recommendations.

Methods
MEDLINE was searched to identify studies evaluating the use of DOACs for thromboprophylaxis or treatment in patients with cancer. Search was limited to peer-reviewed studies published in English. Studies were excluded if they were not RCTs or subgroup analyses of data derived from RCTs, if they did not report efficacy and safety data on patients with active cancer, or if they were published as an abstract. New VTE or VTE recurrence, and major or clinically relevant non-major bleeding (CRNMB) were used to assess the efficacy and safety, respectively. The Mantel-Haenszel random-effects model risk ratios (RRs) and the corresponding 95% confidence intervals (CIs) were calculated to estimate the pooled treatment effects of DOACs.

Results
Four studies evaluating DOACs use for thromboprophylaxis and four – for treatment of CA-VTE were included. Thromboprophylaxis with DOACs was associated with a significant reduction in the risk of symptomatic VTE (RR = 0.58; 95%CI 0.37,0.91) but with an incremental risk of major bleeding or CRNMB (RR = 1.57; 95%CI 1.10,2.26). CA-VTE treatment with DOACs was linked with a significant reduction in VTE recurrence (RR = 0.62; 95%CI 0.44,0.87) but with an incremental risk of CRNMB (RR = 1.58; 95%CI 1.11,2.24).

Conclusions
The DOACs are associated with a lower risk of symptomatic VTE and VTE recurrence, but the risk of bleeding remains a considerable concern. Clinical decisions should be made by assessing individual patient’s risk of VTE and bleeding.
Malignant tumor is the greatest risk factor for pulmonary embolism in hospitalized patients: a single-center study
Authors: Fujieda Kaoru , Nozue Akiko , Watanabe Akie , Shi Keiko , Itagaki Hiroya , Hosokawa Yoshihiko , Nishida Keiko , Tasaka Nobutaka , Satoh Toyomi , Nishide Ken 
Published: October 2021

Abstract
Background
This study aimed to investigate the background of patients who presented with pulmonary embolism (PE) on contrast-enhanced chest computed tomography (CT) and to explore the risk factors for PE.

Methods
This study included a review of the medical records of all 50,621 patients who were admitted to one community hospital between January 1, 2013 and December 31, 2017. Data on sex, age, risk factors related to blood flow stagnation (obesity, long-term bed rest, cardiopulmonary disease, cast fixation, long-term sitting), risk factors related to vascular endothelial disorder (surgery, trauma/fracture, central venous catheterization, catheter tests/treatments, vasculitis, antiphospholipid antibody syndrome, history of venous thromboembolism (VTE)), and risk factors related to hypercoagulability (malignant tumor, use of oral contraceptives/low-dose estrogen progestin/steroids, infection, inflammatory enteric disease, polycythemia, protein C or protein S deficiency, dehydration) were evaluated.

Results
Of all inpatients, 179(0.35%) out of 50,621 were diagnosed with PE after contrast-enhanced chest CT examination, in which 74 patients were symptomatic and 105 patients had no symptom. Among asymptomatic 105 patients, 71 patients got CT scans for other reasons including cancer screening and searching infection focus, and 34 patients got CT scans for searching PE due to either apparent or suspicious DVT. The rate of discovering PE was significantly greater in women (0.46%, 90/19,409) than men (0.29%, 89/31,212) (P = 0.008). Of the 179 patients with PE, 164 (92%) had some type of risk factor. For both men and women, the most frequent risk factor was a malignant tumor, followed by obesity, long-term bed rest and infection for men and long-term bed rest, obesity and infection for women. The most common malignant tumor was lung cancer. Although taking antipsychotic agent is not advocated as a risk factor, there is a possibility of involvement.

Conclusions
The risk factors for PE were identified in this single-center, retrospective study.
Gene therapy for cystic fibrosis: new tools for precision medicine
Authors: Lee Jin-A , Cho Alex , Huang Elena N. , Xu Yiming , Quach Henry , Hu Jim , Wong Amy P. 
Published: October 2021

AbstractThe discovery of the Cystic fibrosis (CF) gene in 1989 has paved the way for incredible progress in treating the disease such that the mean survival age of individuals living with CF is now ~58 years in Canada. Recent developments in gene targeting tools and new cell and animal models have re-ignited the search for a permanent genetic cure for all CF. In this review, we highlight some of the more recent gene therapy approaches as well as new models that will provide insight into personalized therapies for CF.
Single-cell analysis revealed that IL4I1 promoted ovarian cancer progression
Authors: Zhao Hongyu , Teng Yu , Hao Wende , Li Jie , Li Zhefeng , Chen Qi , Yin Chenghong , Yue Wentao 
Published: October 2021

Abstract
Background
Ovarian cancer was one of the leading causes of female deaths. Patients with OC were essentially incurable and portends a poor prognosis, presumably because of profound genetic heterogeneity limiting reproducible prognostic classifications.

Methods
We comprehensively analyzed an ovarian cancer single-cell RNA sequencing dataset, GSE118828, and identified nine major cell types. Relationship between the clusters was explored with CellPhoneDB. A malignant epithelial cluster was confirmed using pseudotime analysis, CNV and GSVA. Furthermore, we constructed the prediction model (i.e., RiskScore) consisted of 10 prognosis-specific genes from 2397 malignant epithelial genes using the LASSO Cox regression algorithm based on public datasets. Then, the prognostic value of Riskscore was assessed with Kaplan–Meier survival analysis and time-dependent ROC curves. At last, a series of in-vitro assays were conducted to explore the roles of IL4I1, an important gene in Riskscore, in OC progression.

Results
We found that macrophages possessed the most interaction pairs with other clusters, and M2-like TAMs were the dominant type of macrophages. C0 was identified as the malignant epithelial cluster. Patients with a lower RiskScore had a greater OS (log-rank P < 0.01). In training set, the AUC of RiskScore was 0.666, 0.743 and 0.809 in 1-year, 3-year and 5-year survival, respectively. This was also validated in another two cohorts. Moreover, downregulation of IL4I1 inhibited OC cells proliferation, migration and invasion.

Conclusions
Our work provide novel insights into our understanding of the heterogeneity among OCs, and would help elucidate the biology of OC and provide clinical guidance in prognosis for OC patients.