bluuebunny/crossref_metadata_2025_split huggingface dataset:
Relationship between miR-378c and YY1 expression in patients with gastric cancer and the clinicopathological features
Authors: Zhang Lei , Zou Lei , Sun Peng 
Published: April 2021

Abstract
Background
The purpose of this study was to explore the clinical value of miR-378c and its target gene YY1 in gastric cancer.

Methods
The TCGA database was employed to analyse miR-378c expression in gastric cancer. qRT-PCR was applied to identify miR-378c and YY1 in tissues and serum of patients suffering from gastric cancer. The association of miR-378c with the clinical data of patients with gastric cancer was analysed. Receiver operating characteristics (ROC) curve analysis was used to determine the diagnostic value of miR-378c and YY1 in gastric cancer, and analyse the relationship between miR-378c and YY1 and patients’ survival. Pearson’s test was applied to determine the association between miR-378c and YY1 in tissue and serum of patients. Dual-Luciferase Reporter assay was employed to examine the targeting association between miR-378c and YY1. Finally, independent prognostic factors was determined in patients with gastric cancer using Cox regression analysis.

Results
In the TCGA database, miR-378c was weakly expressed in gastric cancer. Overall, patients with low expression had a lower survival rate. The expression of miR-378c decreased and the expression of YY1 increased in cancer tissues and serum of tumour patients. In patients with low expression of miR-378c the tumour size was ≥ 5 cm. Low differentiation, high TNM staging and lymph node invasion rate increased significantly, but the 5-year survival rate decreased in the patients. miR-378c and YY1 had better diagnostic value in gastric cancer. TargetScan, miRDB, starBase and miRTarBase predicted that YY1 was a potential gene of miR-378c, and the Dual-Luciferase Reporter assay revealed that there was a targeting relationship between the two, which was proved by correlation analysis. Multivariate Cox analysis revealed that differentiation, TNM staging and miR-378c were independent prognostic factors for patients.

Conclusions
MiR-378c is weakly expressed in gastric cancer patients and may be considered as a promising diagnostic and prognostic indicator for gastric cancer.
A high-density genetic map construction and sex-related loci identification in Chinese Giant salamander
Authors: Hu Qiaomu , Liu Yang , Liao Xiaolin , Tian Haifeng , Ji Xiangshan , Zhu Jiajie , Xiao Hanbing 
Published: April 2021

AbstractBackgroundThe Chinese giant salamanderAndrias davidianusis an important amphibian species in China because of its increasing economic value, protection status and special evolutionary position from aquatic to terrestrial animal. Its large genome presents challenges to genetic research. Genetic linkage mapping is an important tool for genome assembly and determination of phenotype-related loci.ResultsIn this study, we constructed a high-density genetic linkage map using ddRAD sequencing technology to obtain SNP genotyping data of members from an full-sib family which sex had been determined. A total of 10,896 markers were grouped and oriented into 30 linkage groups, representing 30 chromosomes ofA. davidianus. The genetic length of LGs ranged from 17.61 cM (LG30) to 280.81 cM (LG1), with a mean inter-locus distance ranging from 0.11(LG3) to 0.48 cM (LG26). The total genetic map length was 2643.10 cM with an average inter-locus distance of 0.24 cM. Three sex-related loci and four sex-related markers were found on LG6 and LG23, respectively.ConclusionWe constructed the first High-density genetic linkage map and identified three sex-related loci in the Chinese giant salamander. Current results are expected to be a useful tool for future genomic studies aiming at the marker-assisted breeding of the species.
Identification of the angiogenesis related genes for predicting prognosis of patients with gastric cancer
Authors: Zheng Sheng , Zhang Zizhen , Ding Ning , Sun Jiawei , Lin Yifeng , Chen Jingyu , Zhong Jing , Shao Liming , Lin Zhenghua , Xue Meng 
Published: April 2021

AbstractIntroductionAngiogenesis is a key factor in promoting tumor growth, invasion and metastasis. In this study we aimed to investigate the prognostic value of angiogenesis-related genes (ARGs) in gastric cancer (GC).MethodsmRNA sequencing data with clinical information of GC were downloaded from The Cancer Genome Atlas (TCGA) and the Gene Expression Omnibus (GEO) databases. The differentially expressed ARGs between normal and tumor tissues were analyzed by limma package, and then prognosis‑associated genes were screened using Cox regression analysis. Nine angiogenesis genes were identified as crucially related to the overall survival (OS) of patients through least absolute shrinkage and selection operator (LASSO) regression. The prognostic model and corresponding nomograms were establish based on 9 ARGs and verified in in both TCGA and GEO GC cohorts respectively.ResultsEighty-five differentially expressed ARGs and their enriched pathways were confirmed. Significant enrichment analysis revealed that ARGs-related signaling pathway genes were highly related to tumor angiogenesis development. Kaplan–Meier analysis revealed that patients in the high-risk group had worse OS rates compared with the low-risk group in training cohort and validation cohort. In addition, RS had a good prognostic effect on GC patients with different clinical features, especially those with advanced GC. Besides, the calibration curves verified fine concordance between the nomogram prediction model and actual observation.ConclusionsWe developed a nine gene signature related to the angiogenesis that can predict overall survival for GC. It’s assumed to be a valuable prognosis model with high efficiency, providing new perspectives in targeted therapy.
Primary dementia care based on the individual needs of the patient: study protocol of the cluster randomized controlled trial, DemStepCare
Authors:   study group DemStepCare, Bablok Isabella , Binder Harald , Stelzer Dominikus , Kaier Klaus , Graf Erika , Wangler Julian , Jansky Michael , Löhr Michael , Schulz Michael , Kockläuner Marie , Geschke Katharina , Wuttke-Linnemann Alexandra , Fellgiebel Andreas , Farin Erik 
Published: April 2021

AbstractBackgroundMost people with dementia (PwD) are cared for at home, with general practitioners (GPs) playing a key part in the treatment. However, primary dementia care suffers from a number of shortcomings: Often, diagnoses are made too late and therapies by GPs do not follow the guidelines. In cases of acute crises, PwD are too often admitted to hospital with adverse effects on the further course of the disease.The aim of this study is to implement and evaluate a new GP-based, complex dementia care model, DemStepCare. DemStepCare aims to ensure demand-oriented, stepped care for PwD and their caregivers.Methods/designIn a cluster randomized controlled trial, the care of PwD receiving a complex intervention, where the GP is supported by a multi-professional team, is compared to (slightly expanded) usual care.GPs are clustered by GP practice, with 120 GP practices participating in total. GP practices are randomized to an intervention or a control group. 800 PwD are to be included per group. Recruitment takes place in Rhineland-Palatinate, Germany. In addition, a second control group with at least 800 PwD will be formed using aggregated routine data from German health insurance companies. The intervention comprises the training of GPs, case management including repeated risk assessment of the patients’ care situation, the demand-oriented service of an outpatient clinic, an electronic case record, external medication analyses and a link to regional support services. The primary aims of the intervention are to positively influence the quality of life for PwD, to reduce the caregivers’ burden, and to reduce the days spent in hospital. Secondary endpoints address medication adequacy and GPs’ attitudes and sensitivity towards dementia, among others.DiscussionThe GP-based dementia care model DemStepCare is intended to combine a number of promising interventions to provide a complex, stepped intervention that follows the individual needs of PwD and their caregivers. Its effectiveness and feasibility will be assessed in a formative and a summative evaluation.Trial registrationGerman Register of Clinical Trials (Deutsches Register Klinischer Studien, DRKS),DRKS00023560. Registered 13 November 2020 - Retrospectively registered. HTML&TRIAL_ID=DRKS00023560.
Does the additional use of clomiphene citrate or letrozole for in vitro fertilization deserve more attention?
Authors: Liang Ying , Guo Qing , Wu Xiao-Hua , Zhang Li-Nan , Ge Jun , Xu Mei-Ling , Feng Zheng-Li , Wu Xiao-Qian 
Published: April 2021

Abstract
Background
Adding clomiphene citrate (CC) and/or letrozole (LE) to in vitro fertilization (IVF) cycles for mild ovarian stimulation is a general approach. Although lots of researches have demonstrated partial benefits of the strategy, all-around effects of oral medications remained deficient. This paper aims to assess whether an addition of oral medication will result in considerable outcomes on T-Gn (total dose of gonadotropin), Gn days, total retrieved ova, high quality embryos, blastocyst number, ovarian hyperstimulation syndrome (OHSS) rate, clinical pregnancy rate and cumulative pregnancy rate, even if it was not conventional mild/minimal stimulations.

Results
Participants were categorized to three diverse populations as high responders, normal responders and poor responders according to basal antral follicle count. T-Gn in patients treated with CC/LE distinctly decreased from 2496.96 IU/d to 1827.68 IU/d, from 2860.28 IU/d to 2119.99 IU/d, and from 3182.15 IU/d to 1802.84 IU/d, respectively. For high ovary responders and normal responders, the OHSS incidence rate also declined from 29.2 to 4.3% (P < 0.001) and from 1.1 to 0.0% (P = 0.090). Other, there was no statistical difference with respect to the T-retrieved ova (total retrieved ova), high quality embryos, cultured blastocyst and blastocyst number in high responders. For normal responders and poor ovary responders, T-Gn, Gn days, T-retrieved ova, high quality embryos, cultured blastocyst and blastocysts number in oral medications group all apparently decreased. Clinical pregnancy rate per fresh cycle of poor responders with prior oral medications was significantly decreased (25.7% vs. 50.8%, P = 0.005), and no significant differences in high responders and normal responders were expressed (52.5% vs. 44.2%, P = 0.310; 51.9% vs. 42.4%, P = 0.163) between two groups of participants. The numbers of cumulative pregnancy rates were lower in the conventional group compared to the add group for high (75.90% versus 81.03%, P = 0.279), normal (62.69% versus 71.36%, P = 0.016) and poor (39.74% versus 68.21%, P < 0.001) responders.

Conclusions
The addition of CC/LE to the ovulation induction during IVF has certain efficacy in terms of low cost, low OHSS incidence. CC/LE deserves more recommendations as a responsible strategy in high responders due to advantageous pregnancy outcomes. For normal responders, the strategy needs to be considered with more comprehensive factors.
Anti-IL17 antibody Secukinumab therapy is associated with ossification in giant cell tumor of bone: a case report of pathologic similarities and therapeutic potential similar to Denosumab
Authors: Chandler Andrew , Bartelstein Meredith K. , Fujiwara Tomohiro , Antonescu Cristina R. , Healey John H. , Vaynrub Max 
Published: April 2021

Abstract
Background
Giant cell tumor of bone is a benign, locally aggressive neoplasm. Surgical resection is the preferred treatment method. However, for cases in which resection poses an increased risk to the patient, denosumab (anti-RANKL monoclonal antibody) is considered. Secukinumab is an anti-IL-17 antibody that is used in psoriatic arthritis to reduce bone resorption and articular damage.

Case presentation
One case of giant cell tumor of bone (GCTB) in a patient treated with secukinumab for psoriatic arthritis demonstrated findings significant for intra-lesional calcifications. Histologic examination showed ossification, new bone formation, and remodeling. A paucity of osteoclast type giant cells was noted. Real-time quantitative polymerase-chain-reaction (qRT-PCR) analysis revealed decreased osteoclast function compared to treatment-naive GCTB.

Conclusions
Secukinumab may play a role in bone remodeling for GCTB. Radiologists, surgeons, and pathologists should be aware of this interaction, which can cause lesional ossification. Further research is required to define the therapeutic potential of this drug for GCTB and osteolytic disease.
Inflammatory indexes in preoperative blood routine to predict early recurrence of hepatocellular carcinoma after curative hepatectomy
Authors: Wu YiFeng , Tu ChaoYong , Shao ChuXiao 
Published: April 2021

Abstract
Background
The inflammation indexes in blood routine play an essential role in evaluating the prognosis of patients with hepatocellular carcinoma, but the effect on early recurrence has not been clarified. The study aimed to investigate the risk factors of early recurrence (within 2 years) and recurrence-free survival after curative hepatectomy and explore the role of inflammatory indexes in predicting early recurrence.

Methods
The baseline data of 161 patients with hepatocellular carcinoma were analyzed retrospectively. The optimal cut-off value of the inflammatory index was determined according to the Youden index. Its predictive performance was compared by the area under the receiver operating characteristic curve. Logistic and Cox regression analyses were used to determine the risk factors of early recurrence and recurrence-free survival.

Results
The area under the curve of monocyte to lymphocyte ratio (MLR) for predicting early recurrence was 0.700, which was better than systemic inflammatory response index (SIRI), neutrophil to lymphocyte ratio (NLR), platelet to lymphocyte ratio (PLR) and systemic immune-inflammatory index (SII). MLR, tumour size, tumour differentiation and BCLC stage are all risk factors for early recurrence and recurrence-free survival of HCC. Combining the above four risk factors to construct a joint index, the area under the curve for predicting early recurrence was 0.829, which was better than single MLR, tumour size, tumour differentiation and BCLC stage. Furthermore, with the increase of risk factors, the recurrence-free survival of patients is worse.

Conclusion
The combination of MLR and clinical risk factors is helpful for clinicians to identify high-risk patients with early recurrence and carry out active postoperative adjuvant therapy to improve the prognosis of patients.
Dietary phytochemical index in relation to risk of glioma: a case-control study in Iranian adults
Authors: Rigi Somaye , Shayanfar Mehdi , Mousavi Seyed Mohammad , Mohammad-Shirazi Minoo , Sharifi Giuve , Esmaillzadeh Ahmad 
Published: April 2021

Abstract
Background & aim
No study is available that explores the association of dietary phytochemical index (DPI) with glioma. The objective of the current study was to assess this association in Iranian adults.

Methods
This hospital-based case-control study included 128 newly-diagnosed cases of glioma and 256 age- and sex-matched controls. Data collection on dietary intakes was done using a 123-item validated food frequency questionnaire. Calculation of DPI was done as (dietary energy derived from phytochemical-rich foods (kcal)/total daily energy intake (kcal)) × 100. Logistic regression models were used to examine the association between DPI and glioma.

Results
Individuals in the top tertile of DPI were more likely to be older and female. Before taking potential confounders into account, subjects in the top tertile of DPI tended to have a 40% reduced chance of glioma than those in the bottom tertile (OR: 0.60; 95% CI: 0.35–1.02, P = 0.06). After controlling for age, sex, energy intake, several demographic variables and dietary intakes, the association between DPI and glioma became strengthened (OR: 0.43; 95% CI: 0.19–0.97, P = 0.04).

Conclusion
High intakes of phytochemical-rich foods were associated with a lower risk of glioma in adults. High consumption of phytochemical-rich foods might be recommended to prevent glioma. However, further studies with a prospective design are needed to confirm our findings.
Low serum vitamin D concentrations are associated with obese but not lean NAFLD: a cross-sectional study
Authors: Wang Qinqiu , Shi Xiaoying , Wang Jinghua , Zhang Juanwen , Xu Chengfu 
Published: April 2021

Abstract
Background
A low serum vitamin D concentration has been reported to be associated with an increased risk of non-alcoholic fatty liver disease (NAFLD); however, whether lean or obese individuals show a similar association between vitamin D and NAFLD remains speculative. This study aimed to explore the relationship between serum vitamin D concentration and NAFLD in lean and obese Chinese adults.

Methods
This cross-sectional study included 2538 participants (1360 men and 1178 women) who underwent health checkups at the First Affiliated Hospital, Zhejiang University School of Medicine in 2019. NAFLD was diagnosed by liver ultrasound excluding other causes. The association of serum vitamin D concentration with NAFLD was analyzed in lean and obese participants.

Results
The overall prevalence of NAFLD was 33.61% (13.10% in lean and 53.32% in obese) in this study population. The serum vitamin D levels of obese NAFLD patients were lower than those of obese NAFLD-free controls. However, the serum vitamin D levels of lean NAFLD patients were comparable to those of lean NAFLD-free controls. Serum vitamin D level was negatively correlated with the prevalence of NAFLD in obese but not lean participants. Serum vitamin D level was independently associated with the risk of NAFLD in obese participants, with an adjusted odds ratio (95% CI) of 0.987 (0.981–0.993). However, serum vitamin D level was not related to the risk of NAFLD in lean participants.

Conclusions
A low serum vitamin D level is associated with NAFLD in obese but not lean participants.
Gene signature and immune cell profiling by high-dimensional, single-cell analysis in COVID-19 patients, presenting Low T3 syndrome and coexistent hematological malignancies
Authors: Sciacchitano Salvatore , De Vitis Claudia , D’Ascanio Michela , Giovagnoli Simonetta , De Dominicis Chiara , Laghi Andrea , Anibaldi Paolo , Petrucca Andrea , Salerno Gerardo , Santino Iolanda , Amodeo Rachele , Simmaco Maurizio , Napoli Christian , Tafuri Agostino , Di Napoli Arianna , Sacconi Andrea , Salvati Valentina , Ciliberto Gennaro , Fanciulli Maurizio , Piaggio Giulia , de Latouliere Luisa , Ricci Alberto , Mancini Rita 
Published: April 2021

Abstract
Background
Low T3 syndrome is frequent in patients admitted to intensive care units for critical illness and pneumonia. It has been reported also in patients with COVID-19, Hodgkin disease and chronic lymphocytic leukemia. We analyzed the clinical relevance of Low T3 syndrome in COVID-19 patients and, in particular, in those with associated hematological malignancies.

Methods
Sixty-two consecutive patients, hospitalized during the first wave of SARS-CoV-2 outbreak in Sant’Andrea University Hospital in Rome, were subdivided in 38 patients (Group A), showing low levels of FT3, and in 24 patients (Group B), with normal FT3 serum values. During the acute phase of the disease, we measured serum, radiologic and clinical disease severity markers and scores, in search of possible correlations with FT3 serum values. In addition, in 6 COVID-19 patients, 4 with Low T3 syndrome, including 2 with a hematological malignancy, and 2 with normal FT3 values, we performed, high-dimensional single-cell analysis by mass cytometry, multiplex cytokine assay and gene expression profiling in peripheral blood mononuclear cells (PBMC).

Results
Low FT3 serum values were correlated with increased Absolute Neutrophil Count, NLR and dNLR ratios and with reduced total count of CD3+, CD4+ and CD8+ T cells. Low FT3 values correlated also with increased levels of inflammation, tissue damage and coagulation serum markers as well as with SOFA, LIPI and TSS scores. The CyTOF analysis demonstrated reduction of the effector memory and terminal effector subtypes of the CD4+ T lymphocytes. Multiplex cytokine assay indicates that mainly IL-6, IP-10 and MCAF changes are associated with FT3 serum levels, particularly in patients with coexistent hematological malignancies. Gene expression analysis using Nanostring identified four genes differently expressed involved in host immune response, namely CD38, CD79B, IFIT3 and NLRP3.

Conclusions
Our study demonstrates that low FT3 serum levels are associated with severe COVID-19. Our multi-omics approach suggests that T3 is involved in the immune response in COVID-19 and coexistent hematological malignancy and new possible T3 target genes in these patients have been identified.
HNRNPA2B1 promotes multiple myeloma progression by increasing AKT3 expression via m6A-dependent stabilization of ILF3 mRNA
Authors: Jiang Fengjie , Tang Xiaozhu , Tang Chao , Hua Zhen , Ke Mengying , Wang Chen , Zhao Jiamin , Gao Shengyao , Jurczyszyn Artur , Janz Siegfried , Beksac Meral , Zhan Fenghuang , Gu Chunyan , Yang Ye 
Published: April 2021

AbstractN6-methyladenosine (m6A) modification is the most prevalent modification in eukaryotic RNAs while accumulating studies suggest that m6A aberrant expression plays an important role in cancer. HNRNPA2B1 is a m6A reader which binds to nascent RNA and thus affects a perplexing array of RNA metabolism exquisitely. Despite unveiled facets that HNRNPA2B1 is deregulated in several tumors and facilitates tumor growth, a clear role of HNRNPA2B1 in multiple myeloma (MM) remains elusive. Herein, we analyzed the function and the regulatory mechanism of HNRNPA2B1 in MM. We found that HNRNPA2B1 was elevated in MM patients and negatively correlated with favorable prognosis. The depletion of HNRNPA2B1 in MM cells inhibited cell proliferation and induced apoptosis. On the contrary, the overexpression of HNRNPA2B1 promoted cell proliferation in vitro and in vivo. Mechanistic studies revealed that HNRNPA2B1 recognized the m6A sites of ILF3 and enhanced the stability of ILF3 mRNA transcripts, while AKT3 downregulation by siRNA abrogated the cellular proliferation induced by HNRNPA2B1 overexpression. Additionally, the expression of HNRNPA2B1, ILF3 and AKT3 was positively associated with each other in MM tissues tested by immunohistochemistry. In summary, our study highlights that HNRNPA2B1 potentially acts as a therapeutic target of MM through regulating AKT3 expression mediated by ILF3-dependent pattern.
libxtc: an efficient library for reading XTC-compressed MD trajectory data
Authors: Krylov Nikolay A. , Efremov Roman G. 
Published: April 2021

Abstract
Objective
The purpose of this work is to optimize the processing of molecular dynamics (MD) trajectory data obtained for large biomolecular systems. Two popular software tools were chosen as the reference: the tng and the xdrfile libraries. Current implementation of tng algorithms and library is either fast or storage efficient and xdrfile is storage efficient but slow. Our aim was to combine speed and storage efficiency through the xdrfile’s code modification.

Results
Here we present libxtc, a ready-to-use library for reading MD trajectory files in xtc format. The effectiveness of libxtc is demonstrated for several biomolecular systems of various sizes (~ 2 × 104 to ~ 2 × 105 atoms). In sequential mode, the performance of libxtc is up to 1.8 times higher and 1.4 times lower than xdrfile and tng, respectively. In parallel mode, libxtc is about 3 and 1.3 times faster than xdrfile and tng. At the same time, MD data stored in the xtc format require about 1.3 times less disk space than those treated with the tng algorithm in the fastest reading mode, which is a noticeable saving especially when the MD trajectory is long and the number of atoms is large—this applies to most biologically relevant systems.