PReD-Bench/PRed-Bench huggingface dataset:
Correlation between surfactant protein B mRNA expression and neonatal respiratory distress syndrome
Authors: Wenwen Qu
Lu Xie
Zhichun Feng
Lihua Li
Xiaojuan Yin
Hanxiao Fan
Journal: Experimental and Therapeutic Medicine (2012)
Discipline: CLINICAL MEDICINE
Keywords: Surfactant-associated protein B (SP-B); mRNA deficiency; neonatal respiratory distress syndrome (RDS); lung tissues; in situ hybridization
Affiliations: Affiliated Bayi Children's Hospital, Beijing Military Region General Hospital, No. 5 Nan Mencang, Dongcheng District, Beijing 100700,  P.R. China.

Abstract:  The aim of this study was to investigate whether surfactant-associated protein B (SP-B) mRNA deficiency is involved in the pathogenesis of neonatal respiratory distress syndrome (RDS). A total of 60 unrelated neonates who died of RDS were recruited as the RDS group and subgrouped into a ≤32-, a 32-36(+6)- and a ≥37-week group (n=20 per group) on the basis of gestational age. In addition, 60 neonates who succumbed to other diseases were enrolled as controls. The lung tissues were collected within 30 min after death. In situ hybridization was conducted to detect SP-B mRNA expression in the lung. The frequency of SP-B mRNA deficiency was also calculated. Among the RDS groups, the SP-B mRNA levels were significantly higher compared to those in the control group (t=7.812, P&lt;0.001), but were comparable among RDS patients with different gestational ages (F=2.348, P&gt;0.105). Among the control groups, the SP-B mRNA levels increased with the increase in gestational age (F=50.124, P&lt;0.001). In the ≤32-week group, the number of cells positive for SP-B mRNA in RDS patients was markedly reduced as compared to that of the controls (t=3.185, P&lt;0.01). In the 32-36(+6)-week group, the number of cells positive for SP-B mRNA in RDS patients was significantly smaller compared to that of the controls (t=9.342, P&lt;0.001). In the ≥37-week group, the number of cells positive for SP-B mRNA in RDS patients was markedly smaller compared to that in the controls (t=4.238, P&lt;0.001). Among RDS neonates, SP-B mRNA deficiency was noted in 35 patients with a frequency of 58.3%. In the control group, SP-B mRNA deficiency was noted in 8 patients with a frequency of 13.3%, which was markedly lower compared to that in the RDS group (χ(2)=26.421, P&lt;0.001). The results of the present study therefore suggest that SP-B mRNA deficiency is involved in the pathogenesis of RDS. 

Retracted: No

PubPeer comments:
 Figure 6D, Cox2 image contains unmarked several splices. Looks like the 2 righthand lanes had blank spaces pasted into image. original on left and contrast enhanced on right ![file] , 
 Figure 4B, COX2 again seems to have several splices with at least 1 blank pasted into image original on top, contrast enhanced on bottom ![file] , 
 Figure 4B. there appear to be couple more splices in UQCRC2 (CIII) ![file] ,
A three-microRNA signature predicts clinical outcome in breast cancer patients
Authors: D Cheng
H He
B Liang
Journal: European review for medical and pharmacological sciences (2018)
Discipline: PHARMACOLOGY & TOXICOLOGY
Keywords: Breast invasive carcinoma; miRNA signature; prognostic markers; BRCA patients; TCGA database
Affiliations: Transfusion Department, The First Hospital of China Medical University, Shenyang, China. .

Abstract:  Objective: Breast invasive carcinoma (BRCA) is a complex polygenic disease characterized by molecular and histological heterogeneity. An effort is underway to explore and investigate multiple reliable prognostic markers to improve management of BRCA patients and provide novel therapeutic targets. The aim of the study is to identify the prognostic miRNA signature in BRCA patients. Patients and methods: The miRNA-sequencing data and clinical information of BRCA patients were downloaded from The Cancer Genome Atlas (TCGA) database. Results: A total of 106 differentially expressed miRNAs were identified between BRCA tissues and matched normal tissues, including 81 up-regulated miRNAs and 25 down-regulated miRNAs. Then, we established a set of three-miRNA signature that was significantly associated with BRCA patients' survival. Using the prognostic three-miRNA signature, we classified the BRCA patients into high-risk and low-risk groups. Multivariate Cox regression demonstrated that the prognostic power of the three-miRNA signature was independent of other clinical variables. Functional enrichment analysis suggested that three prognostic miRNAs may be involved in known BRCA-related KEGG pathways and biological processes. Conclusions: We demonstrated that three-miRNA signature could be a potential biomarker for predicting clinical outcomes for BRCA patients. 

Retracted: No

PubPeer comments:
 This paper describes an analysis done on a TCGA database set of 1103 breast cancer and 104 matched normal tissue samples. The paper also describes an additional set of 1083 enrolled patients which were divided into a training dataset and a validation dataset. Some concerns: * There is no word on IRB approval for the 1083 enrolled patients, or informed consent. * Table I, which lists the 1083 enrolled patients, shows a clear, and expected, gender distribution, with many more females than males with breast cancer. Yet, the Univariate analysis shown in Table II reports that gender was not a significant hazard ratio (HR). Now, statistics is not my fortu00e9, but should it not be very significant? ![file] ![file] ,
HOTAIRM1 competed endogenously with miR-148a to regulate DLGAP1 in head and neck tumor cells
Authors: Mei Zheng
Qin Zhou
Gangli Liu
Xingguang Liu
Journal: Cancer medicine (2018)
Discipline: CLINICAL MEDICINE
Keywords: DLGAP1; HOTAIRM1; head and neck tumors; miR-148a.
Affiliations: Department of Traditional Chinese Medicine, Qianfoshan Hospital Affiliated to Shandong University, Ji'nan, 250014, Shandong, China., Department of Oral and Maxillofacial Surgery, School and Hospital of Stomatology, Shandong University, Ji'nan, 250012, Shandong, China.

Abstract:  This study is aimed to explore the regulatory effect of lncRNA HOTAIR/miR-148a/DLGAP1 axis on head and neck tumor (HNT) cell growth, cell mobility, and invasiveness. HOTAIRM1, miR-148a, and DLGAP1 level in HNT tissues and adjacent normal tissues were measured by qRT-PCR. Cell Counting Kit-8 (CCK-8) and Transwell (migration and invasion) assay were used to survey the influence of HOTAIRM1, miR-148a, and DLGAP1 on Fadu cells. Nude mouse xenograft was utilized to validate the influence of HOTAIRM1 in vivo. Dual-luciferase reporter assay confirms the relationship between HOTAIRM1 and miR-148a, miR-148a, and DLGAP1. The expression level of HOTAIRM1 was downregulated in human HNT tissues and cells. Overexpression of HOTAIRM1 significantly moderated Fadu cells proliferation, apoptosis, migration, and invasion in vitro and impaired the tumorigenesis in vivo. The expression level of miR-148a was upregulated in human HNT tissue compared to the adjacent tissues. We identified that miR-148a was a target of HOTAIRM1 and its expression levels were reduced by HOTAIRM1. Transfection of miR-148a mimics increased proliferation, migration, and invasion of Fadu cells. DLGAP1 was identified as a novel target of miR-148a and its expression level was promoted by either HOTAIRM1 overexpression or miR-148a knockdown. Overexpression of DLGAP1 also facilitated the cell viability and metastasis of Fadu cells. HOTAIRM1 was confirmed as a tumor suppressor via sponging miR-148a and promote the expression of DLGAP1, which could be regarded as an important target for the prevention and treatment of HNT. 

Retracted: No

PubPeer comments:
 ![file] The two pictures seem to be the same , also, the magnificationm is also different in the miR inhibitor group in Fig 6c. ,
Vaccine potential of plasma bead-based dual antigen delivery system against experimental murine candidiasis
Authors: Munazza Tamkeen Fatima
Qamar Zia
Ejaj Ahmad
Mohammad Owais
Mohammed Saleemuddin
Journal: International Journal of Biological Macromolecules (2015)
Discipline: BIOLOGY & BIOCHEMISTRY
Keywords: Biodegradable polymer; Candida albicans; PLGA microspheres; Plasma beads; Prophylactic vaccine.
Affiliations: Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh 202002, India., Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh 202002, India. Electronic address: .

Abstract:  The development of prophylactic anti-candidal vaccine comprising the Candida albicans cytosolic proteins (Cp) as antigen and plasma beads (PB) prepared from plasma as sustained delivery system, is described. The immune-prophylactic potential of various PBs-based dual antigen delivery systems, co-entrapping Cp pre-entrapped in PLGA microspheres were tested in the murine model. Induction of cell mediated immunity was measured by assaying DTH and NO production as well as in vitro proliferation of lymphocytes derived from the immunized animals. Expression of surface markers on APCs (CD80, CD86) and T-cells (CD4+, CD8+) was also evaluated. Humoral immune response was studied by measuring circulating anti-Cp antibodies and their subclasses. When the prophylactic efficacy of the vaccines was tested in mice challenged with virulent C. albicans, the PB-based formulation (PB-PLGA-Cp vaccine) was found to be most effective in the generation of desirable immune response, in terms of suppression of fungal load and facilitating the survival of the immunized animals. 

Retracted: No

PubPeer comments:
 Figure 3A. Much more similar than expected. https: imgur.com Isg7iF4 ,
Transient expressions of doppel and its structural analog prionDelta32-121 in SH-SY5Y cells caused cytotoxicity possibly by triggering similar apoptosis pathway
Authors: H Y Jiang
P Li
K Xu
C Tian
X P Dong
S Shi
G R Wang
Y L Chu
X Wang
R M Zhou
Q Shi
Journal: Molecular biology reports (2010)
Discipline: MOLECULAR BIOLOGY & GENETICS
Keywords: Doppel; Prion; Neurodegenerative diseases; Pathogenic pathway; Cell apoptosis
Affiliations: Department of Microbiology, School of Medicine, Xi'an Jiao-Tong University, 710061 Xi'an, China.

Abstract:  Doppel (Dpl) is a recently identified prion (PrP)-like protein due to the structural and biochemical similarities, however, its natural function and pathogenic role in neurodegenerative diseases remains unclear. To investigate the possible pathogenic pathway of Dpl and its structural analog for cell apoptosis, mammalian expressing recombinant plasmids containing human PRND gene encoding the full-length Dpl and a truncated human PRNP gene deleting the sequences encoding the peptide from aa 32 to 121 (PrPDelta32-121) were generated. MTT assays showed the cell viabilities of the human neuroblastoma cell line SH-SY5Y receiving Dpl and PrPDelta32-121 expressing plasmids were remarkably lower. Obvious apoptosis phenomena were observed to be associated with the cells transient expressing Dpl and PrPDelta32-121, including reduced mitochondrial transmembrane potential (psim), decreased pro-caspase-3 quantity, more numbers of annexin V- and annexin V/PI-double-stained cells and depressed Bcl-2 level. Moreover, we also found that the Dpl- and PrPDelta32-121-induced cytotoxicities and relevant apoptotic events in SH-SY5Y cells could be fully antagonized by co-expression of the human full-length PrP. These data highly indicate that cytotoxicity induced by the expression of Dpl and truncated PrP in neural derived cells are closely related with the apoptosis process, probably triggering the mitochondrial pathway. It also implies that the cell-benefit activity of the full-length PrP may result from its anti-apoptosis capacity. 

Retracted: No

PubPeer comments:
null, 
 Ad #1. Here is an illustration of the oddities in Figure 6A. In both Bax panels, a band is surrounded by sharp background transitions, as illustrated by blue arrows. In addition an area in the right Bax panel appears to be visible twice, as illustrated by red rounded boxes. ![file] , 
 Figure 5A. Some flow cytometry panels look more similar to each other than expected, as illustrated by ellipses of the same color. ![file] ,
Production of monoclonal antibodies against Rickettsia massiliae and their use in antigenic and epidemiological studies
Authors: D Raoult
W Xu
Journal: Journal of Clinical Microbiology (1997)
Discipline: MICROBIOLOGY
Keywords: Rickettsiae; monoclonal antibodies; antigenic relationships; SFG rickettsiae; lipopolysaccharide
Affiliations: Unité des Rickettsies, CNRS UPRES-A 6020, Faculté de Médecine, Université de la Mediterranée, Marseille, France.

Abstract:  Rickettsiae are gram-negative, obligate intracellular bacteria which have historically been divided into three groups: the typhus group, the scrub typhus group, and the spotted fever group (SFG). Recently, several new SFG rickettsiae have been characterized, and most of these species are associated with ticks and have, as yet, no known pathogenicity toward humans. Rickettsia massiliae, which is widely distributed in Europe and Africa, is one such rickettsia. In order to investigate the antigenic relationships between R. massiliae and other rickettsial species and to develop a more convenient methodology for identifying R. massiliae, we produced monoclonal antibodies against the type strain (Mtu1T) of R. massiliae by fusing immunized splenocytes with SP2/0-Ag14 myeloma cells. A panel of 16 representatives were selected from the 163 positive hybridomas identified on initial screening, and their secreted monoclonal antibodies were further characterized. The reactivities of these 16 monoclonal antibodies with a large panel of rickettsial species were assessed by the microimmunofluorescence assay. All species of the SFG rickettsiae reacted with the monoclonal antibodies directed against epitopes on lipopolysaccharide, which is the common antigen among the SFG rickettsiae. Some closely related species of the SFG, such as Bar29, "R. aeschlimanni," and R. rhipicephali, showed strong cross-reactivities with the monoclonal antibodies directed against epitopes on the two major high-molecular-mass heat-labile proteins (106 and 120 kDa). In addition, species-specific monoclonal antibodies demonstrated that R. massiliae is antigenically different from other rickettsial species. Moreover, these species-specific monoclonal antibodies were successfully used for identifying R. massiliae in the ticks collected from southern France, and are therefore potentially useful tools in the identification and investigation of R. massiliae in ticks in large-scale field work. 

Retracted: No

PubPeer comments:
 Figure 4 shows five panels that each represent different blots, incubated with different monoclonals. * Red boxes: Lanes 1 from the MA4-C11 and MA8-F6 blots look remarkably similar. A potential splice can be observed in the MA8-F6 blot between lanes 1 and 5. * Blue boxes: Lanes 1 from the MA2-E3 and MA2-A1 blots look remarkably similar. A potential splice can be observed in the NA2-A1 blot between lanes 1 and 3. ![file] , 
 Consistent with the observations in comment #1, there appears to be an unacknowledged splice between the two lanes of the MA8-F6 panel. Here, with enhanced contrast: ![file] ,
Inhibitory effects of platelet-rich plasma on intervertebral disc degeneration: a preclinical study in a rabbit model
Authors: Keke Gui
Weimin Ren
Jiachun Dong
Xin Li
Yonglin Yu
Wangping Yin
Journal: Medical Science Monitor (2015)
Discipline: CLINICAL MEDICINE
Keywords: Platelet-rich plasma; growth hormones; tissue repair; rabbit model; IDD
Affiliations: Department of Orthopedics, Jinshan Hospital, Affiliated to Fudan University, Shanghai, China (mainland)., Department of Pathology, Jinshan Hospital, Affiliated to Fudan University, Shanghai, China (mainland)., Department of Orthopedics, Huashan Hospital, Affiliated to Fudan University, Shanghai, China (mainland)., Department of Radiology, Jinshan Hospital, affiliated to Fundan University, Shanghai, China (mainland).

Abstract:  Background: Platelet-rich plasma (PRP) contains multiple growth hormones that may stimulate tissue repair. This study aimed to assess the effects of PRP in a rabbit model of IDD (annulus fibrosus puncture). Material/methods: Thirty-six adult New Zealand white rabbits were randomly divided into 3 groups: 0.1 mL PRP (group A), 0.1 mL phosphate-buffered saline (group B), and control (group C) (n=12/group). Annulus fibrosus puncture was performed to establish L4/5 and L5/6 IDD models. Two and 4 weeks later, 6 rabbits from each group were given an IVD injection at L4/5 and L5/6. Two or 4 weeks after injection, rabbits were scanned with X-ray and MRI before being sacrificed. IVDs were collected for hematoxylin and eosin, Masson's trichrome, and Safranin O staining, and type II collagen immunohistochemistry. Results: Over time, IVD height and disc imaging signal intensity decreased gradually in groups B and C, but only slightly in group A (baseline: 100% for all groups; A: 95.9±4.2% at 4 weeks, 90.1±8.4 at 6 weeks; B: 75.3±5.7% at 4 weeks, 70.8±6.4% at 6 weeks; C: 74.7±5.5% at 4 weeks, 69.9±6.2% at 6 weeks; all P&lt;0.001, P&lt;0.01 between A vs. B and C). Degenerative histological changes in IVDs in groups B and C were more severe compared with group A. Conclusions: Platelet-rich plasma interventions can effectively attenuate the IDD process in rabbits. 

Retracted: No

PubPeer comments:
 The images presented in Figs 2 and 3 do not seem to correspond well with the figure description. The image in Fig 2 doesn t look like an MRI image, while those in Fig 3 are far from H E stained slides. ![file] ,
The development of a selective cyclin-dependent kinase inhibitor that shows antitumor activity
Authors: Simak Ali
Bodo Scheiper
Sebastian H B Kroll
Hetal Patel
Jan Brackow
Alekasandra Siwicka
Seshu K Kanneganti
Matthew J Fuchter
Manikandan Periyasamy
James P Snyder
Eric O Aboagye
Dean A Heathcote
Robert S Tolhurst
Dennis C Liotta
R Charles Coombes
Ashutosh S Jogalekar
Anthony G M Barrett
Journal: Cancer Research (2009)
Discipline: CLINICAL MEDICINE
Keywords: cell cycle; CDK inhibitors; CDK-activating kinase; CDK7; anticancer drugs
Affiliations: Department of Oncology and Chemistry, Imperial College London, London, United Kingdom. 

Abstract:  Normal progression through the cell cycle requires the sequential action of cyclin-dependent kinases CDK1, CDK2, CDK4, and CDK6. Direct or indirect deregulation of CDK activity is a feature of almost all cancers and has led to the development of CDK inhibitors as anticancer agents. The CDK-activating kinase (CAK) plays a critical role in regulating cell cycle by mediating the activating phosphorylation of CDK1, CDK2, CDK4, and CDK6. As such, CDK7, which also regulates transcription as part of the TFIIH basal transcription factor, is an attractive target for the development of anticancer drugs. Computer modeling of the CDK7 structure was used to design potential potent CDK7 inhibitors. Here, we show that a pyrazolo[1,5-a]pyrimidine-derived compound, BS-181, inhibited CAK activity with an IC(50) of 21 nmol/L. Testing of other CDKs as well as another 69 kinases showed that BS-181 only inhibited CDK2 at concentrations lower than 1 micromol/L, with CDK2 being inhibited 35-fold less potently (IC(50) 880 nmol/L) than CDK7. In MCF-7 cells, BS-181 inhibited the phosphorylation of CDK7 substrates, promoted cell cycle arrest and apoptosis to inhibit the growth of cancer cell lines, and showed antitumor effects in vivo. The drug was stable in vivo with a plasma elimination half-life in mice of 405 minutes after i.p. administration of 10 mg/kg. The same dose of drug inhibited the growth of MCF-7 human xenografts in nude mice. BS-181 therefore provides the first example of a potent and selective CDK7 inhibitor with potential as an anticancer agent. 

Retracted: No

PubPeer comments:
 Blue and pink spectra are identical. ![file] ,
Antidepressant-like effects of shuyusan in rats exposed to chronic stress: effects on hypothalamic-pituitary-adrenal function
Authors: Hongyan Chen
Zhigao Sun
Fawei Wang
Dongmei Duan
Mengli Chen
Miao Geng
Liping Chen
Huang Quanzhi
Journal: Evidence-based Complementary and Alternative Medicine (2012)
Discipline: CLINICAL MEDICINE
Keywords: Shuyusan; antidepressant activities; rats model; depression; chronic mild stress
Affiliations: Department of Traditional Chinese Medicine, General Hospital of PLA, Beijing 100853, China., Department of Chinese Pharmaceutical, General Hospital of PLA, Beijing 100853, China, Department of Traditional Chinese Medicine, General Hospital of PLA, Beijing 100853, China, Postgraduate Medical School, General Hospital of PLA, Beijing 100853, China, Institute of Gerontology, General Hospital of PLA, Beijing 100853, China

Abstract:  This study was to investigate antidepressant activities of Shuyusan (a Chinese herb), using a rats model of depression induced by unpredictable chronic mild stress (UCMS). The administration groups were treated with Shuyusan decoction for 3 weeks and compared with fluoxetine treatment. In order to understand the potential antidepressant-like activities of Shuyusan, tail suspension test (TST) and forced swimming test (FST) were used as behavioral despair study. The level of corticotropin-releasing factor (CRH), adrenocorticotropic hormone (ACTH), corticosterone (CORT) and hippocampus glucocorticoid receptor expression were examined. After modeling, there was a significant prolongation of immobility time in administration groups with the TST and FST. High-dose Shuyusan could reduce the immobility time measured with the TST and FST. The immobility time in high-dose herbs group and fluoxetine group was increased significantly compared with the model group. After 3 weeks herbs fed, the serum contents level of CRH, ACTH, and CORT in high-dose herb group was significantly decreased compared to the model group. The result indicated that Shuyusan had antidepressant activity effects on UCMS model rats. The potential antidepressant effect may be related to decreasing glucocorticoid levels activity, regulating the function of HPA axis, and inhibiting glucocorticoid receptor expression in hippocampus. 

Retracted: No

PubPeer comments:
 partial image duplication contradicts labels ![file] Disclaimer: These potential image duplications have been detected automatically using ImageTwin http: dx.doi.org 10.1145 3019612.3019875 Although results have been curated, the automatic algorithm may have generated false positive results and cannot take into account all scientific explanations for apparent duplications like stripped and reprobed blots, time series, serial sections and reused controls. ,
Cyclooxygenase-2 in tumor-associated macrophages promotes metastatic potential of breast cancer cells through Akt pathway
Authors: Yunhai Li
Yong Lin
Tingxiu Xiang
Jing Huang
Zhu Qiu
Jingyuan Wan
Hongzhong Li
Guosheng Ren
Lu Gan
Tianli Hui
Hongyan Huang
Journal: International journal of biological sciences (2016)
Discipline: BIOLOGY & BIOCHEMISTRY
Keywords: Tumor microenvironment; breast cancer; cyclooxygenase-2.; macrophages.
Affiliations: Chongqing Key Laboratory of Molecular Oncology and Epigenetics, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China;; Department of Oncology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China., Chongqing Key Laboratory of Molecular Oncology and Epigenetics, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China., Chongqing Key Laboratory of Molecular Oncology and Epigenetics, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China;; Department of Endocrine and Breast Surgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China., Department of Pharmacology, Chongqing Medical University, Chongqing, China.

Abstract:  Tumor-associated macrophages (TAMs) promote cancer development and progression by releasing various cytokines and chemokines. Previously, we have found that the number of COX-2+ TAMs was associated with lymph node metastasis in breast cancer. However, the mechanism remains enigmatic. In this study, we show that COX-2 in breast TAMs enhances the metastatic potential of breast cancer cells. COX-2 in TAMs induces MMP-9 expression and promotes epithelial-mesenchymal transition (EMT) in breast cancer cells. In addition, COX-2/PGE2 induces IL-6 release in macrophages. Furthermore, we find that the activation of Akt pathway in cancer cells is crucial for the pro-metastatic effect of COX-2+ TAMs by regulating MMP-9 and EMT. These findings indicate that TAMs facilitate breast cancer cell metastasis through COX-2-mediated intercellular communication. 

Retracted: No

PubPeer comments:
 There seems to be an accidental duplication of the images from the scratch assay. The authors may want to contact the journal and ensure that duplicated image is replaced. ![file] ,
LncRNA GIHCG promotes development of ovarian cancer by regulating microRNA-429
Authors: N Yao
B Zhu
B-Q Guo
H-Y Gan
L Yu
Journal: European review for medical and pharmacological sciences (2018)
Discipline: PHARMACOLOGY & TOXICOLOGY
Keywords: lncRNA GIHCG; ovarian cancer; microRNA-429; pathogenic progression; cell cycle
Affiliations: Department of Pathology, The First Affiliated of Bengbu Medical College, Bengbu, China. .

Abstract:  Objective: To explore whether lncRNA GIHCG participates in the pathogenic progression of ovarian cancer (OC) and its underlying mechanism. Patients and methods: Expression levels of GIHCG and microRNA-429 in 30 OC tissues and normal ovarian tissues were detected by quantitative Real time-polymerase chain reaction (qRT-PCR). Subsequently, 15 pairs of OC tissues and paracancerous tissues were selected for correlation analyses of GIHCG, microRNA-429 and the overall survival (OS) of OC patients using Kaplan-Meier method. Pearson correlation analyses were conducted for investigating the correlation between GIHCG and microRNA-429. GIHCG expression in OC cell lines (HEY, A2780 and HO8910) and normal epithelial OC cell line (IOSE-386) was detected by qRT-PCR. After transfection of GIHCG overexpression plasmid in HEY cells, cell cycle, proliferation and colony formation ability were detected by flow cytometry, cell counting kit-8 (CCK-8) and colony formation assay. MicroRNA-429 expression in HEY cells overexpressing GIHCG was detected by qRT-PCR. Rescue experiments were conducted by co-transfection of GIHCG overexpression plasmid and microRNA-429 mimics, followed by cell cycle and colony formation detection. Results: GIHCG was highly expressed, whereas microRNA-429 was lowly expressed in OC tissues than that of paracancerous tissues. OC patients with higher expression of GIHCG showed shorter OS than those with lower expression. However, OC patients with higher expression of microRNA-429 had longer OS than those with lower expression. GIHCG expression was positively correlated to microRNA-429. In vitro experiments showed that GIHCG was highly expressed in HEY, A2780 and HO8910 cells than that of IOSE-386 cells. GIHCG overexpression in HEY cells promoted cell cycle and colony formation abilities, which were reversed by microRNA-429 overexpression. Conclusions: GIHCG is highly expressed in OC, which promotes OC development by stimulating cell cycle progression and cell proliferation by regulating microRNA-429. 

Retracted: No

PubPeer comments:
 Figs 1C, 2C.  GIHCG expression is negatively correlated to OS in OC patients ...  OC patients with higher expression of microRNA-429 presented longer OS than those with lower expression . Are these two pairs of K-M plots derived from the same pool of survival data? There are deaths marked in 2C with no corresponding steps in 1C (brown arrows), and vice versa (green arrows). ![file] ,
Upregulation of miR-1254 promotes Hepatocellular Carcinoma Cell Proliferation, Migration, and Invasion via Inactivation of the Hippo-YAP signaling pathway by decreasing PAX5
Authors: Feng Cheng
Jian Xu
Jianhua Rao
Weixin Yu
Yuanchang Hu
Chao Yang
Xu Lu
Chengyu Shi
Journal: Journal of Cancer (2021)
Discipline: CLINICAL MEDICINE
Keywords: HCC; Hippo signaling pathway; Metastasis; PAX5; Progression
Affiliations: Hepatobiliary Center, The First Affiliated Hospital of Nanjing Medical University; Key Laboratory of Liver Transplantation, Chinese Academy of Medical Sciences, NHC Key Laboratory of Living Donor Liver Transplantation; Nanjing 210029, Jiangsu Province, China., Department of General Surgery, Changzhou Jintan District People's Hospital; Changzhou 213200, Jiangsu Province, China.

Abstract:  Increasing evidence suggests that microRNAs (miRNAs) affect the progression of hepatocellular carcinoma (HCC). However, the exact function and mechanism of miR-1254 in HCC remains unclear. This study explored the effects of miR-1254 on the biological behavior of HCC cells and determined the underlying mechanism. RT-qPCR was used to detect the expression of miR-1254. Gain- or loss-of-function assays determined if miR-1254 affected the biological function of HCC cells in vitro. Dual luciferase reporter assays confirmed the target gene of miR-1254. Tumor xenografts in mice were used to explore the effects of miR-1254 on tumorigenesis and metastasis of HCC. miR-1254 was upregulated in HCC tissues and cell lines and linked to larger tumor size, aggressive vascular invasion and higher Edmondson grade. Lentiviral-based overexpression and knockdown experiments indicated that miR-1254 promoted proliferation, migration, invasion, and the epithelial-mesenchymal transition of HCC cells. The paired box gene 5 (PAX5) was downregulated in HCC tissues, negatively correlated with miR-1254 expression, and confirmed to be a direct target of miR-1254. Restoration of PAX5 reversed the effects of miR-1254 on the biological behavior of HCC cells. Advanced mechanism studies suggested that PAX5 might mediate miR-1254 by regulating the Hippo signaling pathway. Tumor xenografts in mice confirmed that miR-1254 promoted tumorigenesis and metastasis, and led to poor survival. In conclusion, miR-1254 promoted proliferation, migration, and invasion of HCC cells via decreasing Hippo signaling through targeting PAX5 in vitro and in vivo. This miRNA might be a therapeutic target for HCC. 

Retracted: No

PubPeer comments:
 Figure 3 appears to have some image duplications. ![file] , 
 3e *** ![file] , 
 8c *** ![file] ,
Head involution defective (Hid)-triggered apoptosis requires caspase-8 but not FADD (Fas-associated death domain) and is regulated by Erk in mammalian cells
Authors: Apurva Sarin
Peter Vandenabeele
Hadassah Sade
Jishy Varghese
Journal: Journal of Biological Chemistry (2002)
Discipline: BIOLOGY & BIOCHEMISTRY
Keywords: apoptosis; Hid; Erk-1/2; Bcl-2; caspase-9
Affiliations: National Centre for Biological Sciences, UAS-GKVK Campus, Bangalore 560065, Karnataka, India.

Abstract:  The molecular machinery of apoptosis is evolutionarily conserved with some exceptions. One such example is the Drosophila proapoptotic gene Head involution defective (Hid), whose mammalian homologue is not known. Hid is apoptotic to mammalian cells, and we have examined the mechanism by which Hid induces death. We demonstrate for the first time a role for the extracellular signal-related kinase-1/2 (Erk-1/2) in the regulation of Hid function in mammalian cells. Bcl-2 and an inhibitor of caspase-9 blocked apoptosis, indicative of a role for the mitochondrion in this pathway, and we provide evidence for a role for caspase-8 in Hid-induced apoptosis. Thus, apoptosis was blocked by an inhibitor of caspase-8, deletion of caspase-8 rendered cells resistant to Hid-induced apoptosis, and Hid associated with caspase-8 in cell lysates. The Fas-associated death domain (FADD) was dispensable for the apoptotic function of Hid, indicating that Hid does not require extracellular death receptor signaling for the activation of caspase-8. In activated T cells, the cytokine interleukin-2 blocked caspase-8 processing and apoptosis, suggesting that survival cues from trophic factors may target a Hid-like intermediate present in mammalian cells. Thus, this study shows that Hid engages with conserved components of cellular death machinery and suggests that apoptotic paradigms characterized by FADD-independent activation of caspase-8 may involve a Hid-like molecule in mammalian cells. 

Retracted: No

PubPeer comments:
 Figure 7E. https: imgur.com SubDTnT , 
 In this experiment, separate membranes (replicates of the same sample) were probed for the different proteins shown. In experiments where membranes ere stripped and re-probed , this is indicated in the accompanying legend. , 
 Dear Dr. Sarin, how does your explanation justify not splicing the third lane? Doesn t it need to be on the same gel? , 
 #3 Since phosphorylated ERK 1 2 and ERK1 2 run in the same region of the gels, the same membrane was not stripped and re-probed, as errors would result from such processing. Gentler strip and re-probe protocols also result in distortions as residual signals interfere with the new probe. Hence, such samples were run in replicates when probing for phosphorylated and total protein in each experiment performed. The total ERK1 2 is a replicate of the same lysates used for phospho ERK and Caspase-8 , 
 I agree with the reply of Apurva Sarin. The experments of the JBC paper were partially performed in my lab when Jishy Varghese had an internship and in the lab of Apurva. ,
Astrocyte-selective AAV gene therapy through the endogenous GFAP promoter results in robust transduction in the rat spinal cord following injury
Authors: Deborah Young
Jarred M Griffin
Dahna M Fong
Simon J O&#x27;Carroll
Barbara Fackelmeier
Alexander Mouravlev
Journal: Gene Therapy (2019)
Discipline: MOLECULAR BIOLOGY & GENETICS
Keywords: AAV vectors; transgene delivery; central nervous system; gene expression; glial cells
Affiliations: Centre for Brain Research, University of Auckland, Auckland, New Zealand., Centre for Brain Research, University of Auckland, Auckland, New Zealand. .

Abstract:  Adeno-associated viral (AAV) vectors are a promising system for transgene delivery into the central nervous system (CNS) based on their safety profile and long-term gene expression. Gene delivery to the CNS has largely been neuron centric but advances in AAV technology are facilitating the development of approaches to enable transduction of glial cells. Considering the role of astrocytes in the on-going secondary damage in spinal cord injury (SCI), an AAV vector that targets astrocytes could show benefit as a potential treatment. Transduction efficiency, transgene expression and cellular tropism were compared for the AAV serotypes AAV5, AAV9 and AAVRec2 whereby destabilised yellow fluorescent protein (dYFP) was controlled by the GFAP or the truncated GfaABC1D promoter. The vectors were tested in primary spinal cord astrocyte cell culture, spinal cord slice culture and an in vivo model of SCI contusion. AAV5 resulted in greater transduction efficiency, transgene expression and astrocyte tropism compared with AAV9 and AAVRec2. In a rodent model of SCI, robust transgene expression by AAV5-GFAP/GfaABC1D-dYFP was observed through 12 mm of spinal cord tissue and expression was largely restricted to astrocytes. Thus, AAV5-GFAP/GfaABC1D carries the potential as a potential gene therapy vector, particularly for transducing astrocytes in the damaged spinal cord. 

Retracted: No

PubPeer comments:
 Figure 1A: Merge panels are duplicated on the bottom right, I ve added the blue rectangles to show where I mean. I think it s just the one duplication, as the individual panels look unique. Would the authors please comment? ![file] ,
TLX controls angiogenesis through interaction with the von Hippel-Lindau protein
Authors: Kimitoshi Kohno
Keiko Funa
Nina Akrap
Takeshi Yoshida
Pavithra L Chavali
Erik Johansson
Hiroto Izumi
Amiko Hayashi
Zhao-Jun Zeng
Journal: Biology open (2012)
Discipline: BIOLOGY & BIOCHEMISTRY
Keywords: Angiogenesis; HIF-2α; Neuroblastoma; TLX; VHL.
Affiliations: Sahlgrenska Cancer Center, University of Gothenburg ,  Box 425, SE 405 30 Gothenburg ,  Sweden ; Molecular Biology Research Center, School of Biological Science and Technology, Central South University ,  Changsha 410078 ,  China.

Abstract:  TLX is known as the orphan nuclear receptor indispensable for maintaining neural stem cells in adult neurogenesis. We report here that neuroblastoma cell lines express high levels of TLX, which further increase in hypoxia to enhance the angiogenic capacity of these cells. The proangiogenetic activity of TLX appears to be induced by its direct binding to the von Hippel-Lindau protein (pVHL), which stabilizes TLX. In turn, TLX competes with hydroxylated hypoxia-inducible factor (HIF-α) for binding to pVHL, which contributes to the stabilization of HIF-2α in neuroblastoma during normoxia. Upon hypoxia, TLX increases in the nucleus where it binds in close proximity of the HIF-response element on the VEGF-promoter chromatin, and, together with HIF-2α, recruits RNA polymerase II to induce VEGF expression. Conversely, depletion of TLX by shRNA decreases the expression of HIF-2α and VEGF as well as the growth-promoting and colony-forming capacity of the neuroblastoma cell lines IMR-32 and SH-SY5Y. On the contrary, silencing HIF-2α will slightly increase TLX, suggesting that TLX acts to maintain a hypoxic environment when HIF-2α is decreasing. Our results demonstrate TLX to play a key role in controlling angiogenesis by regulating HIF-2α. TLX and pVHL might counterbalance each other in important fate decisions such as self-renewal and differentiation, as well as angiogenesis and anti-angiogenesis. 

Retracted: No

PubPeer comments:
 ![file] ,
A short comment on statistical versus mathematical modelling
Authors: Andrea Saltelli
Journal: Nature Communications (2019)
Discipline: Multidisciplinary
Keywords: crisis of statistics; mathematical modelling; sociology of quantification; post-normal science; production of numbers
Affiliations: Centre for the Study of the Sciences and the Humanities (SVT), University of Bergen (UIB), 5020, Bergen, Norway. ., Open Evidence Research, Universitat Oberta de Catalunya (UOC), 08018, Barcelona, Spain. .

Abstract:  While the crisis of statistics has made it to the headlines, that of mathematical modelling hasn’t. Something can be learned comparing the two, and looking at other instances of production of numbers.Sociology of quantification and post-normal science can help. 

Retracted: No

PubPeer comments:
 The author states  Equivalent formulations of Fig. 1 can be seen in many fields of modelling and data analysis. I believe it is appropriate to give credit where credit is due, so here s what I know: The first depiction of Fig.1 that I m aware of appeared in: - **Ou2019Neill, R. V. (1971)**. Error analysis of ecological models. In D. J. Nelson (Ed.), *Radionuclides in ecosystems* (pp. 898u2013908). Springfield, VA: National Technical Information Service. It has been reproduced in e.g.: - **Reynolds, J. F., Acock, B. (1985)**. Predicting the response of plants to increasing carbon dioxide: A critique of plant growth models. *Ecological Modelling*, 29(1u20134), 107u2013129. https: doi.org 10.1016 0304-3800(85)90049-3 and: - **Passioura, J. (1996)**. Simulation models: science, snake oil, education, or engineering? *Agronomy Journal*, 88, 690u2013694. https: dl.sciencesocieties.org publications aj abstracts 88 5 AJ0880050690 , 
 #1 Thanks, very useful! I took it from the book of Turner where it is correctly referred to as O Neil conjecture. ![file] ,
Genetic association of interleukin-10 promoter polymorphisms and susceptibility to diffuse large B-cell lymphoma: a meta-analysis
Authors: Hai-Yan Cao
Ping Zou
Hao Zhou
Journal: Gene (2013)
Discipline: MOLECULAR BIOLOGY & GENETICS
Keywords: IL-10 gene polymorphisms; diffuse large B-cell lymphoma (DLBCL); meta-analysis; promoter region; -3575T/A
Affiliations: Institute of Hematology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, PR China.

Abstract:  Published data on the association between interleukin-10 (IL-10) gene polymorphisms and diffuse large B-cell lymphoma (DLBCL) risk are inconclusive. To derive a more precise estimation of the relationship, a meta-analysis was performed, focusing on four major IL-10 gene variants in the promoter region: -3575T/A, -1082A/G, -819C/T and -592C/A. We applied the false discovery rate (FDR) method to adjust for multiple testing. A significant association between IL-10 -3575T/A polymorphism and the risk of DLBCL was observed in the pooled 10 case-control studies (A vs. T: OR=1.16, 95% CI=1.08-1.25, P&lt;0.0001; AA+TA vs. TT: OR=1.20, 95% CI=1.08-1.33, P=0.0009; AA vs. TA+TT: OR=1.25, 95% CI=1.09-1.44, P=0.001). The results indicated that carriers of -1082G allele (-1082GG/GA genotypes) had a nearly 30% increased risk of DLBCL, as compared with carriers of -1082AA genotype (GG+GA vs. AA: OR=1.30, 95% CI=1.08-1.57, P=0.005). When P-values were not adjusted for multiple testing, the risk was significantly decreased among people with -592AA genotype (AA vs. AC+CC: OR=0.63, 95% CI=0.43-0.94, P=0.02), while carriers with -819TT genotype also modestly weakened the DLBCL susceptibility at a marginal level of significance (TT vs. CT+CC: OR=0.59, 95% CI=0.35-0.99, P=0.05). However, these associations were not significant after correction for multiple testing. This meta-analysis suggests that IL-10 -3575A allele confers a greater risk to DLBCL susceptibility, while -1082A/G polymorphism also has significant association with DLBCL risk. These results may help to further clarify the malignancy-risk gene signature of DLBCL, and thus have prognostic and predictive value especially for early-stage DLBCL. 

Retracted: No

PubPeer comments:
 Hi, Thank you for putting together this paper. In **Figure S3**, I noticed  **Lorem ipsum** in the lower-left corner. **Am I correct that this is a typo**? If so, I guess whether or not you need to have a formal correction depends upon whether you had a template (and intended that to be blank in your own figure) or if something really was supposed to be there (in which case, the relevant information is missing). Thank You, Charles ,
Exploring the DNA interactions, FGF growth receptor interaction and biological screening of metal(II) complexes of NNN donor ligand derived from 2‑(aminomethyl)benzimidazole
Authors: Ganesan Kumaravel
Dharmasivam Mahendiran
Ponya Utthra Ponnukalai
Natarajan Raman
Journal: International Journal of Biological Macromolecules (2019)
Discipline: BIOLOGY & BIOCHEMISTRY
Keywords: 2‑(aminomethyl)benzimidazole; DNA interactions; FGFR kinase receptor.
Affiliations: Research Department of Chemistry, VHNSN College (Autonomous), Virudhunagar 626 001, India., Post-Graduate and Research Department of Chemistry, The New College (Autonomous), Chennai 600 014, India., Research Department of Chemistry, VHNSN College (Autonomous), Virudhunagar 626 001, India. Electronic address: .

Abstract:  This work deals with a series of biologically important novel transition metal(II) Schiff base chelates containing terpyridine. Benzimidazole, a moiety found in broad spectrum of drugs is espoused in a Schiff base ligand system. Eight such metal(II) complexes are designed, synthesized and characterized. An octahedral geometry has been envisaged for all the complexes. DNA-binding behaviours are studied by absorption titration, electrochemical, viscosity, fluorescence and circular dichroism methods. The DNA cleavage ability is also evaluated by agarose gel electrophoresis method. These studies reveal that the complexes show an intercalative mode of binding to CT-DNA and also effectively cleave the supercoiled pBR322 DNA. The molecular docking studies of the complexes against FGF growth receptors indicate that they bind through electrostatic, van der Waals, hydrogen bonding and π-π interactions. The ligand and its complexes are screened for in vitro antimicrobial activities against a few microorganisms. The data exhibit that they are better antimicrobial agents than the ligand. The cytotoxic activity of the complexes is probed in four cell lines wherein the complex 5 has good cytotoxic activity and is partial to MCF-7 cell line which is comparable with the cisplatin drug which can be attributed to the presence of planar terpyridine co-ligand. 

Retracted: No

PubPeer comments:
 Could the authors comment on what appear to be several repeated features in Figure 6 a? ![file] ,
Modulation of nurr1 gene expression in mesencephalic dopaminergic neurones
Authors: Floriana Volpicelli
Umberto di Porzio
Luca Colucci-D&#x27;Amato
Carla Perrone-Capano
Paola Da Pozzo
Journal: Journal of Neurochemistry (2004)
Discipline: NEUROSCIENCE & BEHAVIOR
Keywords: transcription factor; nuclear receptor; Nurr1; midbrain; dopaminergic neurones
Affiliations: Institute of Genetics and Biophysics, Developmental Neurobiology, Naples, Italy.

Abstract:  The transcription factor/nuclear receptor Nurr1 is essential for the differentiation of midbrain dopaminergic neurones. Here we demonstrate that, during the ontogeny of rat ventral mesencephalon, nurr1 gene expression is developmentally regulated and its levels show a sharp peak between embryonic day E13 and E15, when most dopaminergic neurones differentiate. In addition, in primary cultures from embryonic rat mesencephalon, nurr1 gene follows a temporal pattern of expression comparable to that observed in vivo. We also report that exposure of embryonic mesencephalic cultures to depolarizing stimuli leads to a robust increase in nurr1 mRNA and protein. The depolarizing effect is also detected in mesencephalic cultures enriched in dopaminergic neurones by using a combination of bFGF and Sonic hedgehog. The latter further increases the number of dopaminergic neurones in these 'expanded' cultures, an effect abolished in the presence of anti-Sonic hedgehog antibodies. Our data show that nurr1 gene is highly expressed in midbrain dopaminergic neurones in a sharp temporal window and that its expression is plastic, both in vivo and in vitro. In addition we show that Sonic hedgehog can direct dopaminergic differentiation in proliferating dopaminergic neuroblasts in vitro. 

Retracted: No

PubPeer comments:
 Figure 2d contains numerous cases in which multiple lanes are surprisingly similar to each other, raising the possibility that they are duplicates. Illustrated below: Top, original figure image. Middle, colored boxes denote lanes that are similar to each other. Bottom, image after adjusting gradient map to make it easier to visualize the similarities. ![file] Other threads involving shared authors and similar concerns: https: pubpeer.com publications 10B87A862B678879504371094A6A90 https: pubpeer.com publications 812E5C95DA10CF0831016228F930CF https: pubpeer.com publications A8F2B88889CB2BC4D2DCD9B0078EF9 https: pubpeer.com publications 11BAE73B53B4ED62DC0D03F00437C0 ,