PReD-Bench/PRed-Bench huggingface dataset:
HDAC2-mediated upregulation of IL-6 triggers the migration of osteosarcoma cells
Authors: Jing Li
Ming Liu
Wen Wu
Jiaxing Tang
Jian Tang
Yan Wang
Xiuzhong Yan
Journal: Cell Biology and Toxicology (2019)
Discipline: MOLECULAR BIOLOGY & GENETICS
Keywords: HDAC2; IKK-β; IL-6; Osteosarcoma; p65.
Affiliations: Orthopedic Department, TCM Hospital of Rizhao, Rizhao, 276800, China., Orthopedic Department, Shanghai Ninth People's Hospital, School of Medicine, Shanghai Jiaotong University, No.639 Zhizao Ju Road, Shanghai, 200011, China., Orthopedic Department, Shanghai Ninth People's Hospital, School of Medicine, Shanghai Jiaotong University, No.639 Zhizao Ju Road, Shanghai, 200011, China. .

Abstract:  Understanding the mechanisms of advanced metastasis in osteosarcoma (OS) cell is important for the targeted treatment and drug development. Emerging evidence shows that epigenetic factors such as histone deacetylases (HDACs) are involved in the progression and chemoresistance of OS, while their roles are largely unknown. Our data showed that the expression of HDAC2, while not HDAC1, 4, or 8, was significantly increased in OS cells and tissues. OS patients with increased expression of HDAC2 showed reduced overall survival with p value of 0.0001. Targeted inhibition of HDAC2 suppressed the in vitro migration and invasion of OS cells. Our data showed that the inhibition of HDAC2 can decrease the expression and transcription of interleukin-6 (IL-6) in OS cells. Overexpression of IL-6 can reverse si-HDAC2-induced suppression of cell migration. Mechanistical studies showed that inhibition of HDAC2 decreased the phosphorylation and nuclear accumulation of p65, the key factor of NF-κB complex responsible for the transcription of IL-6. This was due to that HDAC2 can activate the transcription of IKK-β in OS cells. Collectively, our data showed that HDAC2-activated NF-κB can increase the expression of IL-6 in OS cells, which resulted in the promotion of cell migration. It suggested that targeted inhibition of HDAC2/NF-κB/IL-6 might be a potential approach for OS therapy. 

Retracted: No

PubPeer comments:
 Three duplications within Fig 4 ![file] ,
Development and characterization of hyaluronic acid decorated PLGA nanoparticles for delivery of 5-fluorouracil
Authors: Anil K Mishra
Abhinav Agarwal
Gopal Rai
Govind P Agrawal
Awesh K Yadav
Pradeep Mishra
Sanyog Jain
Himanshu Agrawal
Journal: Drug delivery (2010)
Discipline: PHARMACOLOGY & TOXICOLOGY
Keywords: PLGA nanoparticles; targeted delivery; 5-fluorouracil; hyaluronic acid; PEG
Affiliations: Pharmaceutics Research Laboratory, Department of Pharmaceutical Sciences, Dr. H. S. Gour University, Sagar, India.

Abstract:  The present investigation was aimed to develop and explore the prospective of engineered PLGA nanoparticles as vehicles for targeted delivery of 5-fluorouracil (5-FU). Nanoparticles of 5-FU-loaded hyaluronic acid-poly(ethylene glycol)-poly(lactide-co-glycolide) (HA-PEG-PLGA-FU) copolymer were prepared and characterized by FTIR, NMR, transmission electron microscopy, particle size analysis, DSC, and X-ray diffractometer measurement studies. The nanoparticulate formulation was evaluated for in vitro release, hemolytic toxicity, and hematological toxicity. Cytotoxicity studies were performed on Ehrlich ascites tumor (EAT) cell lines using MTT cell proliferation assay. Biodistribution studies of 99m Tc labeled formulation were conducted on EAT-bearing mice. The in vivo tumor inhibition study was also performed after i.v. administration of HA-PEG-PLGA-FU nanoparticles. The HA conjugated formulation was found to be less hemolytic but more cytotoxic as compared to free drug. The hematological data suggested that HA-PEG-PLGA-FU formulation was less immunogenic compared to plain drug. The tissue distribution studies displayed that HA-PEG-PLGA-FU were able to deliver a higher concentration of 5-FU in the tumor mass. In addition, the HA-PEG-PLGA-FU nanoparticles reduced tumor volume significantly in comparison with 5-FU. Thus, it was concluded that the conjugation of HA imparts targetability to the formulation, and enhanced permeation and retention effect ruled out its access to the non-tumor tissues, at the same time favored selective entry in tumors, thereby reducing the side-effects both in vitro and in vivo. 

Retracted: No

PubPeer comments:
  Figure 2. TEM photomicrograph of HA-PEG-PLGA nanoparticles ![file] The low resolution here makes it difficult to comment on the similarities among the nanoparticles. It seems fair, though, to say that two areas of background are far more similar than one would expect. ,
Silencing of polo-like kinase (Plk) 1 via siRNA causes inhibition of growth and induction of apoptosis in human esophageal cancer cells
Authors: Quanhai Li
Zhengmei Yang
Youquan Bu
Fangzhou Song
Journal: Oncology (2008)
Discipline: CLINICAL MEDICINE
Keywords: Esophageal cancer; Polo-like kinase 1 (Plk1); therapeutic target; RNA silencing; small interfering RNA (siRNA)
Affiliations: Department of Biochemistry and Molecular Biology, Chongqing Medical University, Chongqing, China.

Abstract:  Esophageal cancer ranks among one of the most frequent causes of cancer death in the world. Polo-like kinase 1 (Plk1) is overexpressed in human tumors and has prognostic value in many cancers including esophageal cancer, indicating its potential as a therapeutic target. In this study, we investigated the therapeutic potential of Plk1 in esophageal cancer using the technique of RNA silencing via small interfering RNA (siRNA). Synthetic siRNA duplexes against Plk1 were introduced into 4 esophageal cancer cell lines, which subsequently resulted in a significant inhibition in Plk1 expression in the cells. We found that the targeted depletion of Plk1 caused a dramatic mitotic catastrophe (mitotic cell cycle arrest as well as defects in several mitotic events such as incomplete separation of sister chromatids and failure of cytokinesis) followed by massive apoptotic cell death, and eventually resulted in a significant decrease in growth and viability of all 4 esophageal cancer cell lines studied. In addition, our results also indicated that the mitotic arrest induced by Plk1 depletion is mediated by the inactivation of the cdc2/cyclin B1 complex. Taken together, our study strongly suggests that Plk1 may serve as a potential therapeutic target in human esophageal cancer. 

Retracted: No

PubPeer comments:
 Fig 2B , these two look very similar. ![file] ![file] ,
[Atypical course in Stickler syndrome]
Authors: S Koehler
J-B Koehler
V Jansson
B Heimkes
Journal: Zeitschrift fur Orthopadie und Unfallchirurgie (0)
Discipline: CLINICAL MEDICINE
Keywords: Stickler syndrome; osteonecrosis; femoral head; dysplasia epiphysealis capitis femoris; retinal detachment
Affiliations: Orthopädische Klinik und Poliklinik, Ludwig-Maximilians-Universität München, Klinikum Grosshadern, München. 

Abstract:  We report about a 12-year-old boy with a Stickler syndrome. Because of osteonecrosis in the femoral head in MRI the initial diagnosis was dysplasia epiphysealis capitis femoris. The patient developed a progressive stiffness of the hip and a retinal detachment. A molecular investigation showed a Stickler syndrome. Stickler syndrome is an autosomal dominant hereditary disease. It has a very low incidence and a rare association with hip disease. Usually the patients suffer from hypermobility. In our case the course was atypical and diagnosis delayed. 

Retracted: No

PubPeer comments:
 Case report without consent of parents and child. MIssing clinical details ophthalmology. No proof of sequencing. Position of mutation unclear. Not reported to any international database. Results of therapy missing. ,
Inhibition of the NF-kappa B transcription factor increases Bax expression in cancer cell lines
Authors: M P Merville
V Bours
C Van Lint
P Viatour
B Froesch
J C Reed
M Bentires-Alj
E Dejardin
Journal: Oncogene (2001)
Discipline: MOLECULAR BIOLOGY & GENETICS
Keywords: NF-kappa B; apoptosis; Bax protein; I kappa B-alpha; gene promoter
Affiliations: Laboratory of Medical Chemistry and Medical Oncology, University of Liège, Belgium.

Abstract:  The NF-kappa B transcription factor has been shown to inhibit apoptosis in several experimental systems. We therefore investigated whether the expression of the Bax proapoptotic protein could be influenced by NF-kappa B activity. Increased Bax protein expression was detected in HCT116, OVCAR-3 and MCF7 cells stably expressing a mutated unresponsive I kappa B-alpha inhibitory protein that blocks NF-kappa B activity. Northern blots showed that bax mRNA expression was increased as a consequence of mutated I kappa B-alpha expression in HCT116 cells. A careful examination of the human bax gene promoter sequence showed three putative binding sites for NF-kappa B, and the kappa B2 site at position -687 could indeed bind NF-kappa B complexes in vitro. Transient transfection of a bax promoter luciferase construct in HCT116 cells showed that NF-kappa B proteins could partially inhibit the transactivation of the bax promoter by p53. Mutations or deletions of the kappa B sites, including kappa B2, indicated that this NF-kappa B-dependent inhibitory effect did not require NF-kappa B DNA-binding, and was thus an indirect effect. However, cotransfection of expression vectors for several known cofactors failed to identify a competition between p53 and NF-kappa B for a transcription coactivator. Our findings thus demonstrate for the first time that NF-kappa B regulates, through an indirect pathway, the bax gene expression. 

Retracted: No

PubPeer comments:
 Figure 6. The 3 graphs, including error bars are indistinguishable, yet the transfections are different. https: imgur.com OEeoCa3 ,
Extreme intrusive force affects the expression of c-Fos and matrix metallopeptidase 9 in human dental pulp tissues
Authors: Guanghong Han
Dongsheng Yu
Huan Jiang
Weiwei Liu
Min Hu
Journal: Medicine (2020)
Discipline: CLINICAL MEDICINE
Keywords: c-Fos; matrix metallopeptidase 9 (MMP-9); dental pulp; orthodontic treatment; wire appliance
Affiliations: Department of Oral Geriatrics, Hospital of Stomatology, Jilin University, Jilin Provincial Key Laboratory of Tooth Development and Bone Remodeling., Jilin Provincial Key Laboratory of Tooth Development and Bone Remodeling, Changchun, PR China., Department of Oral and Maxillofacial Surgery., Department of Orthodontics, Hospital of Stomatology, Jilin University.

Abstract:  This study aimed to investigate the expression of c-Fos and matrix metallopeptidase 9 (MMP-9) in dental pulp of patients receiving orthodontic treatment via wire appliance.Fifteen patients (30 teeth in total) were randomly assigned to five groups: t = 0, t = 1, t = 4, t = 8 and t = 12 (n = 6). The first maxillary premolars of patients in the t = 0 group were extracted without any orthodontic treatment. An intrusive force of 300 g was applied on first maxillary premolars in the other four groups via wire appliances. This force was maintained for 1 week for t = 1 group, 4 weeks for t = 4 group, 8 weeks for t = 8 group, or 12 weeks for t = 12 group, before the teeth were extracted.The expression of c-Fos and MMP-9 in the pulps of each group was analyzed by immunohistochemical staining and real-time PCR. The relationship in the protein expression between c-Fos and MMP-9 in the dental pulp was analyzed by Pearson correlation analysis.Intrusive force of 300 g increased the expression of both c-Fos and MMP-9 in the dental pulp. The protein expression of MMP-9 in the dental pulp was significantly correlated with the expression of c-Fos (P &lt; .001).Extreme intrusive force upregulates c-Fos and MMP-9 expression in the dental pulp. Moreover, protein expression of c-Fos and MMP-9 is significantly correlated under intrusive force. 

Retracted: No

PubPeer comments:
 Could the authors clarify that they intended to use the same negative control image in Figure 2 and 4? *** ![file] *** ![file] , 
 Really thank you very much for your reading our article. We used and stained consecutive sections of the same tissue in the negative control group. We have some other images of the negative control group. According to your suggestion, we will contact to the journal as soon as possible. If the editor thinks it necessary, we will change the other image for the negative control image in Figure 4. Thanks again for your suggestion. ![](http: )![file] ,
Essential role of caspases in epigallocatechin-3-gallate-mediated inhibition of nuclear factor kappa B and induction of apoptosis
Authors: Kedar Hastak
Hasan Mukhtar
Sanjay Gupta
Farrukh Afaq
Nihal Ahmad
Journal: Oncogene (2004)
Discipline: MOLECULAR BIOLOGY & GENETICS
Keywords: Green tea; EGCG; apoptosis; NF-kappa B pathway; caspases
Affiliations: Department of Urology, Case Western Reserve University, Cleveland, OH 44106, USA.

Abstract:  Green tea constituent (-) epigallocatechin-3-gallate (EGCG) has shown remarkable cancer-preventive and some cancer-therapeutic effects. This is partially because of its ability to induce apoptosis in cancer cells without affecting normal cells. Previous studies from our laboratory have shown the involvement of NF-kappa B pathway in EGCG-mediated cell-cycle deregulation and apoptosis of human epidermoid carcinoma A431 cells. Here we show the essential role of caspases in EGCG-mediated inhibition of NF-kappa B and its subsequent apoptosis. Treatment of A431 cells with EGCG (10-40 microg/ml) resulted in dose-dependent inhibition of NF-kappa B/p65, induction of DNA breaks, cleavage of poly(ADP-ribose) polymerase (PARP) and morphological changes consistent with apoptosis. EGCG treatment of cells also resulted in significant activation of caspases, as shown by the dose- and time-dependent increase in DEVDase activity, and protein expression of caspase-3, -8 and -9. EGCG-mediated caspase activation induces proteolytic cleavage of NF-kappa B/p65 subunit, leading to the loss of transactivation domains, and driving the cells towards apoptosis. EGCG-mediated induction of apoptosis was significantly blocked by the caspase inhibitor N-benzyloxycarbonyl-Val-Ala-Asp(OMe)-fluoromethylketone (Z-VAD-FMK), and moderately blocked by the specific caspase-3 inhibitor Z-DEVD-FMK. Further, pretreatment of cells with Z-VAD-FMK was found to suppress the cleavage of NF-kappa B/p65 subunit, thereby increasing nuclear translocation, DNA binding and transcriptional activity, thus protecting the cells from EGCG-induced apoptosis. Taken together, these studies for the first time demonstrate that EGCG-mediated activation of caspases is critical, at least in part, for inhibition of NF-kappa B and subsequent apoptosis. 

Retracted: No

PubPeer comments:
 Figure 7a. Much more similar than expected. https: imgur.com F2Q9vdi ,
Comparative gene expression profiling identifies common molecular signatures of NF-κB activation in canine and human diffuse large B cell lymphoma (DLBCL)
Authors: Karen A L Tan
Gino Miele
Daniel Crowther
Ilene Kurzman
Grant Sellar
Elspeth Milne
Manikhandan A V Mudaliar
John R Goodlad
David M Vail
David J Argyle
Ross D Haggart
Journal: PLoS ONE (2013)
Discipline: Multidisciplinary
Keywords: canine; human; diffuse large B-cell lymphoma; NF-κB pathway; microarray data
Affiliations: Translational Medicine Research Collaboration, Ninewells Hospital, University of Dundee, Dundee, United Kingdom.

Abstract:  We present the first comparison of global transcriptional changes in canine and human diffuse large B-cell lymphoma (DLBCL), with particular reference to the nuclear factor-kappa B (NF-κB) pathway. Microarray data generated from canine DLBCL and normal lymph nodes were used for differential expression, co-expression and pathway analyses, and compared with analysis of microarray data from human healthy and DLBCL lymph nodes. The comparisons at gene level were performed by mapping the probesets in canine microarrays to orthologous genes in humans and vice versa. A considerable number of differentially expressed genes between canine lymphoma and healthy lymph node samples were also found differentially expressed between human DLBCL and healthy lymph node samples. Principal component analysis using a literature-derived NF-κB target gene set mapped to orthologous canine array probesets and human array probesets clearly separated the healthy and cancer samples in both datasets. The analysis demonstrated that for both human and canine DLBCL there is activation of the NF-κB/p65 canonical pathway, indicating that canine lymphoma could be used as a model to study NF-κB-targeted therapeutics for human lymphoma. To validate this, tissue arrays were generated for canine and human NHL and immunohistochemistry was employed to assess NF-κB activation status. In addition, human and canine B-cell lymphoma lines were assessed for NF-κB activity and the effects of NF-κB inhibition. 

Retracted: No

PubPeer comments:
 Figure 8: p65 staining in canine DLBCL weak (c), and p52 staining in human DLBCL weak (e), appear to be the same image. *** ![file] ,
Hsa_circ_0101432 promotes the development of hepatocellular carcinoma (HCC) by adsorbing miR-1258 and miR-622
Authors: Yu Zhang
Guan Wang
Xiaolun Huang
Xiangang Xu
Guangming Xiang
Yutong Yao
Haibo Zou
Le Luo
Lanyun Luo
Journal: Cell Cycle (2019)
Discipline: MOLECULAR BIOLOGY & GENETICS
Keywords: Hepatocellular carcinoma; Hsa_circ_0101432; MAPK1.
Affiliations: Department of Hepatobiliary Surgery, Sichuan Academy of Medical Sciences & Sichuan Provincial People's Hospital , Chengdu , Sichuan , China., Department of Hepatobiliary Surgery, Guizhou Provincial People's Hospital , Guiyang , Guizhou , China., Graduate School, Chengdu Medical College , Chengdu , Sichuan , China.

Abstract:  The present research was major in investigating the regulation association among hsa_circ_0101432 (has_circ_RPPH1), miR-1258, miR-622 and MAPK1 in hepatocellular carcinoma (HCC), and we explored the mechanism underlying pathogenesis of HCC. Microarray analysis was employed to detect hsa_circ_0101432 expression in HCC. Hsa_circ_0101432 was verified as a circRNA by testing divergent primers and RNase R. And qRT-PCR was performed to determine the expression of hsa_circ_0101432, miR-1258, miR-622 and MAPK1 mRNA. Furthermore, miRanda predicted that mRNAs targeted miR-1258 and miR-622. CCK-8 assay, colony formation assay, flow cytometry as well as transwell assay were performed to detect cell viability, proliferation, apoptosis and invasive ability, respectively. Xenograft in nude mice was applied to observe tumor growth in vivo. Up-regulated hsa_circ_0101432 and down-regulated miR-1258 and miR-622 were detected in HCC while Hsa_circ_0101432 enhanced expression of MAPK1 mRNA by targeting miR-1258 and miR-622. Knocking down hsa_circ_0101432 or overexpressing miR-1258 and miR-622 inhibited proliferation and invasive ability of HCC cell and promoted cell apoptosis. Hsa_circ_0101432 was confirmed to promote tumor growth via inhibiting miR-1258 and miR-622 expression and promoting MAPK1 mRNA expression by in vivo experiment. Hsa_circ_0101432 inhibited HCC cell apoptosis, promoted cell proliferation, invasive ability and HCC tumor growth by targeting miR-1258 and miR-622 and upregulating MAPK1 mRNA expression. 

Retracted: Yes

PubPeer comments:
 In supplementary Figure 5, the XRD curves under 700 and 800 degree are duplicated, even the noise background. ![file] ,
Nanocomposite functionalized membranes based on silica nanoparticles cross-linked to electrospun nanofibrous support for arsenic(v) adsorption from contaminated underground water
Authors: A Uheida
K Laxman Kunjali
H Giraldo Mejía
S Pellice
L Yohai
J Dutta
R Procaccini
Journal: RSC Advances (2019)
Discipline: CHEMISTRY
Keywords: Nanocomposite membranes; Arsenic removal; Mesoporous silica nanoparticles; Polyacrylonitrile; Adsorption studies
Affiliations: División Cerámicos, INTEMA, CONICET, UNMdP, B7608FDQ Mar del Plata, Functional Materials Group, Department of Applied Physics, KTH Royal Institute of Technology, Stockholm, Sweden

Abstract:  Nanocomposite functionalized membranes were synthesized using surface functionalized mesoporous silica nanoparticles (MCM-NH2 or MCM-PEI) cross-linked to a modified polyacrylonitrile (mPAN) nanofibrous substrate for the removal of 1 mg L-1 of As(v); a concentration much higher than what has been reported for underground water in Argentina. Adsorption studies were carried out in batch mode at pH 8 with nanoparticles in colloidal form, as well as the nanoparticles supported on the modified PAN membranes (mPAN/MCM-NH2 and mPAN/MCM-PEI). Results indicate a twenty-fold improvement in As(v) adsorption with supported nanoparticles (nanocomposite membranes) as opposed to their colloidal form. The adsorption efficiency could be further enhanced by modifying the nanocomposite membrane surface with Fe3+ (mPAN/MCM-NH2-Fe3+ and mPAN/MCM-PEI-Fe3+) which resulted in more than 95% arsenic being removed within the first 15 minutes and a specific arsenic adsorption capacity of 4.61 mg g-1 and 5.89 mg g-1 for mPAN/MCM-NH2-Fe3+ and mPAN/MCM-PEI-Fe3+ nanocomposite membranes, respectively. The adsorption characteristics were observed to follow a pseudo-first order behavior. The results suggest that the synthesized materials are excellent for quick and efficient reduction of As(v) concentrations below the WHO guidelines and show promise for future applications. 

Retracted: No

PubPeer comments:
 Figure 2 appears to include an image previously published (July 2018 RSC Advances 8(43):24588-24598 DOI:10.1039 C8RA02463D), which also has a PP[ discussion thread] . They appear to be described differently. *** ![file] ,
A Zn(II)-MOF with Suitable Pore Surroundings for Cyanosilylation Reaction and Protective Effect on Bladder Cancer Cells by Regulating miR-130 and CYLD
Authors: Wu, Yu-Ye
Fan, Hai-Qing
Chen, Hui-Jun
Jiang, Li-Xing
Zhang, Wei-Ping
Journal: Journal of Inorganic and Organometallic Polymers and Materials (2021)
Discipline: CHEMISTRY
Keywords: Keywords: porous metal-organic framework; Zn(II); catalytic activity; cyanation; trimethylsilyl cyanohydrin

Abstract: A porous metal–organic framework (MOF) based on Zn(II) metal nodes was prepared via reaction of rigid V-shaped ligand 2,6-di(2′,5′-dicarboxylphenyl)pyridine (H4L) along with Zn(NO3)2·6H2O in water and DMF mixed solvent, and its chemical formula was [Zn3(L)(OH)2(H2O)4](DMF)5 (1). The results show that the obtained activated 1a has catalytic activity for aromatic aldehydes cyanation under the existence of the trimethylsilyl cyanide, thus providing trimethylsilyl cyanohydrin in the form of shape along with size selection. In addition, a feasible synergistic mechanism of 1a for cyanosilylation of aldehyde also has been put forward. Furthermore, the treatment function of the compound on bladder cancer cells was assessed. The reverse transcription-polymerase chain reaction (PT-PCR) was carried out to determine cyclindromatosis (CYLD) and miR-130 relative expression in bladder cancer cells after the combine therapy. Besides, the mechanism of the compound was explored, by evaluating the level of autophagic programed cell death by western blot.

Retracted: No

PubPeer comments:
  To explore the mechanism of the treatment efect of the compound against bladder cancer cells, the western blot was carried out in accordance with the protocols as the previous reported. *[citation required]*  Metalu2013organic frameworks (MOFs) are a kind of crystalline materials of porous with periodic skeleton structures, they are made up of organic ligands along with metal oxide clusters or metal [5u20139]. In this genre,  MOF is used in a broad sense which includes inorganic ceramics. - [9]. H. Du, C. Ma, W. Ma, H. Wang, Process. Appl. Ceram. 12, 303u2013312 (2018) ** Microstructure evolution and dielectric properties of Ce-doped SrBi4Ti4O15 ceramics synthesized via glycine-nitrate process **  Because of their ordered internal microchannels and exceedingly high surface areas as well as highly changeable pore sizes, MOFs are considered to be a prospective functional material with porosity, which has been more and more studied and applied in catalysis, separation and gas storage as well as other fields [10u201313]. - [11]. M. Arshad, H.L. Du, M.S. Javed, A. Maqsood, I. Ashraf, S. Hussain, W.L. Ma, H.P. Ran, Ceram. Int. 46, 2238u20132246 (2020) ** Fabrication, structure, and frequency-dependent electrical and dielectric properties of Sr-doped BaTiO3 ceramics ** Other References in this paper are more relevant but they form a constellation, frequently recurring in other papers of the same  Floor wax **and** a dessert topping genre, almost as if these all have a production-line provenance. ,
Protective effects of triptolide on retinal ganglion cells in a rat model of chronic glaucoma
Authors: Fan Yang
Dongmei Wang
Lingling Wu
Ying Li
Journal: Drug Design Development and Therapy (2015)
Discipline: PHARMACOLOGY & TOXICOLOGY
Keywords: glaucoma; microglia; neuroprotection; triptolide.
Affiliations: Ophthalmology Department, Peking University Third Hospital, Beijing, People's Republic of China.

Abstract:  Purpose: To study the effects of triptolide, a Chinese herb extract, on retinal ganglion cells (RGCs) in a rat model of chronic glaucoma. Methods: Eighty Wistar rats were randomly divided into triptolide group (n=40) and normal saline (NS) group (n=40). Angle photocoagulation was used to establish the model of glaucoma, with right eye as laser treated eye and left eye as control eye. Triptolide group received triptolide intraperitoneally daily, while NS group received NS. Intraocular pressure (IOP), anti-CD11b immunofluorescent stain in retina and optic nerve, RGCs count with Nissel stain and microglia count with anti-CD11b immunofluorescence stain in retina flat mounts, retinal tumor necrosis factor (TNF)-α mRNA detection by reverse transcription-polymerase chain reaction, and double immunofluorescent labeling with anti-TNF-α and anti-CD11b in retinal frozen section were performed. Results: Mean IOP of the laser treated eyes significantly increased 3 weeks after photocoagulation (P&lt;0.05), with no statistical difference between the two groups (P&gt;0.05). RGCs survival in the laser treated eyes was significantly improved in the triptolide group than the NS group (P&lt;0.05). Microglia count in superficial retina of the laser treated eyes was significantly less in the triptolide group (30.40±4.90) than the NS group (35.06±7.59) (P&lt;0.05). TNF-α mRNA expression in the retina of the laser treated eyes in the triptolide group decreased by 60% compared with that in the NS group (P&lt;0.01). The double immunofluorescent labeling showed that TNF-α was mainly distributed around the microglia. Conclusion: Triptolide improved RGCs survival in this rat model of chronic glaucoma, which did not depend on IOP decrease but might be exerted by inhibiting microglia activities and reducing TNF-α secretion. 

Retracted: No

PubPeer comments:
 Figure 7 has an apparently repeated blot. More easily seen when image is inverted, see red boxes below. Top: Showing areas of concern; Bottom: Original image. *** ![file] *** ![file] , 
  Figure 3 H E staining of the retinal frozen sections of the laser treated eyes in the two groups . ![file] B and H differ only by a horizontal flip. ,
Hyaluronic acid conjugated multi-walled carbon nanotubes for colon cancer targeting
Authors: Ashish Kumar Jain
Shiv Kumar Prajapati
Ankit Jain
Chirag Shrivastava
Journal: International journal of biological macromolecules (2019)
Discipline: BIOLOGY & BIOCHEMISTRY
Keywords: Gemcitabine; Hyaluronic acid; Multi-walled carbon nanotubes.
Affiliations: Adina Institute of Pharmaceutical Sciences, Sagar, 470002, M.P., India., Department of Pharmaceutics, Institute of Pharmaceutical Research, GLA University, Mathura, 281406, U.P., India. Electronic address: .

Abstract:  Purpose of the present research was to evaluate in vitro and in vivo potential of gemcitabine (GEM) loaded hyaluronic acid (HA) conjugated PEGylated multi-walled carbon nanotubes (GEM/HA-PEG-MWCNTs) for effective colon cancer targeting. HA was conjugated onto the surface of aminated or PEGylated MWCNTs which were evaluated for size, surface morphology, entrapment efficiency (~90%), in vitro drug release, in vitro cytotoxicity and in vivo performance in Sprague Dawley rats. In vitro release showed that the release rate of GEM in acidic conditions (pH 5.3) was faster than physiological conditions (PBS, pH 7.4) followed by a sustained release pattern. The developed GEM/HA-PEG-MWCNTs indicated significantly less hemolytic toxicity (7.73 ± 0.4%) paralleled to free GEM (18.71 ± 0.44%) and showed higher cytotoxicity against HT-29 colon cancer cell line. The antitumor study assured that GEM/HA-PEG-MWCNTs significantly reduced tumor volume as compared to free GEM and increased survival rate without noticeable loss in body weight. In vivo studies showed an improvement in pharmacokinetics in terms of remarkable escalation in mean residence time, half-life, AUC, AUMC, median survival time in tumor bearing rats treated with GEM/HA-MWCNTs and GEM/HA-PEG-MWCNTs as compared to free GEM (p ˂ 0.001). These outcomes proved engineered MWCNTs as a safe and effective nanomedicine in colon cancer targeting. 

Retracted: No

PubPeer comments:
  Figure 3 TEM photomicrographs of (a) Purified MWCNTs (b) GEM HA-MWCNTs (c) GEM HA-PEG-MWCNTs. ![file] A close-up of (c) reveals repeating graphic elements that are not compatible with actual transmission electron microscopy. Other repeated elements are left as an exercise for the reader. ![file] , 
  Figure 6 Fluorescence photomicrograph of colon tissue sac after 6 hr administration of FITC loaded (a) GEM-MWCNTs (b) GEM PEG-MWCNTs (c) GEM HA-PEG-MWCNTs (d) GEM HA-MWCNTs . Duplicated cell in (a) is marked. ![file] , 
 #1 Intriguing partial symmetry in 3(a). ![file] ,
An in vitro and in vivo study of the role of long non-coding RNA-HOST2 in the proliferation, migration, and invasion of human glioma cells
Authors: Ji-Qiang Ma
Yi-Ming Cheng
Chun-Long Zhong
Kui-Ming Zhang
Shi-Yi Xu
Zhong-Wei Zhuang
Qi Wang
Journal: IUBMB life (2019)
Discipline: BIOLOGY & BIOCHEMISTRY
Keywords: cell invasion; cell migration; cell proliferation; clone formation; glioma
Affiliations: Department of Neurosurgery, Shanghai East Hospital Affiliated to Tongji University, Shanghai, 200120, China.

Abstract:  Gliomas are the most commonly occurring primary malignant brain tumors in the central nervous system of adults. They are rarely curable and the prognosis for high grade gliomas is generally poor. Recently, long non-coding RNA (lncRNA) human ovarian cancer-specific transcript 2 (HOST2) has been reported to be expressed at high levels in human ovarian cancer, involving tumorigenesis. However, little is still known about whether and how HOST2 regulates glioma development and progression. Therefore, this study aims to investigate the role of HOST2 in human glioma cells. Reverse transcription quantitative real-time polymerase chain reaction (RT-qPCR) was used to determine the expression of lncRNA HOST2, let-7b, and PBX3 in human glioma cells. Cultured human glioma cells were treated with siRNA (si)-lncRNA HOST2, let-7b mimic, si-lncRNA HOST2 + let-7b inhibitor, and si-PBX3. Parameters including cell viability, colony formation, cell migration, and cell invasion were detected by cell counting kit-8 assay, colony formation assay, scratch test, and Transwell assay respectively to determine the effects of down-regulated HOST2 on glioma cells. Tumor formation in nude mice was evaluated by subcutaneous tumor formation experiment. Results showed that HOST2 and PBX3 were highly expressed in glioma tissue whereas let-7b was expressed at much lower levels. In response to treatment with si-lncRNA HOST2, si-PBX3, and let-7b mimic, glioma cell lines exhibited decreased cell viability, suppressed cell migration, invasion, and reduced colony formation of glioma cells. This was accompanied by an attenuated tumor formation with smaller volume and weight in nude mice, suggesting that down-regulated HOST2 could inhibit the tumorigenicity of glioma cells. Lastly, we found that lncRNA HOST2 was highly expressed in glioma tissues and its down-regulation could inhibit the growth and invasion of glioma cells. © 2018 IUBMB Life, 71(1):93-104, 2019. 

Retracted: No

PubPeer comments:
 Fig 7A.  LncRNA HOST2 silencing represses U251and U87 cell invasion as detected by Transwell assay. (A) The cells passing through the bottom chamber were stained with crystal violet . ![file] Fig 6 from [Liu et al (2017)] .  The migration and invasion ability of the SK-NEP-1 cells after transfection in each group as detected by the Transwell assay . ![file] Different cell types, different treatments, different authors, same panel. ,
HSP27 is a ubiquitin-binding protein involved in I-kappaBalpha proteasomal degradation
Authors: Arnaud Parcellier
Sandeep Gurbuxani
Daphné Seigneurin-Berny
Aurélie Chantôme
Elise Schmitt
Eric Solary
Saadi Khochbin
Carmen Garrido
Alena Pance
Stéphanie Plenchette
Journal: Molecular and Cellular Biology (2003)
Discipline: MOLECULAR BIOLOGY & GENETICS
Keywords: HSP27; chaperone; apoptosis; ubiquitinated proteins; 26S proteasome
Affiliations: INSERM U517, UFR Médecine et Pharmacie, 21033 Dijon, France., INSERM U517, UFR Médecine et Pharmacie, 21033 Dijon, INSERM U309, Institut Albert Bonniot, Faculté de Médecine, 38706 La Tronche Cedex, France

Abstract:  HSP27 is an ATP-independent chaperone that confers protection against apoptosis through various mechanisms, including a direct interaction with cytochrome c. Here we show that HSP27 overexpression in various cell types enhances the degradation of ubiquitinated proteins by the 26S proteasome in response to stressful stimuli, such as etoposide or tumor necrosis factor alpha (TNF-alpha). We demonstrate that HSP27 binds to polyubiquitin chains and to the 26S proteasome in vitro and in vivo. The ubiquitin-proteasome pathway is involved in the activation of transcription factor NF-kappaB by degrading its main inhibitor, I-kappaBalpha. HSP27 overexpression increases NF-kappaB nuclear relocalization, DNA binding, and transcriptional activity induced by etoposide, TNF-alpha, and interleukin 1beta. HSP27 does not affect I-kappaBalpha phosphorylation but enhances the degradation of phosphorylated I-kappaBalpha by the proteasome. The interaction of HSP27 with the 26S proteasome is required to activate the proteasome and the degradation of phosphorylated I-kappaBalpha. A protein complex that includes HSP27, phosphorylated I-kappaBalpha, and the 26S proteasome is formed. Based on these observations, we propose that HSP27, under stress conditions, favors the degradation of ubiquitinated proteins, such as phosphorylated I-kappaBalpha. This novel function of HSP27 would account for its antiapoptotic properties through the enhancement of NF-kappaB activity. 

Retracted: No

PubPeer comments:
 Figure 6A. Much more similar than expected. ![file] ,
Broad frequency sensitivity and complex neural coding in the larval zebrafish auditory system
Authors: Lena Constantin
Leandro A Scholz
Itia Favre-Bulle
Rebecca E Poulsen
Ethan K Scott
Gilles C Vanwalleghem
Journal: Current Biology (2021)
Discipline: BIOLOGY & BIOCHEMISTRY
Keywords: GCaMP; acoustics; auditory processing; calcium imaging; frequency selectivity
Affiliations: Queensland Brain Institute, The University of Queensland, Brisbane, QLD 4072, Australia., Queensland Brain Institute, The University of Queensland, Brisbane, QLD 4072, Australia; School of Mathematics and Physics, The University of Queensland, Brisbane, QLD 4072, Australia., Queensland Brain Institute, The University of Queensland, Brisbane, QLD 4072, Australia. Electronic address: .

Abstract:  Most animals have complex auditory systems that identify salient features of the acoustic landscape to direct appropriate responses. In fish, these features include the volume, frequency, complexity, and temporal structure of acoustic stimuli transmitted through water. Larval fish have simple brains compared to adults but swim freely and depend on sophisticated sensory processing for survival.1-5 Zebrafish larvae, an important model for studying brain-wide neural networks, have thus far been found to possess a rudimentary auditory system, sensitive to a narrow range of frequencies and without evident sensitivity to acoustic features that are salient and ethologically important to adult fish.6,7 Here, we have combined a novel method for delivering water-borne sounds, a diverse assembly of acoustic stimuli, and whole-brain calcium imaging to describe the responses of individual auditory-responsive neurons across the brains of zebrafish larvae. Our results reveal responses to frequencies ranging from 100 Hz to 4 kHz, with evidence of frequency discrimination from 100 Hz to 2.5 kHz. Frequency-selective neurons are located in numerous regions of the brain, and neurons responsive to the same frequency are spatially grouped in some regions. Using functional clustering, we identified categories of neurons that are selective for a single pure-tone frequency, white noise, the sharp onset of acoustic stimuli, and stimuli involving a gradual crescendo. These results suggest a more nuanced auditory system than has previously been described in larval fish and provide insights into how a young animal's auditory system can both function acutely and serve as the scaffold for a more complex adult system. 

Retracted: No

PubPeer comments:
 I have a few questions regarding stimulus amplitudes (Figure S1): - Hydrophone data are relative to an arbitrary reference. What was the absolute stimulus pressure amplitude in Pascal (or dB re 1 u00b5Pa)? - Accelerometer data are given in units of pressure ( dB re 20 u00b5Pau201d), rather than acceleration (m s^2). Is this a typo? (How can an accelerometer return pressure data?) Can you please provide absolute pressure and acceleration data in SI units? ,
RETRACTED: A novel class of specific Hsp90 small molecule inhibitors demonstrate in vitro and in vivo anti-tumor activity in human melanoma cells
Authors: Tod Smeal
Gerrit Los
Pei-Pei Kung
Pramod P Mehta
Andrea Shen
Min-Jean Yin
Leslie Nguyen
Marlena Walls
Shinji Yamazaki
Michael R Gehring
Journal: Cancer letters (2011)
Discipline: CLINICAL MEDICINE
Keywords: Retracted article; Elsevier Policy; Article Withdrawal; Investigation; Pfizer
Affiliations: Pfizer Worldwide Research and Development, Oncology Research, 10724 Science Center Drive, San Diego, CA 92121, United States.

Abstract:  This article has been retracted: please see Elsevier Policy on Article Withdrawal (http://www.elsevier.com/locate/withdrawalpolicy). This article has been retracted at the request of the Authors. Following an investigation by Pfizer, Figures 2, 5B and 5C appear to be duplications and hence the conclusions in the manuscript cannot be verified. The Authors apologize for this inconvenience. 

Retracted: Yes

PubPeer comments:
null, 
 Retraction notice. https: www.ncbi.nlm.nih.gov pubmed 20926183 , 
null, 
 New upload of figures that disappeared during a PubPeer upgrade.  Concerns about Figure 5B. * Two splices appear to be visible in the left AKT panel (purple arrows). * A mirrored duplication appears to be visible between the left and right AKT panels (salmon boxes). * A duplication appears to be visible within the left Actin panel (green boxes). ![file] , 
  Concerns about Figure 5C. * Several duplications appear to be visible within or between the two AKT panels (teal, purple, and yellow boxes). * A duplication appears to be visible within the left Actin panel (red boxes). Note some features highlighted with red arrows. ![file] ,
Preliminary study of pancreatic cancer associated with Helicobacter pylori infection
Authors: Yefu Liu
Jie Lin
Fulu Ai
Xiangdong Hua
Zhaoqiang Feng
Journal: Cell Biochemistry and Biophysics (2015)
Discipline: BIOLOGY & BIOCHEMISTRY
Keywords: Helicobacter pylori; pancreatic cancer; infection rate; CagA-Hp; risk factors
Affiliations: Department of Hepato-Biliary-Pancreatic Surgery, Liaoning Cancer Hospital & Institute, 44 Xiaoheyan Road, Dadong District, Shenyang, 110042, China, .

Abstract:  Little is known about the relationship about Helicobacter pylori (H. pylori) infection and pancreatic, and this study was set to investigate how H. pylori infection is correlated with pancreatic cancer and provide references for the clinical prevention and treatment of pancreatic cancer. 56 cases of pancreatic cancer patients admitted to the hospital from August 2012 to August 2013 were collected as the observation group. The anti-Hp IgG (H. pylori-specific antibodies), Hp IgM (H. pylori antibodies), and CagA-Hp-IgG (H. pylori serotoxin-associated protein a antibody) in the serum were measured and compared with the related indicators of control group (60 cases of healthy subjects). The H. pylori infection rate was 64.29% in the observation group, and that in the control group was 46.67%. Our results showed that the H. pylori infection rate in the observation group was significantly higher than that in the control group, which was statistically different (P &lt; 0.01). The positive rate of CagA-Hp in the observation group was 38.88, and 21.53% in the control group, for which the observation group was significantly higher than the control group (P &lt; 0.05). The occurrence of H. pylori infection in patients with pancreatic cancer was also positively correlated with the smoking history and the history of chronic pancreatitis (P &lt; 0.05). Helicobacter pylori infection is one of the risk factors for pancreatic cancer, and the patients with positive CagA-Hp have the higher risk, so the prevention and treatment of H. pylori infection would be beneficial for the prevention and treatment of pancreatic cancer. 

Retracted: No

PubPeer comments:
 This paper appears to draw extensively from a previously published paper in a Chinese journal: 10.11816 cn.ni.2014-135064. Example below shows data from Table 1 and 2. *** Table 1 ![file] ![file] *** Table 2 ![file] ![file] ,
Apoptosis of hematopoietic cells induced by growth factor withdrawal is associated with caspase-9 mediated cleavage of Raf-1
Authors: Rudi Beyaert
Xavier Saelens
Geert Van Loo
Peter Vandenabeele
Sigrid Cornelis
Yanik Bruynooghe
Journal: Oncogene (2005)
Discipline: MOLECULAR BIOLOGY & GENETICS
Keywords: Raf-1; apoptosis; hematopoietic cells; IL-3; cleavage
Affiliations: Unit of Molecular Signal Transduction in Inflammation, Department for Molecular Biomedical Research, VIB-Ghent University, Technologiepark 927, B-9052 Ghent-Zwijnaarde, Belgium.

Abstract:  The Raf-1 serine/threonine kinase is a key protein that is implicated in the transmission of many growth and cell survival signals. In the present study we demonstrate that apoptosis of hematopoietic cells induced by IL-3-deprivation is associated with the cleavage of Raf-1, resulting in the separation of the N-terminal regulatory domain and the C-terminal kinase domain. Raf-1 cleavage specifically occurs upon triggering of the mitochondrial death pathway, and coincides with the activation of specific caspases. Moreover, Bcl-2 overexpression or treatment with the caspase inhibitor z-VAD.fmk completely prevented Raf-1 cleavage, whereas caspase inhibition by treatment of cells with Ac-DEVD.fmk or z-IETD.fmk, or CrmA overexpression had no effect. Furthermore, in vitro cleavage studies indicate that caspase-9, which is the apical protease in the mitochondrial death pathway, is able to cleave Raf-1 at position D279. Cell fractionation studies showed that the Raf-1 C-terminal fragment that is generated upon IL-3 withdrawal is localized predominantly to the mitochondria. In addition, constitutive expression of this C-terminal Raf-1 fragment fused to a mitochondrial targeting sequence in Ba/F3 pre-B cells significantly delays apoptosis induced by IL-3 withdrawal. These results suggest an important role for caspase-9 mediated cleavage of Raf-1 in the negative feedback regulation of hematopoietic cell apoptosis induced by growth factor withdrawal. 

Retracted: No

PubPeer comments:
 Figure 6. https: imgur.com YHta8Uy ,
A novel approach of decoding EEG four-class motor imagery tasks via scout ESI and CNN
Authors: Shuyue Jia
Yimin Hou
Lu Zhou
Xiangmin Lun
Journal: Journal of Neural Engineering (2020)
Discipline: NEUROSCIENCE & BEHAVIOR
Keywords: Scout EEG source imaging; Convolutional neural network; Motor imagery tasks; Boundary element method; Weighted minimum norm estimation
Affiliations: School of Automation Engineering, Northeast Electric Power University, Jilin, People's Republic of China.

Abstract:  Objective: To develop and implement a novel approach which combines the technique of scout EEG source imaging (ESI) with convolutional neural network (CNN) for the classification of motor imagery (MI) tasks. Approach: The technique of ESI uses a boundary element method (BEM) and weighted minimum norm estimation (WMNE) to solve the EEG forward and inverse problems, respectively. Ten scouts are then created within the motor cortex to select the region of interest (ROI). We extract features from the time series of scouts using a Morlet wavelet approach. Lastly, CNN is employed for classifying MI tasks. Main results: The overall mean accuracy on the Physionet database reaches 94.5% and the individual accuracy of each task reaches 95.3%, 93.3%, 93.6%, 96% for the left fist, right fist, both fists and both feet, correspondingly, validated using ten-fold cross validation. We report an increase of up to 14.4% for overall classification compared with the competitive results from the state-of-the-art MI classification methods. Then, we add four new subjects to verify the validity of the method and the overall mean accuracy is 92.5%. Furthermore, the global classifier was adapted to single subjects improving the overall mean accuracy to 94.54%. Significance: The combination of scout ESI and CNN enhances BCI performance of decoding EEG four-class MI tasks. 

Retracted: No

PubPeer comments:
 Would you mind providing code on github? ,
Polymer–Drug Nanoparticles Combine Doxorubicin Carrier and Heparin Bioactivity Functionalities for Primary and Metastatic Cancer Treatment
Authors: Qin He
Chunyu Xia
Yayuan Liu
Zhirong Zhang
Ling Mei
Yubei Zhou
Journal: Molecular Pharmaceutics (2017)
Discipline: PHARMACOLOGY & TOXICOLOGY
Keywords: drug delivery; low molecular weight heparin; metastasis; pH sensitive; self-assembly.
Affiliations: Key Laboratory of Drug Targeting and Drug Delivery Systems, West China School of Pharmacy, Sichuan University, No. 17, Block 3, Southern Renmin Road, Chengdu 610041, China

Abstract:  Here, a biocompatible amphiphilic copolymer of low molecular weight heparin (LMWH) and doxorubicin (DOX) connected by an acid-sensitive hydrazone bond for enhanced tumor treatment efficacy and safety has been designed and tested. The conjugate combines DOX delivery with LMWH antimetastatic capabilities. After the nanoparticles reach the tumor site, the acidic tumor microenvironment triggers the breakage of the hydrazone bond releasing DOX from the nanoparticles, which results in an increase in the cellular uptake and enhanced in vivo antitumor efficacy. A 3.4-fold and 1.5-fold increase in tumor growth inhibition were observed compared to the saline-treated control group and free DOX treated group, respectively. The LMWH-based nanoparticles effectively inhibited interactions between tumor cells and platelets mediated by P-selectin reducing metastasis of cells in both in vitro and in vivo models. The improved safety and therapeutic effect of LMWW-DOX nanoparticles offers new potential for tumor therapy. 

Retracted: No

PubPeer comments:
 Fig. 4C LMWH and DOX overlapped with dimension adjustment ![file] In the entire figure 4: ![file] ,
Stickler syndrome. Report of a second Australian family
Authors: K Kozlowski
G Turner
Journal: Pediatric radiology (1975)
Discipline: CLINICAL MEDICINE
Keywords: Stickler Syndrome; hereditary; progressive; arthro-ophthalmopathy; dominant gene

Abstract:  Three cases of Stickler Syndrome (hereditary progressive arthro-ophthalmopathy) in a family are described. This disease is caused by a dominant gene with incomplete penetrance, and shows variability in its symptomatology and clinical and radiographic findings among members of the same families. The radiographic appearances, although seldom diagnostic, are often suggestive of the disease or supportive in doubtful cases. 

Retracted: Yes

PubPeer comments:
 Retracted on 10 July 2020. See for backgrounds https: retractionwatch.com 2020 07 23 why-did-a-journal-suddenly-retract-a-45-year-old-paper-over-lack-of-informed-consent ,