PReD-Bench/PRed-Bench huggingface dataset:
Controlled release calcium silicate based floating granular delivery system of ranitidine hydrochloride
Authors: Govind P Agrawal
Ashish K Jain
Sunil K Jain
Awesh Yadav
Journal: Current Drug Delivery (2006)
Discipline: PHARMACOLOGY & TOXICOLOGY
Keywords: floating granular delivery system; calcium silicate; ranitidine hydrochloride; hydroxypropyl methylcellulose K4M; ethylcellulose
Affiliations: Department of Pharmaceutical Sciences, Dr. Hari Singh Gour Vishwavidyalaya, Sagar, India.

Abstract:  The objective of the present investigation was to prepare and evaluate floating granular delivery system consisting of (i) calcium silicate (CS) as porous carrier; (ii) ranitidine hydrochloride (RH), an anti-ulcer agent; and (iii) hydroxypropyl methylcellulose K4M (HPMC) and ethylcellulose (EC) as matrix forming polymers. The effect of various formulation and process variables on the particle morphology, particle size, micromeritic properties, percent drug content, in vitro floating behavior, and in vitro drug release from the floating granules was studied. The scanning electron microscopy (SEM) of granules revealed that that more pores of CS in secondary coated granules (SCG) were covered by the polymer film than those in primary coated granules (PCG). The formulation demonstrated favorable in vitro floating and drug release characteristics. The in vivo evaluation for the determination of pharmacokinetic parameters was performed in albino rats. Higher plasma concentration was maintained throughout the study period from the floating granules of RH. The enhanced bioavailability and elimination half-life observed in the present study may be due to the floating nature of the dosage form. The results suggested that CS is a useful carrier for the development of floating and sustained release preparations. 

Retracted: No

PubPeer comments:
 Fig 5 and Table 2: ![file] Table 2 and Fig 4 from [Jain et al (2008)] ![file] The latter paper does specify the number of albino rats in each group as 3, so it is not a complete duplicate publication. , 
 Figs 3 and 4: ![file] Figs 2 and 3 from Jain et al (2008): ![file] These appear to be reporting data from the same experiment, except that cumulative *in-vitro* drug release progresses from ~25% to ~70% in the present Fig 4, but from ~25% to ~50% in the 2008 Fig 3. Why the change in scale? ,
Multiple attribute group decision-making based on interval-valued q-rung orthopair uncertain linguistic power Muirhead mean operators and linguistic scale functions
Authors: Jun Wang
Shifeng Liu
Yuan Xu
Journal: PLoS ONE (2021)
Discipline: Multidisciplinary
Keywords: Fuzzy set theory; MAGDM; interval-valued q-rung orthopair fuzzy sets; IVq-ROFSs; interval-valued q-rung orthopair uncertain linguistic sets
Affiliations: School of Economics and Management, Beijing Jiaotong University, Beijing, China., School of Economics and Management, Beijing University of Chemical Technology, Beijing, China.

Abstract:  Fuzzy set theory and its extended form have been widely used in multiple-attribute group decision-making (MAGDM) problems, among which the interval-valued q-rung orthopair fuzzy sets (IVq-ROFSs) got a lot of attention for its ability of capturing information denoted by interval values. Based on the previous studies, to find a better solution for fusing qualitative quantization information with fuzzy numbers, we propose a novel definition of interval-valued q-rung orthopair uncertain linguistic sets (IVq-ROULSs) based on the linguistic scale functions, as well as its corresponding properties, such as operational rules and the comparison method. Furthermore, we utilize the power Muirhead mean operators to construct the information fusion method, and provide a variety of aggregation operators based on the proposed information description environment. A model framework is constructed for solving the MAGDM problem utilizing the proposed method. Finally, we illustrate the performance of the new method and investigate its advantages and superiorities through comparative analysis. 

Retracted: No

PubPeer comments:
 This paper presents a generalization of the results in the paper (doi: 10.1109 access.2020.3026474) The term $$(s_{theta}, [a,b], [c,d])$$ is generalized to $$([s_{theta},s_{tau}], [a,b], [c,d])$$ and the case $q=2$ is generalized to the general scenario of $q$ being an integer. However, it is flawed at best according to the comment on https: pubpeer.com publications 65E7240FCA5E1E54F2B91FB074E34B A decision making theory based on such notions makes no sense. ![file] ,
Down-regulation of miR-675-5p contributes to tumor progression and development by targeting pro-tumorigenic GPR55 in non-small cell lung cancer
Authors: Xiyun Deng
Dan He
Chunfang Zhang
Wei Chen
Chaojun Duan
Yang Gao
Jun Wang
Bin Li
Yanwu Zhou
Zhuchu Chen
Jidong Hong
Bin Shan
Journal: Molecular Cancer (2015)
Discipline: MOLECULAR BIOLOGY & GENETICS
Keywords: microRNAs; miR-675-5p; non-small cell lung cancer; proliferation; invasion
Affiliations: Key Laboratory of Cancer Proteomics of Chinese Ministry of Health, Institute of Medical Sciences, Xiangya Hospital, Central South University, Xiangya Road 87th, Changsha, 410008, Hunan, PR China. ., College of Medical Sciences, Washington State University Spokane, 412 E.Spokane Falls Boulevard, Spokane, WA, 99202, USA. ., Faculty of Basic Medical Sciences, College of Medicine, Hunan Normal University, Changsha, 410013, PR China. .

Abstract:  Background: microRNAs are small noncoding RNAs that modulate a variety of cellular processes by regulating multiple targets, which can promote or inhibit the development of malignant behaviors. Accumulating evidence suggests that miR-675-5p plays important roles in human carcinogenesis. However, its precise biological role remains largely elusive. This study examined the role of miR-675-5p in non- small cell lung cancer (NSCLC). Methods: The expression of miR-675-5p was analyzed by real-time quantitative PCR (qRT-PCR). The effect of miR-675-5p on proliferation was evaluated through MTT and colony formation assays, and cell migration and invasion were evaluated through transwell assays. The expression of target proteins and downstream molecules was analyzed by western blotting and immunohistochemical staining. The luciferase reporter assay was used to assess the target genes of miR-675-5p in non-small cell lung cancer cells. Results: The expression levels of miR-675-5p in NSCLC tissues were significantly reduced compared to those in adjacent non-cancerous tissues (P &lt; 0.001). The expression of miR-675-5p in patients with non-small cell lung cancer had a negative correlation with lymph node metastasis (P &lt; 0.01) and TNM stage (P &lt; 0.05). Down-regulation of miR-675-5p promoted cell growth, proliferation, colony formation, invasion and migration, and promoted the tumorigenicity graft growth of nude mice in vivo (P &lt; 0.01); whereas up-regulation of miR-675-5p had the contrary effects. The luciferase reporter assay showed that GPR55 was a direct target gene of miR-675-5p. Overexpression of miR-675-5p can lead to the down-regulation of GPR55 and its signaling pathway, whereas the effect can be reversed by down-regulation of miR-675-5p expression. Conclusions: miR-675-5p functions as a novel tumor suppressor in NSCLC and the anti-oncogenic activity may involve its inhibition of the target gene GPR55. These findings suggest the possibility for miR-675-5p as a therapeutic target in NSCLC. 

Retracted: No

PubPeer comments:
 I have some concerns about figure 3: there appear to be overlaps between different treatments ![file] , 
 Figure 6: ![file] ,
Mitochondrial TCA cycle metabolites control physiology and disease
Authors: Navdeep S Chandel
Inmaculada Martínez-Reyes
Journal: Nature Communications (2020)
Discipline: Multidisciplinary
Keywords: Mitochondria; signaling organelles; cellular functions; cell fate; TCA cycle intermediates
Affiliations: Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA., Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA. .

Abstract:  Mitochondria are signaling organelles that regulate a wide variety of cellular functions and can dictate cell fate. Multiple mechanisms contribute to communicate mitochondrial fitness to the rest of the cell. Recent evidence confers a new role for TCA cycle intermediates, generally thought to be important for biosynthetic purposes, as signaling molecules with functions controlling chromatin modifications, DNA methylation, the hypoxic response, and immunity. This review summarizes the mechanisms by which the abundance of different TCA cycle metabolites controls cellular function and fate in different contexts. We will focus on how these metabolites mediated signaling can affect physiology and disease. 

Retracted: No

PubPeer comments:
 u03b1-ketoglutarate In the context of the review, it is important to add that u03b1-ketoglutarate inhibits ATP-synthase which has a number of important implications for cell energy balance, signaling and longevity: Chin, R., Fu, X., Pai, M. et al. The metabolite u03b1-ketoglutarate extends lifespan by inhibiting ATP synthase and TOR. Nature 510, 397u2013401 (2014). https: doi.org 10.1038 nature13264 ,
<p>Ultrasound-microbubbles-mediated microRNA-449a inhibits lung cancer cell growth via the regulation of Notch1</p>
Authors: Lingwu Meng
Shaofei Yuan
Zongxiao ShangGuan
Renguo Zhao
Linjia Zhu
Journal: OncoTargets and Therapy (2019)
Discipline: CLINICAL MEDICINE
Keywords: H1299; Notch1; lung cancer; microRNA-449a; ultrasound-mediated microbubbles.
Affiliations: Department of Minimally Invasive Therapy, First People's Hospital of Shangqiu, Shangqiu 476100, People's Republic of China., Department of Thoracic Oncology, The Third Affiliated Hospital of Wenzhou Medical University, Ruian, Zhejiang Province 325200, People's Republic of China.

Abstract:  Background: The application of gene-loaded microbubbles (MBs) combined with ultrasound that results in increased delivery efficiency may be an excellent method of gene delivery. This study aimed to discuss the effects of ultrasound-MB-mediated microRNA (miR)-449a on lung cancer (LC) development by targeting Notch1. Methods: Initially, miR-449a expression in LC tissues, paracancerous tissues, LC cell lines, and lung epithelial cells was detected and its association with LC patients' clinical characteristics was analyzed. The gain-of-function studies were performed to probe the roles of miR-449a and ultrasound-MB-mediated miR-449a in LC progression. Then, RT-qPCR combined with Western blot analysis was applied to verify the levels of miR-449a, Notch1, proliferation- and apoptosis-related proteins. Moreover, xenograft tumors in nude mice were also applied for in vivo experiments. Results: Poorly expressed miR-449a was observed in LC, and its expression was associated with clinical staging, differentiation and lymph node metastasis of LC patients. Overexpression of miR-449a suppressed LC cell proliferation and promoted G2/M arrest and apoptosis. Ultrasound-MB-mediated miR-449a strengthened inhibitory effects of miR-449a on cell growth and resistance to apoptosis. miR-449a inhibited H1299 cell activity by targeting Notch1. Conclusion: Our data supported that miR-449a overexpression inhibited LC cell growth, and ultrasound-MB-mediated miR-449a reinforced the repressive effects of miR-449a on LC progression. This investigation may offer new insight for LC treatment. 

Retracted: No

PubPeer comments:
 Fig 7E.  H1299 apoptosis was determined by flow cytometry . ![file] Panels are the same in their left-hand quadrants. , 
 Fig 5C.  Relative Ki67-positive rate measured by immunohistochemistry, the brown events indicating Ki67 positive and blue events indicating negative. Repeated area is marked. ![file] Can the authors reassure us that no other areas are repeated within or between panels? ,
Evidence that TNF-TNFR1-TRADD-TRAF2-RIP-TAK1-IKK pathway mediates constitutive NF-kappaB activation and proliferation in human head and neck squamous cell carcinoma
Authors: B B Aggarwal
D G Jackson-Bernitsas
H Ichikawa
Y Takada
B G Darnay
X L Lin
M M Chaturvedi
J N Myers
Journal: Oncogene (2007)
Discipline: MOLECULAR BIOLOGY & GENETICS
Keywords: NF-kappaB; HNSCC; activation; IkappaBalpha; IKK
Affiliations: Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.

Abstract:  Constitutively activated nuclear factor-kappaB (NF-kappaB) has been associated with a variety of aggressive tumor types, including head and neck squamous cell carcinoma (HNSCC); however, the mechanism of its activation is not fully understood. Therefore, we investigated the molecular pathway that mediates constitutive activation of NF-kappaB in a series of HNSCC cell lines. We confirmed that NF-kappaB was constitutively active in all HNSCC cell lines (FaDu, LICR-LON-HN5 and SCC4) examined as indicated by DNA binding, immunocytochemical localization of p65, by NF-kappaB-dependent reporter gene expression and its inhibition by dominant-negative (DN)-inhibitory subunit of NF-kappaB (IkappaBalpha), the natural inhibitor of NF-kappaB. Constitutive NF-kappaB activation in HNSCC was found to be due to constitutive activation of IkappaBalpha kinase (IKK); and this correlated with constitutive expression of phosphorylated forms of IkappaBalpha and p65 proteins. All HNSCC showed the expression of p50, p52, p100 and receptor-interacting protein; all linked with NF-kappaB activation. The expression of constitutively active NF-kappaB in HNSCC is mediated through the tumor necrosis factor (TNF) signaling pathway, as NF-kappaB reporter activity was inhibited by DN-TNF receptor-associated death domain (TRADD), DN-TNF receptor-associated factor (TRAF)2, DN-receptor-interacting protein (RIP), DN-transforming growth factor-beta-activated kinase 1 (TAK1), DN-kappa-Ras, DN-AKT and DN-IKK but not by DN-TRAF5 or DN-TRAF6. Constitutive NF-kappaB activation was also associated with the autocrine expression of TNF, TNF receptors and receptor-activator of NF-kappaB and its ligand in HNSCC cells but not interleukin (IL)-1beta. All HNSCC cell lines expressed IL-6, a NF-kappaB-regulated gene product. Furthermore, treatment of HNSCC cells with anti-TNF antibody downregulated constitutively active NF-kappaB, and this was associated with inhibition of IL-6 expression and cell proliferation. Our results clearly demonstrate that constitutive activation of NF-kappaB is mediated through the TRADD-TRAF2-RIP-TAK1-IKK pathway, making TNF a novel target in the treatment of head and neck cancer. 

Retracted: No

PubPeer comments:
 Identified by another reader. *** ![file] ,
Overexpression of Fli-1 is associated with adverse prognosis of endometrial cancer
Authors: Jiuwei Cui
Na Wang
Lingyi Zhang
Yan Li
Ailing Li
Tianyang Zhang
Wei Li
Wei Song
Baofeng Jin
Rui Mu
Journal: Cancer Investigation (2015)
Discipline: CLINICAL MEDICINE
Keywords: Endometrial cancer; Fli-1; Prognostic factor; Tumor grade.
Affiliations: a Cancer Center, the First Hospital of Jilin University , Changchun , China., b Institute of Basic Medical Sciences , National Center of Biomedical Analysis , Beijing , China., c Obstetrics and Gynecology , the Second Hospital of Jilin University , Changchun , China.

Abstract:  This study aimed to investigate the expression of Friend leukemia virus integration 1 (Fli-1) and its correlation with the prognosis of endometrial cancer (EC). Thirty-two EC tissue samples were evaluated for Fli-1 expression using immunohistochemistry. Fli-1 showed significantly high expression in EC cells, followed by hyperplasia cells, and was negative in adjacent normal tissues. The high expression of Fli-1 was significantly associated with a high differentiation grade, mutated P53 expression, and histological subtype (p &lt; .05). Downregulation of Fli-1 in AN3CN cells using RNA interference inhibited cell clone formation and proliferation but did not affect apoptosis and migration of the cells. This study provides the first evidence that Fli-1 expression gradually increases in parallel with disease progression, and its overexpression might predict poor prognosis in EC. 

Retracted: No

PubPeer comments:
 All these images do not have scale bar! ![file] ![file] , 
 Dear Dr. Lychnophora Markgravii: Thank you for raising this concern, which we have looked into very carefully and discussed.u00a0In the figure 1 and 2, Fli-1 expression was examined in EC tissues by using immunohistochemistry. Fli-1 is negative in normal tissue, weak positive in endometrial hyperplastic tissue, and highly expressed in EC. Each stained result was evaluated by two pathologists, who lacked the clinical information, independently. The proportion of positive cells ranged 10u2013100% while the intensity of staining was scored as 0 (negative), 1 (weak), 2 (moderate), and 3 (intense). There is no requirement about scale bar of immunohistochemistryu00a0in the Journal of Cancer Investigation. The immunoreactivity score for each sample was taken as a percentage of positive cells multiplied by the intensity of staining. The images were extendedu00a0at the same scale, which does not affect the interpretation of the results. Thank you for your attention. Best regardsuff01Wei Song ,
An oligonucleotide probe incorporating the chromophore of green fluorescent protein is useful for the detection of HER-2 mRNA breast cancer marker
Authors: Yaron Shav-Tal
Eli Varon
Bilha Fischer
Verena Böttner
Christian Ducho
Melissa Meng
Abed Saady
Journal: European Journal of Medicinal Chemistry (2019)
Discipline: CHEMISTRY
Keywords: Diagnosis; treatment; breast cancer; mRNA markers; fluorescent oligonucleotide probe
Affiliations: Department of Chemistry, Bar-Ilan University, Ramat-Gan, 52900, Israel., Department of Pharmacy, Pharmaceutical and Medicinal Chemistry, Saarland University, 66123, Saarbrücken, Germany., Faculty of Life Sciences & Institute of Nanotechnology, Bar-Ilan University, Ramat-Gan, 52900, Israel., Department of Chemistry, Bar-Ilan University, Ramat-Gan, 52900, Israel. Electronic address: .

Abstract:  Diagnosis and treatment of breast cancer can be greatly enhanced and personalized based on the quantitative detection of mRNA markers. Here, we targeted the development of a fluorescent oligonucleotide probe to detect specifically the HER-2 mRNA breast cancer marker. We have selected the chromophore of the Green Fluorescent Protein (GFP), 4-hydroxybenzylidene imidazolinone (HBI), as a fluorophore covalently bound to an oligonucleotide probe and potentially capable of intercalating within a probe-mRNA duplex. We first synthesized the two-ring scaffold of the HBI chromophore 5 and coupled it to 2'-deoxyuridine at C5-position via a 7-atom-spacer, to give 4. Indeed, in the highly viscous glycerol used to mimic the reduced conformational flexibility of the intercalated HBI, chromophore 4 displayed a quantum yield of 0.29 and brightness of 20600 M-1cm-1, while no fluorescent signal was observed in methanol. Next, we synthesized a 20-mer oligonucleotide probe incorporating 4 at position 6 (5'-CCCGTUTCAACAGGAGTTTC-3'), ONHBI, targeting nucleotides 1233-1253 of HER-2 mRNA. A 16-fold enhancement of ONHBI emission intensity upon hybridization with the complementary RNA vs that of the oligonucleotide probe alone indicated the presence of target oligonucleotide and proved the intercalation of the chromophore (quantum yield 0.52; brightness 23500 M-1cm-1). Even more, an 11-fold enhancement of ONHBI emission (quantum yield 0.50; brightness 23200 M-1cm-1) was observed when the probe was mixed with total RNA extract from a human cell line that has high levels of HER2 mRNA expression. Thus, we propose ONHBI as a promising probe potentially useful for the sensitive and specific detection of HER2 mRNA breast cancer marker. 

Retracted: No

PubPeer comments:
 Figure 4: ASCs transduced with AAV2 and AAV6 appear to show the same image, albeit with different colour contrast. I ve added a contrast adjusted comparison with coloured shapes below. Would the authors please comment? ![file] ,
Effects of ranolazine on cardiac function in rats with heart failure
Authors: Z-Q Yu
H Li
G-T Wang
X-N He
Journal: European review for medical and pharmacological sciences (2019)
Discipline: PHARMACOLOGY & TOXICOLOGY
Keywords: ranolazine; cardiac function; myocardial apoptosis; heart failure; AKT phosphorylation
Affiliations: Daqing Campus of Harbin Medical University, Daqing, China. .

Abstract:  Objective: To investigate the effects of ranolazine on the cardiac function and myocardial apoptosis in rats with heart failure and its possible mechanisms. Materials and methods: Thirty Wistar rats were randomly divided into sham operation (negative control; NC), chronic heart failure (CHF), and ranolazine groups. Suprarenal abdominal aortic coarctation was used to induce CHF in rats. Five weeks later, rats in the ranolazine group received ranolazine (50 mg/kg) daily, whereas those in the CHF group received normal saline. After 4 weeks, changes in hemodynamic parameters, cardiac structure and pathology, myocardial apoptosis, and protein expression were assessed. Results: The left ventricular end-diastolic pressure (LVEDP) significantly increased in the CHF group; whereas the maximal rate of left ventricular pressure rise and fall (±dp/dtmax) decreased, compared to those in the NC group. Ranolazine significantly reduced LVEDP and increased ±dp/dtmax (p&lt;0.01), compared to those in the CHF group. Severe impairment of cardiomyocytes was observed in the CHF group with evident inflammation; however, ranolazine reversed these deficits. Rats in the CHF group exhibited an increase in TUNEL-positive cells, which was inhibited by ranolazine, where the apoptotic index significantly decreased in ranolazine-treated rats (p&lt;0.01). Also, ranolazine downregulated caspase-9 expression and upregulated pAKT and Bcl-2 expression in rat cardiomyocytes. Moreover, ranolazine significantly inhibited myocardial apoptosis and caspase-9 expression, promoted AKT phosphorylation, and upregulated pAKT and Bcl-2 expression in vitro, compared to those in the control group (p&lt;0.001). LY294002 inhibited ranolazine-induced suppression of myocardial apoptosis (p&lt;0.001). Conclusions: Ranolazine improved cardiac function and inhibited myocardial apoptosis in rats with CHF, which could be attributed to the regulation of AKT phosphorylation. 

Retracted: No

PubPeer comments:
 Figure 2.  Myocardial apoptosis in rats of all groups, visualized by TUNEL staining (400u00d7). A, NC group; B, CHF model group; C, ranolazine group . Repeated nuclei within 2B. ![file] ,
RETRACTED ARTICLE: The effect of soil nutrients and moisture during ontogeny on apparent wood density of Eucalyptus grandis
Authors: Vinicius Resende Castro
Antonio José Vinha Zanuncio
José Cola Zanuncio
Mario Tommasiello Filho
Paula Gabriella Surdi
Roger Chambi-Legoas
Journal: Scientific Reports (2020)
Discipline: Multidisciplinary
Keywords: soil nutrients; water availability; wood properties; Eucalyptus grandis; apparent wood density
Affiliations: Universidade Federal de Viçosa, Departamento de Engenharia Florestal, Viçosa, 36570-900, Brasil. ., Escola Superior de Agricultura, Luiz de Queiroz, Departamento de Engenharia Florestal, Piracicaba, 13418-900, Brasil., Universidade Federal de Viçosa, Departamento de Engenharia Florestal, Viçosa, 36570-900, Brasil., Universidade Federal de Viçosa, Departamento de Entomologia/BIOAGRO, Viçosa, 36570-900, Brasil., Universidade Federal de Uberlândia, Instituto de Ciências Agrárias-ICIAG, Monte Carmelo, 38500-000, Brasil.

Abstract:  Knowledge of the effect of soil nutrients, such as K and Na and their interaction with water availability, on the growth and wood properties of the eucalypts, is needed to increase the productivity of commercial plantation forests in Brazil that generate employment and taxes. The present study evaluates the apparent wood density (at 12% wood moisture) of Eucalyptus grandis trees at 12, 24, 36 and 48 months old under ambient and lower than ambient (66%) rainfall conditions and K and Na nutrient enrichment. The treatments were two water availability (100 and 66% of the rainfall) and the three nutrient treatments were: K (4.5 kmol/ha), Na (4.5 kmol/ha) and a control (natural conditions). The apparent wood density of samples at breast height (1.3 m) was determined by X-ray densitometry and digital images. Increased nutrients at all four ages and water availability at 36 and 48 months reduced apparent wood density in E. grandis trees, however, effects of nutrients are lower under water availability reduction. The radial profile of wood density was higher in four-year-old trees, but there was radial variation in apparent wood density at all ages. These findings predict that, under water stress, apparent wood density will not decline in commercial E. grandis plantations fertilized with potassium. The use of sodium, as a substitute of potassium, should consider their negative impacts on wood density of Eucalyptus grandis trees. 

Retracted: Yes

PubPeer comments:
 2021 retraction. https: www.nature.com articles s41598-021-91048-y The Editors have retracted this article. After publication it was brought to the Editorsu2019 attention that this article reports data that have previously been published1, specifically the data for 12, 24 and 36 months shown in Table 1, Table 2 and Figure 2. The Editors therefore consider this article to be redundant. All authors agree to this retraction. Reference 1. Castro, V. R. et al. Application effect of potassium, sodium and water availability in the apparent density at 12% humidity of juvenile wood of Eucalyptus grandis trees. Ciu00eanc. Florest. 27, 1017u20131027 (2017). ,
RETRACTED ARTICLE: Strategies for efficient production of heterologous proteins in Escherichia coli
Authors: S Jana
J K Deb
Journal: Applied Microbiology and Biotechnology (2005)
Discipline: BIOLOGY & BIOCHEMISTRY
Keywords: Recombinant proteins; Escherichia coli; therapeutic applications; production; expression vectors
Affiliations: Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology-Delhi, Hauz Khas, New Delhi 110016, India.

Abstract:  In recent years, the number of recombinant proteins used for therapeutic applications has increased dramatically. Production of these proteins has a remarkable demand in the market. Escherichia coli offers a means for the rapid and economical production of recombinant proteins. These advantages, coupled with a wealth of biochemical and genetic knowledge, have enabled the production of such economically therapeutic proteins such as insulin and bovine growth hormone. These demands have driven the development of a variety of strategies for achieving high-level expression of protein, particularly involving several aspects such as expression vectors design, gene dosage, promoter strength (transcriptional regulation), mRNA stability, translation initiation and termination (translational regulation), host design considerations, codon usage, and fermentation factors available for manipulating the expression conditions, which are the major challenges is obtaining the high yield of protein at low cost. 

Retracted: Yes

PubPeer comments:
 This paper was retracted.  Upon investigation carried out according to the Committee on Publication Ethics guidelines, it has been found that the authors have duplicated substantial parts from the following article: Strategies for Achieving High-Level Expression of Genes in Escherichia coli Savvas C. Makrides MICROBIOLOGICAL REVIEWS, Sept. 1996, p. 512u2013538 Vol. 60, No. 3 Copyright u00a91996, American Society for Microbiology In particular the authors duplicated (1) Fig. 1 (incl. legend) (2) The subchapter u201cTranslational regulationu201d (3) The subchapter u201cmRNA stabilityu201d As it was not possible to contact the authors the retraction had to be executed without their approval. https: link.springer.com article 10.1007%2Fs00253-014-5822-4 I commented here so that this paper shows up using the browser extension. ,
MiR-122 regulates cell apoptosis and ROS by targeting DJ-1 in renal ischemic reperfusion injury rat models
Authors: X-H Qu
K Zhang
Journal: European review for medical and pharmacological sciences (2020)
Discipline: PHARMACOLOGY & TOXICOLOGY
Keywords: research misconduct; MiR-122; cell apoptosis; ROS; DJ-1
Affiliations: Department of Kidney Medicine, Affiliated Hospital of Jining Medical University, Jining, Shandong, China.

Abstract:  Since this article has been suspected of research misconduct and the corresponding authors did not respond to our request to prove originality of data and figures, "MiR-122 regulates cell apoptosis and ROS by targeting DJ-1 in renal ischemic reperfusion injury rat models, by X.-H. Qu, K. Zhang, published in Eur Rev Med Pharmacol Sci 2018; 22 (24): 8830-8838-DOI: 10.26355/eurrev_201812_16651-PMID: 30575925" has been withdrawn. The Publisher apologizes for any inconvenience this may cause. https://www.europeanreview.org/article/16651. 

Retracted: No

PubPeer comments:
 This article has been withdrawn and the link to the PDF has been removed. The journal writes:  *Since this article has been suspected of research misconduct and the corresponding authors did not respond to our request to prove originality of data and figures, u201cMiR-122 regulates cell apoptosis and ROS by targeting DJ-1 in renal ischemic reperfusion injury rat models, by X.-H. Qu, K. Zhang, published in Eur Rev Med Pharmacol Sci 2018; 22 (24): 8830-8838u2013DOI: 10.26355 eurrev_201812_16651u2013PMID: 30575925u201d has been withdrawn. The Publisher apologizes for any inconvenience this may cause. * It is unfortunate, and not according to COPE guideline, that the journal has removed the PDF. Luckily, the PDF was captured by the WayBackMachine, and can be found here: https: web.archive.org web 20200210111107 https: www.europeanreview.org wp wp-content uploads 8830-8838.pdf It appears to be part of the Paper Mill #2, AKA the Paint It Black Paper Mill, described by Smut Clyde on Leonid Schneider s blog For Better Science: https: forbetterscience.com 2020 02 27 dark-satanic-papermills Here is part of Figure 4 as an illustration of the soft-focus Western blots and particular shape of the flow cytometry plots. ![file] ,
Dexamethasone enhances the lung metastasis of breast cancer via a PI3K-SGK1-CTGF pathway
Authors: Yujing Zhang
Huiling Wang
Jia Xu
Pengyi Shi
Hantao Zhang
Lin Cheng
Yiming Li
Shuang Zhang
Jieyan Luo
Yong Zhang
Fuyi Cheng
Hongxin Deng
Na Chen
Lei Dai
Dechao Yu
Jiamei Fu
Yang Yang
Qi Xiong
Gang Shi
Journal: Oncogene (2021)
Discipline: MOLECULAR BIOLOGY & GENETICS
Keywords: Dexamethasone; breast cancer; metastasis; chemotherapy; mouse models
Affiliations: State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, PR China., Department of Biotherapy, Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan, PR China., State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, PR China. .

Abstract:  Dexamethasone (Dex), as a pretreatment agent, is widely used to attenuate the side effects of chemotherapy in breast cancer treatment. However, whether and how Dex affects breast cancer metastasis remain to be furtherly understood. In this study, we established several mouse breast cancer metastatic models to study the effect of Dex in vitro and in vivo. Transwell, Western Blot and RNA interference were applied to study the molecular mechanism of Dex in promoting breast cancer cell migration. Meanwhile, the effect of Dex on lung metastasis of breast cancer in Dex combined with PTX chemotherapy was discussed. Our results confirmed that Dex could promote breast cancer cell metastasis both in vitro and in vivo. Mechanistic studies revealed that this pro-metastatic effect of Dex was mediated by the GR-PI3K-SGK1-CTGF pathway in tumor cells. Ligation of Dex and glucocorticoid receptor (GR) on tumor cells activated the PI3K signaling pathway and upregulated serum glucocorticoid-inducible kinase 1 (SGK1) expression, and then increased the expression of connective tissue growth factor (CTGF) through Nedd4l-Smad2. Moreover, Dex was the leading factor for lung metastasis in a standard regimen for breast cancer treatment with paclitaxel and Dex. Importantly, targeting SGK1 with the inhibitor GSK650394 remarkably reduced lung metastasis in this regimen. Our present data provide new insights into Dex-induced breast cancer metastasis and indicate that SGK1 could be a candidate target for the treatment of breast cancer metastasis. 

Retracted: No

PubPeer comments:
 ![file] Fig S9 B and Fig 5D have duplicates, could the authors make comments. Thanks! ,
Recognition of apoptotic cells by epithelial cells: conserved versus tissue-specific signaling responses
Authors: Angelika Antoni
Wilfred Lieberthal
David S Ucker
Lanfei Feng
Joyce Rauch
Jerrold S Levine
John H Schwartz
Vimal A Patel
Daniel J Lee
Journal: Journal of Biological Chemistry (2010)
Discipline: BIOLOGY & BIOCHEMISTRY
Keywords: apoptosis; phagocytes; macrophages; signaling events; MAPK modules
Affiliations: Section of Nephrology, Department of Medicine, University of Illinois, Chicago, Illinois 60612, USA.

Abstract:  During apoptosis, cells acquire new activities that enable them to modulate the fate and function of interacting phagocytes, particularly macrophages (m). Although the best known of these activities is anti-inflammatory, apoptotic targets also influence m survival and proliferation by modulating proximal signaling events, such as MAPK modules and Akt. We asked whether modulation of these same signaling events extends to epithelial cells, a minimally phagocytic cell type. We used BU.MPT cells, a mouse kidney epithelial cell line, as our primary model, but we also evaluated several epithelial cell lines of distinct tissue origins. Like m, mouse kidney epithelial cells recognized apoptotic and necrotic targets through distinct non-competing receptors, albeit with lower binding capacity and markedly reduced phagocytosis. Also, modulation of inflammatory activity and MAPK-dependent signaling by apoptotic and necrotic targets was indistinguishable in kidney epithelial cells and m. In contrast, modulation of Akt-dependent signaling differed dramatically between kidney epithelial cells and m. In kidney epithelial cells, modulation of Akt was linked to target cell recognition, independently of phagocytosis, whereas in m, modulation was linked to phagocytosis. Moreover, recognition of apoptotic and necrotic targets by kidney epithelial cells elicited opposite responses; apoptotic targets inhibited whereas necrotic targets stimulated Akt activity. These data confirm that nonprofessional phagocytes recognize and respond to dying cells, albeit in a manner partially distinct from m. By acting as sentinels of environmental change, apoptotic and necrotic targets may permit neighboring viable cells, especially non-migratory epithelial cells, to monitor and adapt to local stresses. 

Retracted: No

PubPeer comments:
 Fig 1A, the ERK1 2 and p38 panels (marked with blue boxes) in -EGF and +EGF group were cut and pasted from other WB blots. Sharp margins could be noted. Fig.4D, sharp margins around one band from the Akt panel could be seen. Could the author explain what happened? ![file] ![file] ,
Phylogenetic analyses of Klebsiella species delineate Klebsiella and Raoultella gen. nov., with description of Raoultella ornithinolytica comb. nov., Raoultella terrigena comb. nov. and Raoultella planticola comb. nov
Authors: A Carta
P Rousselier
C Bollet
M Drancourt
Journal: INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY (2001)
Discipline: MICROBIOLOGY
Keywords: phylogenetic relationships; Klebsiella species; Enterobacteriaceae; 16S rRNA; rpoB genes

Abstract:  The phylogenetic relationships of the type strains of 9 Klebsiella species and 20 species from 11 genera of the family Enterobacteriaceae were investigated by performing a comparative analysis of the sequences of the 16S rRNA and rpoB genes. The sequence data were phylogenetically analysed by the neighbourjoining and parsimony methods. The phylogenetic inference of the sequence comparison confirmed that the genus Klebsiella is heterogeneous and composed of species which form three clusters that also included members of other genera, including Enterobacter aerogenes, Erwinia clusters I and II and Tatumella. Cluster I contained the type strains of Klebsiella pneumoniae subsp. pneumoniae, Klebsiella pneumoniae subsp. rhinoscleromatis and Klebsiella pneumoniae subsp. ozaenae. Cluster II contained Klebsiella ornithinolytica, Klebsiella planticola, Klebsiella trevisanii and Klebsiella terrigena, organisms characterized by growth at 10 degrees C and utilization of L-sorbose as carbon source. Cluster III contained Klebsiella oxytoca. The data from the sequence analyses along with previously reported biochemical and DNA-DNA hybridization data support the division of the genus Klebsiella into two genera and one genogroup. The name Raoultella is proposed as a genus name for species of cluster II and emended definitions of Klebsiella species are proposed. 

Retracted: No

PubPeer comments:
 Copy pasted from the Abstract of https: doi.org 10.1016 j.resmic.2021.103851 : (...) Therefore, we propose to reunify Klebsiella and Raoultella to the single genus Klebsiella and reclassify Raoultella electrica as Klebsiella electrica comb. nov. (...) ,
Association Between ApoA-I (Apolipoprotein A-I) Immune Complexes and Adverse Cardiovascular Events—Brief Report
Authors: Arshed Ali Quyyumi
Ayman Samman Tahhan
David Nardo
Vincent J Venditto
David Henson
Journal: Arteriosclerosis Thrombosis and Vascular Biology (2019)
Discipline: CLINICAL MEDICINE
Keywords: antibodies; apolipoprotein A-I; autoantibodies; cardiovascular disease; immunoglobulin G.
Affiliations: From the Department of Pharmaceutical Sciences, University of Kentucky, Lexington (D.H., D.N., V.J.V.)., Division of Cardiology, Emory Clinical Cardiovascular Research Institute, Emory University School of Medicine, Atlanta, GA (A.S.T., A.A.Q.).

Abstract:  Objective: The immune response is linked to the progression of atherosclerotic cardiovascular disease (CVD). Free autoantibodies targeting ApoA-I (apolipoprotein A-I) have been identified as a component of the inflammatory milieu in patients and have a moderate association with CVD progression. Based on the presence of these antibodies and the high concentration of circulating ApoA-I, we hypothesized that antibodies bound to ApoA-I as an immune complex would be predictive of incident adverse CVD outcomes. Approach and Results: The presence of ApoA-I/IgG immune complexes (ICs) in plasma was confirmed by ELISA in 3 subject cohorts. Characterization of the protein components of ApoAI/IgG ICs indicate that ICs are not correlated with total ApoA-I concentration and are enriched in the anti-inflammatory subclass, IgG4, relative to total plasma IgG (&gt;30% versus 6%). In 359 patients with coronary artery disease (CAD), there were 71 incident adverse CVD events (death, myocardial infarction, and stroke) during a median 4.1-year follow-up. In Cox proportional hazard regression analysis, low levels of ApoA-I/IgG ICs were independent predictors of adverse cardiovascular outcomes after adjustment for age, sex, diabetes mellitus, estimated glomerular filtration rate, presence of obstructive CAD, heart failure, total cholesterol, and HDL (high-density lipoprotein) cholesterol (adjusted hazard ratio of 1.90 [95% CI, 1.03-3.49; P=0.038] between the lowest and the highest tertiles). Conclusions: Low levels of ApoA-I/IgG ICs are associated with an increased risk of adverse events in patients with CAD, raising their potential to be used as a biomarker to predict CVD progression. 

Retracted: Yes

PubPeer comments:
 2021 retraction. https: www.ahajournals.org doi pdf 10.1161 ATV.0000000000000141 After publication, the authors identified misinterpreted data that impacts the conclusion of the article that apoliu0002poprotein A-I and IgG immune complexes are inversely associated with disease progression. Although the observed association with disease outcomes remains, the authors have strong evidence that the analyte measured is not apoliu0002poprotein A-I and IgG immune complexes. Therefore, the authors have requested to retract the article. ,
Synthesis and characterization of an octaarginine functionalized graphene oxide nano-carrier for gene delivery applications
Authors: Shahab Faghihi
Rana Imani
Shahriar Hojjati Emami
Journal: Physical Chemistry Chemical Physics (2015)
Discipline: CHEMISTRY
Keywords: gene therapy; cell-penetrating peptides; nano-carrier; gene delivery; octaarginine
Affiliations: Department of Biomedical Engineering, Amirkabir University of Technology, Tehran 15875/4413, Iran, Tissue Engineering and Biomaterials Division, National Institute of Genetic Engineering and Biotechnology, Tehran 14965/161

Abstract:  The success of gene therapy is largely dependent on the development of a gene carrier. Recently cell-penetrating peptides (CPPs) have been employed for enhancing the gene and drug delivery efficacy of nano-particles. The feasibility of octaarginine (R8) functionalized graphene oxide (GO) as a novel nano-carrier for gene delivery is investigated. A DNA plasmid expressing enhanced green fluorescent protein (pEGFP) is used as a model gene to study the R8-GO transfection ability into mammalian cells. R8 peptide is conjugated in different ratios (0.1-1.5 μmol per mg of GO) to carboxylated graphene oxide by a two step amidation process. The process of peptide conjugation is analyzed by Fourier transform infrared (FTIR), atomic force microscopy (AFM), UV-vis spectroscopy and X-ray diffraction (XRD). In order to obtain the highest transfection of pEGFP into the cells, the amount of peptide bound to GO is optimized which is evidenced by dynamic light scattering (DLS), zeta potential, TNBS and gel retardation assays. The cytotoxicity of R8-functionalized GO is also tested by MTT assay. The results confirm the successful attachment of R8 peptide to GO. The AFM and XRD results show a significant increase in the thickness of nano graphene oxide sheets (NGOS) from 0.8 to 2-7 nm as well as an increase in the GO interlying space after the R8-functionalization process. A reduction in nano-carrier stability in both aqueous solution and cell culture media is observed when the amount of peptide is increased to more than 1 μmol mg(-1). Gel electrophoresis analysis shows the highest DNA loading on the peptide functionalized GO at the ratios of 0.5 and 1 μmol mg(-1). As a result, the conjugated peptide sample with a peptide molar ratio of 1 μmol per mg of GO shows the highest conjugational efficiency and EGFP gene expression along with improved dispersibility and biocompatibility. Overall, the findings reveal the importance of peptide density on the surface of NGOS in order to obtain the most efficient cell transfection. It is concluded that the R8-conjugated GO could be a promising nano-carrier for gene delivery with relevance in biotechnology therapeutics and clinical applications. 

Retracted: No

PubPeer comments:
 Figure 3. XRD patterns recorded using copy- paste. ![file] , 
 #1 Also surprisingly similar to the modified graphene-oxide XRDs reported in [ Nano-graphene oxide carboxylation for efficient bioconjugation applications: a quantitative optimization approach (2015)] , by the same authors. ![] ,
LncRNA KCNQ1OT1 facilitates the progression of bladder cancer by targeting MiR-218-5p/HS3ST3B1
Authors: Benkang Shi
Yongzhi Li
Fengming Dong
Bing Liu
Yili Liu
Xingwang Zhu
Journal: Cancer Gene Therapy (2020)
Discipline: CLINICAL MEDICINE
Keywords: Long non-coding RNA; lncRNA; KCNQ1OT1; bladder cancer; miR-218-5p
Affiliations: Department of Urology, The Fourth Affiliated Hospital of China Medical University, Shenyang, 110032, China., Department of Urology, Qilu Hospital of Shandong University, Jinan, 250000, China., Department of Urology, The Fourth Affiliated Hospital of China Medical University, Shenyang, 110032, China. .

Abstract:  Long non-coding RNA (lncRNA) is characterized by biological function in diverse cancers. LncRNA KCNQ1 opposite strand/antisense transcript 1 (KCNQ1OT1) is well acknowledged to regulate various cancers, while its role in bladder cancer remains unclear. In the present study, we aimed at probing into the impact and detailed mechanisms of KCNQ1OT1 in bladder cancer progression. In this study, we demonstrated that KCNQ1OT1 expression in bladder cancer tissues was notably up-regulated compared with in normal adjacent tissues, and KCNQ1OT1 modulated the malignant phenotypes of bladder cancer cells. Moreover, it was validated that KCNQ1OT1 could specifically bind to miR-218-5p and reduce its expression. Overexpressed miR-218-5p would inhibit the proliferation and metastasis of bladder cancer cells while facilitating apoptosis. In terms of Mechanism, Heparan Sulfate-Glucosamine 3-Sulfotransferase 3B1 (HS3ST3B1) was validated as a target gene of miR-218-5p, and could be regulated by KCNQ1OT1 indirectly. In conclusion, KCNQ1OT1 can promote the progression of bladder cancer through regulation of miR-218-5p/HS3ST3B1, which is expected to serve as a new therapeutic target for bladder cancer. 

Retracted: No

PubPeer comments:
 Can the authors please explain how versican (VCAN), a  significant protein of extracellular matrix can be  a prominent cancer drug for GC patients ?! And also why one of the merged micrographs in Figure 4A does not correspond with the single stained micrographs (red staining)? ![file] ![file] ,