PReD-Bench/PRed-Bench huggingface dataset:
The best time to argue about what a replication means? Before you do it
Authors: Timothy M Errington
Brian A Nosek
Journal: Nature (2020)
Discipline: Multidisciplinary
Keywords: Publishing; Research data; Research management.

Abstract: To avoid stalemates and provide lessons, replicators and original researchers must reach agreement on a study design and set out expectations ahead of time. To avoid stalemates and provide lessons, replicators and original researchers must reach agreement on a study design and set out expectations ahead of time.

Retracted: No

PubPeer comments:
 The best time to decide what an original study means? Before you do it. Authors are normally supposed to make clear the relevant independent, dependent variables in their report of a original study, such that anyone choosing to attempt a replication has all the necessary information. Would-be replicators should not be required first to complete negotiations with these authors - who may, moreover, be unwilling or unable to oblige. In putting the burden for clarity and interpretability on the replication stage in other words, Nosek and Errington seem to be giving original studies a huge implicit pass as to clarity and interpretability - their meaning doesn t need to be clarified until and unless someone else decides to replicate. An interesting further implication of this view - perhaps the most interesting - is that *even reviewers and editors* of papers will apparently not to be required to understand the claims of authors enough to potentially perform a replication without entering into new discussions - because if they do understand, why not insist authors provide readers of the article with that same clarity? Are reviewers really to accept papers for publication whose interpretation is not clear to them? Is this really supposed to promote the publication of reliable studies? Very puzzling indeed. , 
 Even more bizarre, the same authors have proposed redefining  replication to mean any study that has a bearing on a published articles  claims. That article  What is replication, has also been commented on. https: pubpeer.com publications E2DFDA0621664BA2517561DE65E71D ,
Measuring the Hubble constant with a sample of kilonovae
Authors: Mattia Bulla
Tim Dietrich
Michael W Coughlin
David A Coulter
Lina Issa
Nelson Christensen
Jack Heinzel
Nandita Khetan
Sarah Antier
Ryan J Foley
Journal: Nature Communications (2020)
Discipline: Multidisciplinary
Keywords: Kilonovae; compact binaries; neutron star; standard sirens; Hubble constant
Affiliations: School of Physics and Astronomy, University of Minnesota, Minneapolis, MN, 55455, USA. ., Division of Physics, Math, and Astronomy, California Institute of Technology, Pasadena, CA, 91125, USA. ., APC, UMR 7164, 10 rue Alice Domon et Léonie Duquet, 75205, Paris, France., Institut für Physik und Astronomie, Universität Potsdam, Haus 28, Karl-Liebknecht-Str. 24/25, 14476, Potsdam, Germany., Nikhef, Science Park 105, 1098 XG, Amsterdam, The Netherlands., Department of Astronomy and Astrophysics, University of California, Santa Cruz, CA, 95064, USA., Artemis, Université Côte d'Azur, Observatoire Côte d'Azur, CNRS, CS 34229, F-06304, Nice Cedex 4, France., Physics and Astronomy, Carleton College, Northfield, MN, 55057, USA., Nordita, KTH Royal Institute of Technology and Stockholm University, Roslagstullsbacken 23, SE-106 91, Stockholm, Sweden., Département de Phyisque, Université Paris-Saclay, ENS Paris-Saclay, 91190, Gif-sur-Yvette, France., Gran Sasso Science Institute (GSSI), I-67100, L'Aquila, Italy.

Abstract:  Kilonovae produced by the coalescence of compact binaries with at least one neutron star are promising standard sirens for an independent measurement of the Hubble constant (H0). Through their detection via follow-up of gravitational-wave (GW), short gamma-ray bursts (sGRBs) or optical surveys, a large sample of kilonovae (even without GW data) can be used for H0 contraints. Here, we show measurement of H0 using light curves associated with four sGRBs, assuming these are attributable to kilonovae, combined with GW170817. Including a systematic uncertainty on the models that is as large as the statistical ones, we find [Formula: see text] and [Formula: see text] for two different kilonova models that are consistent with the local and inverse-distance ladder measurements. For a given model, this measurement is about a factor of 2-3 more precise than the standard-siren measurement for GW170817 using only GWs. 

Retracted: No

PubPeer comments:
 You base your results on analysis of the semi-log relationships as presented in your Figure 3: so-called  Hubble-Lemaitre diagram... . This is claimed by you to be a Hubble-Lemaitre diagram, which is NOT true. There are several fatal errors in your analysis, so your concluding value for H0 is wrong and not useful. For more details please read the comments in https: pubpeer.com publications 74D29B06206B17E658D5558FB4F84D https: pubpeer.com publications 9ECC6F3838DA848551D01DB9DF5E07 , 
 The authors should also read and think about the Hubble-Lemaitre diagram as properly used in this article 10.3847 1538-4357 ab2f73 , 
 Figure 7 of article 10.3847 1538-4357 ab2f73 which properly used the Hubble-Lemaitre method. ,
Inhibition of hepatitis C virus replication by intracellular delivery of multiple siRNAs by nanosomes
Authors: Partha K Chandra
Tarun K Mandal
Tara Ooms
Anup K Kundu
Tong Wu
Sidhartha Hazari
Lili Bao
Gilbert F Morris
Srikanta Dash
Sruti Chandra
Journal: Molecular Therapy (2012)
Discipline: CLINICAL MEDICINE
Keywords: antiviral response; HCV infection; siRNA; nanosome; drug-resistant variants
Affiliations: Department of Pathology and Laboratory Medicine, Tulane University Health Sciences Center, New Orleans, Louisiana 70112, USA.

Abstract:  Sustained antiviral responses of chronic hepatitis C virus (HCV) infection have improved recently by the use of direct-acting antiviral agents along with interferon (IFN)-α and ribavirin. However, the emergence of drug-resistant variants is expected to be a major problem. We describe here a novel combinatorial small interfering RNA (siRNA) nanosome-based antiviral approach to clear HCV infection. Multiple siRNAs targeted to the highly conserved 5'-untranslated region (UTR) of the HCV genome were synthesized and encapsulated into lipid nanoparticles called nanosomes. We show that siRNA can be repeatedly delivered to 100% of cells in culture using nanosomes without toxicity. Six siRNAs dramatically reduced HCV replication in both the replicon and infectious cell culture model. Repeated treatments with two siRNAs were better than a single siRNA treatment in minimizing the development of an escape mutant, resulting in rapid inhibition of viral replication. Systemic administration of combinatorial siRNA-nanosomes is well tolerated in BALB/c mice without liver injury or histological toxicity. As a proof-of-principle, we showed that systemic injections of siRNA nanosomes significantly reduced HCV replication in a liver tumor-xenotransplant mouse model of HCV. Our results indicate that systemic delivery of combinatorial siRNA nanosomes can be used to minimize the development of escape mutants and inhibition of HCV infection. 

Retracted: No

PubPeer comments:
 Figure 6B. * Some panels appear to show areas of overlap, as analyzed via ImageTwin. ![file] , 
 Figure 7E. * Cyan boxes: A small possible overlap between two panels as detected by ImageTwin ![file] , 
 Figures 3A, 3D, and 6C. * Boxes of the same color highlight panels that look similar to each other. Sometimes rotated, mirrored, or squashed. ![file] ,
Light-emitting-diode induced retinal damage and its wavelength dependency in vivo
Authors: Chang-Hao Yang
Gen-Shuh Wang
Li-Ling Lee
David H Sliney
Yu-Man Shang
Journal: International Journal of Ophthalmology (2017)
Discipline: CLINICAL MEDICINE
Keywords: LED light injury; blue light injury; iron; light injury mechanisms; oxidative stress
Affiliations: Institute of Environmental Health, National Taiwan University, Taipei 10051, Taiwan, China., Army Medical Department, Consulting Medical Physicist, Aberdeen Proving Ground, Maryland, MD 21010-5403, USA., Department of Ophthalmology, National Taiwan University School of Medicine, Taipei 10051, Taiwan, China; Department of Ophthalmology, National Taiwan University Hospital, Taipei 10051, Taiwan, China., Green Energy and Environment Research Laboratories, Industrial Technology Research Institute, Chutung, Hsinchu 31040, Taiwan, China.

Abstract:  Aim: To examine light-emitting-diode (LED)-induced retinal neuronal cell damage and its wavelength-driven pathogenic mechanisms. Methods: Sprague-Dawley rats were exposed to blue LEDs (460 nm), green LEDs (530 nm), and red LEDs (620 nm). Electroretinography (ERG), Hematoxylin and eosin (H&amp;E) staining, transmission electron microscopy (TEM), terminal deoxynucleotidyl transferase dUTP nick end labeling (TUNEL), and immunohistochemical (IHC) staining, Western blotting (WB) and the detection of superoxide anion (O2-·), hydrogen peroxide (H2O2), total iron, and ferric (Fe3+) levels were applied. Results: ERG results showed the blue LED group induced more functional damage than that of green or red LED groups. H&amp;E staining, TUNEL, IHC, and TEM revealed apoptosis and necrosis of photoreceptors and RPE, which indicated blue LED also induced more photochemical injury. Free radical production and iron-related molecular marker expressions demonstrated that oxidative stress and iron-overload were associated with retinal injury. WB assays correspondingly showed that defense gene expression was up-regulated after the LED light exposure with a wavelength dependency. Conclusion: The study results indicate that LED blue-light exposure poses a great risk of retinal injury in awake, task-oriented rod-dominant animals. The wavelength-dependent effect should be considered carefully when switching to LED lighting applications. 

Retracted: No

PubPeer comments:
 ![file] ,
Secretion of the recombination α-amylase in Escherichia coli and purification by the gram-positive enhancer matrix (GEM) particles
Authors: Zhijiang Zhou
Qiaozhi Song
Renpeng Du
Ye Han
Fangkun Zhao
Binbin Wang
Journal: International Journal of Biological Macromolecules (2019)
Discipline: BIOLOGY & BIOCHEMISTRY
Keywords: Gram-positive enhancer matrix particles; Purification; Recombination expression; Secretion; α-Amylase.
Affiliations: School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, PR China., School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, PR China. Electronic address: .

Abstract:  α-Amylases are important enzymes in industry. A recombinant α-amylase with a secretion signal peptide and an AcmA tag was expressed in Escherichia coli to improve the yield. The induction concentrations were optimized, and the temperature had a significant influence on soluble expression and secretion. A visible band could be obtained when the induction was conducted at 16 °C. The gram-positive enhancer matrix (GEM) particles could separate and purify the recombinant α-amylase with the AcmA tag, and no visible band could be seen in the culture even after the culture was concentrated ten times. The solution and concentration of the recombinant α-amylase could be adjusted by GEM particles. The recombinant untagged α-amylase was obtained after digestion. The α-amylase was characterized. The recombinant α-amylase was a thermophilic enzyme with a broad pH tolerance. In addition, the enzyme activity of the recombinant α-amylase was independent of Ca2+. The recombinant α-amylase contained the OmpA signal peptide and the AcmA tag and was expressed and purified quickly and easily. 

Retracted: No

PubPeer comments:
 Concerns about images in Figure 1b and 1d. Comparison image includes vertical and horizontal resizing. *** ![file] *** original image ![file] ,
Cefazolin-loaded mesoporous silicon microparticles show sustained bactericidal effect against Staphylococcus aureus
Authors: Bradley K Weiner
Mauro Ferrari
Christopher Loo
Xuewu Liu
Iman K Yazdi
Matthew B Murphy
Ennio Tasciotti
Journal: Journal of tissue engineering (2014)
Discipline: MOLECULAR BIOLOGY & GENETICS
Keywords: Antibiotics; controlled release; drug delivery; mesoporous silicon; microparticles.
Affiliations: Department of Nanomedicine, Houston Methodist Research Institute, Houston, TX, USA ; Department of Biomedical Engineering, University of Houston, Houston, TX, USA., Department of Nanomedicine, Houston Methodist Research Institute, Houston, TX, USA., Department of Nanomedicine, Houston Methodist Research Institute, Houston, TX, USA ; Department of Orthopedic Surgery, Houston Methodist Hospital, Houston, TX, USA.

Abstract:  Cefazolin is an antibiotic frequently used in preoperative prophylaxis of orthopedic surgery and to fight secondary infections post-operatively. Although its systemic delivery in a bulk or bolus dose is usually effective, the local and controlled release can increase its effectiveness by lowering dosages, minimizing total drug exposure, abating the development of antibiotic resistance and avoiding the cytotoxic effect. A delivery system based on mesoporous silicon microparticles was developed that is capable of efficiently loading and continuously releasing cefazolin over several days. The in vitro release kinetics from mesoporous silicon microparticles with three different nanopore sizes was evaluated, and minimal inhibitory concentration of cefazolin necessary to eliminate a culture of Staphylococcus aureus was identified to be 250 µg/mL. A milder toxicity toward mesenchymal stem cells was observed from mesoporous silicon microparticles over a 7-day period. Medium pore size-loaded mesoporous silicon microparticles exhibited long-lasting bactericidal properties in a zone inhibition assay while they were able to kill all the bacteria growing in suspension cultures within 24 h. This study demonstrates that the sustained release of cefazolin from mesoporous silicon microparticles provides immediate and long-term control over bacterial growth both in suspension and adhesion while causing minimal toxicity to a population of mesenchymal stem cell. Mesoporous silicon microparticles offer significant advantageous properties for drug delivery applications in tissue engineering as it favorably extends drug bioavailability and stability, while reducing concomitant cytotoxicity to the surrounding tissues. 

Retracted: No

PubPeer comments:
 Figure 5 appears to have a repeated image, when flipped horizontally and vertically. *** ![file] *** Full figure ![file] ,
The mechanisms of regulation of Hdm2 protein level by serum growth factors
Authors: Anna Phillips
Jeremy P Blaydes
Chris J Jones
Journal: FEBS letters (2006)
Discipline: BIOLOGY & BIOCHEMISTRY
Keywords: Cell cycle progression; serum growth factors; Hdm2; p53-dependent transcription; anti-proliferative genes
Affiliations: Cancer Sciences Division, Somers Cancer Research Building, School of Medicine, University of Southampton, MP 824, Southampton General Hospital, Southampton SO16 6YD, UK.

Abstract:  Cell cycle progression in response to serum growth factors is dependent on the expression of functional Hdm2 (Mdm2), which inhibits p53-dependent transcription of anti-proliferative genes. In a well characterised non-transformed human fibroblast model, growth factors induce the expression of Hdm2 with rapid kinetics. Here we dissect the mechanistic basis for this critical response. In contrast to previous studies in which components of the growth factor signalling pathways were overexpressed, hdm2 mRNA expression is not induced with immediate-early kinetics in these cells. Rather, the elevated Hdm2 protein levels which follow growth factor stimulation are primarily a consequence of phosphatidylinositol-3 kinase-dependent stabilisation of the Hdm2 protein combined with a global increase in protein synthesis. 

Retracted: No

PubPeer comments:
 Figure 3C. Much more similar than expected. ![file] ,
RETRACTED ARTICLE: Circular RNA ABCB10 promotes hepatocellularcarcinoma progression by increasing HMG20A expression by spongingmiR-670-3p
Authors: Dunwei Wang
Yu Fu
Limin Cai
Xuexue Lei
Journal: Cancer Cell International (2019)
Discipline: MOLECULAR BIOLOGY & GENETICS
Keywords: HMG20A; Liver cancer; Proliferation; circABCB10; miR-670-3p.
Affiliations: 1Department of Hepatobiliary and Pancreas Surgery, The First Hospital of Jilin University, Changchun, 130021 Jilin People's Republic of China., 2Department of Anesthesiology, The First Hospital of Jilin University, No. 71 Xinmin Street, Changchun, 130021 Jilin People's Republic of China.

Abstract:  Background/aims: The dysregulation of circABCB10 may play an critical role in tumor progression. However, its function in liver cancer (HCC) is still unclear. Therefore, this experimental design is based on circABCB10 to explore the pathogenesis of HCC. Methods: The expression of circABCB10 and miR-670-3p in HCC tissues was detected by RT-qPCR. CCK-8, Brdu incorporation, colony formation and transwell assays were used to determine the effect of circABCB10 on HCC cell proliferation and migration. Target gene prediction and screening, luciferase reporter assays were used to validate downstream target genes of circABCB10 and miR-670-3p. HMG20A expression was detected by RT-qPCR and Western blotting. The tumor changes in mice were detected by in nude mice. Results: CircABCB10 was significantly increased in HCC tissues and cell lines, and high CircABCB10 expression was directly associated with low survival in HCC patients. Silencing of circABCB10 inhibited proliferation and invasion of hepatocellular carcinoma. In addition, circABCB10 acted as a sponge of miR-670-3p to upregulate HMG20A expression. In addition, overexpression of miR-670-3p or knockdown of HMG20A reversed the carcinogenic effects of circABCB10 in HCC. There was a negative correlation between the expression of circABCB10 and miR-670-3p, and a positive correlation between the expression of circABCB10 and HMG20A in HCC tissues. Conclusion: circABCB10 promoted HCC progression by modulating the miR-670-3p/HMG20A axis, and circABCB10 may be a potential therapeutic target for HCC.Trail registration JL1H384739, registered at Sep 09, 2014. 

Retracted: Yes

PubPeer comments:
 https: cosmocoffee.info viewtopic.php?f=2 t=3293 p=9012 sid=b54746c8486443e45cf0018447acf98c#p9012 ,
The v-Jun point mutation allows c-Jun to escape GSK3-dependent recognition and destruction by the Fbw7 ubiquitin ligase
Authors: Susanne Schlisio
Jianping Jin
William G Kaelin Jr
Wenyi Wei
J Wade Harper
Journal: Cancer Cell (2005)
Discipline: MOLECULAR BIOLOGY & GENETICS
Keywords: c-Jun; c-Myc; oncogenic transcription factors; polyubiquitination; GSK3
Affiliations: Department of Medical Oncology, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA.

Abstract:  The c-Jun and c-Myc oncogenic transcription factors are highly unstable proteins due to polyubiquitination. Similar to c-Myc, we report here that phosphorylation of c-Jun by GSK3 creates a high-affinity binding site for the E3 ligase Fbw7, which targets c-Jun for polyubiquitination and proteasomal degradation. In keeping with this, we found that c-Jun levels were inversely related to GSK3 activity in mammalian cells that had entered the cell cycle. Importantly, phosphorylation of c-Jun by GSK3 requires a priming phosphorylation event at Ser-243. Ser-243 is mutated to phenylalanine in v-Jun and allows it to escape recognition by Fbw7. These findings explain the enhanced stability and oncogenicity of v-Jun relative to its cellular counterpart and reveal that GSK3 and Fbw7 coordinately regulate c-Jun and c-Myc. 

Retracted: No

PubPeer comments:
 Figure 3. Undisclosed splices. ![file] ,
pH-sensitive metal-phenolic network capsules for targeted photodynamic therapy against cancer cells
Authors: Wei Wei
Zhenzhen Wei
Peicheng Luo
Yuanqing Wei
Songqin Liu
Journal: Artificial Cells Nanomedicine and Biotechnology (2017)
Discipline: BIOLOGY & BIOCHEMISTRY
Keywords: Photodynamic therapy; cancer targeting drug delivery; haematoporphyrin monomethyl ether; polyethylene glycol metal-phenolic network.
Affiliations: Ministry of Education, Key Laboratory of Environmental Medicine Engineering, Jiangsu Engineering Laboratory of Smart Carbon-Rich Materials and Device, School of Chemistry and Chemical Engineering, Southeast University, Nanjing, P. R. China

Abstract:  Photodynamic therapy (PDT) is an effective and promising method for cancer treatment, which is proposed for more than one century. However, the specific delivery of photosensitizer to target carcinoma cells to reduce the side effect is still a great challenge. This work provides a strategy to deliver photosensitizers to cancer cells by utilizing pH-sensitive polyethylene glycol metal-phenolic network (PEG-MPN) capsules to encapsulate haematoporphyrin monomethyl ether (HMME). With the assistance of folic acid (FA), HMME-doped PEG-MPN capsules (MPN@HMMEs) accumulate in carcinoma cells selectively followed by releasing HMME in the lysosomes because of the physiologically relevant acidic pH environment. From the fluorescent ratiometric sensing and reactive oxygen species (ROS) regionality distribution of MPN@HMMEs, we demonstrated the encapsulated photosensitizers are diffused from lysosomes to cytoplasm. Under irradiation at 638 nm laser, ROS generated from the photosensitizers induced cancer cells undergoing apoptosis while normal cells survive. Therefore, MPN@HMME could be applied as a new strategy for targeted PDT against cancer and PEG-MPN capsules are expected to be general carries for drug delivering. 

Retracted: No

PubPeer comments:
 Figure 4. * Blank and Ni 2+ appear to be showing the same spectrum * Ba2+ and Cr3+ appear to be showing the same spectrum * Mg2+ and Ti3+ appear to be showing the same spectrum ![file] , 
 #1 Dear Elisabeth M Bik, We thank you for pointing out this. This issue has been brought to our attention. We are seriously checking all the raw data related to this article and will respond as soon as possible. Sincerely Bingyang , 
 September 17, 2021, correction: https: pubs.rsc.org en content articlelanding 2021 NR D1NR90196F  The authors regret that in the original manuscript, Fig. 4C contained some errors caused by duplicate spectra data being incorrectly inserted into the figure. Three incorrect spectra were displayed for Ni2+, Ba2+and Ti3+. A correct version of Fig. 4C with the associated caption is as displayed below: {...} The Royal Society of Chemistry apologises for these errors and any consequent inconvenience to authors and readers. I thank the authors, journal, and publisher for correcting this. ,
Retracted : miR‐124a enhances therapeutic effects of bone marrow stromal cells transplant on diabetic nephropathy‐related epithelial‐to‐mesenchymal transition and fibrosis
Authors: Xiaojun Cai
Fengyan Hou
Xuling Wang
Lei Wang
Journal: Journal of Cellular Biochemistry (2020)
Discipline: MOLECULAR BIOLOGY & GENETICS
Keywords: BMSCs; DN; EMT; miR-124a; podocytes
Affiliations: Department of Endocrinology, Heilongjiang Provincial Academy of Chinese Medical Science, Harbin, Heilongjiang, China.

Abstract:  Background: Epithelial-to-mesenchymal transition (EMT) has been gradually considered as one of the major pathways that causes the production of interstitial myofibroblasts in diseased kidneys. Materials and methods: The study was done to investigate the effect of a bone marrow stromal cell (BMSCs) transplant on rat podocytes and diabetic nephropathy (DN) rats in high-glucose concentration, and to explore the effect of miR-124a on BMSC therapy. High glucose-injured podocytes and streptozotocin-induced DN rats have been respectively used as injury models in in vitro and in vivo studies. Podocyte viability was measured using the Cell Counting Kit-8 assay. Renal pathological examination was observed by HE staining and Masson staining. The messenger RNA and protein levels were determined via real-time polymerase chain reaction and Western blotting, respectively. Results: By mediating the activation of caveolin-1 (cav-1) and β-catenin and affecting the expression levels of EMT biomarkers including p-cadherin, synaptopodin, fibroblast-specific protein-1, α-smooth muscle actin and snail, our in vitro study confirmed that miR-124a played a significant role in the treatment of high glucose-induced podocyte injury by BMSCs. The therapeutic effects of the BMSC transplant on DN rats were also proved to be further enhanced by miR-124a overexpression in BMSCs, and such a phenomenon was accompanied by the improvement of renal fibrosis and mitigation of DN-related kidney impairment. Regulation of fibronectin, collagen1, and EMT-related proteins was closely implicated with the mechanism, and the activation of cav-1 and β-catenin was also possibly involved. Conclusion: The study demonstrated the pivotal effect of miR-124a on BMSC therapy for DN rats via mitigating EMT and fibrosis. Our results provide a novel insight into how therapeutic effects of BMSCs can be improved at the posttranscriptional level. 

Retracted: Yes

PubPeer comments:
 Retracted [30 June 2021] . -------------------------------- The above article, published online on 12 June 2019 in Wiley Online Library , has been retracted by agreement between the authors, the journal s Editor in Chief, Prof. Dr. Christian Behl, and Wiley Periodicals LLC. The authors asked to retract their article. A detailed investigation revealed several inconsistencies in the figures. Since original data could not be provided, the overall validity of the results could not be confirmed. The authors were not available for a final confirmation of the retraction. ,
Pretreatment of MQA, a caffeoylquinic acid derivative compound, protects against H2O2-induced oxidative stress in SH-SY5Y cells
Authors: Li An
Weihong Meng
Qingchun Zhao
Xiaowen Jiang
Lingyue Gao
Jian Huang
Junpeng Bai
Xing Tian
Journal: Neurological Research (2016)
Discipline: NEUROSCIENCE & BEHAVIOR
Keywords: Apoptosis; Caffeoylquinic acid; Hydrogen peroxide; Oxidative stress; SH-SY5Y cells.
Affiliations: a Department of Pharmacy , General Hospital of Shenyang Military Area Command , Shenyang , China., b Department of Pharmacy , Shihezi University , Shihezi , China., c Department of Life Science and Biochemistry , Shenyang Pharmaceutical University , Shenyang , China.

Abstract:  Objectives: Compound MQA (1,5-O-dicaffeoyl-3-O-[4-malic acid methyl ester]-quinic acid) is a natural caffeoylquinic acid derivative isolated from Arctium lappa L. roots. This study aims to explore the neuroprotective effects of MQA against hydrogen peroxide (H2O2)-induced oxidative stress in SH-SY5Y neuroblastoma cells. Methods: The SH-SY5Y cells were divided into four groups, including control, 20 μM MQA, 200 μM H2O2, 200 μM H2O2 + 20 μM MQA groups. The effects of MQA on H2O2-induced cell death were measured by MTT and LDH assays. Hoechst 33342 and Annexin V-PI double staining were used to observed H2O2-induced apoptosis. Also, the effects of MQA on antioxidant system and mitochondrial pathway were explored. Further, steady-state phosphorylation levels of ERK1/2, Akt and GSK-3β were examined by Western blot analysis. Results: Pretreatment with MQA prevented cell death in SH-SY5Y cells exposed to 200 μM H2O2 for 3 h. Meanwhile, Hoechst 33342 and Annexin V-PI double staining showed that MQA attenuated H2O2-induced apoptosis. These changes are related to elevation in SOD activity, reduction in MDA production and ROS formation, and increases in mitochondrial membrane potential (MMP). In addition, the potential mechanisms of MQA against H2O2-induced apoptosis are associated with increases in the Bcl-2/Bax ratio, decreases in cytochrome c release, caspase-3 and caspase-9 expressions, phosphorylation of ERK1/2, and dephosphorylation of AKT and GSK-3β. Conclusion: These findings suggest that protective effects of MQA against H2O2-induced apoptosis might be associated with mitochondrial apoptosis, ERK1/2 and AKT/GSK-3β pathway. 

Retracted: No

PubPeer comments:
 Two images in Figure 4 appear to overlap, although the brightness is different. This group seems to have a difficult time keeping their laboratory results organized. *** ![file] ,
Salidroside Attenuates LPS-Induced Acute Lung Injury in Rats
Authors: Miao Mingxing
Yang Yiming
Yan Tianhua
Zhu Lingpeng
Liu Jingyan
Guo Yujuan
Journal: Inflammation (2017)
Discipline: IMMUNOLOGY
Keywords: LPS; TLR/NF-κB; caveolin-1; lung injury; salidroside.
Affiliations: Department of Physiology and Pharmacology, China Pharmaceutical University, Nanjing, China., Department of Physiology and Pharmacology, China Pharmaceutical University, Nanjing, China. ., National Experimental Teaching Demonstration Center of Pharmacy, China Pharmaceutical University, Nanjing, China. .

Abstract:  The purpose of the present study was to investigate the effects of salidroside (Sal) on lung injury in lipopolysaccharide (LPS)-induced endotoxemic in vitro and in vivo. SD rats were randomly divided into five groups: control group, LPS group (15 mg kg-1), LPS plus dexamethasone (2 mg kg-1), and LPS plus Sal groups with different Sal doses (20 mg kg-1, 40 mg kg-1). Wet-to-dry weight (W/D) ratio was performed. Hematoxylin-eosin (HE) staining of lung was performed. Lung level of myeloperoxidase (MPO) was measured. Serum levels of the activities of the anti-oxidant superoxide dismutase (SOD), glutathione peroxidase (GSH-px), glutathione (GSH), tumor necrosis factor-α (TNF-α), interleukin-6 (IL-6), and interleukin-1β (IL-1β) were measured. Caveolin-1 and TLR/NF-κB pathway proteins were detected by Western blot. In vitro, we evaluated the protective effect of Sal on A549 cell line induced by LPS. The activities of the antioxidant SOD, CAT, GSH and GPX, TNF-α, IL-6, and IL-1β in cellular supernatant were measured. Caveolin-1 and TLR/NF-κB pathway was examined by Western blot. As a result, Sal significantly attenuated the above indices. In addition, Sal exerts pronounced protective effects in rats subjected to LPS possibly through inhibiting the caveolin-1 and TLR/NF-κB pathway in vivo. Our results indicated that Sal could be a potential therapeutic agent for the treatment of lung injury disease. 

Retracted: No

PubPeer comments:
 Brought to my attention by a reader. Figure 9. * Red boxes: Two bands, in the TLR4 and MyD99 panels, look remarkably similar. Could the authors take away any concerns by posting the high resolution, uncropped blot images here, please? ![file] ,
Renoprotective activity of sivelestat in severe acute pancreatitis in rats
Authors: Xiaowen Li
Li Chen
Longyun Ye
A-Mao Tang
Houhong Wang
Chao Li
Daren Liu
Guogang Li
Journal: Experimental and Therapeutic Medicine (2013)
Discipline: CLINICAL MEDICINE
Keywords: acute pancreatitis; neutrophil elastase; renoprotection; sivelestat.
Affiliations: Department of Surgery, Zhejiang University School of Medicine, Second Affiliated Hospital, Hangzhou, Zhejiang 310009;

Abstract:  Acute pancreatitis, affecting 382,014 individuals annually in China, is life-threatening in its severe form. Since acute pancreatitis-associated morbidity or mortality is attributable mainly to functional failure of the vital organs, significant research efforts have focused on the identification of novel agents with potential organ-protective properties in the hope of developing approaches to improve the outcome of acute pancreatitis. In a previous study, we demonstrated that sivelestat, a specific inhibitor of neutrophil elastase (NE), is effective in protecting against lung failure in rats with taurocholate-induced acute pancreatitis. As part of the analyses extended from that study, the present study aimed to evaluate the role of sivelestat in the protection against acute pancreatitis-associated renal injury. Renal histopathology and major renal function parameters were analyzed in renal tissue and blood specimens collected from rats with acute pancreatitis induced by the surgical administration of sodium taurocholate in the presence or absence of sivelestat treatment and in sham-operated control rats at various time-points. The extended analyses demonstrated that: i) sodium taurocholate induced apparent renal injury and dysfunction manifested by histological anomalies, including vacuolization and apoptosis of the cells of the tubular epithelial lining in the kidney, as well as biochemical aberrations in the blood (increases in levels of blood urea nitrogen, creatinine and tumor necrosis factor-α) and renal tissue (robust increases in NE activity and induced neutrophil chemoattractant-1 levels); and ii) sivelestat treatment effectively attenuated all taurocholate-induced histological anomalies and biochemical aberrations. These observations strongly suggest that the NE inhibitor, sivelestat, is effective in protecting against acute pancreatitis-associated renal injury. 

Retracted: No

PubPeer comments:
 unexpected image duplication ![file] Disclaimer: These potential image duplications have been detected automatically using ImageTwin http: dx.doi.org 10.1145 3019612.3019875 Although results have been curated, the automatic algorithm may have generated false positive results and cannot take into account all scientific explanations for apparent duplications like stripped and reprobed blots, time series, serial sections and reused controls. ,
Consistent Detection of 2019 Novel Coronavirus in Saliva
Authors: Ivan Fan-Ngai Hung
Jasper Fuk-Woo Chan
Darshana H Kandamby
Wai-Shing Leung
Chris Yau-Chung Choi
Owen Tak-Yin Tsang
Tak-Chiu Wu
Kwok-Hung Chan
Kelvin Kai-Wang To
David Christopher Lung
Agnes Yim-Fong Fung
Kwok-Yung Yuen
Thomas Shiu-Hong Chik
Rosana Wing-Shan Poon
Vincent Chi-Chung Cheng
Anthony Raymond Tam
Jacky Man-Chun Chan
Cyril Chik-Yan Yip
Journal: Clinical Infectious Diseases (2020)
Discipline: IMMUNOLOGY
Keywords: 2019 novel coronavirus; COVID-19; diagnostics; saliva; transmission
Affiliations: State Key Laboratory for Emerging Infectious Diseases, Department of Microbiology, Carol Yu Centre for Infection, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China., Department of Microbiology, Queen Mary Hospital, Hong Kong Special Administrative Region, China., Department of Clinical Microbiology and Infection Control, The University of Hong Kong-Shenzhen Hospital, Shenzhen, China., Department of Medicine and Geriatrics, Princess Margaret Hospital, Hong Kong Special Administrative Region, China., Department of Medicine, Queen Elizabeth Hospital, Hong Kong Special Administrative Region, China., Intensive Care Unit, Princess Margaret Hospital, Hong Kong Special Administrative Region, China., Department of Pathology, Queen Elizabeth Hospital, Hong Kong Special Administrative Region, China., Department of Medicine, Queen Mary Hospital, Hong Kong Special Administrative Region, China.

Abstract:  The 2019 novel coronavirus (2019-nCoV) was detected in the self-collected saliva of 91.7% (11/12) of patients. Serial saliva viral load monitoring generally showed a declining trend. Live virus was detected in saliva by viral culture. Saliva is a promising noninvasive specimen for diagnosis, monitoring, and infection control in patients with 2019-nCoV infection. 

Retracted: No

PubPeer comments:
 The authors state: u201cIn-house 1-step real-time reverse tran-scriptionu2013quantitative polymerase chain reaction (RT-qPCR) assay targeting the S gene of 2019-nCoV was performed using QuantiNova SYBR Green RT-PCR Kit (Qiagen) in a LightCycler 480 Real-Time PCR System (Roche), as we de-scribed previously [2].u201d [2] refers to Yu et al. (2020), which states u201cThe 2019-nCoV nucleic acid test was conducted by means of real-time reverse-transcription polymerase chain reaction, using detection reagents from Zhuo Cheng Hui Sheng Biotechnology and Berger Medical Technology.u201d The reagents and protocols used appear to be incomplete. In addition, the manufacturers appear to be different. Could the authors offer a full and detailed protocol, indicating all the precise primers used, RT-PCR assay conditions and pertinent manufacturer details, including product codes, for replication trials. Yu P, Zhu J, Zhang Z, Han Y, Huang L. A familial cluster of infection associated with the 2019 novel coronavirus indicating potential person-to-person transmission during the incubation period. J Infect Dis. 2020 Feb 18. pii: jiaa077. doi: 10.1093 infdis jiaa077 ,
RETRACTED: Combination of carvacrol and rosiglitazone ameliorates high fat diet induced changes in lipids and inflammatory markers in C57BL/6J mice
Authors: Muthukrishnan Ezhumalai
Natarajan Ashokkumar
Kodukkur Viswanathan Pugalendi
Journal: Biochimie (2015)
Discipline: BIOLOGY & BIOCHEMISTRY
Keywords: Carvacrol; Diabetes mellitus; High fat diet; Rosiglitazone.
Affiliations: Department of Biochemistry and Biotechnology, Faculty of Science, Annamalai University, Annamalainagar 608 002, Tamilnadu, India., Department of Biochemistry and Biotechnology, Faculty of Science, Annamalai University, Annamalainagar 608 002, Tamilnadu, India. Electronic address: .

Abstract:  This article has been retracted: please see Elsevier Policy on Article Withdrawal (https://www.elsevier.com/about/our-business/policies/article-withdrawal). This article has been retracted at the request of the Editor-in-Chief. Following concerns raised by Dr. E. Bik, the journal conducted an investigation and found evidence that there had been improper manipulation and duplication of images in Figure 4. The editors would like to thank Dr. Bik for her valuable insight in this matter. The authors have not responded to requests for an explanation of these irregularities so this article is retracted without their approval. 

Retracted: Yes

PubPeer comments:
 Figure 4. Panels D (HFD+CVL) and F (HFD+CVL+RSG) appear to look unexpectedly similar. Shown with red boxes. Panels A (Control) and B (Control +CVL+RSG) appear to show an area of overlap when one of the panels is rotated 180 degrees. Shown with blue boxes. ![file] , 
 2020 retraction. https: www.sciencedirect.com science article pii S0300908420300547?via%3Dihub This article has been retracted at the request of the Editor-in-Chief. Following concerns raised by Dr. E. Bik, the journal conducted an investigation and found evidence that there had been improper manipulation and duplication of images in Figure 4. The editors would like to thank Dr. Bik for her valuable insight in this matter. The authors have not responded to requests for an explanation of these irregularities so this article is retracted without their approval. ,
The protein ENH is a cytoplasmic sequestration factor for Id2 in normal and tumor cells from the nervous system
Authors: Anna Lasorella
Antonio Iavarone
Journal: Proceedings of the National Academy of Sciences of the United States of America (2006)
Discipline: Multidisciplinary
Keywords: Id2; transcription factors; retinoblastoma tumor suppressor protein; differentiation; cell-cycle progression
Affiliations: Institute for Cancer Genetics, Department of Pathology, Pediatrics, and Neurology, Columbia University Medical Center, New York, NY 10032, USA.

Abstract:  Id2 is a natural inhibitor of the basic helix-loop-helix transcription factors and the retinoblastoma tumor suppressor protein. Active Id2 prevents differentiation and promotes cell-cycle progression and tumorigenesis in the nervous system. A key event that regulates Id2 activity during differentiation is translocation from the nucleus to the cytoplasm. Here we show that the actin-associated protein enigma homolog (ENH) is a cytoplasmic retention factor for Id2. ENH contains three LIM domains, which bind to the helix-loop-helix domain of Id proteins in vitro and in vivo. ENH is up-regulated during neural differentiation, and its ectopic expression in neuroblastoma cells leads to translocation of Id2 from the nucleus to the cytoplasm, with consequent inactivation of transcriptional and cell-cycle-promoting functions of Id2. Conversely, silencing of ENH by RNA interference prevents cytoplasmic relocation of Id2 in neuroblastoma cells differentiated with retinoic acid. Finally, the differentiated neural crest-derived tumor ganglioneuroblastoma coexpresses Id2 and ENH in the cytoplasm of ganglionic cells. These data indicate that ENH contributes to differentiation of the nervous system through cytoplasmic sequestration of Id2. They also suggest that ENH is a restraining factor of the oncogenic activity of Id proteins in neural tumors. 

Retracted: No

PubPeer comments:
 Could the authors provide the web-based official organizational (owner s data) source reference for their presented RAW DATA in Table 4? ![file] ,
Dental findings and identification of undiagnosed hyperglycemia
Authors: I B Lamster
C Kunzel
S Burkett
E Lalla
B Cheng
Journal: Journal of dental research (2013)
Discipline: CLINICAL MEDICINE
Keywords: diabetes; periodontal disease(s)/periodontitis; periodontal medicine; pre-diabetes; prevention
Affiliations: Division of Periodontics, College of Dental Medicine.

Abstract:  A change in the American Diabetes Association guidelines added hemoglobin A1c (HbA1c) to the assays for diabetes diagnosis, but evidence suggests that glucose vs. HbA1c criteria may identify different segments of the affected population. We previously demonstrated that oral findings offer an opportunity for the detection of undiagnosed abnormal fasting plasma glucose (FPG) among dental patients who present with diabetes risk factors. In this new cross-sectional study, we sought to extend these observations. The first goal, using data from 591 new participants, was to assess our previously identified hyperglycemia detection models when HbA1c is used for case definition. The second goal, using data from our total cohort of 1,097 participants, was to evaluate the models' performance regardless of whether an FPG or an HbA1c is used for diagnosis. The presence of ≥ 26% teeth with deep pockets or ≥ 4 missing teeth correctly identified 72% of pre-diabetes or diabetes cases in the HbA1c sample and 75% in the total population. The addition of a point-of-care HbA1c ≥ 5.7% increased correct identification to 87% and 90%, respectively. These results demonstrate the validity of our prediction models regardless of the test used for diabetes or pre-diabetes diagnosis in the clinical setting and underscore the contribution dentists can make. 

Retracted: No

PubPeer comments:
 According to the Press, this paper was funded by  The Jeffrey Epstein VI Foundation amongst others . Could authors explain why this information was omitted in the publication? https: www.aegisdentalnetwork.com news 2013 10 9 Early-Detection-of-Diabetes-in-Teeth-Funded-by-Columbia-University-and-Jeffrey-Epstein-VI-Foundation ![file] ,
Overlapping and enzyme-specific contributions of matrix metalloproteinases-9 and -12 in IL-13-induced inflammation and remodeling
Authors: Lesley A Rabach
Tao Zheng
Zhou Zhu
Wei Liu
Robert J Homer
Jack A Elias
Bing Ma
Morgan E Rabach
Sophie Lanone
Robert M Senior
J Michael Shipley
Chun Geun Lee
Qingsheng Chen
Jingming Wang
Steven D Shapiro
Journal: Journal of Clinical Investigation (2002)
Discipline: CLINICAL MEDICINE
Keywords: IL-13; inflammation; alveolar remodeling; MMP-9; MMP-12
Affiliations: Section of Pulmonary and Critical Care Medicine, Department of Internal Medicine, and. Department of Pathology, Yale University School of Medicine, New Haven, Connecticut 06520, USA.

Abstract:  IL-13 potently stimulates eosinophilic and lymphocytic inflammation and alveolar remodeling in the lung, effects that depend on the induction of various matrix metalloproteinases (MMPs). Here, we compared the remodeling and inflammatory effects of an IL-13 transgene in lungs of wild-type, MMP-9-deficient, or MMP-12-deficient mice. IL-13-induced alveolar enlargement, lung enlargement, compliance alterations, and respiratory failure and death were markedly decreased in the absence of MMP-9 or MMP-12. Moreover, IL-13 potently induced MMPs-2, -12, -13, and -14 in the absence of MMP-9, while induction of MMPs-2, -9, -13, and -14 by IL-13 was diminished in the absence of MMP-12. A deficiency in MMP-9 did not alter eosinophil, macrophage, or lymphocyte recovery, but increased the recovery of total leukocytes and neutrophils in bronchoalveolar lavage (BAL) fluids from IL-13 transgenic mice. In contrast, a deficiency in MMP-12 decreased the recovery of leukocytes, eosinophils, and macrophages, but not lymphocytes or neutrophils. These studies demonstrate that IL-13 acts via MMPs-9 and -12 to induce alveolar remodeling, respiratory failure, and death and that IL-13 induction of MMPs-2, -9, -13, and -14 is mediated at least partially by an MMP-12-dependent pathway. The also demonstrate that MMPs-9 and -12 play different roles in the generation of IL-13-induced inflammation, with MMP-9 inhibiting neutrophil accumulation and MMP-12 contributing to the accumulation of eosinophils and macrophages. 

Retracted: No

PubPeer comments:
 Figure 6. Splicing in some panels, but not others makes comparison between panels problematic. https: imgur.com yCa5zyh ,
Where Are We With Human Lice? A Review of the Current State of Knowledge
Authors: Oleg Mediannikov
Didier Raoult
Nadia Amanzougaghene
Florence Fenollar
Journal: Frontiers in Cellular and Infection Microbiology (2020)
Discipline: MICROBIOLOGY
Keywords: Pediculus humanus; biology; control; disease-vector; epidemiology
Affiliations: Aix Marseille Univ, IRD, AP-HM, SSA, VITROME, Marseille, France., IHU-Méditerranée Infection, Marseille, France., Aix Marseille Univ, IRD, AP-HM, MEPHI, Marseille, France.

Abstract:  Pediculus humanus is an obligate bloodsucking ectoparasite of human that includes two ecotypes, head louse and body louse, which differ slightly in morphology and biology, but have distinct ecologies. Phylogenetically, they are classified on six mitochondrial clades (A, B, C, D, E, and F), head louse encompasses the full genetic diversity of clades, while body louse belongs to clades A and D. Recent studies suggested that not only body louse, but also head louse can transmit disease, which warrants greater attention as a serious public health problem. The recent sequencing of body louse genome confirmed that P. humanus has the smallest genome of any hemimetabolous insect reported to date, and also revealed numerous interesting characteristics in the nuclear and mitochondrial genomes. The transcriptome analyses showed that body and head lice were almost genetically identical. Indeed, the phenotypic flexibility associated with the emergence of body lice, is probably a result of regulatory changes, perhaps epigenetic in origin, triggered by environmental signals. Current lice control strategies have proven unsuccessful. For instance, ivermectin represents a relatively new and very promising pediculicide. However, ivermectin resistance in the field has begun to be reported. Therefore, novel opportunities for pest control strategies are needed. Our objective here is to review the current state of knowledge on the biology, epidemiology, phylogeny, disease-vector and control of this fascinating and very intimate human parasite. 

Retracted: No

PubPeer comments:
 The scope of this paper is the treatment of lice. This paper covers the use of ivermectin. The authors declared no competing interests. However, according to a poster from the Institut Hospitalo-Universitaire de Marseille (see below), 1 of the author seems to be the founders of a pharmaceutical company called Arthrobac Pharma. This pharmaceutical company is dedicated to the treatment of lice using ivermectin in combination with other products. Being a founder of a pharmaceutical company dedicated to the treatment of lice may be considered as a competing interest when the article address the treatment of lice. Can the author explain if they still had any interest in this pharmaceutical company when the manuscript was submitted? ![Poster](http: backup.mediterranee-infection.com arkotheque client ihumed _depot_arko articles 579 poster_img.jpg) ,