PReD-Bench/PRed-Bench huggingface dataset:
The ISG15 isopeptidase UBP43 is regulated by proteolysis via the SCFSkp2 ubiquitin ligase
Authors: Sara Tokarz
Kevin Friedman
Dong-Er Zhang
Catherine Berset
Kei-Ichi Nakayama
Keiko Nakayama
Stefan Lanker
Janna La Rue
Journal: Journal of Biological Chemistry (2004)
Discipline: BIOLOGY & BIOCHEMISTRY
Keywords: Skp2; UBP43; ubiquitination; ISG15; SCFSkp2
Affiliations: Department of Molecular and Medical Genetics, School of Medicine, Oregon Health and Sciences University, Portland, Oregon 97239, USA.

Abstract:  The Skp2 oncoprotein belongs to the family of F-box proteins that function as substrate recognition factors for SCF (Skp1, cullin, F-box protein) E3 ubiquitin-ligase complexes. Binding of the substrate to the SCFSkp2 complex catalyzes the conjugation of ubiquitin molecules to the bound substrate, resulting in multi-ubiquitination and rapid degradation by the 26 S proteasome. Using Skp2 as bait in a yeast two-hybrid screen, we have identified UBP43 as a novel substrate for Skp2. UBP43 belongs to the family of ubiquitin isopeptidases and specifically cleaves ISG15, a ubiquitin-like molecule that is induced by cellular stresses, such as type 1 interferons (IFN), nephrotoxic damage, and bacterial infection. UBP43 was originally identified as an up-regulated gene in knock-in mice expressing an acute myelogenous leukemia fusion protein, AML1-ETO, as well as in melanoma cell lines treated with IFN-beta. The phenotype of UBP43 knockout mice includes shortened life span, hypersensitivity to IFN, and neuronal damage, suggesting that tight regulation of ISG15 conjugation is critical for normal cellular function. In this study, we demonstrate that UBP43 is ubiquitinated in vivo and accumulates in cells treated with proteasome inhibitors. We also show that Skp2 promotes UBP43 ubiquitination and degradation, resulting in higher levels of ISG15 conjugates. In Skp2-/- mouse cells, levels of UBP43 are consistently up-regulated, whereas levels of ISG15 conjugates are reduced. Our results demonstrate that the SCFSkp2 is involved in controlling UBP43 protein levels and may therefore play an important role in modulating type 1 IFN signaling. 

Retracted: No

PubPeer comments:
 ![file] ,
Non-bioengineered silk fibroin protein 3D scaffolds for potential biotechnological and tissue engineering applications
Authors: Subhas C Kundu
Biman B Mandal
Journal: Macromolecular Bioscience (2008)
Discipline: BIOLOGY & BIOCHEMISTRY
Keywords: silk gland fibroin; 3D scaffolds; tasar silkworm; SDS; mechanical properties
Affiliations: Department of Biotechnology, Indian Institute of Technology, Kharagpur-721302, India. 

Abstract:  This paper describes a new source for fabricating high-strength, non-bioengineered silk gland fibroin 3D scaffolds from Indian tropical tasar silkworm, Antheraea mylitta using SDS for dissolution. The scaffolds were fabricated by freeze drying at different prefreezing temperatures for pore size and porosity optimization. Superior mechanical properties with compressive strength in the range of 972 kPa were observed. The matrices were degraded by proteases within 28 d of incubation. Biocompatibility was assessed by feline fibroblast culture in vitro and confocal microscopy further confirmed adherence, spreading, and proliferation of primary dermal fibroblasts. Results indicate nonmulberry 3D silk gland fibroin protein as an inexpensive, high-strength, slow biodegradable, biocompatible, and alternative natural biomaterial. [Figure: see text]. 

Retracted: No

PubPeer comments:
 Reuse of images ![file] ,
Management of diabetes during Ramadan fasting in children and adolescents: A survey of physicians’ perceptions and practices in the Arab Society for Paediatric Endocrinology and Diabetes (ASPED) countries
Authors: Asma Deeb
Salem A Beshyah
Nancy Elbarbary
Abdelhadi Habeb
Journal: Diabetes Research and Clinical Practice (2019)
Discipline: CLINICAL MEDICINE
Keywords: ASPED; Adolescents; Attitudes; Children; Diabetes
Affiliations: Ain Shams University, Cairo, Egypt. Electronic address: ., Paediatric Endocrinology Department, Mafraq Hospital, Abu Dhabi, United Arab Emirates., Prince Mohammed bin Abdulaziz Hospital for National Guard, Madinah, KSA., Sheikh Khalifa Medical City, Abu Dhabi, United Arab Emirates; Dubai Medical College, Dubai, United Arab Emirates.

Abstract:  Aim: To ascertain the pattern of diabetes management during Ramadan fasting in childhood and adolescence among physicians in Arab countries. Methods: An online electronic survey questionnaire was distributed to physicians registered in the Arab society for Paediatric Endocrinology and Diabetes (ASPED). Results: Of the 167 responders, 114 (86.0%) were paediatricians and the remaining 14.4% were adult physicians. 117 (79.6%) would allow patients to fast and 60.7% of them emphasized providing education before fasting. 69.1% of physicians thought that their patients complete &gt;50% of fasting days. 46.9% recognized those with hypoglycemia unawareness among the very high-risk group for fasting. 62% reported that fasting should be broken if symptomatic hypoglycemia regardless of glucose level and 48.2% indicated that blood glucose above 300 mg/dl is another indication. 63.4% of respondents would decrease basal insulin by 25%, and 52.8% reported that using insulin pump during fasting reduced the frequency of hypoglycemia. 81.1% recommend several dietary adjustments and 56.4% used rapid-acting insulin analog according to carbohydrate counting. Conclusions: There is a wide variation in the management of children and adolescents with diabetes during Ramadan in ASPED countries. A targeted educational program for physicians and establishing a guideline for this challenging area is needed. 

Retracted: No

PubPeer comments:
 The author list in this paper is indicated as: Nancy Elbarbary, Asma Deeb, Abdelhadi Habeb, Salem A. Beshyah https: www.diabetesresearchclinicalpractice.com article S0168-8227(18)31885-0 fulltext But the accepted paper was: Abdelhadi M Habeb, Asma Deeb, Nancy Elbarbary, Salem A Beshyah https: sci-hub.tw 10.1016 j.diabres.2019.107975 What was the reason for this radical change in authorship order? ,
Public availability of published research data in high-impact journals
Authors: Alawi A Alsheikh-Ali
Mouaz H Al-Mallah
Waqas Qureshi
John P A Ioannidis
Journal: PloS one (2011)
Discipline: Multidisciplinary
Keywords: research data availability; data sharing policies; high-impact journals; primary data; data availability instructions
Affiliations: Institute of Cardiac Sciences, Sheikh Khalifa Medical City, Abu Dhabi, United Arab Emirates.

Abstract:  Background: There is increasing interest to make primary data from published research publicly available. We aimed to assess the current status of making research data available in highly-cited journals across the scientific literature. Methods and results: We reviewed the first 10 original research papers of 2009 published in the 50 original research journals with the highest impact factor. For each journal we documented the policies related to public availability and sharing of data. Of the 50 journals, 44 (88%) had a statement in their instructions to authors related to public availability and sharing of data. However, there was wide variation in journal requirements, ranging from requiring the sharing of all primary data related to the research to just including a statement in the published manuscript that data can be available on request. Of the 500 assessed papers, 149 (30%) were not subject to any data availability policy. Of the remaining 351 papers that were covered by some data availability policy, 208 papers (59%) did not fully adhere to the data availability instructions of the journals they were published in, most commonly (73%) by not publicly depositing microarray data. The other 143 papers that adhered to the data availability instructions did so by publicly depositing only the specific data type as required, making a statement of willingness to share, or actually sharing all the primary data. Overall, only 47 papers (9%) deposited full primary raw data online. None of the 149 papers not subject to data availability policies made their full primary data publicly available. Conclusion: A substantial proportion of original research papers published in high-impact journals are either not subject to any data availability policies, or do not adhere to the data availability instructions in their respective journals. This empiric evaluation highlights opportunities for improvement. 

Retracted: No

PubPeer comments:
 The final column of Figure 1 is labeled  Full data deposited, percentage of papers . Numbers in this column range from 0 to 9. These are not percentages but rather the number of articles out of 10 from each journal that publicly deposited data. To convert these to percentages, multiply by 10. ,
Septin ring assembly is regulated by Spt20, a structural subunit of the SAGA complex
Authors: Hong Lu
Yuchen Guo
Bingkun Lei
Yan-Wen Tan
Wenqi Zhao
Yao Yu
Nan Zhou
Journal: Journal of Cell Science (2014)
Discipline: MOLECULAR BIOLOGY & GENETICS
Keywords: Fission yeast; Mid2; SAGA; Septin; Spt20.
Affiliations: State Key Laboratory of Genetic Engineering, School of Life Sciences, and Institute of Biomedical Sciences, Shanghai 200433, China., State Key Laboratory of Surface Physics and Department of Physics, Fudan University, Shanghai 200433, China., State Key Laboratory of Genetic Engineering, School of Life Sciences, and Institute of Biomedical Sciences, Shanghai 200433, China Shanghai Engineering Research Center of Industrial Microorganisms, Shanghai 200433, China  ., State Key Laboratory of Genetic Engineering, School of Life Sciences, and Institute of Biomedical Sciences, Shanghai 200433, China Shanghai Engineering Research Center of Industrial Microorganisms, Shanghai 200433, China Shanghai Collaborative Innovation Center for Biomanufacturing Technology, Shanghai 200237, China  .

Abstract:  Accurate cell division requires the proper assembly of high-order septin structures. In fission yeast (Schizosaccharomyces pombe), Spn1-Spn4 are assembled into a primary septin ring at the division site, and the subsequent recruitment of Mid2 to the structure results in a stable septin ring. However, not much is known about the regulation of this key process. Here, we found that deletion of Spt20, a structural subunit of the Spt-Ada-Gcn5-acetyltransferase (SAGA) transcriptional activation complex, caused a severe cell separation defect. The defect was mainly due to impaired septin ring assembly, as 80% of spt20Δ cells lost septin rings at the division sites. Spt20 regulates septin ring assembly partially through the transcriptional activation of mid2(+). Spt20 also interacted with Spn2 and Mid2 in vitro and was associated with other components of the ring in vivo. Spt20 colocalized with the septin ring, but did not separate when the septin ring split. Importantly, Spt20 regulated the stability of the septin ring and was required for the recruitment of Mid2. The transcription-dependent and -independent roles of Spt20 in septin ring assembly highlight a multifaceted regulation of one process by a SAGA subunit. 

Retracted: No

PubPeer comments:
 An image in Figure 3A and Figure 6B appear to overlap. *** 3A closeup ![file] 6B closeup ![file] ,
Dexmedetomidine protects PC12 cells from oxidative damage through regulation of miR-199a/HIF-1α
Authors: Qinglong Kong
Yalin Xi
Ling Wu
Journal: Artificial Cells Nanomedicine and Biotechnology (2020)
Discipline: BIOLOGY & BIOCHEMISTRY
Keywords: HIF-1α; PC12 cells; dexmedetomidine; miR-199a; oxidative damage.
Affiliations: Department of Clinical Pharmacy, Dalian Central Hospital, Dalian, China, Department of Thoracic Surgery, Dalian Central Hospital, Dalian, China

Abstract:  Background: Although dexmedetomidine (Dex) has a significant neuroprotective effect in various nerve-damage models, the exact mechanism of which Dex protects cells from oxidative damage is not fully clear. This article recommended the protective effect of Dex on oxidative damage in PC12 cells.Methods: The PC12 cells were incubated by hydrogen peroxide (H2O2) for 24 h and pre-treated by Dex for 30 min. Cell viability, apoptosis, HIF-1α expression and ROS level were detected by CCK-8, apoptosis assay, Western blot and ROS assay, respectively. The miR-199a expression was tested by qRT-PCR. Targeting relationship between miR-199a and HIF-1α was performed by dual luciferase activity assay. The activation of PI3K/AKT/mTOR and Wnt/β-catenin pathways was tested by western blot.Results: Dex attenuated H2O2-induced oxidative damage, including the decline of cell viability, the raise of apoptosis and the generation of ROS in PC12 cells by down-regulating miR-199a expression. Moreover, Dex up-regulated HIF-1α expression via decreasing miR-199a level in PC12 cells and miR-199a targeted the 3'-UTR of HIF-1α. In addition, Dex activated PI3K/AKT/mTOR and Wnt/β-catenin pathways by declining miR-199a level.Conclusions: This article illustrated the protective effect of Dex on oxidative damage in PC12 cells. Furthermore, Dex prevented PC12 cells from oxidative injury through the regulation of miR-199a/HIF-1α. 

Retracted: No

PubPeer comments:
 The Western Blots in this paper all display the curious, stylised form, like tadpoles or performing sardines, familiar from products of the celebrated  Tadpole Papermill. Here, Fig 6. ![file] Is it possible for the authors to upload or link to scans of the original gels? ,
TRAF2 facilitates vaccinia virus replication by promoting rapid virus entry
Authors: Juergen Haas
Samantha J Griffiths
Philippa M Beard
Ismar R Haga
Tali Pechenick Jowers
Journal: Journal of Virology (2014)
Discipline: MICROBIOLOGY
Keywords: TRAF2; vaccinia virus; replication; virus entry; proviral factor
Affiliations: The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, United Kingdom.

Abstract:  Tumor necrosis factor receptor (TNFR)-associated factor 2 (TRAF2) is a pivotal intracellular mediator of signaling pathways downstream of TNFR1 and -2 with known pro- and antiviral effects. We investigated its role in the replication of the prototype poxvirus vaccinia virus (VACV). Loss of TRAF2 expression, either through small interfering RNA treatment of HeLa cells or through genetic knockout in murine embryonic fibroblasts (MEFs), led to significant reductions in VACV growth following low-multiplicity infection. In single-cycle infections, there was delayed production of both early and late VACV proteins as well as accelerated virus-induced alterations to cell morphology, indicating that TRAF2 influences early stages of virus replication. Consistent with an early role, uncoating assays showed normal virus attachment but delayed virus entry in the absence of TRAF2. Although alterations to c-Jun N-terminal kinase (JNK) signaling were apparent in VACV-infected TRAF2(-/-) MEFs, treatment of wild-type cells with a JNK inhibitor did not affect virus entry. Instead, treatment with an inhibitor of endosomal acidification greatly reduced virus entry into TRAF2(-/-) MEFs, suggesting that VACV is reliant on the endosomal route of entry in the absence of TRAF2. Thus, TRAF2 is a proviral factor for VACV that plays a role in promoting efficient viral entry, most likely via the plasma membrane. Importance: Tumor necrosis factor receptor-associated factors (TRAFs) are key facilitators of intracellular signaling with roles in innate and adaptive immunity and stress responses. We have discovered that TRAF2 is a proviral factor in vaccinia virus replication in both HeLa cells and mouse embryonic fibroblasts and that its influence is exercised through promotion of efficient virus entry. 

Retracted: No

PubPeer comments:
 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. , 
 #1 It is not clear why the same Mock infection image was used or why the dimensions differ, but this does not seem likely to affect the conclusions. *** ![file] ,
Role of synbiotics in polysaccharide assisted colon targeted microspheres of mesalamine for the treatment of ulcerative colitis
Authors: Sachin Kumar Singh
Rupinderjeet Kaur
Monica Gulati
Journal: International Journal of Biological Macromolecules (2017)
Discipline: BIOLOGY & BIOCHEMISTRY
Keywords: Co-administration; Guar gum; Mesalamine; Microspheres; Probiotics
Affiliations: School of Pharmaceutical Sciences, Lovely Professional University, Punjab, 144 401, India., School of Pharmaceutical Sciences, Lovely Professional University, Punjab, 144 401, India. Electronic address: .

Abstract:  The present study explains the effect of concomitant administration of synbiotics with the polysaccharide based colon targeted delivery system. As the gut microflora get deranged on administration of mesalamine, drug release from such delivery systems is expected to be jeopardised because the release trigger is dependent solely on the colonic microbiota. To overcome this limitation, mesalamine was formulated as microspheres with guar gum and xanthan gum (prebiotics). These were combined with probiotics containing Lactobacillus acidophilus, L. rhamnosus, Bifidobacterium longumand Saccharomyces boulardi. Dissolution studies of the prepared formulation conducted in simulated colonic fluid clearly demonstrated its superiority over the marketed, delayed release dosage forms of mesalamine. The therapeutic benefit of the concomitant administration of synbiotic with mesalamine was evidenced by the comparative evaluation of faecal contents, weight gain trend and histopathological studies conducted in rats. The results suggest that co-administration of synbiotics with mesalamine can be used as a convenient methodology to achieve efficient and cost-effective targeting of the drug to colon. 

Retracted: No

PubPeer comments:
 ![file] ![file] The histological colon sections in Fig.7 IIa and Fig.9 Va are duplicated for different treatment groups. Could the authors clarify the duplication of the same image? ,
Low-intensity ultrasound increases FAK, ERK-1/2, and IRS-1 expression of intact rat bones in a noncumulative manner
Authors: José Rodrigo Pauli
Carlos Vinícius Buarque de Gusmão
William Dias Belangero
José Marcos Alves
Mario José Abdalla Saad
Journal: Clinical Orthopaedics and Related Research (2010)
Discipline: CLINICAL MEDICINE
Keywords: Low-intensity pulsed ultrasound stimulation (LIPUS); osteogenesis; intact bone; mechanotransduction; growth factor pathways
Affiliations: Department of Orthopaedics and Traumatology, Faculty of Medical Sciences, The State University of Campinas (UNICAMP), Campinas, São Paulo, Brazil. 

Abstract:  Background: Low-intensity pulsed ultrasound stimulation (LIPUS) reportedly increases osteogenesis in fracture models but fails in intact bone, suggesting LIPUS does not act on mechanotransduction and growth factor pathways of intact bone. Questions/purposes: We asked whether daily 20-minute LIPUS applied to intact tibias would act on bone proteins involved in mechanotransduction (focal adhesion kinase [FAK], and extracellular signal-regulated kinase-1/2 [ERK-1/2]), and growth factor signaling (insulin receptor substrate-1 [IRS-1]) pathways at 7, 14, and 21 days of treatment. Methods: Immunoblotting was performed to detect FAK, ERK-1/2, and IRS-1 expression and activation from the stimulated intact tibias at 7, 14, and 21 days of daily 20-minute LIPUS. Results: LIPUS increased FAK expression (at 7 days), ERK-1/2 (at 14 days), and IRS-1 (at 7 days), but expression decreased 7 days later, indicating a noncumulative effect of LIPUS. As only FAK expression was detected at 21 days, these observations suggest LIPUS influences nuclear reactions that may be modulated by a major cellular mechanism preferentially inhibiting IRS-1 expression and not FAK expression. Increased ERK-1/2 expression at 14 days suggests the differing mechanisms for promoting ERK-1/2, FAK, and IRS-1 syntheses. IRS-1 expression behaved similarly to FAK expression; therefore, LIPUS may modulate growth factor pathways. LIPUS increased sustained FAK and ERK-1/2 activation, but not IRS-1, suggesting sustained ERK-1/2 activation is not the result of mechanically induced growth factor activation. Conclusions: LIPUS acts on mechanotransduction and growth factor pathways in intact bone in a noncumulative manner. Clinical relevance These data suggest LIPUS applied to intact bone acts on proteins involved in osteogenesis. 

Retracted: No

PubPeer comments:
 Figure 4A FAK and pFAK are much more similar than expected ![file] ,
Silence of lncRNA XIST represses myocardial cell apoptosis in rats with acute myocardial infarction through regulating miR-449
Authors: M-J Zhang
H-Y Liu
D-D Zhai
C-Z Liang
M Zhang
T Ma
Y-L Han
L Wang
Y Shen
Journal: European review for medical and pharmacological sciences (2019)
Discipline: PHARMACOLOGY & TOXICOLOGY
Keywords: lncRNA XIST; acute myocardial infarction; rat; miR-449; Notch1
Affiliations: Heart Center, Aerospace Center Hospital, Beijing, China. .

Abstract:  Objective: To study the influences of long non-coding ribonucleic acid (lncRNA) X-inactive specific transcript (XIST) on rats with acute myocardial infarction (AMI), and its regulatory mechanism. Materials and methods: A total of 30 Sprague-Dawley rats were randomly assigned into Sham group, Model group, and lncRNA XIST small interfering RNA (XIST siRNA) group. The AMI rat model was prepared through ligating the left anterior descending coronary artery. The left ventricular end-diastolic volume (LVEDV), left ventricular end-systolic volume (LVESV), left ventricular systolic diameter (LVDs), and left ventricular diastolic diameter (LVDd) of rats were determined using a color Doppler ultrasound system. Reverse transcription-polymerase chain reaction was performed to measure the expression levels of lncRNA XIST, microRNA (miR)-449, and Notch1 in rat heart tissues in each group. Pathological morphology of rat heart tissues in each group was observed via hematoxylin-eosin (HE) staining. Cell apoptosis in rat heart tissues was evaluated through terminal deoxynucleotidyl transferase-mediated dUTP nick end labeling (TUNEL) assay. Results: Compared with those in Sham group, rats in Model group had significantly increased LVEDV, LVESV, LVDs, and LVDd. After transfection with lncRNA XIST siRNA, XIST level in rat heart tissues was remarkably declined in XIST siRNA group compared with that in Model group. According to HE staining results, the pathological injuries in rat heart tissues were greatly improved in XIST siRNA group compared with those in Model group. TUNEL staining results revealed that the apoptosis rate of cells in rat heart tissues in XIST siRNA group was markedly lower than that in Model group. Higher level of miR-449 and lower level of Notch1 were observed in rats of XIST siRNA group than those of Model group. Conclusions: Knockdown of lncRNA XIST can repress the myocardial cell apoptosis in AMI model rats by downregulating miR-449 level. 

Retracted: No

PubPeer comments:
 The authors in this paper applied a method called the best-worst method to determine the weights of criteria in multi-criteria decision making. The authors introduced the model in eq.(12) from Ref[23] and introduced the notion u201cconsistency ratiou201d and table 2 from Ref[23] and Ref[24]. However, according to the content in Ref[23] and Ref[24], **Table 2 does not correspond to the model in eq.(12).** Could the authors address this issue? ![file] ![file] ![file] **The following information is from Ref[23]** ![file] ,
Effects of different components of Mao Dongqing’s total flavonoids and total saponins on transient ischemic attack (TIA) model of rats
Authors: Ming Bai
Bao-Song Liu
Meng-Fan Peng
Ming-San Miao
Rui-Juan Ma
Journal: Saudi Journal of Biological Sciences (2018)
Discipline: BIOLOGY & BIOCHEMISTRY
Keywords: Mao Dongqing'stotal flavonoids; Optimal active ratio components; TIA animal model; Total saponins.
Affiliations: Henan University of Chinese Medicine College of Pharmacy, Zhengzhou, Henan 450046, China.

Abstract:  Objective: To study the effects of the different components of the total flavonoids and total saponins from Mao Dongqing's active site on the rats of TIA model, determine the optimal reactive components ratio of Mao Dongqing on the rats of TIA. Methods: TIA rat model was induced by tail vein injection of tert butyl alcohol, the blank group was injected with the same amount of physiological saline, then behavioral score wasevaluated. Determination the level of glutamic acid in serum, the activity of Na+-K+-ATP enzyme, CA++-ATP enzyme and Mg++-ATP enzyme in Brain tissue, observe the changes of hippocampus in brain tissue, the comprehensive weight method was used to evaluate the efficacy of each component finally. Results: The contents of total flavonoids and total saponins in the active part of Mao Dongqing can significantly improve the pathological changes of brain tissue in rats, improve the activity of Na+-K+-ATP enzyme, Ca++-ATP enzyme and Mg++-ATP enzyme in the brain of rats, and reduce the level of glutamic acid in serum. The most significant of the contents was the ratio of 10:6. Conclusion: The different proportions of total flavonoids and total saponins in the active part of Mao Dongqing all has a better effect on the rats with TIA, and the ratio of 10:6 is the best active component for preventing and controlling TIA. 

Retracted: No

PubPeer comments:
 Figure 1: middel dose is a duplicate of large dose. I ve added yellow rectangles to show where I mean. Would the authors please comment? ![file] , 
 Dear Mycosphaerella arachidis. Thank you for your reminder. A photo pasting error has been found. The editorial department has been contacted and an errata will be issued in the near future. ,
TNF stimulates nuclear export and secretion of IL-15 by acting on CRM1 and ARF6
Authors: Hung Hsuchou
Weihong Pan
Abba J Kastin
Suidong Ouyang
Journal: PLoS ONE (2013)
Discipline: Multidisciplinary
Keywords: Interleukin-15; tumor necrosis factor-α; nuclear export; leptomycine B; CRM1
Affiliations: Pennington Biomedical Research Center, Baton Rouge, Louisana, United States of America.

Abstract:  Interleukin (IL)-15 is a ubiquitously expressed cytokine that in the basal state is mainly localized intracellularly, including the nucleus. Unexpectedly, tumor necrosis factor-α (TNF) time-dependently induced nuclear export of IL-15Rα and IL15. This process was inhibited by leptomycine B (LMB), a specific inhibitor of nuclear export receptor chromosomal region maintenance 1 (CRM1). In the presence of TNF, LMB co-treatment led to accumulation of both IL-15Rα and IL-15 in the nucleus of HeLa cells, suggesting that CRM1 facilitates nuclear export and that TNF enhances CRM1 activity. Once in the cytoplasm, IL-15 showed partial co-localization with late endosomes but very little with other organelles tested 4 h after TNF treatment. IL-15Rα showed co-localization with both early and late endosomes, and to a lesser extent with endoplasmic reticulum and Golgi. This indicates different kinetics and possibly different trafficking routes of IL-15 from its specific receptor. The TNF-induced secretion of IL-15 was attenuated by pretreatment of cells by brefeldin A that inhibits ER-to-Golgi transport, or by use of domain negative ADP-ribosylation factor 6 (ARF6) that interferes with exocytotic sorting. We conclude that TNF abolishes nuclear localization of IL-15 and IL-15Rα by acting on CRM1, and it facilitates exocytosis of IL-15 with the involvement of ARF6. 

Retracted: No

PubPeer comments:
 Concern about Figure 4A which was reported to the journal in October 2015. Figure 4A. The IL-15 blot looks very similar to the IgG blot, when one of the 2 is flipped horizontally and slightly compressed. Note the presence of a small air bubble under the 2nd band, an irregularity in the background of the 3rd lane, and two vertical stripes in the position of the 4th lane. Shown with red boxes. ![file] ,
Two Novel Pyran Derivatives: Crystal Structures, Anti-Liver Cancer Activity, and Docking Study
Authors: Li, D.
Guo, Q.
Chen, W. -H.
Wang, H. -Y.
Journal: Journal of Structural Chemistry (2020)
Discipline: CHEMISTRY
Keywords: synthesis; characterization; pyran derivatives; infrared; 1H nuclear magnetic resonance spectroscopy

Abstract: The synthesis and characterization of two new pyran derivatives (1 and 2) are characterized by infrared (IR) and 1H nuclear magnetic resonance spectroscopy (1H NMR), high resolution mass spectrum (HRMS), and single crystal X-ray crystallography. The anticancer activity of compounds is investigated against four human liver cancer cells (Hep G2, SMMC-7721, HHCC, and HB611) by 3-(4,5)-dimethylthiahiazo(-z-y1)-3,5-di-phenytetrazoliumbromide (MTT) assay. Furthermore, molecular docking studies support the biological assay data and suggest that the two compounds have a similar interaction strength with protein.

Retracted: No

PubPeer comments:
 The opening References are absurd, and seemingly taken from a strip of  References wallpaper used by a large number of other papers.  Cancer is one of the most serious clinical problems, particularly in developed countries, despite advances in biomedical research and technology [1, 2]. - [1]. D. Zhang, H. Q. Zhang, S. Zhao, Z. G. Li, and S. X. Hou. Int. J. Electrochem. Sci., 2019, 14, 4659. ** Electrochemical Impedance Spectroscopy Evaluation of Corrosion Protection of X65 Carbon Steel by Halloysite Nanotube-Filled Epoxy Composite Coatings in 3.5% NaCl Solution ** - [2]. S. Guo, R. Chen, H. Li, T. Zhang, and Y. Liu. Int. J. Softw. Eng. Know., 2019, 29, 139. ** Identify Severity Bug Report with Distribution Imbalance by CR-SMOTE and ELM **  According to the World Health Organization (WHO), the incidence of this disease is about 6 million cases per year [3, 4]. - [3]. J. Su, Z. Sheng, L. Xie, G. Li, and A. X. Liu. IEEE T. Commun., 2019, 67, 2527. ** Fast Splitting-Based Tag Identification Algorithm For Anti-Collision in UHF RFID System ** - [4]. J. Su, Z. Sheng, V. C. M. Leung, and Y. Chen. IEEE Wirel. Commun., 2019, 26, 118. ** Energy Efficient Tag Identification Algorithms For RFID: Survey, Motivation And New Design **  Cancer cannot be defined as a single disease, but rather a collection of diseases [5]. - [5]. H. Li, G. Gao, R. Chen, X. Ge, S. Guo, L. and Y. Hao. Int. J. Softw. Eng. Know., 2019, 29, 93. ** The Influence Ranking for Testers in Bug Tracking Systems ** ,
Long non‑coding RNA TUG1 promotes osteosarcoma cell proliferation and invasion through inhibition of microRNA‑212‑3p expression
Authors: Heng Li
Guofeng Tian
Lin Shao
Feipeng Tian
Journal: Experimental and therapeutic medicine (2018)
Discipline: CLINICAL MEDICINE
Keywords: long non-coding RNA; microRNA; migration; osteosarcoma; proliferation.
Affiliations: Department of Orthopedics, Daqing Longnan Hospital, Daqing, Heilongjiang 163453, P.R. China.

Abstract:  Taurine upregulated gene 1 (TUG1), a long non-coding RNA (lncRNA), has recently been suggested to be associated with the development of osteosarcoma (OS), but the underlying molecular mechanism still remains largely unclear. In the present study, it was revealed that TUG1 was significantly upregulated whereas miR-212-3p was significantly downregulated in OS tissues and cell lines, when compared with adjacent non-tumor tissues and normal osteoblasts cell lines, respectively. An inverse association between the TUG1 and miR-212-3p expression was also observed in OS tissues. Furthermore, TUG1 directly interacted with miR-212-3p and negatively regulated the expression of miR-212-3p in OS cells. In vitro experiments further indicated that inhibition of TUG1 suppressed the proliferation and invasion of OS cells. Furthermore, knockdown of miR-212-3p eliminated the suppressive effects of TUG1 inhibition on the proliferation and invasion of OS cells. Taken together, these findings demonstrate that TUG1 promotes OS cell proliferation and invasion by inhibition of miR-212-3p expression, thus suggesting that TUG1 may become a potential therapeutic target for OS. 

Retracted: Yes

PubPeer comments:
 Figs 5C,D and 7A,B. ![file] Could the authors comment on the shared panels with Figs 2C, 3C, 7C of [Feng et al (2017)] ? ![file] And Figs 5C, 6E of [Zhou et al (2018)] ? ![file] , 
 Retracted [14 February 2022] .  Following the publication of this paper, it was drawn to the Editors attention by a concerned reader that the Transwell cell migration assay data shown in Figs. 5C and D, and 7A and B, were strikingly similar to data appearing in different form in other articles by different authors. Owing to the fact that the contentious data in the above article had already been published elsewhere, or were already under consideration for publication, prior to its submission to *Experimental and Therapeutic Medicine*, the Editor has decided that this paper should be retracted from the Journal. The authors were asked for an explanation to account for these concerns, but the Editorial Office did not receive any reply. The Editor apologizes to the readership for any inconvenience caused. ,
Ultra-Processed Diets Cause Excess Calorie Intake and Weight Gain: An Inpatient Randomized Controlled Trial of Ad Libitum Food Intake
Authors: Shanna Yang
Rebecca Howard
Megan Zhou
Juen Guo
Stephanie T Chung
Michael Stagliano
Irene Rozga
Ciaran G Forde
Hongyi Cai
Thomas Cassimatis
Mary Walter
Elise Costa
Kong Y Chen
Valerie Darcey
Klaudia Raisinger
Paule V Joseph
Amber Courville
Suzanne McGehee
Laura A Fletcher
Kevin D Hall
Alexis Ayuketah
Ronald Ouwerkerk
Peter J Walter
Robert Brychta
Ahmed M Gharib
Journal: Cell Metabolism (2019)
Discipline: MOLECULAR BIOLOGY & GENETICS
Keywords: diet quality; energy balance; energy intake; processed food; weight gain
Affiliations: National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, MD, USA. Electronic address: ., National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, MD, USA., National Institutes of Health Clinical Center, Bethesda, MD, USA., Singapore Institute for Clinical Sciences, Singapore, Singapore., National Institute of Nursing Research, Bethesda, MD, USA.

Abstract:  We investigated whether ultra-processed foods affect energy intake in 20 weight-stable adults, aged (mean ± SE) 31.2 ± 1.6 years and BMI = 27 ± 1.5 kg/m2. Subjects were admitted to the NIH Clinical Center and randomized to receive either ultra-processed or unprocessed diets for 2 weeks immediately followed by the alternate diet for 2 weeks. Meals were designed to be matched for presented calories, energy density, macronutrients, sugar, sodium, and fiber. Subjects were instructed to consume as much or as little as desired. Energy intake was greater during the ultra-processed diet (508 ± 106 kcal/day; p = 0.0001), with increased consumption of carbohydrate (280 ± 54 kcal/day; p &lt; 0.0001) and fat (230 ± 53 kcal/day; p = 0.0004), but not protein (-2 ± 12 kcal/day; p = 0.85). Weight changes were highly correlated with energy intake (r = 0.8, p &lt; 0.0001), with participants gaining 0.9 ± 0.3 kg (p = 0.009) during the ultra-processed diet and losing 0.9 ± 0.3 kg (p = 0.007) during the unprocessed diet. Limiting consumption of ultra-processed foods may be an effective strategy for obesity prevention and treatment. 

Retracted: No

PubPeer comments:
 https: steamtraen.blogspot.com 2021 01 some-problems-in-high-profile-study-of.html Includes a useful reply from an author. ,
Upregulation of miR-376c-3p alleviates oxygen-glucose deprivation-induced cell injury by targeting ING5
Authors: Heng Zhang
Jie Zhou
Bing He
Yanjie Yi
Mingxia Zhang
Journal: Cellular & Molecular Biology Letters (2019)
Discipline: MOLECULAR BIOLOGY & GENETICS
Keywords: Apoptosis; Cell cycle; ING5; Oxygen–glucose deprivation; miR-376c-3p.
Affiliations: Department of Pediatrics, Renmin Hospital of Wuhan University, Hubei Province, 430060 China.

Abstract:  Background: The expression level of miR-376c-3p is significantly lower in infants with neonatal hypoxic-ischemic encephalopathy (HIE) than in healthy infants. However, the biological function of this microRNA remains largely elusive. Methods: We used PC-12 and SH-SY5Y cells to establish an oxygen-glucose deprivation (OGD) cell injury model to mimic HIE in vitro. The miR-376c-3p expression levels were measured using quantitative reverse transcription PCR. The CCK-8 assay and flow cytometry were utilized to evaluate OGD-induced cell injury. The association between miR-376c-3p and inhibitor of growth 5 (ING5) was validated using the luciferase reporter assay. Western blotting was conducted to determine the protein expression of CDK4, cyclin D1, Bcl-2 and Bax. Results: MiR-376c-3p was significantly downregulated in the OGD-induced cell injury model. Its overexpression elevated cell viability and impaired cell cycle G0/G1 phase arrest and apoptosis in PC-12 and SH-SY5Y cells after OGD. Downregulation of miR-376c-3p gave the opposite results. We further demonstrated that ING5 was a negatively regulated target gene of miR-376c-3p. Importantly, ING5 knockdown had a similar effect to miR-376c-3p-mediated protective effects against cell injury induced by OGD. Its overexpression abolished these protective effects. Conclusion: Our data suggest that miR-376c-3p downregulated ING5 to exert protective effects against OGD-induced cell injury in PC-12 and SH-SY5Y cells. This might represent a novel therapeutic approach for neonatal HIE treatment. 

Retracted: No

PubPeer comments:
 This article appears to be computer-generated with [SCIgen] . ![file] --- This comment was written by Guillaume Cabanac and Cyril Labbu00e9. Contact: [SeekAndBlastn-Operators@univ-grenoble-alpes.fr](mailto:SeekAndBlastn-Operators@univ-grenoble-alpes.fr). ,
A critical role for phosphoinositide 3-kinase upstream of Gab1 and SHP2 in the activation of ras and mitogen-activated protein kinases by epidermal growth factor
Authors: C Peres
S Chretien
B Payrastre
N Tonks
S Roche
M Laffargue
H Chap
P Raynal
P Mayeux
A Yart
Journal: Journal of Biological Chemistry (2001)
Discipline: BIOLOGY & BIOCHEMISTRY
Keywords: MAPK activation; PI3K; EGF stimulation; Ras activation; SHP2
Affiliations: INSERM U326, IFR 30, Hôpital Purpan, Toulouse 31059, INSERM U363, Hôpital Cochin, 27 rue du Faubourg Saint-Jacques, Paris 75014, France.

Abstract:  Although the mechanisms involved in the activation of mitogen-activated protein kinases (MAPK) by receptor tyrosine kinases do not display an obvious role for phosphoinositide 3-kinases (PI3Ks), we have observed in the nontransformed cell line Vero stimulated with epidermal growth factor (EGF) that wortmannin and LY294002 nearly abolished MAPK activation. The effect was observed under strong stimulation and was independent of EGF concentration. In addition, three mutants of class Ia PI3Ks were found to inhibit MAPK activation to an extent similar to their effect on Akt/protein kinase B activation. To determine the importance of PI3K lipid kinase activity in MAPK activation, we have used the phosphatase PTEN and the pleckstrin homology domain of Tec kinase. Overexpression of these proteins, but not control mutants, was found to inhibit MAPK activation, suggesting that the lipid products of class Ia PI3K are necessary for MAPK signaling. We next investigated the location of PI3K in the MAPK cascade. Pharmacological inhibitors and dominant negative forms of PI3K were found to block the activation of Ras induced by EGF. Upstream from Ras, although association of Grb2 with its conventional effectors was independent of PI3K, we have observed that the recruitment of the tyrosine phosphatase SHP2 required PI3K. Because SHP2 was also essential for Ras activation, this suggested the existence of a PI3K/SHP2 pathway leading to the activation of Ras. In addition, we have observed that the docking protein Gab1, which is involved in PI3K activation during EGF stimulation, is also implicated in this pathway downstream of PI3K. Indeed, the association of Gab1 with SHP2 was blocked by PI3K inhibitors, and expression of Gab1 mutant deficient for binding to SHP2 was found to inhibit Ras stimulation without interfering with PI3K activation. These results show that, in addition to Shc and Grb2, a PI3K-dependent pathway involving Gab1 and SHP2 is essential for Ras activation under EGF stimulation. 

Retracted: No

PubPeer comments:
 Figure 2D appears to have two images which overlap. This is sometimes seen in papermill or u201coutsourcedu201d papers. *** ![file] , 
 Images in Figure 2E and 6D appear to overlap, with altered dimensions. *** ![file] , 
 Two images and figure 6C appear to overlap, although the color has been altered in one. There may be more issues in this paper, but Iu2019ll stop for now. Perhaps the authors could comment. *** ![file] ,
LncRNA PTAR promotes EMT and invasion-metastasis in serous ovarian cancer by competitively binding miR-101-3p to regulate ZEB1 expression
Authors: Haihai Liang
Rui Yang
Tianyi You
Chengyu Wang
Tong Yu
Hua Jiang
Hongli Shan
Xiaoguang Zhao
Yue Han
Lida Yang
Yunyan Gu
Huitong Shan
Journal: Molecular Cancer (2018)
Discipline: MOLECULAR BIOLOGY & GENETICS
Keywords: Epithelial-mesenchymal transition; Ovarian cancer; ZEB1; lncRNA PTAR; miR-101.
Affiliations: Department of Pharmacology (State-Province Key Laboratories of Biomedicine-Pharmaceutics of China, Key Laboratory of Cardiovascular Research, Ministry of Education), College of Pharmacy, Harbin Medical University, Harbin, China., Translational Medicine Research and Cooperation Center of Northern China, Heilongjiang Academy of Medical Sciences, Harbin, 150081, China., Department of Systems Biology, College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150001, China., Department of Systems Biology, College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150086, China. ., Training Center for Students Innovation and Entrepreneurship Education, Harbin Medical University, Harbin, 150086, China. .

Abstract:  Background: Ovarian cancer (OvCa) is one of the most common malignant diseases of the female reproductive system in the world. The majority of OvCa is diagnosed with metastasis in the abdominal cavity. Epithelial-to-mesenchymal transition (EMT) plays a key role in tumor cell metastasis. However, it is still unclear whether long non-coding RNA (lncRNA) is implicated in EMT and influences cell invasion and metastasis in OvCa. Results: In this study, using bioinformatcis analysis, we constructed a lncRNA-mediated competing endogenous RNA (ceRNA) network for mesenchymal OvCa and identified lncRNA AP000695.4, which we named pro-transition associated RNA (PTAR). PTAR was significantly up-regulated in the mesenchymal subtype samples compared with the epithelial subtype samples from the TCGA OvCa data sets. In addition, our study showed that PTAR expression was positively correlated with the expression level of ZEB1 in the mesenchymal OvCa samples. Meanwhile, we found that silencing miR-101 promoted cell migration, whereas the overexpression of miR-101 suppressed EMT and cell migration in OvCa cell lines through the regulation of ZEB1. Further analysis showed that enhanced expression of PTAR promoted EMT and metastasis through the regulation of miR-101, whereas silencing PTAR led to the attenuation of TGF-β1-induced tumorigenicity in ovarian cancer cells. Mechanistically, we found that PTAR acted as a ceRNA of miR-101, as forced expression of PTAR reduced the expression and activity of miR-101. More importantly, the knockdown of PTAR reduced tumorigenicity and metastasis in vivo. Conclusions: Taken together, the results from our study highlight a role for the PTAR-miR-101-ZEB1 axis in OvCa, which offers novel strategies for the prevention of metastasis in OvCa. 

Retracted: No

PubPeer comments:
 Figures 3A, 3B, 4A, 4D and 7D appear to have overlapping images ![file] ![file] ![file] ![file] ,
The dual 980‐nm and 1470‐nm diode laser for vascular lesions
Authors: Uwe Wollina
Alberto Goldman
Journal: Dermatologic Therapy (2020)
Discipline: CLINICAL MEDICINE
Keywords: diode laser; dual laser; vascular lesions.
Affiliations: Department of Dermatology and AllergologyStädtisches Klinikum Dresden Dresden Germany, Division of Plastic SurgeryDoctoral Student on Medicine and Sciences of Health in the Pontifical Catholic University of Rio Grande do Sul Porto Alegre Brazil

Abstract:  Transcutaneous use of dual diode lasers is a new option in dermatology. The aim of the study was to demonstrate the transcutaneous application of a dual laser in dermatologic outpatients. We used a laser system that combines 980 nm and 1470 nm wavelengths for treatment of vascular lesions. Fifty-six adult Caucasian patients of Fitzpatrick skin type I-III, 32 females and 24 males with mean age of (41 ± 3.7) years were included. We treated 497 vascular lesions of skin and lips. Complete clearance was achieved in cherry angiomas, venous lakes, lip hemangioma, and spider nevi in 100% after a single treatment. Patients with couperose and/or facial telangiectasia needed several treatment sessions. Mild to moderate pain during the laser shots was noted in all patients. No adverse events were recorded. The dual 980-nm/1470-nm diode laser is a safe and effective tool for common vascular lesions. 

Retracted: No

PubPeer comments:
 Unexpected similarity. ![file] , 
 1) ![file] 2) ![file] 3) ![file] , 
 Reproduced with minor changes on numbers! ![file] , 
 Reproduced with minor changes on numbers! ![file] , 
 **Duplication and Materials Recycling!** ![file] ![file] , 
 ![file] , 
 **Copying or reproduction of materials without permission of the copyright owner (copyright infringement)!** ![file] ![file] ,
Sheep with scrapie and mastitis transmit infectious prions through the milk
Authors: Ciriaco Ligios
Francesca Demontis
Christina J Sigurdson
Antonello Carta
Maria Giovanna Cancedda
Caterina Maestrale
Cinzia Santucciu
Adriano Aguzzi
James C DeMartini
Mariangela Saba
Cristiana Patta
Journal: Journal of Virology (2011)
Discipline: MICROBIOLOGY
Keywords: Prions; Misfolded proteins; Infectious; Neurological disease; Prion shedding routes
Affiliations: Istituto Zooprofilattico Sperimentale della Sardegna, Sassari, Italy.

Abstract:  Prions are misfolded proteins that are infectious and naturally transmitted, causing a fatal neurological disease in humans and animals. Prion shedding routes have been shown to be modified by inflammation in excretory organs, such as the kidney. Here, we show that sheep with scrapie and lentiviral mastitis secrete prions into the milk and infect nearly 90% of naïve suckling lambs. Thus, lentiviruses may enhance prion transmission, conceivably sustaining prion infections in flocks for generations. This study also indicates a risk of prion spread to sheep and potentially to other animals through dietary exposure to pooled sheep milk or milk products. 

Retracted: No

PubPeer comments:
 Figure 2B. In the right two panels ( Scapie), both blots appear to show some repetitive elements. Marked with rounded boxes in four different colors. Image made darker to bring out some details. Could the authors please comment or provide original blots? ![file] , 
 We are looking into these blots as a high priority. , 
 #2 The western blots in Figure 2B were performed in the Ligios lab. Dr. Aguzzi and I have asked Dr. Ligios to provide the original high resolution, uncropped blots to PubPeer. , 
 Dear Dr Sigurdson and Dr Aguzzi, It has been two years. Any updates on this case, please? There are serious concerns about these blots, and I have not yet seen any updates to take away my concerns. It would be great to post the original blots here, or, a link to these images on an online file share site. ,