PReD-Bench/PRed-Bench huggingface dataset:
Silencing of AP-4 inhibits proliferation, induces cell cycle arrest and promotes apoptosis in human lung cancer cells
Authors: Wei Guo
Shanshan Chen
Guojun Zhang
Yizhuo Xu
Heying Chu
Guoqiang Zhao
Xiaonan Chen
Ping Li
Yuwen DU
Juan Li
Xuanyu Hu
Huaqi Wang
Journal: Oncology Letters (2016)
Discipline: CLINICAL MEDICINE
Keywords: RNA interference; activating enhancer-binding protein-4; lung cancer.
Affiliations: Department of Microbiology and Immunology, College of Basic Medical Sciences, Zhengzhou University, Zhengzhou, Henan 450001, P.R. China., Department of Microbiology and Immunology, Henan Academy of Medical and Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, Henan 450052, P.R. China., Department of Respiratory Medicine, The First Affiliated Hospital, Zhengzhou University, Zhengzhou, Henan 450052, P.R. China.

Abstract:  Activating enhancer-binding protein (AP)-4 is a member of the basic helix-loop-helix transcription factors, and is involved in tumor biology. However, the role of AP-4 in human lung cancer remains to be fully elucidated. In the present study, the expression of AP-4 in human lung cancer tissues and cells was investigated by reverse transcription-quantitative polymerase chain reaction, and it was observed that the level of AP-4 was increased in tumor tissues and cells compared with their normal counterparts. AP-4 expression was knocked down by transfection with a specific small interfering RNA (siRNA) in lung cancer cells, and this indicated that siRNA-mediated silencing of AP-4 inhibited cell proliferation, arrested the cell cycle at the G0/G1 phase and induced apoptosis by modulating the expression of p21 and cyclin D1. The results of the present study suggest that AP-4 may be an oncoprotein that has a significant role in lung cancer, and that siRNA-mediated silencing of AP-4 may have therapeutic potential as a strategy for the treatment of lung cancer. 

Retracted: No

PubPeer comments:
 [Right]: Fig 3A. At [left]: Figure 7 from  Effect of miR-451 on the biological behavior of the esophageal carcinoma cell line EC9706 [(Wang et al 2013)] . The Scramble A549 control FACS is unexpectedly similar to the Blank and Liposome controls of Wang et al. The Blank A549 control FACS is unexpectedly similar to the Scramble control of Wang et al. ![file] , 
 [Perhaps a systemic problem] . Journals and readers may wish to proceed with caution. ,
Integrative analyses identify osteopontin, LAMB3 and ITGB1 as critical pro-metastatic genes for lung cancer
Authors: Xiao-Min Wang
De-Shui Jia
He-Chun Lin
Qin Geng
Ming Yao
Jin-Jun Li
Ming-Xia Yan
Lei Liu
Jing Li
Xiang-Huo He
Journal: PloS one (2013)
Discipline: Multidisciplinary
Keywords: Regulatory genes; Lung cancer; Metastasis; Gene array; Bioinformatics analyses
Affiliations: State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.

Abstract:  Objective: To explore the key regulatory genes associated with lung cancer in order to reduce its occurrence and progress through silencing these key genes. Methods: To identify the key regulatory genes involved in lung cancer, we performed a combination of gene array and bioinformatics analyses to compare gene transcription profiles in 3 monoclonal cell strains with high, medium or low metastatic abilities, which were separated from the SPC-A-1sci and SPC-A-1 cell lines by limiting dilution monoclone assay. We then analyzed those genes' biological activities by knocking down their expression in SPC-A-1sci cells using siRNA and lenti-viral shRNA vectors, followed by determinations of the invasion and migration capabilities of the resulting cell lines in vitro as well as their potential for inducing occurrence and metastasis of lung cancer in vivo. To examine the clinical relevance of these findings, we analyzed the expression levels of the identified genes in human lung cancer tissues (n = 135) and matched adjacent normal tissues by immunohistochemical (IHC) staining. Results: Three monoclonal cell strains characterized with high, medium or low metastatic abilities were successfully selected. Gene array and bioinformatics analyses implied that osteopontin, LAMB3 and ITGB1 were key genes involved in lung cancer. Knockdown of these genes suppressed human lung cancer cell invasion and metastasis in vitro and in vivo. Clinical sample analyses indicated that osteopontin, LAMB3 and ITGB1 protein expression levels were higher in lung cancer patients, compared to non-cancerous adjacent tissues, and correlated with lymphatic metastasis. Conclusions: We confirmed that osteopontin, LAMB3 and ITGB1 played important roles in the occurrence and metastasis of lung cancer, thus provided important clues to understanding the molecular mechanism of metastasis and contributing to the therapeutic treatment of lung cancer. 

Retracted: No

PubPeer comments:
 Figure 3. Some panels representing different experiments (e.g., invasion vs migration, or Mock vs. NC) appear to show areas of overlap, as highlighted with blue and green boxes. ![file] ,
Utilization of Saccharomyces cerevisiae recombinant strain incapable of both ethanol and glycerol biosynthesis for anaerobic bioproduction
Authors: Takashi Hirasawa
Hiroshi Shimizu
Yoshihiro Ida
Chikara Furusawa
Journal: Applied microbiology and biotechnology (2013)
Discipline: BIOLOGY & BIOCHEMISTRY
Keywords: Yeast; Saccharomyces cerevisiae; Ethanol; Glycerol; Bioproduction
Affiliations: Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, 1-5 Yamadaoka, Suita, Osaka 565-0871, Japan.

Abstract:  The yeast Saccharomyces cerevisiae produces ethanol and glycerol as major unwanted byproducts, unless ethanol and glycerol are the target compounds. Minimizing the levels of these byproducts is important for bioproduction processes using yeast cells. In this study, we constructed a yeast strain in which both ethanol and glycerol production pathways were disrupted and examined its culture characteristics. In wild-type yeast strain, metabolic pathways that produce ethanol and glycerol play an important role in reoxidizing nicotinamide adenine dinucleotide (NADH) generated during glycolysis, particularly under anaerobic conditions. Strains in which both pathways were disrupted therefore failed to grow and consume glucose under anaerobic conditions. Introduction of desired metabolic reaction(s) coupled with NADH oxidation enabled the engineered strain to consume substrate and produce target compound(s). Here we introduced NADH-oxidization-coupled L-lactate production mechanisms into a yeast strain incapable of ethanol and glycerol biosynthesis, based on in silico simulation using a genome-scale metabolic model of S. cerevisiae. From the results of in silico simulation based on flux balance analysis, a feasible anaerobic non-growing metabolic state, in which L-lactate yield approached the theoretical maximum, was identified and this phenomenon was verified experimentally. The yeast strain incapable of both ethanol and glycerol biosynthesis is a potentially valuable host for bioproduction coupled with NADH oxidation under anaerobic conditions. 

Retracted: No

PubPeer comments:
 This title is misleading. All strains described still produce ethanol. Even though the strain produces much less ethanol than the WT, it is misleading to claim that it is  incapable of producing ethanol. The engineered strains still produce 4.8% and 6.8% of the theoretical ethanol yield. ,
RETRACTED ARTICLE: Complete mitochondrial genome of the Swan Goose (Anser cygnoides L.) and its phylogenetic analysis
Authors: Xing You Liu
Jian He Hu
Guang Hui Wei
Chang Zhong Liu
Journal: Mitochondrial DNA Part A (2016)
Discipline: MOLECULAR BIOLOGY & GENETICS
Keywords: Anser cygnoides; genome; mitochondrion; phylogenetic analysis.
Affiliations: a College of Animal Science, Henan Institute of Science and Technology , Xinxiang , Henan Province , China.

Abstract:  In this study, we undertook the first complete the Swan Goose (Anser cygnoides L.) mitochondrial genome. The total length of the mitogenome is 16,739 bp. It contains the typical structure, including 13 protein-coding genes, 22 transfer RNA genes, two ribosomal RNA genes, and one D-loop region. The overall composition of the mitogenome is A (29.2%), G (15.8%), C (32.8%), and T (22.2%). Besides, the base preference of AT was not determined. Twenty-two kinds of tRNA were all typically cloverleaf structures. According to the phylogenetic analysis, A. cygnoides L. has a closer relationship with Anser anser. 

Retracted: Yes

PubPeer comments:
 Retracted, see https: www.tandfonline.com doi full 10.1080 24701394.2020.1758395 ( The above article has been retracted as, subsequent to publication, duplication has been found in the article content and figure 1 has been reused from the following earlier published article ). Backgrounds in a technical report at https: www.researchgate.net publication 337063445 ,
Evaluation of the Newcastle disease virus F and HN proteins in protective immunity by using a recombinant avian paramyxovirus type 3 vector in chickens
Authors: Peter L Collins
Siba K Samal
Sachin Kumar
Baibaswata Nayak
Journal: Journal of Virology (2011)
Discipline: MICROBIOLOGY
Keywords: Newcastle disease virus; avian paramyxoviruses; viral vector vaccine; reverse-genetics system; recombinant viruses
Affiliations: Virginia-Maryland Regional College of Veterinary Medicine, University of Maryland, College Park, MD 20742, USA.

Abstract:  Newcastle disease virus (NDV) belongs to serotype 1 of the avian paramyxoviruses (APMV-1) and causes severe disease in chickens. Current live attenuated NDV vaccines are not fully satisfactory. An alternative is to use a viral vector vaccine that infects chickens but does not cause disease. APMV serotype 3 infects a wide variety of avian species but does not cause any apparent disease in chickens. In this study, we constructed a reverse-genetics system for recovery of infectious APMV-3 strain Netherlands from cloned cDNAs. Two recombinant viruses, rAPMV3-F and rAPMV3-HN, were generated expressing the NDV fusion (F) and hemagglutinin-neuraminidase (HN) proteins, respectively, from added genes. These viruses were used to immunize 2-week-old chickens by the oculonasal route in order to evaluate the contribution of each protein to the induction of NDV-specific neutralizing antibodies and protective immunity. Each virus induced high titers of NDV-specific hemagglutination inhibition and serum neutralizing antibodies, but the response to F protein was greater. Protective immunity was evaluated by challenging the immunized birds 21 days later with virulent NDV via the oculonasal, intramuscular, or intravenous route. With oculonasal or intramuscular challenge, all three recombinant viruses (rAPMV3, rAPMV3-F, and rAPMV3-HN) were protective, while all unvaccinated birds succumbed to death. These results indicated that rAPMV3 alone can provide cross-protection against NDV challenge. However, with intravenous challenge, birds immunized with rAPMV3 were not protected, whereas birds immunized with rAPMV3-F alone or in combination with rAPMV3-HN were completely protected, and birds immunized with rAPMV3-HN alone were partially protected. These results indicate that the NDV F and HN proteins are independent neutralization and protective antigens, but the contribution by F is greater. rAMPV3 represents an avirulent vaccine vector that can be used against NDV and other poultry pathogens. 

Retracted: Yes

PubPeer comments:
null, 
 2020 retraction. https: jvi.asm.org content 94 6 e01867-19 It has been called to our attention that in Fig. 6C, lanes 4 and 10 (top blot) and lanes 9 and 10 (bottom blot) are duplicates. Since the samples used for this figure are no longer available, we are taking responsibility for the mistakes and retracting the paper. ,
ACADL Functions as a Tumor Suppressor in Hepatocellular Carcinoma Metastasis by Inhibiting Matrix Metalloproteinase 14
Authors: Danfeng Guo
Huapeng Zhang
Jie Li
Xiaodan Zhang
Wenzhi Guo
Dongsheng Yu
Shuijun Zhang
Chun Pang
Honglei Cui
Xiaoyi Shi
Journal: Frontiers in Oncology (2022)
Discipline: CLINICAL MEDICINE
Keywords: ACADL; MMP14; STAT3; hepatocellular carcinoma; metastasis.
Affiliations: Henan Key Laboratory for Digestive Organ Transplantation, Zhengzhou, China.

Abstract:  High aggressiveness is the main reason for the poor prognosis of hepatocellular carcinoma (HCC) patients. However, its molecular mechanisms still remain largely unexplored. ACADL, a mitochondrial enzyme that facilitates the primary regulated step in mitochondrial fatty acid oxidation, plays a role in HCC growth inhibition. However, the function of ACADL in tumor metastasis is not well elucidated. We found that the reduced expression of ACADL is closely associated with the loss of tumor encapsulation, extrahepatic metastasis, and poor prognosis in HCC patients. Upregulation of ACADL significantly inhibited HCC migration and invasion ability. Whereas knockdown of ACADL markedly enhanced cell invasive capability. Expression of matrix metalloproteinase-14 (MMP14) was negatively associated with the content of ACADL in HCC specimens. MMP14-positive patients with a low expression of ACADL showed worse outcome. Treatment with MMP14 agonist reversed the inhibitory effect of ACADL on HCC metastasis. In addition, ACADL negatively regulated MMP14 expression by inhibiting the STAT3 signaling pathway, as the sustained activation of STAT3 effectively restored the level of MMP14 in ACADL-overexpressed cells. Collectively, these findings disclose that ACADL represses HCC metastasis via STAT3-MMP14 pathway. This study may propose a promising strategy for the precise treatment of metastatic HCC patients. 

Retracted: No

PubPeer comments:
 There seems to be a image that appears in both Figure 2 and Figure 4. *** ![file] ,
A nicotinic hypothesis for Covid-19 with preventive and therapeutic implications
Authors: Makoto Miyara
Felix A Rey
Jean-Pierre Changeux
Zahir Amoura
Journal: Comptes Rendus Biologies (2020)
Discipline: BIOLOGY & BIOCHEMISTRY
Keywords: Covid-19; clinical trials of nicotine patches; nicotinic receptors; smoking.
Affiliations: Institut Pasteur CNRS UMR 3571 Department of Neuroscience and Collège de France, Paris France.

Abstract:  SARS-CoV-2 epidemics raises a considerable issue of public health at the planetary scale. There is a pressing urgency to find treatments based upon currently available scientific knowledge. Therefore, we tentatively propose a hypothesis which hopefully might ultimately help save lives. Based on the current scientific literature and on new epidemiological data which reveal that current smoking status appears to be a protective factor against the infection by SARS-CoV-2 [1], we hypothesize that the nicotinic acetylcholine receptor (nAChR) plays a key role in the pathophysiology of Covid-19 infection and might represent a target for the prevention and control of Covid-19 infection. 

Retracted: No

PubPeer comments:
 Figure 1B. * Red boxes: The two  Triptolide panels appear to look very similar to each other. Yet, the percentages appear to be different. ![file] ,
Pre- and post-operative evaluation: percentages of circulating myeloid-derived suppressor cells in rectal cancer patients
Authors: L Yuan
P Zhao
Z Suo
B Xu
H Fan
P Yuan
Journal: Neoplasma (2015)
Discipline: CLINICAL MEDICINE
Keywords: myeloid-derived suppressor cells, rectal cancer, plasma arginase I, local recurrence, disease free survival.

Abstract:  This study aims to explore whether pre-operative or post-operative percentages of circulating myeloid-derived suppressor cells (MDSC) have any correlations with clinicopathological parameters in patients with rectal cancer and have any predictive values for local recurrence and disease free survival. Lin-/HLADR-/CD11b+/CD33+ MDSCs were analyzed in the study. Blood samples before and after surgery were measured by flow cytometry to determine the MDSC percentages. Plasma arginase I levels were analyzed using an enzyme-linked immunosorbent assay. Digital rectal examination, abdominal ultrasonography, or computed tomography was performed every three months after surgery to monitor local recurrence. Prior to surgery, cancer patients presented with higher levels of circulating MDSC compared to healthy controls (medians of 3.89% and 0.57%, respectively). Seven days after operation, we observed an immediate increase in MDSC followed by a downtrend. Local recurrence was observed in 11 of 41 patients (26.8%) with stage I/II cancer and 11 of 23 patients (47.8%) with stage III cancer. Significantly higher percentages of MDSC were observed in patients who had local recurrence versus patients without local recurrence. Multivariate analysis further verified that the pre-operative level of MDSC was significantly associated with local recurrence (P=0.038). Therefore, our results indicate that pre-operative percentage of MDSC appears to be a reliable prognostic marker for local recurrence and poor disease free survival in rectal cancer patients with curative resection. Keywords: myeloid-derived suppressor cells, rectal cancer, plasma arginase I, local recurrence, disease free survival. 

Retracted: No

PubPeer comments:
 Two flow cytometry results, SSC vs FSC, presented as A) Healthy donor and B) Patient with rectal cancer are in fact the same: internal replication. The corresponding author has multiple issues with data manupilations, which is documented at Pubpeer. As the data in this paper is based on patient materials and may have clinical implications it is paramount that the authors disclose their raw data. ![file] ![file] , 
 One year and no correction. I can add that I think there is lack of ethical approval from principal investigators current home institution (Oslo University Hospital). Only approval from China is listed. ,
Poor dental hygiene and periodontal health in nursing home residents with dementia: an observational study
Authors: Johannes Schröder
Dominik Baumgart
Andreas Zenthöfer
Peter Rammelsberg
Nicoleta Corcodel
Alexander Jochen Hassel
Tomas Cabrera
Journal: Odontology (2017)
Discipline: CLINICAL MEDICINE
Keywords: Dementia; Elderly; Nursing home; Oral health; Oral hygiene.
Affiliations: Department of Prosthodontics, Dental School, University of Heidelberg, Im Neuenheimer Feld 400, 69120, Heidelberg, Germany. ., Department of Prosthodontics, Dental School, University of Heidelberg, Im Neuenheimer Feld 400, 69120, Heidelberg, Germany., Institute of Gerontology, University of Heidelberg, Heidelberg, Germany., Section of Geriatric Psychiatry, University of Heidelberg, Heidelberg, Germany.

Abstract:  Poor oral health conditions are well documented in the institutionalized elderly, but the literature is lacking research on relationships between dementia and periodontal health in nursing home residents. The purpose of this cohort study, therefore, was to assess whether dementia is associated with poor oral health/denture hygiene and an increased risk of periodontal disease in the institutionalized elderly. A total of 219 participants were assessed using the Mini Mental State Examination (MMSE) to determine cognitive state. According to the MMSE outcome, participants scoring ≤20 were assigned to dementia group (D) and those scoring &gt;20 to the non-dementia group (ND), respectively. For each of the groups D and ND, Gingival Bleeding Index (GBI) and Denture Hygiene Index (DHI) linear regression models were used with the confounders age, gender, dementia, number of comorbidities and number of permanent medications. To assess the risk factors for severe periodontitis as measured by the Community Index of Periodontal Treatment Needs, a logistic regression analysis was performed. Statistical analysis revealed no significant differences of GBI as well of DHI for demented and healthy subjects (p &gt; 0.05). Severe periodontitis was detected in 66 % of participants with dementia. The logistic regression showed a 2.9 times increased risk among demented participants (p = 0.006). Oral hygiene, denture hygiene and periodontal health are poor in nursing home residents. The severity of oral problems, primarily periodontitis, seems to be enhanced in subjects suffering from dementia. Longitudinal observations are needed to clarify the cause-reaction relationship. 

Retracted: No

PubPeer comments:
 what was the follow up period of cohort in your papeR ,
The Potential Role of Complement System in the Progression of Ovarian Clear Cell Carcinoma Inferred from the Gene Ontology-Based Immunofunctionome Analysis
Authors: Yi-Pin Yang
Chia-Ming Chang
Tzu-Wei Lin
Mu-Hsien Yu
Kuo-Min Su
Peng-Hui Wang
Cheng-Chang Chang
Li-Chun Liu
Ping-Hsing Tsai
Mong-Lien Wang
Journal: International Journal of Molecular Sciences (2020)
Discipline: CHEMISTRY
Keywords: complement system; gene ontology (GO); immunological function; machine learning; ovarian clear cell carcinoma (OCCC).
Affiliations: Department of Obstetrics and Gynecology, Tri-service General Hospital, National Defense Medical Center, Taipei 114, Taiwan., Department of Medical Research, Taipei Veterans General Hospital, Taipei 112, Taiwan., School of Medicine, National Yang-Ming University, Taipei 112, Taiwan.

Abstract:  Ovarian clear cell carcinoma (OCCC) is the second most common epithelial ovarian carcinoma (EOC). It is refractory to chemotherapy with a worse prognosis after the preliminary optimal debulking operation, such that the treatment of OCCC remains a challenge. OCCC is believed to evolve from endometriosis, a chronic immune/inflammation-related disease, so that immunotherapy may be a potential alternative treatment. Here, gene set-based analysis was used to investigate the immunofunctionomes of OCCC in early and advanced stages. Quantified biological functions defined by 5917 Gene Ontology (GO) terms downloaded from the Gene Expression Omnibus (GEO) database were used. DNA microarray gene expression profiles were used to convert 85 OCCCs and 136 normal controls into to the functionome. Relevant offspring were as extracted and the immunofunctionomes were rebuilt at different stages by machine learning. Several dysregulated pathogenic functions were found to coexist in the immunopathogenesis of early and advanced OCCC, wherein the complement-activation-alternative-pathway may be the headmost dysfunctional immunological pathway in duality for carcinogenesis at all OCCC stages. Several immunological genes involved in the complement system had dual influences on patients' survival, and immunohistochemistrical analysis implied the higher expression of C3a receptor (C3aR) and C5a receptor (C5aR) levels in OCCC than in controls. 

Retracted: No

PubPeer comments:
 Dear colleagues, I wonder what causes the difference in PFS for a small cohort of ovarian clear cell carcinoma patients (n=25) reanalyzed in this paper compared to the original paper (Uehara 2015)? Maybe censored data were labelled as events? If a correct analysis leads to other results I think the paper should be corrected or retracted as it seems to be an important validation for the bioinformatic analysis. ![file] ,
MiR-27a targets sFRP1 in hFOB cells to regulate proliferation, apoptosis and differentiation
Authors: Jieruo Gu
Qiuxia Li
Qing Lv
Donggeng Guo
Qiujing Wei
Shuangyan Cao
Journal: PloS one (2014)
Discipline: Multidisciplinary
Keywords: MicroRNAs; miR-27; osteoblast differentiation; bone formation; Wnt signaling pathway
Affiliations: Department of Rheumatology, Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, China.

Abstract:  MicroRNAs (miRNAs) play a key role in the regulation of almost all the physiological and pathological processes, including bone metabolism. Recent studies have suggested that miR-27 might play a key role in osteoblast differentiation and bone formation. Increasing evidence indicates that the canonical Wnt signaling pathway contributes to different stages of bone formation. In this study, we identify miR-27a can promote osteoblast differentiation by repressing a new target, secreted frizzled-related proteins 1 (sFRP1) expression at the transcriptional level. Here, 21 candidate targets of miR-27a involved in canonical Wnt/β-catenin signaling were predicted, and a significant decrease in sFRP1 luciferase activity was observed both in 293T and MG63 cells co-transfected with the matched luciferase reporter constructs and miR-27a mimic. Furthermore, the presence of exogenous miR-27a significantly decreased sFRP1 mRNA and protein expression in hFOB1.19 cells during both proliferation and osteogenic differentiation. The over-expression of miR-27a or knockdown sFRP1 significantly increased the percentage of apoptotic hFOBs, the percentage of cells in the G2-M phase of the cell cycle and the expression of key osteoblastic markers, including ALP, SPP1, RUNX2 and ALP activity. Over-expression of miR-27a or knockdown of endogenous sFRP1 led to an accumulation of β-catenin in hFOBs. In the present study, we demonstrate that miR-27a induced gene silencing effect is a vital mechanism contributing to bone metabolism in hFOB cells in vitro, which is partly affected by the post-transcriptional regulation of sFRP1, during osteoblast proliferation, apoptosis and differentiation. 

Retracted: No

PubPeer comments:
 Figure 6. * Blue boxes: the left panel in Figure 6A and the left panel in Figure 6C appear to look identical. ![file] ,
Transcriptional profiling of developing mouse epidermis reveals novel patterns of coordinated gene expression
Authors: Gavin D Richardson
Colin A B Jahoda
Katherine A Fantauzzo
Angela M Christiano
Hisham Bazzi
Journal: Developmental Dynamics (2007)
Discipline: MOLECULAR BIOLOGY & GENETICS
Keywords: mammalian epidermis; epidermal morphogenesis; keratinocytes; stratification; differentiation
Affiliations: Departments of Genetics and Development, Columbia University, New York, New York 10032, USA.

Abstract:  The mammalian epidermis is the first line of defense against external environmental challenges including dehydration. The epidermis undergoes a highly intricate developmental program in utero, transforming from a simple to a complex stratified epithelium. During this process of stratification and differentiation, epidermal keratinocytes express a defined set of structural proteins, mainly keratins, whose expression is controlled by largely unknown mechanisms. In order to identify novel factors contributing to epidermal morphogenesis, we performed a global transcriptional analysis of the developing mouse epidermis after separating it from the underlying dermis (E12.5-E15.5). Unexpectedly, the recently identified genes encoding secreted peptides dermokine (Dmkn), keratinocyte differentiation-associated protein (krtdap), and suprabasin (Sbsn) as well as a largely uncharacterized embryonic keratin (Krt77), were among the most highly differentially expressed genes. The three genes encoding the secreted proteins form a cluster in an approximately 40-Kb locus on human chromosome 19 and the syntenic region on mouse chromosome 7 known as the stratified epithelium secreted peptides complex (SSC). Using whole mount in situ hybridization, we show that these genes show a coordinated spatio-temporal expression pattern during epidermal morphogenesis. The expression of these genes initiates in the nasal epithelium and correlates with the initiation of other epidermal differentiation markers such as K1 and loricrin (Byrne et al. [1994] Development 120:2369-2383), as well as the initiation of barrier formation. Our observations reveal a coordinated mode of expression of the SSC genes as well as the correlation of their initiation in the nasal epithelium with the initiation of barrier formation at this site. 

Retracted: No

PubPeer comments:
null, 
null, 
null, 
null, 
 24 hr aspirin treatment in Fig. 5B causes unexpectedly similar Cyt c release to 48 hr aspirin treatment in Fig. 6B.![file] ,
The effect of alcohol cue exposure and acute intoxication on inhibitory control processes and ad libitum alcohol consumption
Authors: Laura Baines
Andrew Jones
Matt Field
Paul Christiansen
Journal: Psychopharmacology (2019)
Discipline: NEUROSCIENCE & BEHAVIOR
Keywords: Alcohol; Craving; Cue reactivity; Inhibitory control; Proactive slowing
Affiliations: Department of Psychological Sciences, University of Liverpool, L69 7ZA, Liverpool, UK. ., UK Centre for Tobacco and Alcohol Studies, University of Liverpool, Liverpool, UK. ., UK Centre for Tobacco and Alcohol Studies, University of Liverpool, Liverpool, UK., Department of Psychology, University of Sheffield, Sheffield, UK., Department of Psychological Sciences, University of Liverpool, L69 7ZA, Liverpool, UK.

Abstract:  Rationale: Alcohol intoxication and alcohol cue exposure impair 'reactive' inhibitory control and increase motivation to drink. However, inhibitory control is a multi-component process that also comprises signal detection and proactive control. It is unknown whether intoxication and cue exposure selectively influence these subprocesses in heavy drinkers. Objectives: In two pre-registered studies, we investigated whether exposure to alcohol-related cues (study 1) and alcohol priming (study 2) impair each of these subprocesses of inhibitory control and increase motivation to drink. Methods: In study 1, 64 heavy drinkers completed a modified stop-signal task in an alcohol context (with embedded alcohol cues) and a neutral context (with embedded neutral cues) followed by a subjective measure of craving and a bogus taste test to measure ad libitum alcohol consumption. In study 2, 36 heavy drinkers consumed an alcoholic beverage (0.6 g/kg body weight), an alcohol-placebo beverage, and water on a within-subjects basis, followed by the modified stop-signal task and a bogus taste test. Results: In study 1, alcohol cue exposure did not impair inhibitory control subprocesses. Reactive control was unexpectedly better following alcohol cue exposure (compared to neutral cue exposure). However, craving and ad libitum consumption increased as expected. In study 2, reactive control was significantly impaired following the alcohol and control primes, relative to the placebo, but there was no effect on proactive slowing or signal detection. As expected, intoxication increased motivation to drink and ad libitum consumption (compared to placebo and control). Conclusions: Alcohol intoxication and cue exposure increase motivation to drink in the absence of impairments in subcomponents of inhibitory control. 

Retracted: No

PubPeer comments:
 Although it was not made clear in this paper - both studies calculated Stop Signal Reaction time using the mean method. ,
AtKP1, a kinesin-like protein, mainly localizes to mitochondria in Arabidopsis thaliana
Authors: Hai Qing Wang
Tao Xu
Zhe Qu
Cheng Zhi Ni
Guo Qin Liu
Journal: Cell Research (2005)
Discipline: MOLECULAR BIOLOGY & GENETICS
Keywords: Kinesins; Kinesin-like proteins; AtKP1; Antibody; Immunoblot analysis
Affiliations: State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing.

Abstract:  Kinesins and kinesin-like proteins (KLPs) constitute a large family of microtubule-based motors that play important roles in many fundamental cellular and developmental processes. To date, a number of kinesins or KLPs have been identified in plants including Arabidopsis thaliana. Here, a polyclonal antibody against AtKP1 (kinesin-like protein 1 in A. thaliana) was raised by injection the expressed AtKP1 specific C-terminal polypeptides in rabbits, and immunoblot analysis was conducted with the affinity-purified anti-AtKP1 antibody. The results indicated that this antibody recognized the AtKP1 fusion proteins expressed in E. coli and proteins of ~125 kDa in the soluble fractions of Arabidopsis extracts. The molecular weight was consistent with the calculated molecular weight based on deduced amino acids sequence of AtKP1. To acquire the subcellular localization of the protein, AtKP1 in Arabidopsis root cells was observed by indirect immunofluorescence microscopy. AtKP1 was localized to particle-like organelles in interphase or dividing cells, but not to mitotic microtubule arrays. Relatively more AtKP1 was found in isolated mitochondria fraction on immunoblot of the subcellular fractions. The AtKP1 protein could not be released following a 0.6 M KI washing, indicating that AtKP1 is tightly bind to mitochondria and might function associated with this kind of organelles. 

Retracted: No

PubPeer comments:
 Figure 1: it appears as some images were duplicated (boxes of same color), as suggested by bands shape, darker areas within bands, and features in the background at 43 kDa. Legend (below) though says antibodies were different. Could the authors please check, clarify, and eventually post the original uncropped scans of blots at better resolution? ![file] , 
 Figure 4A, much more similar than expected (orange boxes), and it seems a brush tool was used around the right-most band. Could the authors please post the uncropped scan of the blot? ![file] ,
Preventing BRCA 1/ ZBRK 1 repressor complex binding to the GOT2 promoter results in accelerated aspartate biosynthesis and promotion of cell proliferation
Authors: Kai Zhang
Mengjiao Wu
Jinting Li
Ruoxi Hong
Weimin Zhang
Jiawen Fan
Fei Xu
Wen Xia
Yan Wang
Shusen Wang
Qimin Zhan
Xi Xia
Jie Chen
Journal: Molecular Oncology (2019)
Discipline: MOLECULAR BIOLOGY & GENETICS
Keywords: BRCA1; GOT2; ZBRK1; aspartate; breast cancer
Affiliations: State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China., Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Laboratory of Molecular Oncology, Peking University Cancer Hospital & Institute, Beijing, China., Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Veterinary Medicine, China Agricultural University, Beijing, China., Beijing Key Laboratory of Detection Technology for Animal-Derived Food Safety and Beijing Laboratory for Food Quality and Safety, China Agricultural University, Beijing, China., State Key Laboratory of Molecular Oncology, National Cancer Institute and Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.

Abstract:  Breast cancer susceptibility gene 1 (BRCA1) has been implicated in modulating metabolism via transcriptional regulation. However, direct metabolic targets of BRCA1 and the underlying regulatory mechanisms are still unknown. Here, we identified several metabolic genes, including the gene which encodes glutamate-oxaloacetate transaminase 2 (GOT2), a key enzyme for aspartate biosynthesis, which are repressed by BRCA1. We report that BRCA1 forms a co-repressor complex with ZBRK1 that coordinately represses GOT2 expression via a ZBRK1 recognition element in the promoter of GOT2. Impairment of this complex results in upregulation of GOT2, which in turn increases aspartate and alpha ketoglutarate production, leading to rapid cell proliferation of breast cancer cells. Importantly, we found that GOT2 can serve as an independent prognostic factor for overall survival and disease-free survival of patients with breast cancer, especially triple-negative breast cancer. Interestingly, we also demonstrated that GOT2 overexpression sensitized breast cancer cells to methotrexate, suggesting a promising precision therapeutic strategy for breast cancer treatment. In summary, our findings reveal that BRCA1 modulates aspartate biosynthesis through transcriptional repression of GOT2, and provides a biological basis for treatment choices in breast cancer. 

Retracted: No

PubPeer comments:
 Apparently there is some controversy on the naming of this variant: https: www.nytimes.com 2022 03 11 science deltacron-coronavirus-variant.html ,
Canine Mammary Cancer Stem Cells are Radio- and Chemo- Resistant and Exhibit an Epithelial-Mesenchymal Transition Phenotype
Authors: Rod W Else
Lisa Y Pang
Alejandro Cervantes-Arias
David J Argyle
Journal: Cancers (2011)
Discipline: CLINICAL MEDICINE
Keywords: Canine mammary carcinoma; cancer stem cells; stem cell characteristics; tumor growth; metastasis
Affiliations: Royal (Dick) School of Veterinary Studies and Roslin Institute, The University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, UK. .

Abstract:  Canine mammary carcinoma is the most common cancer among female dogs and is often fatal due to the development of distant metastases. In humans, solid tumors are made up of heterogeneous cell populations, which perform different roles in the tumor economy. A small subset of tumor cells can hold or acquire stem cell characteristics, enabling them to drive tumor growth, recurrence and metastasis. In veterinary medicine, the molecular drivers of canine mammary carcinoma are as yet undefined. Here we report that putative cancer stem cells (CSCs) can be isolated form a canine mammary carcinoma cell line, REM134. We show that these cells have an increased ability to form tumorspheres, a characteristic of stem cells, and that they express embryonic stem cell markers associated with pluripotency. Moreover, canine CSCs are relatively resistant to the cytotoxic effects of common chemotherapeutic drugs and ionizing radiation, indicating that failure of clinical therapy to eradicate canine mammary cancer may be due to the survival of CSCs. The epithelial to mesenchymal transition (EMT) has been associated with cancer invasion, metastasis, and the acquisition of stem cell characteristics. Our results show that canine CSCs predominantly express mesenchymal markers and are more invasive than parental cells, indicating that these cells have a mesenchymal phenotype. Furthermore, we show that canine mammary cancer cells can be induced to undergo EMT by TGFβ and that these cells have an increased ability to form tumorspheres. Our findings indicate that EMT induction can enrich for cells with CSC properties, and provide further insight into canine CSC biology. 

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. ,
Production Calculation Model of Thermal Recovery after Hydraulic Fracturing and Packing in Tight Reservoir
Authors: Tomas Pieler
Annette Borchers
Journal: Processes (2021)
Discipline: CHEMISTRY
Keywords: Xenopus embryos; pluripotent cells; organogenesis; human embryonic stem cells; animal cap cells

Abstract:  Xenopus embryos provide a rich source of pluripotent cells that can be differentiated into functional organs. Since the molecular principles of vertebrate organogenesis appear to be conserved between Xenopus and mammals, this system can provide useful guidelines for the directional manipulation of human embryonic stem cells. Pluripotent Xenopus cells can be easily isolated from the animal pole of blastula stage Xenopus embryos. These so called "animal cap" cells represent prospective ectodermal cells, but give rise to endodermal, mesodermal and neuro-ectodermal derivatives if treated with the appropriate factors. These factors include evolutionary conserved modulators of the key developmental signal transduction pathways that can be supplied either by mRNA microinjection or direct application of recombinant proteins. This relatively simple system has added to our understanding of pancreas, liver, kidney, eye and heart development. In particular, recent studies have used animal cap cells to generate ectopic eyes and hearts, setting the stage for future work aimed at programming pluripotent cells for regenerative medicine. 

Retracted: No

PubPeer comments:
 In a series of MDPI papers, this paper too shows non-relevant references to the subject at hand. For example, the references [9] and [10] are irrelevant to the Specific Calculation Formula (!) as the formula was not found in either one of the references [9, 10]! ![file] ![file] , 
 Could the authors please provide the relevant source references for the formulas boxed in the text below? ![file] ,
A critical evaluation of glucocorticoids in the management of severe COVID-19
Authors: Laura Perra
Nicola Petrosillo
Marco Aiello
Edoardo Migliori
Cinzia Solinas
Journal: Cytokine & growth factor reviews (2020)
Discipline: MOLECULAR BIOLOGY & GENETICS
Keywords: ARDS; COVID-19; Glucocorticoids; Immune response; SARS-CoV-2.
Affiliations: Azienda Tutela Salute Sardegna, Hospital Antonio Segni, via Cappuccini, 7, Ozieri (SS), Italy. Electronic address: ., Azienda Tutela Salute Sardegna, via Enrico Costa n. 57, Sassari, Italy. Electronic address: ., Azienda Ospedaliero Universitaria Policlinico Vittorio Emanuele, Via Santa Sofia, 78, Catania, Italy. Electronic address: ., Columbia University Medical Center, Columbia Center for Translational Immunology, 650 West 168th St., New York, NY 10032, United States. Electronic address: ., National Institute for Infectious Diseases 'L. Spallanzani', IRCCS, Via Portuense, 292, Rome, Italy. Electronic address: .

Abstract:  The viral infection by SARS-CoV-2 has irrevocably altered the life of the majority of human beings, challenging national health systems worldwide, and pushing researchers to rapidly find adequate preventive and treatment strategies. No therapies have been shown effective with the exception of dexamethasone, a glucocorticoid that was recently proved to be the first life-saving drug in this disease. Remarkably, around 20 % of infected people develop a severe form of COVID-19, giving rise to respiratory and multi-organ failures requiring subintensive and intensive care interventions. This phenomenon is due to an excessive immune response that damages pulmonary alveoli, leading to a cytokine and chemokine storm with systemic effects. Indeed glucocorticoids' role in regulating this immune response is controversial, and they have been used in clinical practice in a variety of countries, even without a previous clear consensus on their evidence-based benefit. 

Retracted: No

PubPeer comments:
 The legend that accompanies Table 2 (below) refers to u201cFMTVDM: Fleming Method for Tissue and Vascular Differentiation and Metabolism,u201d however I do not see this abbreviation used in the table. I presume the authors had a reference to Dr. Flemingu2019s supposed clinical trial but removed that reference from the published manuscript. This may be just as well, as explained here: https: retractionwatch.com 2020 05 29 a-convicted-felon-wants-people-to-enroll-in-a-covid-19-clinical-trial-what-could-go-wrong ,
JNK2 and IKKbeta are required for activating the innate response to viral infection
Authors: W M Chu
Y Hu
J Perrault
Z W Li
M Karin
Y Chen
D Ostertag
L Chang
B Williams
Journal: Immunity (1999)
Discipline: IMMUNOLOGY
Keywords: Viral infection; double-stranded RNA; interferons; cytokines; transcription factors
Affiliations: Department of Pharmacology, University of California, San Diego, La Jolla 92093-0636, USA.

Abstract:  Viral infection or double-stranded (ds) RNA induce interferons (IFN) and other cytokines. Transcription factors mediating IFN induction are known, but the signaling pathways that regulate them are less clear. We now describe two such pathways. The first pathway leading to NF-kappaB depends on the dsRNA-responsive protein kinase (PKR), which in turn activates IKB kinase (IKK) through the IKKbeta subunit. The second viral-and dsRNA-responsive pathway is PKR independent and involves Jun kinase (JNK) activation leading to stimulation of AP-1. Both IKKbeta and JNK2 are essential for efficient induction of type I IFN and other cytokines in response to viral infection or dsRNA. This study establishes a general role for these kinases in activation of innate immune responses. 

Retracted: No

PubPeer comments:
null, 
null, 
 Identified by another reader. *** ![file] ,
EZH2 inhibition promotes methyl jasmonate‑induced apoptosis of human colorectal cancer through the Wnt/β‑catenin pathway
Authors: Yongkun Wang
Yao Wang
Chunguo Cui
Tingting Liang
Li Fan
Journal: Oncology Letters (2018)
Discipline: CLINICAL MEDICINE
Keywords: Wnt/β-catenin; enhancer of zeste 2 polycomb repressive complex 2 subunit; human colorectal cancer; methyl jasmonate.
Affiliations: Department of Urology, The China‑Japan Union Hospital of Jilin University, Changchun, Jilin 130033, P.R. China, Department of Galactophore, The China‑Japan Union Hospital of Jilin University, Changchun, Jilin 130033, P.R. China, Department of Orthopedics, The China‑Japan Union Hospital of Jilin University, Changchun, Jilin 130033, P.R. China, Cancer Center, The First Hospital of Jilin University, Changchun, Jilin 130021, P.R. China

Abstract:  Methyl jasmonate potentially induces the differentiation of human myeloid leukemia cells and inhibits their proliferation; it may induce the differentiation and apoptosis of human lymphocytic leukemia cells, but does not exert a damaging effect on normal lymphocytes. In the present study, the anticancer effect of methyl jasmonate on human colorectal cancer cells was investigated. Cell viability and apoptosis was assessed using a Cell Counting kit-8 assay and flow cytometry, respectively. Methyl jasmonate suppressed cell viability and induced apoptosis in human colorectal cancer cells. Additionally, methyl jasmonate increased the activation of caspase-3, inhibited the expression levels of enhancer of zeste 2 polycomb repressive complex 2 subunit (EZH2) and the Wnt/β-catenin pathway in human colorectal cancer. Downregulation of EZH2 expression enhanced the anticancer effect of methyl jasmonate on human colorectal cancer cells through suppression of the Wnt/β-catenin pathway. Thus, EZH2 downregulation promotes the anticancer effect of methyl jasmonate by inducing apoptosis in human colorectal cancer cells through the Wnt/β-catenin pathway. 

Retracted: Yes

PubPeer comments:
 Retracted [2 June 2021] .  Subsequently to the publication of the above paper, the authors have requested that the paper be retracted on account of a lack of coordination among different members of the research group who were performing experiments simultaneously, and the fact that an inappropriate cell line was selected for some of the experiments (T24, which is a bladder cancer cell line, was used instead of the SW480 cell line). Consequently, the authors no longer feel confident about the reported results, and consider the conclusions of this study to be unreliable. The Editor has granted the authorsu2019 request that the paper be retracted, and all the named authors agree to this retraction. The authors sincerely apologize for their errors, and regret any inconvenience caused. ,