bluuebunny/crossref_metadata_2025_split huggingface dataset:
Biomarkers and Targets Identification Among CXC Chemokines in the Colon Adenocarcinoma
Authors: wang heng , guo ChangQing , luo jun , Li Quan , fubuqing BuQing , Jiang Wei 
Published: May 2022

Abstract
Background: COAD is among the most prevalent malignancy, with a very high incidence rate. Crosstalk between cancer and interstitial cells significantly affects cancer development, modulated partly by chemokines production. When present in the tumor microenvironment, CXC chemokines have been shown to regulate tumor cell activity and influence immune cell transport, resulting in anti-tumor immune mechanisms and influencing the outcomes of the patient; nonetheless, the CXC chemokines expression levels in COAD, as well as their prognostic significance, have not yet been established.Methods: This study used UALCAN, GeneMANIA, STRING, TRRUST, cBioPortal, TIMER, and GEPIA,Results: The expression of CXC1/2/3/5/6/11/12/13/14/16/17 in COAD patients was shown to be significantly correlated with the pathological stage. A considerably improved prognosis was observed in patients with low transcriptional levels of CXCL9/10/11. Differentially expressed CXC chemokines exert roles that are predominantly correlated with the chemokine signaling pathway and interactions of cytokine–cytokine receptors. Our findings indicated that the transcriptional factors, including SP1, RELA, and NFKB1 are essential for the production of CXC chemokines. Furthermore, we discovered a substantial association between the CXC chemokines production and infiltration of 6 kinds of immune cells (CD8+ T cells, dendritic cells, B cells, CD4+ T cells, neutrophils, and macrophages,). Conclusions: These findings might be useful in identifying prognostic indicators and immunotherapeutic targets for colon cancer.
Multicenter case-control study evaluating the safety of anti-SARS-CoV-2 vaccines in a cohort of patients with systemic vasculitis
Authors: Simoncelli Edoardo , Conticini Edoardo , Colafrancesco Serena , Gattamelata Aneglica , Spinelli Francesca Romana , Garufi Cristina , Truglia Simona , Grazzini Silvia , Giardina Federico , Izzo Raffaella , Cantarini Luca , Frediani Bruno , Conti Fabrizio , Priori Roberta 
Published: May 2022

Abstract
Objective: Data on the safety of anti-SARS-CoV-2 vaccines in patients with rare rheumatic diseases, such as systemic vasculitis (SV), are limited. Aim of this study was to evaluate the occurrence of a disease flare and the appearance of adverse events (AEs) following administration of anti-SARS-CoV-2 vaccine in a multicenter cohort of patients with SV. Methods: Patients with SV and healthy controls (HCs) from two different Italian rheumatology centers were asked to complete a questionnaire assessing disease flares occurrence, defined as new onset of clinical manifestations related to vasculitis needing an implementation of therapy, and local/systemic AEs appearance following anti SARS-CoV-2 vaccination.Results: 107 patients with SV (57 ANCA-associated) and 107 HCs were enrolled. A disease flare occurred in only one patient (0.93%) with microscopic polyangiitis after the first dose of an mRNA vaccine. Both after the first and the second vaccine dose administration, no significant differences in AEs between patients with SV and HCs were observed; no serious AEs were reported as well. Conclusions: This data suggest a good risk profile for anti-SARS-CoV-2 vaccine in patients with systemic vasculitis.
Fungal communities are more sensitive to the simulated environmental changes than bacterial communities in a subtropical forest: the single and interactive effects of nitrogen addition and precipitation seasonality change
Authors: He Dan , Guo Zhiming , Shen Weijun , Ren Lijuan , Sun Dan , Yao Qing , Zhu Honghui 
Published: May 2022

Abstract
Increased nitrogen (N) deposition and changes in precipitation seasonality can greatly impact soil microbial communities in tropical/subtropical forests. Although knowledge about the effects of a single factor on soil microbial communities is growing rapidly, little is understood about the interactive effects of these two environmental change factors. In this study, we investigated the responses of soil bacterial and fungal communities to the simulated environmental changes (nitrogen addition, precipitation seasonality change, and their combination) in a subtropical forest in South China. The interaction between N and water treatments was significant for affecting some soil physicochemical properties (such as pH, soil water and NO3 − contents). Fungi were more susceptible to treatment than bacteria in a variety of community traits (alpha, beta diversity, and network topological features). The N and water treatments act antagonistically to affect fungal alpha diversity, and the interaction effect was detected significant for the dry season. The topological features of the meta-community (containing both bacteria and fungi) network overrode the alpha and beta diversity of bacterial or fungal communities in explaining the variation of soil enzyme activities. The associations between Ascomycota fungi and Gammaproteobacteria or Alphaproteobacteria might be important in mediating the inter-kingdom interactions. In summary, our results suggested that fungal communities were more sensitive to N addition and precipitation seasonality change (and their interaction) than bacterial communities, and the treatments’ effects were more prominent in the dry season, which may have great consequences in soil processes and ecosystem functions in subtropical forests.
Nasal microbiome disruption and recovery after mupirocin treatment in Staphylococcus aureus carriers and noncarriers
Authors: Baede Valérie O. , Barray Anaïs , Tavakol Mehri , Lina Gérard , Vos Margreet C. , Rasigade Jean-Philippe 
Published: May 2022

Abstract
Background: Nasal decolonization procedures against the opportunistic pathogen Staphylococcus aureus rely on topical antimicrobial drug usage, whose impact on the nasal microbiota is poorly understood. We examined this impact in healthy S. aureus carriers and noncarriers.Methods: This is a prospective interventional cohort study of 8 S. aureus carriers and 8 noncarriers treated with nasal mupirocin and chlorhexidine baths. Sequential nasal swabs were taken over 6 months. S. aureus was detected by quantitative culture and genotyped using spa typing. RNA-based 16S species-level metabarcoding was used to assess the living microbial diversity.Results: The species Dolosigranulum pigrum, Moraxella nonliquefaciens and Corynebacterium propinquum correlated negatively with S. aureus carriage. Mupirocin treatment effectively eliminated S. aureus, D. pigrum and M. nonliquefaciens, but not corynebacteria. S. aureus recolonization in carriers occurred more rapidly than recolonization by the dominant species in noncarriers (median 3 vs. 6 months, respectively). Recolonizing S. aureus isolates had the same spa type as the initial isolate. Conclusions: Mupirocin-chlorhexidine treatment had a long-lasting impact on the nasal microbiota. S. aureus recolonization predated microbiota recovery, emphasizing the strong adaptation of this pathogen to the nasal niche and the transient efficacy of the decolonization procedure.
The effects of a truncated form of Staphylococcus aureus protein A (SpA) on the expression of cytokines of autoimmune patients and healthy individuals
Authors: Rigi Garshasb , Kardar Gholamali , Hajizade Abbas , Zamani Javad , Ahmadian Gholamreza 
Published: May 2022

Abstract
Background: The recombinant Staphylococcal protein A (SpA) is widely used in biotechnology to purify polyclonal and monoclonal IgG antibodies. At very low concentrations, the highly-purified form of the protein A can down-regulate the activation of human B-lymphocytes and macrophages which are the key cells in determining autoimmune diseases. Methods: In the present study, the efficiency of three different forms of protein A, including native SpA, the recombinant full-length SpA, and a truncated form of SpA on the reduction of 4 inflammatory cytokines, including IL-8, IL-1β, TNF-α, and IL-6 by peripheral blood mononuclear cell (PBMCs) were studied and compared to an anti-rheumatoid arthritis commercial drug, Enbrel. The recombinant proteins were expressed in E. coli expression vector and the native form of SpA was commercially provided. PBMCs were obtained from adult patients with active rheumatoid arthritis (RA) and healthy control donors. Then, the effect of different doses of the three pure forms of SpA in comparison with Enbrel was investigated by analyzing the expression of selected cytokines using ELISA. Results: The results showed that the recombinant truncated form of SpA significantly reduced the expression of the cytokines more effectively than other full-length formulations as well as the commercial drug Enbrel. In silico analysis suggests that in the truncated protein, by increasing the radius of gyration, the IgG-binding domains find a more open structure and are more exposed to IgG. Conclusion: In conclusion, our results showed that the truncated form of protein A is the most potent form of SpA that reduces the secretion of the evaluated cytokines from PBMCs in vitro.
Mortality in Psoriatic Arthritis patients, changes over time and the impact of COVID-19: Results from a multicenter Psoriatic Arthritis Registry (PsART-ID)
Authors: Erden Abdulsamet , Ayan Gizem , Kilic Levent , Solmaz Dilek , Bakirci Sibel , Kimyon Gezmis , Günal Esen Kasapoglu , Dogru Atalay , Bayindir Özün , Dalkilic Ediz , Özisler Cem , Akar Servet , Cetin Gözde Yildirim , Tarhan Emine Figen , Küçüksahin Orhan , Omma Ahmet , Gonullu Emel , Yildiz Fatih , Ersozlu Emine Duygu , Cinar Muhammed , Tufan Abdurrahman , Pehlevan Seval , Esmen Serpil Ergulu , Yilmaz Sema , Duruoz Tuncay , Kasifoglu Timucin , Yazısız Veli , Aksu Kenan , Aydin Sibel Zehra , Kalyoncu Umut 
Published: May 2022

Abstract
BackgroundThis study aimed to assess the mortality of PsA before and during the COVID-19 pandemic.MethodsFrom the prospective, multicenter PsART-ID (Psoriatic Arthritis Registry-International Database), patients from Turkey were analyzed by linking the registry to the Turkish Cause of Death Registry. The outcome of interest was death from any cause, pre-pandemic (since the onset of registry – March 2014- March 2020), and during the pandemic (March 2020-May 2021). The crude mortality rate and standardized mortality ratio (SMR) were determined. ResultsThere were 1216 PsA patients with a follow-up of 7500 patient-years. Overall, 46 deaths (26 males) were observed. In the pre-pandemic period, SMR for PsA vs the general population was 0.95 (0.61-1.49), being higher in males [1.56 (0.92-2.63)] than females [0.62 (0.33-1.17)]. The crude mortality rate in PsA doubled during the pandemic (pre-pandemic crude mortality rate: 5.07 vs 10.76 during the pandemic) with a higher increase in females (2.9 vs 8.72) than males (9.07 vs 14.73).Conclusion The mortality in PsA was found similar to the general population in the pre-pandemic era. The mortality rates in PsA doubled during the pandemic. Whether PsA patients have more risk of mortality than the general population due to COVID-19, needs further studies.
A prospective observational study comparing the pediatric post anesthesia discharge scoring system with clinical discharge criteria in pediatric day surgical patients in Western China
Authors: Yang Chen , Wu Tingting , Tang Linrui , Zhang Xuebing 
Published: May 2022

Abstract
Objective: To evaluate the safety and efficacy of the pediatric post-anesthesia discharge scoring system (Ped-PADSS), and compared with the existing clinical discharge criteria (CDC) in the day surgery ward of our hospital. Methods: After the patient completed the operation and returned to the day surgery ward, the initial assessment was conducted by an independent observer using the Ped-PADSS and CDC. This process was repeated at 1 hour intervals until the patient achieved a Ped-PADSS score of 9 and met the CDC. Results: From July to December 2021, 721 pediatric patients. One hour after returning from PACU to the day surgery ward, 92.65% of pediatric patients were dischargeable based on the Ped-PADSS scores. Two hour after returning from PACU to the day surgery ward, 100.00% of pediatric patients were dischargeable. The median length of stay in the day surgery ward (n=720) was reduced by 1 hour after surgery compared with the median length of stay in the day surgery ward before the use of the output score (P<0.05); and there were 9 (1.25%) adverse events occurred in the interval between Ped-PADSS and CDC time.Conclusion: This prospective study reveals that the Ped-PADSS-based discharge decision greatly speeds the transit of pediatric patients through the day surgery ward, thus improving day surgery ward efficiency and medical resource utilization.
ABCC6P1 pseudogene induces chemotherapy resistance in breast cancer: a new insight into the role of pseudogene in drug resistance
Authors: Hashemi Mahnaz , Golalipour Masoud 
Published: May 2022

Abstract
Background: The elevated drug efflux by ABC transports has been considered the primary mechanism of drug resistance in cancer. Recently, non-coding RNAs, such as pseudogenes, have been proposed to be involved in transporter-mediated drug resistance in cancer. The human genome has 22 ABC transporter pseudogenes. Among these pseudogenes, ABCC6P1, has co-expression with the ancestral gene in various human tissues. Methods and Results: In present study, we assessed the effect of ABCC6P1 pseudogene on ABCC6 expression and drug resistance. The ABCC6P1 transfected into MCF-7 cells. In ABCC6P1-overexpressing cells, the ABCC6 mRNA level increased up to 9.45-fold. The results of cell treatment with Doxorubicin, 5FU, Cisplatin, and Paclitaxel showed that the survival of ABCC6P1-overexpressing cells was higher than normal cells. Furthermore, uptake of Doxorubicin was lower after ABCC6P1 overexpression. Conclusions: In conclusion, our results show that overexpression of ABCC6P1 pseudogene induces the drug resistance phenotype, possibly through activation of the ancestral gene.
Prediction of Type 2 Diabetes mellitus using soft computing.
Authors: Punjabi Poonam , Yadav Anuradha , Sankhla Manisha , Mamta  , Mathur Sandeep , Dave Harsh S , Patel Vaishnavi , Chavhan Tushar , Manisha  , Tak Amit 
Published: May 2022

Abstract
Background
Type 2 Diabetes Mellitus (DM) is another pandemic of 21 century, and its control is of immense importance. Researchers developed many predictor models using soft computing techniques. The present study developed a prediction model for Type 2 DM using machine learning classifiers. The analysis excludes plasma glucose concentration and insulin concentration as predictors to explore relationships with other predictors.
Methods
This cross-sectional study enrolled 108 participants aged 25 to 67 years from SMS Medical College, Jaipur (Rajasthan, India), after approval from the ethics committee. The study developed a prediction model using machine learning techniques. The classifiers used in the application include decision trees, support vector machines, K-nearest neighbors, and ensemble learning classifiers. A total of 25 predictors were collected and underwent feature reduction. The response levels include diabetes mellitus, prediabetes, and no diabetes mellitus. The models were run using three predictors and a response variable. The prediction model with the best accuracy and area under the receiver operator characteristic curve was selected.
Results
The features that vary among the three groups include age, WHR, biceps skinfold thickness, total lipids, phospholipids, triglycerides, total cholesterol, LDL, VLDL, and serum creatinine, and family history of DM. After feature reduction, the age, biceps skinfold thickness, and serum creatinine were run on the Classification learner application to predict the diabetic category. The best model was subspace discriminant with accuracy, sensitivity, specificity, and AUC under the ROC curve was 62.4%, 74%, 94%, and 0.70, respectively.
Conclusion
The present study concludes that age, biceps skinfold thickness, and serum creatinine combination have higher specificity in predicting type 2 DM. The study emphasized the selection of appropriate predictors along with newer machine learning algorithms.
Graph Neural Networks: a bibliometrics overview
Authors: Keramatfar Abdalsamad , Rafiee Mohadeseh , Amirkhani Hossein 
Published: May 2022

Abstract
Recently, graph neural networks (GNN) have become a hot topic in machine learning community. This paper presents a Scopus-based bibliometric overview of the GNNs’ research since 2004, when GNN papers were first published. The study aims to evaluate GNN research trend, both quantitatively and qualitatively. We provide the trend of research, distribution of subjects, active and influential authors and institutions, sources of publications, most cited documents, and hot topics. Our investigations reveal that the most frequent subject categories in this field are computer science, engineering, telecommunications, linguistics, operations research and management science, information science and library science, business and economics, automation and control systems, robotics, and social sciences. In addition, the most active source of GNN publications is Lecture Notes in Computer Science. The most prolific or impactful institutions are found in the United States, China, and Canada. We also provide must-read papers and future directions. Finally, the application of graph convolutional networks and attention mechanism are now among hot topics of GNN research.
Biocatalytic Strategy for Construction of sp3-Rich Polycyclic Compounds from Directed Evolution and Computational Modeling
Authors: Fasan Rudi , Vargas David A. , Ren Xinkun , Sengupta Arkajyoti , Zhu Ledong , Garcia-Borràs Marc , Houk Kendall 
Published: May 2022

Abstract
Catalysis with engineered enzymes has provided more efficient and streamlined routes for the synthesis and manufacturing of drug molecules. Despite landmark achievements, the potential of biocatalysis toward assisting early-stage drug discovery campaigns remains largely untapped. We have developed a novel biocatalytic strategy for the construction of sp3-rich polycyclic compounds via an intramolecular cyclopropanation of benzothiophenes and related heterocycles. Despite the inherent challenge presented by this reaction, two regiocomplementary carbene transferases were evolved to catalyze the highly stereoselective cyclization of benzothienyl substrates bearing diazo ester groups at either the C2 or C3 position of the heterocycle. The detailed mechanisms of these reactions were obtained by a combination of crystallographic and computational (quantum mechanics calculations and molecular dynamics simulations) analyses. Leveraging these insights, the narrow substrate scope of one of the biocatalysts could be expanded to include previously unreactive substrates, highlighting the value of integrating evolutionary and rational strategies for the development of enzymes useful for new-to-nature enzyme transformations. The molecular scaffolds made accessible by the present strategy feature a combination of 3D and stereochemical complexity with ‘rule-of-3’ properties, which should make them highly valuable for fragment-based drug discovery campaigns.
Qualitative study of process in daily life of patients with larynx/pharyngeal cancer before total laryngectomy
Authors: Kotake Kumiko , Haba Kaori , Kurita Mami , Ota Ichiro , Suzukamo Yoshimi , Kai Ichiro , Iwanaga Kazuyo , Takahashi Aya , Ishibashi Yoko , Uemura Hirokazu , Hara Yoriko , Atrata Yukiko , Kinoshita Yasuhito 
Published: May 2022

Abstract
Background: Many patients with larynx/pharyngeal cancer only become aware of the disease in an advanced stage due to hoarseness and a strange feeling upon swallowing. The aim of this study was to discuss what kinds of support are required for these patients by clarifying the process in their daily life prior to total laryngectomy.Methods: A qualitative study was performed using the Modified Grounded Theory Approach in patients with larynx/pharyngeal cancer before total laryngectomy. In a semi-structured interview, patients were asked to talk freely about their health conditions, problems, and anxieties. Information on age, sex, family members living with the patient, occupation, diagnosis, staging, and subjective symptoms was also obtained in the interview. Results: The analysis theme of “How do cancer patients live before surgery?” had a storyline centered on {surviving surgery}. The patients had a [strange feeling] caused by a sense of a lump in the throat and pain of hoarseness, as well as [unexperienced anxiety] for their first experience of hospitalization and surgery. The core category and the two categories interacted with each other and recurred. [Unexperienced anxiety] was related to [cannot imagine] daily life after hospital discharge, and transitioned to [not knowing what will happen after surgery] until the time comes. The core category of {surviving surgery} and the three categories interacted with each other and recurred. The patients also had a positive mindset of [having a purpose in life after hospital discharge] and were [looking for positives] at that time, while making a [request of support from physicians] to improve their [strange feeling]. Quality of life (QOL) prior to laryngectomy is influenced by negative mental and physical feelings caused by cancer and by anxieties about postoperative life, but with hope for social support.Conclusions: Patients experience a “transition” before total laryngectomy, and at this turning point they try to think positively about surviving the surgery, but also feel loneliness, fear, and anxiety. These findings suggest the need for a healthcare team approach for pre- and postoperative support by staying close to a patient, even after hospital discharge.
Usefulness and limitations of cryopreservation for immunocytochemical staining of cytological specimens
Authors: Furusawa Yu , Shima-Sawa Mariko , Hifumi Tatsuro , Miyoshi Noriaki , Yamato Osamu , Yabuki Akira 
Published: May 2022

Abstract
Immunocytochemistry is an advanced diagnostic tool used to identify the origin of tumor cells. The present study aimed to clarify the usefulness of cryopreserved, air-dried cytology samples for the detection of cytokeratin and vimentin. Air-dried smear samples were prepared from canine tumors and stored at –30°C or room temperature without fixation. The duration of cryopreservation varied from 2 months to 4 years and 8 months. Formalin-fixed paraffin sections were also prepared from these tumors. These samples underwent enzymatic immunocytochemistry and immunohistochemistry for the detection of cytokeratin and vimentin. Immunoreactivity for cytokeratin was detected in samples cryopreserved for a maximum of 3 years and 10 months. Immunosignals for vimentin were clearly detected for 2 years. Expression of cytokeratin and vimentin was not detected in samples stored at room temperature for 1 week. Immunoreactivity was observed in all specimens using immunohistochemistry. These findings suggest that immunocytochemistry for cytokeratin and vimentin can be safely applied to air-dried smears that have been cryopreserved at –30°C for at least 2 years. This simple method may be useful for retrospective cytological studies and/or re-evaluation of cytology results.
Three SARS-CoV-2 recombinants identified in Brazilian children
Authors: Silva Luciane Sussuchi da , de Oliveira Cristina Mendes , Cota Bianca Della Croce Vieira , Romano Camila Malta , Levi José Eduardo 
Published: May 2022

Abstract
Since the emergence of the variant of concern (VOC) B.1.1.529 (Omicron) in November 20211, nearly 100 sublineages have been assigned by Pango. Recently, the co-circulation of Omicron and Delta lineages, as well as its diverse set of sublineages, has brought to attention the identification of several recombinant events. A putative new recombinant and two XE recombinants were identified in children by the GENOV surveillance program (https://dasa.com.br/en/genov/) from Dasa, Brazil. All three children haven’t traveled abroad nor their relatives, indicating that the infections by recombinants likely occurred in São Paulo city.