bluuebunny/crossref_metadata_2025_split huggingface dataset:
Profiling non-coding RNA levels with clinical classifiers in pediatric Crohn’s disease
Authors: Pelia Ranjit , Venkateswaran Suresh , Matthews Jason D. , Haberman Yael , Cutler David J. , Hyams Jeffrey S. , Denson Lee A. , Kugathasan Subra 
Published: July 2021

Abstract
Background
Crohn’s disease (CD) is a heritable chronic inflammatory disorder. Non-coding RNAs (ncRNAs) play an important role in epigenetic regulation by affecting gene expression, but can also directly affect protein function, thus having a substantial impact on biological processes. We investigated whether non-coding RNAs (ncRNA) at diagnosis are dysregulated during CD at different CD locations and future disease behaviors to determine if ncRNA signatures can serve as an index to outcomes.

Methods
Using subjects belonging to the RISK cohort, we analyzed ncRNA from the ileal biopsies of 345 CD and 71 non-IBD controls, and ncRNA from rectal biopsies of 329 CD and 61 non-IBD controls. Sequence alignment was done (STAR package) using Human Genome version 38 (hg38) as reference panel. The differential expression (DE) analysis was performed with EdgeR package and DE ncRNAs were identified with a threshold of fold change (FC) > 2 and FDR < 0.05 after multiple test corrections.

Results
In total, we identified 130 CD specific DE ncRNAs (89 in ileum and 41 in rectum) when compared to non-IBD controls. Similarly, 35 DE ncRNAs were identified between B1 and B2 in ileum, whereas no differences among CD disease behaviors were noticed in rectum. We also found inflammation specific ncRNAs between inflamed and non-inflamed groups in ileal biopsies. Overall, we observed that expression of mir1244-2, mir1244-3, mir1244-4, and RN7SL2 were increased during CD, regardless of disease behavior, location, or inflammatory status. Lastly, we tested ncRNA expression at baseline as potential tool to predict the disease status, disease behaviors and disease inflammation at 3-year follow up.

Conclusions
We have identified ncRNAs that are specific to disease location, disease behavior, and disease inflammation in CD. Both ileal and rectal specific ncRNA are changing over the course of CD, specifically during the disease progression in the intestinal mucosa. Collectively, our findings show changes in ncRNA during CD and may have a clinical utility in early identification and characterization of disease progression.
Circular RNA circIKBKB promotes breast cancer bone metastasis through sustaining NF-κB/bone remodeling factors signaling
Authors: Xu Yingru , Zhang Shuxia , Liao Xinyi , Li Man , Chen Suwen , Li Xincheng , Wu Xingui , Yang Meisongzhu , Tang Miaoling , Hu Yameng , Li Ziwen , Yu Ruyuan , Huang Mudan , Song Libing , Li Jun 
Published: July 2021

Abstract
Background
Breast cancer (BC) has a marked tendency to spread to the bone, resulting in significant skeletal complications and mortality. Recently, circular RNAs (circRNAs) have been reported to contribute to cancer initiation and progression. However, the function and mechanism of circRNAs in BC bone metastasis (BC-BM) remain largely unknown.

Methods
Bone-metastatic circRNAs were screened using circRNAs deep sequencing and validated using in situ hybridization in BC tissues with or without bone metastasis. The role of circIKBKB in inducing bone pre-metastatic niche formation and bone metastasis was determined using osteoclastogenesis, immunofluorescence and bone resorption pit assays. The mechanism underlying circIKBKB-mediated activation of NF-κB/bone remodeling factors signaling and EIF4A3-induced circIKBKB were investigated using RNA pull-down, luciferase reporter, chromatin isolation by RNA purification and enzyme-linked immunosorbent assays.

Results
We identified that a novel circRNA, circIKBKB, was upregulated significantly in bone-metastatic BC tissues. Overexpressing circIKBKB enhanced the capability of BC cells to induce formation of bone pre-metastatic niche dramatically by promoting osteoclastogenesis in vivo and in vitro. Mechanically, circIKBKB activated NF-κB pathway via promoting IKKβ-mediated IκBα phosphorylation, inhibiting IκBα feedback loop and facilitating NF-κB to the promoters of multiple bone remodeling factors. Moreover, EIF4A3, acted acting as a pre-mRNA splicing factor, promoted cyclization of circIKBKB by directly binding to the circIKBKB flanking region. Importantly, treatment with inhibitor eIF4A3-IN-2 reduced circIKBKB expression and inhibited breast cancer bone metastasis effectively.

Conclusion
We revealed a plausible mechanism for circIKBKB-mediated NF-κB hyperactivation in bone-metastatic BC, which might represent a potential strategy to treat breast cancer bone metastasis.
GenoVault: a cloud based genomics repository
Authors: Jain Sankalp , Saxena Amit , Hesarur Suprit , Bhadhadhara Kirti , Bharti Neeraj , Kasibhatla Sunitha Manjari , Sonavane Uddhavesh , Joshi Rajendra 
Published: July 2021

AbstractGenoVault is a cloud-based repository for handling Next Generation Sequencing (NGS) data. It is developed using OpenStack-based private cloud with various services like keystone for authentication, cinder for block storage, neutron for networking and nova for managing compute instances for the Cloud. GenoVault uses object-based storage, which enables data to be stored as objects instead of files or blocks for faster retrieval from different distributed object nodes. Along with a web-based interface, a JavaFX-based desktop client has also been developed to meet the requirements of large file uploads that are usually seen in NGS datasets. Users can store files in their respective object-based storage areas and the metadata provided by the user during file uploads is used for querying the database. GenoVault repository is designed taking into account future needs and hence can scale both vertically and horizontally using OpenStack-based cloud features. Users have an option to make the data shareable to the public or restrict the access as private. Data security is ensured as every container is a separate entity in object-based storage architecture which is also supported by Secure File Transfer Protocol (SFTP) for data upload and download. The data is uploaded by the user in individual containers that include raw read files (fastq), processed alignment files (bam, sam, bed) and the output of variation detection (vcf). GenoVault architecture allows verification of the data in terms of integrity and authentication before making it available to collaborators as per the user’s permissions. GenoVault is useful for maintaining the organization-wide NGS data generated in various labs which is not yet published and submitted to public repositories like NCBI. GenoVault also provides support to share NGS data among the collaborating institutions. GenoVault can thus manage vast volumes of NGS data on any OpenStack-based private cloud.
IL-7 and CCL19-secreting CAR-T cell therapy for tumors with positive glypican-3 or mesothelin
Authors: Pang Nengzhi , Shi Jingxuan , Qin Le , Chen Aiming , Tang Yuou , Yang Hainan , Huang Yufeng , Wu Qingde , Li Xufeng , He Bingjia , Li Tianheng , Liang Baoxia , Zhang Jinglin , Cao Bihui , Liu Manting , Feng Yunfei , Ye Xiaodie , Chen Xiaopei , Wang Lu , Tian Yu , Li Hao , Li Junping , Hu Hong , He Jingping , Hu Yuling , Zhi Cheng , Tang Zhaoyang , Gong Yibo , Xu Fangting , Xu Linfeng , Fan Weijun , Zhao Ming , Chen Deji , Lian Hui , Yang Lili , Li Peng , Zhang Zhenfeng 
Published: July 2021

AbstractAlthough chimeric antigen receptor (CAR)-engineered T cells have shown great success in the treatment of B cell malignancies, this strategy has limited efficacy in patients with solid tumors. In mouse CAR-T cells, IL-7 and CCL19 expression have been demonstrated to improve T cell infiltration and CAR-T cell survival in mouse tumors. Therefore, in the current study, we engineered human CAR-T cells to secrete human IL-7 and CCL19 (7 × 19) and found that these 7 × 19 CAR-T cells showed enhanced capacities of expansion and migration in vitro. Furthermore, 7 × 19 CAR-T cells showed superior tumor suppression ability compared to conventional CAR-T cells in xenografts of hepatocellular carcinoma (HCC) cell lines, primary HCC tissue samples and pancreatic carcinoma (PC) cell lines. We then initiated a phase 1 clinical trial in advanced HCC/PC/ovarian carcinoma (OC) patients with glypican-3 (GPC3) or mesothelin (MSLN) expression. In a patient with advanced HCC, anti-GPC3-7 × 19 CAR-T treatment resulted in complete tumor disappearance 30 days post intratumor injection. In a patient with advanced PC, anti-MSLN-7 × 19 CAR-T treatment resulted in almost complete tumor disappearance 240 days post-intravenous infusion. Our results demonstrated that the incorporation of 7 × 19 into CAR-T cells significantly enhanced the antitumor activity against human solid tumor. Trial registration: NCT03198546. Registered 26 June 2017, https://clinicaltrials.gov/ct2/show/NCT03198546?term=NCT03198546&draw=2&rank=1
Cellular senescence or stemness: hypoxia flips the coin
Authors: Otero-Albiol Daniel , Carnero Amancio 
Published: July 2021

AbstractCellular senescence is a complex physiological state whose main feature is proliferative arrest. Cellular senescence can be considered the reverse of cell immortalization and continuous tumor growth. However, cellular senescence has many physiological functions beyond being a putative tumor suppressive trait. It remains unknown whether low levels of oxygen or hypoxia, which is a feature of every tissue in the organism, modulate cellular senescence, altering its capacity to suppress the limitation of proliferation. It has been observed that the lifespan of mammalian primary cells is increased under low oxygen conditions. Additionally, hypoxia promotes self-renewal and pluripotency maintenance in adult and embryonic stem cells (ESCs), induced pluripotent stem cells (iPSCs) and cancer stem cells (CSCs). In this study, we discuss the role of hypoxia facilitating senescence bypass during malignant transformation and acquisition of stemness properties, which all contribute to tumor development and cancer disease aggressiveness.
Clinical practice recommendations on the management of perioperative cardiac arrest: A report from the PERIOPCA Consortium
Authors: Chalkias Athanasios , Mongardon Nicolas , Boboshko Vladimir , Cerny Vladimir , Constant Anne-Laure , De Roux Quentin , Finco Gabriele , Fumagalli Francesca , Gkamprela Eleana , Legriel Stéphane , Lomivorotov Vladimir , Magliocca Aurora , Makaronis Panagiotis , Mamais Ioannis , Mani Iliana , Mavridis Theodoros , Mura Paolo , Ristagno Giuseppe , Sardo Salvatore , Papagiannakis Nikolaos , Xanthos Theodoros ,   for the PERIOPCA Consortium, Chalkias Athanasios , Mongardon Nicolas , Boboshko Vladimir , Cerny Vladimir , Constant Anne-Laure , De Roux Quentin , Finco Gabriele , Fumagalli Francesca , Gkamprela Eleana , Legriel Stéphane , Lomivorotov Vladimir , Magliocca Aurora , Makaronis Panagiotis , Mamais Ioannis , Mani Iliana , Mavridis Theodoros , Mura Paolo , Ristagno Giuseppe , Sardo Salvatore , Papagiannakis Nikolaos , Xanthos Theodoros 
Published: July 2021

Abstract
Background
Perioperative cardiac arrest is a rare complication with an incidence of around 1 in 1400 cases, but it carries a high burden of mortality reaching up to 70% at 30 days. Despite its specificities, guidelines for treatment of perioperative cardiac arrest are lacking. Gathering the available literature may improve quality of care and outcome of patients.

Methods
The PERIOPCA Task Force identified major clinical questions about the management of perioperative cardiac arrest and framed them into the therapy population [P], intervention [I], comparator [C], and outcome [O] (PICO) format. Systematic searches of PubMed, Embase, and the Cochrane Library for articles published until September 2020 were performed. Consensus-based treatment recommendations were created using the Grading of Recommendations, Assessment, Development, and Evaluation (GRADE) system. The strength of consensus among the Task Force members about the recommendations was assessed through a modified Delphi consensus process.

Results
Twenty-two PICO questions were addressed, and the recommendations were validated in two Delphi rounds. A summary of evidence for each outcome is reported and accompanied by an overall assessment of the evidence to guide healthcare providers.

Conclusions
The main limitations of our work lie in the scarcity of good quality evidence on this topic. Still, these recommendations provide a basis for decision making, as well as a guide for future research on perioperative cardiac arrest.
Asystolic cardiac arrest following liposomal amphotericin B infusion: anaphylaxis or compliment activation-related pseudoallergy?
Authors: Drewett George P. , Copaescu Ana , DeLuca Joseph , Holmes Natasha E. , Trubiano Jason A. 
Published: July 2021

AbstractAllergic reaction to liposomal amphotericin B is rare. We report a case of cardiac arrest in a 64-year-old woman following liposomal amphotericin B infusion, requiring resuscitation. We also present the results of subsequent skin prick and intradermal testing to liposomal amphotericin on the patient and three healthy controls, highlighting the need for further research into the immunopathogenesis of this reaction.
Acute poisoning with acetamiprid: a case report
Authors: Pirasath Selladurai , Senthuran Rajaram , Athirayan Chandrakulasegeran , Gevakaran Mathyasekeran , Guruparan Mahesan , Gnanathasan Ariaranee 
Published: July 2021

Abstract
Background
Acetamiprid is a potent new first-generation neonicotinoid insecticide in agricultural practices. It is well described that it has low toxicity among animals and is lethal if consumed in large amounts. However, toxicity in humans is rarely reported in literature. Here, we describe acetamiprid toxicity complicated with severe lactic acidosis, myocardial ischemia, refractory hypotension, and severe hypokalemia in a middle-aged man who presented with deliberate self-harming with acetamiprid poisoning in Sri Lanka.

Case presentation
We describe a case of acute poisoning with an acetamiprid in a middle-aged Sri Lankan Tamil farmer for suicidal purposes following family conflicts with his wife. He presented with severe nausea, vomiting, and altered level of consciousness. He had electrocardiogram changes, hypoxia, and lactic acidosis. With intensive care management including ventilatory support, inotropic therapy along with intraarterial blood pressure monitoring, correction of acidosis, and administration of electrolytes, he made good clinical recovery. He was discharged without any further complications 6 days after ingestion of acetamiprid.

Conclusions
This case illustrates a rare, acute poisoning with acetamiprid in human, as well as its clinical manifestations and successful management with supportive therapy. This will be helpful for clinicians to identify clinical manifestations and to guide management of acute poisoning with acetamiprid in the future.
Zoster-associated limb paralysis mimicking acute stroke: a case report
Authors: Dalugama Chamara , Jayasinghe Ruwanthi , Rathnayaka Nimanthi , Medagama Arjuna 
Published: July 2021

Abstract
Background
Varicella zoster virus is a Deoxyribonucleic acid (DNA) virus exclusively affecting humans. Reactivation of varicella zoster virus causes herpes zoster with vesicular eruptions in a restricted dermatomal distribution. Peripheral motor neuropathy is a very rare complication of varicella zoster virus.

Case presentation
A 57-year-old previously well Sri Lankan female presented with acute onset painful weakness of the left upper limb with a preceding history of a febrile illness. Subsequently she developed vesicular eruptions in the dermatomal distribution of cervical 5, 6, and 7. Electromyography was suggestive of acute denervation of cervical 5, 6, and 7 myotomes. Diagnosis of zoster-associated brachial plexopathy was made, and the patient was treated with acyclovir, steroids, and analgesics. She made a good recovery.

Conclusion
Brachial plexus neuritis due to varicella zoster infection should be considered in an acute monoparesis of a limb as it is a treatable and reversible condition
Potential advantages and limitations of using information fusion in media forensics—a discussion on the example of detecting face morphing attacks
Authors: Kraetzer Christian , Makrushin Andrey , Dittmann Jana , Hildebrandt Mario 
Published: July 2021

AbstractInformation fusion, i.e., the combination of expert systems, has a huge potential to improve the accuracy of pattern recognition systems. During the last decades, various application fields started to use different fusion concepts extensively. The forensic sciences are still hesitant if it comes to blindly applying information fusion. Here, a potentially negative impact on the classification accuracy, if wrongly used or parameterized, as well as the increased complexity (and the inherently higher costs for plausibility validation) of fusion is in conflict with the fundamental requirements for forensics.The goals of this paper are to explain the reasons for this reluctance to accept such a potentially very beneficial technique and to illustrate the practical issues arising when applying fusion. For those practical discussions the exemplary application scenario of morphing attack detection (MAD) is selected with the goal to facilitate the understanding between the media forensics community and forensic practitioners.As general contributions, it is illustrated why the naive assumption that fusion would make the detection more reliable can fail in practice, i.e., why fusion behaves in a field application sometimes differently than in the lab. As a result, the constraints and limitations of the application of fusion are discussed and its impact to (media) forensics is reflected upon.As technical contributions, the current state of the art of MAD is expanded by:The introduction of the likelihood-based fusion and an fusion ensemble composition experiment to extend the set of methods (majority voting, sum-rule, and Dempster-Shafer Theory of evidence) used previouslyThe direct comparison of the two evaluation scenarios “MAD in document issuing” and “MAD in identity verification” using a realistic and some less restrictive evaluation setupsA thorough analysis and discussion of the detection performance issues and the reasons why fusion in a majority of the test cases discussed here leads to worse classification accuracy than the best individual classifier
Pregnancy complications, substance abuse, and prenatal care predict birthweight in adolescent mothers
Authors: Hacker Miriam , Firk Christine , Konrad Kerstin , Paschke Kerstin , Neulen Joseph , Herpertz-Dahlmann Beate , Dahmen Brigitte 
Published: July 2021

AbstractBackgroundReduced birthweight is associated with adverse physical and mental health outcomes later in life. Children of adolescent mothers are at higher risk for reduced birthweight. The current study aimed to identify the key risk factors affecting birthweight in a well-characterized sample of adolescent mothers to inform preventive public health efforts.MethodsSixty-four adolescent mothers (≤ 21 years of age) provided detailed data on pregnancy, birth and psychosocial risk. Separate regression analyses with (1) birthweight and (2) low birthweight (LBW) as outcomes, and pregnancy complications, prenatal care, maternal age, substance abuse during pregnancy, socioeconomic risk, stressful life events and the child’s sex as independent variables were conducted. Exploratively, a receiver operating characteristic (ROC) analysis was performed to investigate the quality of the discriminatory power of the risk factors.ResultsThe following variables explained variance in birthweight significantly: prenatal care attendance (p = .006), pregnancy complications (p = .006), and maternal substance abuse during pregnancy (p = .044). Prenatal care attendance (p = .023) and complications during pregnancy (p = .027) were identified as significant contributors to LBW. Substance abuse (p = .013), pregnancy complications (p = .022), and prenatal care attendance (p = .044) showed reasonable accuracy in predicting low birthweight in the ROC analysis.ConclusionsAmong high-risk adolescent mothers, both biological factors, such as pregnancy complications, and behavioural factors amenable to intervention, such as substance abuse and insufficient prenatal care, seem to contribute to reduced birthweight in their children, a predisposing factor for poorer health outcomes later in life. More tailored intervention programmes targeting the specific needs of this high-risk group are needed.
Determinants of diabetic retinopathy in Tikur Anbessa Hospital, Ethiopia: a case–control study
Authors: Seid Kalid , Tesfaye Temamen , Belay Admasu , Mohammed Hayat 
Published: July 2021

AbstractBackgroundDiabetic retinopathy is the most frequent complication of Diabetes Mellitus and remains the leading cause of preventable blindness. However, there are limited studies on the determinants of diabetic retinopathy in the study area as well in Ethiopia. Hence, this study aimed to assess the determinants of diabetic retinopathy among diabetic patients at Tikur Anbessa Hospital.MethodsAn institution-based unmatched case–control study design was conducted at Tikur Anbessa Hospital from May 11 to June 26, 2020. Diabetic patients who developed retinopathy within 2 years were cases in the study. Patients who were free of retinopathy were controls in this study. Data were collected using a pretested interviewer-administered questionnaire, Topcon retinal examination, and a record review. The collected data were entered into Epi Data version 3.1 software, and analyzed using SPSS version 25. Binary logistic regression analysis was used to assess the determinants of diabetic retinopathy.ResultsA total of 282 patients (142 cases and 140 controls) were included in the study. The mean age (± Standard deviation) for the cases and the controls were 50.6 (SD: ± 18.7) and 44.9 (SD: ± 17.65) respectively. Patients who had a glucometer at home (AOR = 0.048; 95% CI: 0.005–0.492), exercise adherence (AOR = 0.075; 95% CI: 0.007–0.84), diabetes duration < 5 years (AOR = 0.005; 95% CI: 0.00–0.10) and 5–10 years (AOR = 0.041; 95% CI: 0.003–0.57), health information on diabetic complications (AOR = 0.002; 95% CI: 0.00–0.042) and appointments every month (AOR = 0.004; 95% CI: 0.00–0.073) and every 3 months (AOR = 0.022; 95% CI: 0.002–0.23) were less likely to develop diabetic retinopathy. Participants who had poor glycemic control (AOR = 19.9; 95% CI: 2.34–168.69), systolic hypertension (AOR = 23.4; 95% CI: 2.56–215.36) and nephropathy (AOR = 17.85; 95% CI: 2.01–158.1), had a higher risk of developing diabetic retinopathy.ConclusionsPatients who had a glucometer at home, exercise adherence, diabetes duration < 10 years, health information on diabetic complications, and frequent follow-up had a preventive role. However, poor glycemic control, systolic hypertension, and nephropathy increase the risk of diabetic retinopathy. A concerted effort should be made to improve the health status of patients with Diabetes Mellitus, with particular emphasis on lifestyle modification practices to prevent diabetic retinopathy.