bluuebunny/crossref_metadata_2025_split huggingface dataset:
In Vivo HSC Gene Therapy with Base Editors Allows for Efficient Reactivation of Fetal Globin in Beta-Yac Mice
Authors: Li Chang , Georgakopoulou Afrodite , Gil Sucheol , Lieber Andre 
Published: February 2021

Base editors are capable of installing precise nucleotide mutations at targeted genomic loci and present the advantage of avoiding double-stranded DNA breaks. Here, we aimed to target critical motifs regulating gamma-globin reactivation with base editors delivered via HDAd5/35++ vectors. Through optimized design, we successfully rescued a panel of cytidine and adenine base editors (CBE and ABE) targeting the BCL11A enhancer or recreating naturally occurring Hereditary Persistence of Fetal Hemoglobin (HPFH) mutations in the HBG1/2 promoter. In HUDEP-2 cells, all five tested vectors efficiently installed target base conversion and led to gamma-globin reactivation. We observed significant gamma-globin protein production (~23% over β-globin) by using an ABE vector HDAd-ABE-sgHBG#2 specific to the -113A to G HPFH mutation in HBG1/2 promoter. This vector was therefore chosen for downstream in vivo hematopoietic progenitor/stem cell (HSPC) transduction studies in mice that carry 248kb of the human β-globin locus (β-YAC mice) and thus accurately reflect globin switching. An EF1a-mgmtP140K expression cassette flanked by frt and transposon sites was included in the vector for allowing in vivo selection of transduced cells. After in vivo HSPC transduction with HDAd-ABE-HBG#2 + HDAd-SB and low doses of chemoselection, an average of over 40% HbF-positive cells in peripheral red blood cells was measured. This corresponded to ~21% gamma-globin production over human β-globin. The -113 A to G conversion in total bone marrow cells was on average 20%. Compared to untransduced mice, no alterations in hematological parameters, erythropoiesis and bone marrow cellular composition were observed after treatment, demonstrating a good safety profile of our approach. No detectable editing was found at top-scored potential off-target genomic sites. Bone marrow lineage-negative cells, isolated from primary mice at week 16 after transduction, were capable of reconstituting secondary transplanted mice with stable HbF expression. Importantly, the advantage of base editing over CRISPR/Cas9 was reflected by the markedly lower rates of intergenic 4.9kb deletion and no detectable toxicity in human CD34+ stem cells. Our observations demonstrate that base editors delivered by HDAd5/35++ vectors represent a promising strategy for precise in vivo genome engineering for the treatment of hemoglobinopathies.

Disclosures
Lieber: Ensoma, Inc: Consultancy, Research Funding.
Alternative Consolidation Strategy after High Dose Methotrexate, Rituximab and Temozolamide in Primary CNS Lymphoma - the Henry Ford Experience
Authors: Philip Joyce , Sharma Shivani , Donthireddy Vijayalakshmi 
Published: February 2021

Background: Treatment for primary CNS lymphoma involves a methotrexate-based induction therapy followed by consolidation. The optimal consolidation treatment after induction with a high dose Methotrexate (HD-MTX), Rituximab and Temozolomide regimen has not been fully established. The CALGB 50202 regimen using Etoposide and Cytarabine consolidation was associated with significant toxicity. We sought to review the results of alternative consolidation regimens and evaluate the progression free survival and overall survival.
Methods: A retrospective cohort study was conducted to evaluate the efficacy of alternative consolidation regimens such as autologous stem cell transplant and HDMTx alone. Patients diagnosed with primary CNS lymphoma between November 2012 and March 2019 were identified. All patients received the same induction chemotherapy based on the CALGB 50202 protocol. Data was collected for baseline characteristics, progression free survival and overall survival.
Results: 38 patients had a diagnosis of primary CNS lymphoma. 15 patients received treatment as per the CALBG 50202 induction protocol with high dose Methotrexate, Rituximab and Temozolomide. Of the 15 patients, 11 patients (69%) achieved a complete remission (CR) after induction therapy. 7 patients received an autologous stem cell transplant for consolidation, 5 patients received HD-MTX alone for consolidation and one patient was placed on Lenalidomide maintenance. 2 patients did not receive any consolidation therapy due to progressive disease and/or death. At a median follow up of 2.7 years for the entire cohort, median PFS was 31.7+ months and median OS was 32.5+ months. At a median follow up of 2.7 years for patients who were consolidated with an autologous stem cell transplant, median PFS and median OS was 27.2+ and 32.5+ months respectively. At a median follow up of 5.5 years for patients who were consolidated with treatments other than transplant, median PFS and OS was 65.6+ months. There were no deaths attributed to treatment related toxicity. To date, 4 patients of the entire cohort have died, with a median survival time among surviving patients of 3.6 years (range, 0.68-7.05 years). There were no deaths attributed to treatment related toxicity.
Conclusion: Patients with primary CNS lymphoma who received induction therapy as per CALGB 50202 regimen and received alternative consolidation therapies with either autologous stem cell transplant or HD-MTX based consolidation achieved prolonged PFS and OS comparable if not superior to the Etoposide and Cytarabine consolidation. Results of the ongoing CALGB 51101 trial will determine the utility of EA consolidation.

Disclosures
No relevant conflicts of interest to declare.
Long non-coding RNA CIR inhibits chondrogenic differentiation of mesenchymal stem cells by epigenetically suppressing ATOH8 via methyltransferase EZH2
Authors: Liu Feng , Song De-Ye , Huang Jun , Yang Hong-Qi , You Di , Ni Jiang-Dong 
Published: February 2021

AbstractBackgroundOsteoarthritis (OA) is the most common articular disorder, leading to joint malfunction and disability. Although the incidence of OA is increasing globally, the treatment of OA is very limited. LncRNA CIR has been implicated in OA through unclear mechanisms. Here, we investigated the role of lncRNA CIR in chondrogenic differentiation.MethodsHuman umbilical-cord-derived mesenchymal stem cells (hUC-MSCs) were obtained from human umbilical cords. Flow cytometry was used to analyze the surface markers of hUC-MSCs. Various culture conditions and corresponding staining assays were employed to assess the differentiation abilities of hUC-MSC. qRT-PCR, western blot, and immunostaining were used to measure expression levels of related genes and proteins such as lncRNA CIR, ATOH8, EZH2, and H3K27me3. RNA immunoprecipitation assay, biotin pull-down, and chromatin immunoprecipitaion assay were performed to analyze the interactions of lncRNA CIR, EZH2, H3K27me3 and ATOH8 promoter.ResultshUC-MSCs exhibited MSCs features and could differentiate into chondrocytes under specific conditions. LncRNA CIR was downregulated while ATOH8 was upregulated during the chondrogenic differentiation of hUC-MSCs. Knockdown lncRNA CIR or overexpression of ATOH8 promoted chondrogenic differentiation. Further, lncRNA CIR bound to EZH2 and repressed ATOH8 expression via EZH2-mediated H3K27me3, which promotes the methylation of ATOH8. Inhibition of ATOH8 reversed the effects of knockdown lncRNA CIR on chondrogenic differentiation.ConclusionLncRNA CIR suppresses chondrogenic differentiation of hUC-MSCs. Mechanistically, lncRNA CIR could inhibit ATOH8 expression that functions to promote chondrogenic differentiation through EZH2-mediated epigenetic modifications.
Plant Co-expression Annotation Resource: a web server for identifying targets for genetically modified crop breeding pipelines
Authors: José Andrade Viana Marcos , Zerlotini Adhemar , de Alvarenga Mudadu Mauricio 
Published: February 2021

AbstractThe development of genetically modified crops (GM) includes the discovery of candidate genes through bioinformatics analysis using genomics data, gene expression, and others. Proteins of unknown function (PUFs) are interesting targets for GM crops breeding pipelines for the novelty associated with such targets and also to avoid copyright protection. One method of inferring the putative function of PUFs is by relating them to factors of interest such as abiotic stresses using orthology and co-expression networks, in a guilt-by-association manner. In this regard, we have downloaded, analyzed, and processed genomics data of 53 angiosperms, totaling 1,862,010 genes and 2,332,974 RNA. Diamond and InterproScan were used to discover 72,266 PUFs for all organisms. RNA-seq datasets related to abiotic stresses were downloaded from NCBI/GEO. The RNA-seq data was used as input to the LSTrAP software to construct co-expression networks. LSTrAP also created clusters of transcripts with correlated expression, whose members are more probably related to the molecular mechanisms associated with abiotic stresses in the plants. Orthologous groups were created (OrhtoMCL) using all 2,332,974 proteins in order to associate PUFs to abiotic stress-related clusters of co-expression and therefore infer their function in a guilt-by-association manner. A freely available web resource named “Plant Co-expression Annotation Resource” (https://www.machado.cnptia.embrapa.br/plantannot), Plantannot, was created to provide indexed queries to search for PUF putatively associated with abiotic stresses. The web interface also allows browsing, querying, and retrieving of public genomics data from 53 plants. We hope Plantannot to be useful for researchers trying to obtain novel GM crops resistant to climate change hazards.
Investigating the relevance of major signaling pathways in cancer survival using a biologically meaningful deep learning model
Authors: Feng Jiarui , Zhang Heming , Li Fuhai 
Published: February 2021

AbstractBackgroundSurvival analysis is an important part of cancer studies. In addition to the existing Cox proportional hazards model, deep learning models have recently been proposed in survival prediction, which directly integrates multi-omics data of a large number of genes using the fully connected dense deep neural network layers, which are hard to interpret. On the other hand, cancer signaling pathways are important and interpretable concepts that define the signaling cascades regulating cancer development and drug resistance. Thus, it is important to investigate potential associations between patient survival and individual signaling pathways, which can help domain experts to understand deep learning models making specific predictions.ResultsIn this exploratory study, we proposed to investigate the relevance and influence of a set of core cancer signaling pathways in the survival analysis of cancer patients. Specifically, we built a simplified and partially biologically meaningful deep neural network, DeepSigSurvNet, for survival prediction. In the model, the gene expression and copy number data of 1967 genes from 46 major signaling pathways were integrated in the model. We applied the model to four types of cancer and investigated the influence of the 46 signaling pathways in the cancers. Interestingly, the interpretable analysis identified the distinct patterns of these signaling pathways, which are helpful in understanding the relevance of signaling pathways in terms of their application to the prediction of cancer patients’ survival time. These highly relevant signaling pathways, when combined with other essential signaling pathways inhibitors, can be novel targets for drug and drug combination prediction to improve cancer patients’ survival time.ConclusionThe proposed DeepSigSurvNet model can facilitate the understanding of the implications of signaling pathways on cancer patients’ survival by integrating multi-omics data and clinical factors.
Melatonin confers heavy metal-induced tolerance by alleviating oxidative stress and reducing the heavy metal accumulation in Exophiala pisciphila, a dark septate endophyte (DSE)
Authors: Yu Yang , Teng Zhaowei , Mou Zongmin , Lv Yan , Li Tao , Chen Suiyun , Zhao Dake , Zhao Zhiwei 
Published: February 2021

Abstract
Background
Melatonin (MT), ubiquitous in almost all organisms, functions as a free radical scavenger. Despite several reports on its role as an antioxidant in animals, plants, and some microorganisms, extensive studies in filamentous fungi are limited. Based upon the role of melatonin as an antioxidant, we investigated its role in heavy metal-induced stress tolerance in Exophiala pisciphila, a dark septate endophyte (DSE), by studying the underlying mechanisms in alleviating oxidative stress and reducing heavy metal accumulation.

Results
A significant decrease in malondialdehyde (MDA) and oxygen free radical (OFR) in E. pisciphila was recorded under Cd, Zn, and Pb stresses as compared to the control. Pretreatment of E. pisciphila with 200.0 μM exogenous melatonin significantly increased the activity of superoxide dismutase (SOD) under Zn and Pb stresses. Pretreatment with 200.0 μM melatonin also lowered Cd, Zn, and Pb concentrations significantly. Melatonin production was enhanced by Cd, Cu, and Zn after 2 d, and melatonin biosynthetic enzyme genes, E. pisciphila tryptophan decarboxylase (EpTDC1) and serotonin N-acetyltransferase (EpSNAT1), were transcriptionally upregulated. The overexpression of EpTDC1 and N-acetylserotonin O-methyltransferase (EpASMT1) in Escherichia coli and Arabidopsis thaliana enhanced its heavy metal-induced stress tolerance. The overexpression of EpTDC1 and EpASMT1 reduced the Cd accumulation in the whole A. thaliana plants, especially in the roots.

Conclusions
Melatonin conferred heavy metal-induced stress tolerance by alleviating oxidative stress, activating antioxidant enzyme SOD, and reducing heavy metal accumulation in E. pisciphila. Melatonin biosynthetic enzyme genes of E. pisciphila also played key roles in limiting excessive heavy metal accumulation in A. thaliana. These findings can be extended to understand the role of melatonin in other DSEs associated with economically important plants and help develop new strategies in sustainable agriculture practice where plants can grow in soils contaminated with heavy metals.
Intergenerational caring: a systematic literature review on young and young adult caregivers of older people
Authors: D’Amen Barbara , Socci Marco , Santini Sara 
Published: February 2021

Abstract
Background
The theme of young family caregivers of older relatives is still partially uncovered, although the phenomenon is increasing worldwide. This Systematic Literature Review discusses methodological and content issues of ten articles covering this topic, in order to contribute to increase the knowledge and provide suggestions for designing effective support services for adolescent young caregivers. To this purpose, the findings of this review are framed within the caregiving stress appraisal model (renamed CSA model) elaborated by Yates’ and collegues, in order to highlight differences between young caregivers and the older ones.

Methods
Multiple databases including PubMed, Web of Science, Scopus, ProQuest - Psychology Database, CINAHL Complete - EBSCOHost were used to carry out a systematic review of the literature. Additional references were retrieved from experts contacted and research knowledge. The selected articles underwent both methodological appraisal and contents analysis: for every article an appraisal score was calculated and themes and sub-themes were identified.

Results
Out of the ten included studies three were mixed methods, six qualitative and one quantitative. Nine reached a high quality methodological score and one medium. Four main themes emerged from the content analysis: aspects of the caregiving relationship; effects of caregiving; coping strategies; recommendations for services, policy and research.

Conclusions
Selected studies explored practical features of the relationship between young caregivers and older family members (tasks performed, motivations, coping strategies) and highlighted both positive and negative outcomes on young people’s everyday life condition and future development. Nevertheless, these evidences were often limited to small samples that did not allow to make generalizations. More studies are needed including large samples in order to deepen the different aspects of caregiving and design tailored support services.
Infection pattern, case fatality rate and spread of Lassa virus in Nigeria
Authors: Yaro Clement Ameh , Kogi Ezekiel , Opara Kenneth Nnamdi , Batiha Gaber El-Saber , Baty Roua S. , Albrakati Ashraf , Altalbawy Farag M. A. , Etuh Innocent Utenwojo , Oni James Paul 
Published: February 2021

AbstractBackgroundLassa fever (LF) is a zoonotic infectious disease of public concern in Nigeria. The infection dynamics of the disease is not well elucidated in Nigeria. This study was carried out to describe the pattern of infection, case fatality rate and spread of lassa virus (LASV) from 2017 to 2020.MethodsWeekly epidemiological data on LF from December, 2016 to September, 2020 were obtained from Nigeria Centre for Disease Control. The number of confirmed cases and deaths were computed according to months and states. Descriptive statistics was performed and case fatality rate was calculated. Distribution and spread maps of LF over the four years period was performed on ArcMap 10.7.ResultsA total of 2787 confirmed cases and 516 deaths were reported in Nigeria from December, 2016 to September, 2020. Increase in number of cases and deaths were observed with 298, 528, 796 and 1165 confirmed cases and 79, 125, 158 and 158 deaths in 2017, 2018, 2019 and 2020 respectively. Over 60% of the cases were reported in two states, Edo and Ondo states. The LF cases spread from 19 states in 2017 to 32 states and Federal Capital Territory (FCT) in 2020. Ondo state (25.39%) had the highest of deaths rate from LF over the four years. Case fatality rate (CFR) of LF was highest in 2017 (26.5%) with CFR of 23.7, 19.6 and 13.4% in 2018, 2019 and 2020 respectively. The peak of infection was in the month of February for the four years. Infections increases at the onset of dry season in November and decline till April when the wet season sets-in.ConclusionThere is an annual increase in the number of LASV infection across the states in Nigeria. There is need to heighten control strategies through the use of integrated approach, ranging from vector control, health education and early diagnosis.
Prognostic role of preoperative D-dimer, fibrinogen and platelet levels in patients with oral squamous cell carcinoma
Authors: Liang Yu-jie , Mei Xue-ying , Zeng Bin , Zhang Si-en , Yang Le , Lao Xiao-mei , Liao Gui-qing 
Published: February 2021

Abstract
Background
The relationship between cancer and coagulation has been intensively studied in recent years; however, the effects of coagulation factors on oral squamous cell carcinoma (OSCC) have rarely been reported. This study aimed to investigate the relationship between preoperative D-dimer (DD), fibrinogen (FIB), platelets (PLT) and OSCC, as well as the prognostic value of DD, FIB and PLT in OSCC.

Methods
We retrospectively investigated a total of 202 patients with OSCC treated at Guanghua Hospital of Stomatology, Sun Yat-sen University. Baseline demographic and clinicopathological information as well as both preoperative and postoperative DD, FIB and PLT results were collected from each patient, and patients with primary OSCC were followed up for disease progression, death or the end of the study. The correlations between preoperative DD, FIB, PLT and other clinical features, as well as the therapeutic effect and PFS were analysed statistically, and postoperative DD and surgical parameters were also analysed.

Results
Preoperative DD was significantly correlated with T stage, N stage, clinical stage and relapse of OSCC (P = 0.000, 0.001, 0.000 and 0.000, respectively). Univariate Cox regression analyses showed that high preoperative DD predicted poor prognosis in patients with OSCC (HR = 2.1, P = 0.033), while FIB and PLT showed no prognostic values. Postoperative DD was significantly correlated with preoperative DD and surgical type but not the duration of surgery (P = 0.005, 0.001 and 0.244, respectively).

Conclusion
In this study, we suggested that high preoperative DD level may serve as an indicator for synchronous neck dissection in patients with T1, 2 OSCC, and the elevated DD level might be the marker of disease progression in patient follow up.
A cross-sectional survey of knowledge, attitude and practice (KAP) towards COVID-19 pandemic among the Syrian residents
Authors: Al ahdab Sanaa 
Published: February 2021

Abstract
Background
Effective COVID-19 pandemic management requires adequate understanding of factors that influence behavioral changes. This study aims to assess knowledge, attitudes and practices towards COVID-19 among Syrians in a post-conflict context.

Method
A cross sectional web-based survey was conducted on the Syrian residents of 16 years and above. It contains questions on knowledge, attitudes and practices (KAP) with respect to COVID-19. Participants’ demographic characteristics are recorded and analyzed. The study is conducted during the global outbreak of COVID-19.

Results
A total of 706 participants (female, 444; male, 262) were enrolled. This study included 405 participants aged between 16 and 29, 204 aged between 30 and 49, and 97 aged above 60 years. There were 642 who have a university degree and 61 who have high school degree. Among the participants 253 were students, 316 were employed, 75 work as freelancers, and 62 were unemployed. Results showed that overall knowledge score towards the disease was about 60% (mean score 3.54 ± 1.20; range 0–6). Knowledge scores significantly differed across age groups (P < 0.05), education levels (P = 0.001), and occupations (P < 0.05). Attitude and practice scores were 2.45 ± 0.81 (range 0–4), 5.90 ± 1.52 (range 0–8), respectively. Attitude scores were significantly different between males and females (P < 0.05), whereas practice scores varied significantly across gender (P < 0.05), age groups (P = 0.01), education levels (P = 0.015), occupations (P < 0.05), and according to knowledge score (P = 0.000). Results from multiple linear regression indicated that lower knowledge scores were significantly associated with lower education level (P < 0.05), whereas poor preventive practices were common among male, young and unemployed participants with significance levels of P < 0.01, P = .000, P < 0.01, respectively.

Conclusion
The findings of this study suggest that the Syrian residents demonstrate modest knowledge, attitudes and practices towards COVID-19 at the time of its global outbreak. Efforts should be directed towards raising the awareness of the disease to improve their practices in the current COVID-19 pandemic, as well as for future epidemics.