bluuebunny/crossref_metadata_2025_split huggingface dataset:
Contextual reprogramming of CAR-T cells for treatment of HER2+ cancers
Authors: Yang Zhifen , Li Lingyu , Turkoz Ahu , Chen Pohan , Harari-Steinfeld Rona , Bobbin Maggie , Stefanson Ofir , Choi Hana , Pietrobon Violena , Alphson Bennett , Goswami Angshumala , Balan Vitaly , Kearney Alper , Patel Dharmesh , Yang Jin , Inel Damla , Vinod Veena , Cesano Alessandra , Wang Bing , Roh Kyung-Ho , Qi Lei S. , Marincola Francesco M. 
Published: November 2021

Abstract
Background
Adoptive transfer of chimeric antigen receptor (CAR)-engineered T cells combined with checkpoint inhibition may prevent T cell exhaustion and improve clinical outcomes. However, the approach is limited by cumulative costs and toxicities.

Methods
To overcome this drawback, we created a CAR-T (RB-340-1) that unites in one product the two modalities: a CRISPR interference-(CRISPRi) circuit prevents programmed cell death protein 1 (PD-1) expression upon antigen-encounter. RB-340-1 is engineered to express an anti-human epidermal growth factor receptor 2 (HER2) CAR single chain variable fragment (scFv), with CD28 and CD3ζ co-stimulatory domains linked to the tobacco etch virus (TEV) protease and a single guide RNA (sgRNA) targeting the PD-1 transcription start site (TSS). A second constructs includes linker for activation of T cells (LAT) fused to nuclease-deactivated spCas9 (dCas9)-Kruppel-associated box (KRAB) via a TEV-cleavable sequence (TCS). Upon antigen encounter, the LAT-dCas9-KRAB (LdCK) complex is cleaved by TEV allowing targeting of dCas9-KRAB to the PD-1 gene TSS.

Results
Here, we show that RB-340-1 consistently demonstrated higher production of homeostatic cytokines, enhanced expansion of CAR-T cells in vitro, prolonged in vivo persistence and more efficient suppression of HER2+ FaDu oropharyngeal cancer growth compared to the respective conventional CAR-T cell product.

Conclusions
As the first application of CRISPRi toward a clinically relevant product, RB-340-1 with the conditional, non-gene editing and reversible suppression promotes CAR-T cells resilience to checkpoint inhibition, and their persistence and effectiveness against HER2-expressing cancer xenografts.
DSS-induced inflammation in the colon drives a proinflammatory signature in the brain that is ameliorated by prophylactic treatment with the S100A9 inhibitor paquinimod
Authors: Talley Sarah , Valiauga Rasa , Anderson Lillian , Cannon Abigail R. , Choudhry Mashkoor A. , Campbell Edward M. 
Published: November 2021

Abstract
Background
Inflammatory bowel disease (IBD) is established to drive pathological sequelae in organ systems outside the intestine, including the central nervous system (CNS). Many patients exhibit cognitive deficits, particularly during disease flare. The connection between colonic inflammation and neuroinflammation remains unclear and characterization of the neuroinflammatory phenotype in the brain during colitis is ill-defined.

Methods
Transgenic mice expressing a bioluminescent reporter of active caspase-1 were treated with 2% dextran sodium sulfate (DSS) for 7 days to induce acute colitis, and colonic, systemic and neuroinflammation were assessed. In some experiments, mice were prophylactically treated with paquinimod (ABR-215757) to inhibit S100A9 inflammatory signaling. As a positive control for peripheral-induced neuroinflammation, mice were injected with lipopolysaccharide (LPS). Colonic, systemic and brain inflammatory cytokines and chemokines were measured by cytokine bead array (CBA) and Proteome profiler mouse cytokine array. Bioluminescence was quantified in the brain and caspase activation was confirmed by immunoblot. Immune cell infiltration into the CNS was measured by flow cytometry, while light sheet microscopy was used to monitor changes in resident microglia localization in intact brains during DSS or LPS-induced neuroinflammation. RNA sequencing was performed to identify transcriptomic changes occurring in the CNS of DSS-treated mice. Expression of inflammatory biomarkers were quantified in the brain and serum by qRT-PCR, ELISA and WB.

Results
DSS-treated mice exhibited clinical hallmarks of colitis, including weight loss, colonic shortening and inflammation in the colon. We also detected a significant increase in inflammatory cytokines in the serum and brain, as well as caspase and microglia activation in the brain of mice with ongoing colitis. RNA sequencing of brains isolated from DSS-treated mice revealed differential expression of genes involved in the regulation of inflammatory responses. This inflammatory phenotype was similar to the signature detected in LPS-treated mice, albeit less robust and transient, as inflammatory gene expression returned to baseline following cessation of DSS. Pharmacological inhibition of S100A9, one of the transcripts identified by RNA sequencing, attenuated colitis severity and systemic and neuroinflammation.

Conclusions
Our findings suggest that local inflammation in the colon drives systemic inflammation and neuroinflammation, and this can be ameliorated by inhibition of the S100 alarmin, S100A9.
An ancient retroviral RNA element hidden in mammalian genomes and its involvement in co-opted retroviral gene regulation
Authors: Kitao Koichi , Nakagawa So , Miyazawa Takayuki 
Published: November 2021

Abstract
Background
Retroviruses utilize multiple unique RNA elements to control RNA processing and translation. However, it is unclear what functional RNA elements are present in endogenous retroviruses (ERVs). Gene co-option from ERVs sometimes entails the conservation of viral cis-elements required for gene expression, which might reveal the RNA regulation in ERVs.

Results
Here, we characterized an RNA element found in ERVs consisting of three specific sequence motifs, called SPRE. The SPRE-like elements were found in different ERV families but not in any exogenous viral sequences examined. We observed more than a thousand of copies of the SPRE-like elements in several mammalian genomes; in human and marmoset genomes, they overlapped with lineage-specific ERVs. SPRE was originally found in human syncytin-1 and syncytin-2. Indeed, several mammalian syncytin genes: mac-syncytin-3 of macaque, syncytin-Ten1 of tenrec, and syncytin-Car1 of Carnivora, contained the SPRE-like elements. A reporter assay revealed that the enhancement of gene expression by SPRE depended on the reporter genes. Mutation of SPRE impaired the wild-type syncytin-2 expression while the same mutation did not affect codon-optimized syncytin-2, suggesting that SPRE activity depends on the coding sequence.

Conclusions
These results indicate multiple independent invasions of various mammalian genomes by retroviruses harboring SPRE-like elements. Functional SPRE-like elements are found in several syncytin genes derived from these retroviruses. This element may facilitate the expression of viral genes, which were suppressed due to inefficient codon frequency or repressive elements within the coding sequences. These findings provide new insights into the long-term evolution of RNA elements and molecular mechanisms of gene expression in retroviruses.
Commentary: What should referral pathways have to improve healthcare experiences of women with female genital mutilation in Australia?
Authors: Njue Carolyne , Ameyaw Edward K. , Ahinkorah Bright O. , Seidu Abdul-Aziz , Kimani Samuel 
Published: November 2021

Abstract
Background
We examined the evidence derived from healthcare professionals’ interfacing with women with female genital mutilation (FGM) to comprehend the referral pathways available to these women in Australia.

Main body
Clinicians encountered FGM-related complications that included ruptured bladder and total urinary incontinence. Midwives and paediatricians indicated a lack of referral pathways for FGM, but used their discretion to refer such cases to social work departments, obstetric/gynaecological units, child protection service providers, psychological counsellors and surgeons. The continuum of care for women with FGM is characterised by inadequate and lack of clear referral pathways. This underscores the need to develop and strengthen referral pathways in response to physical, birthing and psychological complications of women with FGM to improve their care experiences in Australia.

Short conclusion
Capacity building initiatives on FGM-prevention and care for trainees and practising health providers and community involvement in high burden areas/populations should be implemented to promote uptake and utilization of the referral services. Provision of infrastructural support, including clinical management tools, job aids, posters, referral algorithms and electronic patient records with "drop-down menus" for referral sites for health complications of FGM to reinforce the providers’ efforts are critical.
Magnitude of child sexual abuse and its associated factors among high school female students in Dire Dawa, Eastern Ethiopia: a cross-sectional study
Authors: Abera Legesse , Aliye Abdulahi , Tadesse Kalbesse , Guta Alemu 
Published: November 2021

Abstract
Background
Child sexual abuse (CSA) refers to the involvement of a child (< 18 years) in sexual activity that he or she does not fully comprehend, is unable to give informed consent to, or for which the child is not developmentally prepared and cannot give consent, or that violates the laws or social taboos of society. It is a serious public health problem affecting millions of people each year worldwide but the most neglected and least documented form of violence in Ethiopia among school girls. Therefore, this study aimed to assess the magnitude of child sexual abuse and its associated factors among female high school students in the Dire Dawa administration, Eastern Ethiopia.

Methods
An institutional-based cross-sectional study was conducted among female high school students in Dire Dawa administration between March 1 and 23/2021. We employed stratified and multistage sampling techniques to include 794 participants from selected high schools. A pretested self-administered questionnaire was used, and the data were analyzed using the SPSS software version 24.

Results
The proportion of students who reported at least one form of sexual abuse was 384 (48.9%) and approximately 19% of the students reported rape from the total respondents. Students who live alone 4.3 times (AOR 4.30; 95% CI 1.81–10.24), those who live with their friends five times (AOR 5.02; 95% CI 2.24–8.04), and those who live with their single parent three times (AOR 3.31; 95% CI 1.23–8.89) more likely to experience sexual abuse than those living with both parents. The odds of experiencing sexual abuse among students of rural residence were 3.2 times higher than their urban counterparts (AOR 3.2; 95% CI 2.02–4.51). Students who didn’t drink alcohol were 70% more protective than those who drank alcohol (AOR 0.70; 95% CI 0.28–0.97). Among rape survivors (64, 37.9%) developed unwanted pregnancies, 26.0% of them underwent an abortion, and (39, 26.0%) developed STI as an outcome of sexual abuse.

Conclusion
This study demonstrated that the magnitude of child sexual abuse among female students in Dire Dawa was high. Lack of discussion about sexual issues with parents, living without both parents, drinking alcohol, and being a rural residence had a significant association with child sexual abuse. Unwanted pregnancy, abortion, and STIs have been reported as reproductive health outcomes of rape. Therefore, policymakers should introduce and strengthen comprehensive sexual and reproductive health education both in school and out of school, in addition to formal education to reduce the magnitude of the problem. Parents should discuss all sexual and reproductive health issues with their children to reduce the magnitude and consequences of child sexual abuse.
High throughput sequencing of whole transcriptome and construct of ceRNA regulatory network in RD cells infected with enterovirus D68
Authors: Si Junzhuo , Tang Xia , Xu Lei , Fu Huichao , Li Huayi , He Yonglin , Bao Jiajia , Tang Jialing , Li Anlong , Lu Nan , Yang Chun 
Published: November 2021

Abstract
Background
With the advancement of sequencing technologies, a plethora of noncoding RNA (ncRNA) species have been widely discovered, including microRNAs (miRNAs), circular RNAs (circRNAs), and long ncRNAs (lncRNAs). However, the mechanism of these non-coding RNAs in diseases caused by enterovirus d68 (EV-D68) remains unclear. The goal of this research was to identify significantly altered circRNAs, lncRNAs, miRNAs, and mRNAs pathways in RD cells infected with EV-D68, analyze their target relationships, demonstrate the competing endogenous RNA (ceRNA) regulatory network, and evaluate their biological functions.

Methods
The total RNAs were sequenced by high-throughput sequencing technology, and differentially expressed genes between control and infection groups were screened using bioinformatics method. We discovered the targeting relationship between three ncRNAs and mRNA using bioinformatics methods, and then built a ceRNA regulatory network centered on miRNA. The biological functions of differentially expressed mRNAs (DEmRNAs) were discovered through GO and KEGG enrichment analysis. Create a protein interaction network (PPI) to seek for hub mRNAs and learn more about protein–protein interactions. The relative expression was verified using RT-qPCR. The effects of Fos and ARRDC3 on virus replication were confirmed using RT-qPCR, virus titer (TCID50/ml), Western blotting.

Results
375 lncRNAs (154 upregulated and 221 downregulated), 33 circRNAs (32 upregulated and 1 downregulated), 96 miRNAs (49 upregulated and 47 downregulated), and 239 mRNAs (135 upregulated and 104 downregulated) were identified as differently in infected group compare to no-infected group. A single lncRNA or circRNA can be connected with numerous miRNAs, which subsequently coregulate additional mRNAs, according to the ceRNA regulatory network. The majority of DEmRNAs were shown to be connected to DNA binding, transcription regulation by RNA polymerase II, transcription factor, MAPK signaling pathways, Hippo signal pathway, and apoptosis pathway, according to GO and KEGG pathway enrichment analysis. The hub mRNAs with EGR1, Fos and Jun as the core were screened through PPI interaction network. We preliminarily demonstrated that the Fos and ARRDC3 genes can suppress EV-D68 viral replication in order to further verify the results of full transcriptome sequencing.

Conclusion
The results of whole transcriptome analysis after EV-D68 infection of RD cells were first reported in this study, and for the first time, a ceRNA regulation network containing miRNA at its center was established for the first time. The Fos and ARRDC3 genes were found to hinder viral in RD cells. This study establishes a novel insight host response during EV-D68 infection and further investigated potential drug targets.
Developing and validating a measurement tool to self-report perceived barriers in substance use treatment: the substance use treatment barriers questionnaire (SUTBQ)
Authors: Ghouchani Hamid Tavakoli , Lashkardoost Hossein , Saadati Hassan , Hojjat Seyed Kaveh , Kaviyani Faezeh , Razaghi Kazem , Asghari Dordane , Gholizadeh Nazanin 
Published: November 2021

Abstract
Background
Substance using often cause a wide range of social, health, and psychological problems. This study aimed to develop and validate a questionnaire of barriers of treatment in substance users.

Methods
In this cross-sectional study, the initial questionnaire was designed based on the evaluation of previous studies. The preliminary tool including 35 Likert-scaled items. After assuring the face validity of the questionnaire, 13 experts’ opinions were obtained for assessing or improving the content validity. The reliability was investigated by internal consistency methods using Cronbach’s alpha. For measuring the structural validity, the exploratory factor analysis was performed to determine the dimensionality of the questionnaire using principal components extraction and Varimax rotation.

Results
The preliminary questionnaire consisted of 35 items. After completing the face validity and summarizing the experts’ suggestions, 8 items were removed. By calculating the content validity ratio and coefficient, 11 questions were deleted. The internal consistency was calculated to be 0.84 using Cronbach’s alpha. In the last stage and according to the results of the factor analysis, three factors fear of or unawareness of treatment, doubt or inefficiency, and social stigma were identified from the 10-items questionnaire, which explained 67.34% of the total variance.

Conclusion
Considering the necessity of using a validated tool for planning and evaluating effective interventions on people who use substance is inevitable. The Substance use Treatment Barriers Questionnaire is designed with 10 items and 3 dimensions, which has appropriate validity and reliability and can be used to determine the obstacles for treatment or factors that lead to discontinuing treatment.
Study on the relationship between the timing of conversion from external fixation to internal fixation and infection in the treatment of open fractures of extremities
Authors: Ye Zelin , Zhao Shanwen , Zeng Canjun , Luo Ziheng , Yuan Song , Li Runguang 
Published: November 2021

Abstract
Objective
To investigate the relationship between the infection rate and the timing of replacement of temporary external fixators with internal fixation, and the timing of immediate or delayed internal fixation after removal of temporary external fixation in the staging treatment modality of open fractures of extremities.

Methods
A retrospective analysis was performed on 122 cases of open fractures of extremities. External fixators were applied at the early stage and replaced with internal fixation when the condition of soft tissues improved and inflammatory indexes dropped to the normal range or showed a steady downward trend. Depending on the carrying time of external fixators after wound closure or healing, the patients were divided into three groups; the carrying time of groups A, B, and C was ≤ 14 days, 15–28 days, and > 28 days, respectively. Depending on the immediate or delayed internal fixation after removal of external fixator, patients were divided into group a (immediate internal fixation after removal of external fixator) and group b (delayed internal fixation after removal of external fixator, 5–7 days later).

Results
The infection rates of groups A, B, and C were 6.5%, 5.9%, and 23.3%, respectively. The differences among the three groups were statistically significant (P < 0.05). The infection rates of different Gustilo–Anderson fractures were as follows: no cases of infection out of 10 cases with type I fracture (0%); two cases of infection out of 35 cases with type II fracture (5.7%); three cases of infection out of 36 cases with IIIa fracture (8.3%); five cases of infection out of 28 cases with IIIB fracture (17.9%); and five cases of infection out of 13 cases with IIIC fracture (38.5%). The differences among the five groups were statistically significant.

Conclusions
The occurrence of infection of open fractures of extremities is associated with the fracture severity (Gustilo classification). For open fractures of Gustilo types I and II, the final internal fixation should be placed as soon as possible when the recovery of general and local conditions is good and the infection is controlled.
Silencing of UBE2D1 inhibited cell migration in gastric cancer, decreasing ubiquitination of SMAD4
Authors: Xie Honghu , He Yu , Wu Yugang , Lu Qicheng 
Published: November 2021

Abstract
Background
Gastric cancer (GC) is the second leading cause of cancer-related deaths. Because it is hard to diagnose at early stage, the overall 5 years survival rate is lower than 25%. High migration is the main hallmark of malignant cells at advanced stage of GC. Thus, it is urgent to find biomarkers for early diagnosis and more effective therapy of GC.

Methods
In this study, lentivirus-mediated silencing and overexpression lentiviruses targeting the ubiquitin-conjugating enzyme E2 D1 (UBE2D1), transwell, wound healing, and pulmonary metastasis mouse model were applied to analyze the function of UBE2D1 in vitro and in vivo. Real-time PCR and immunohistochemistry were used to elucidate the level of UBE2D1 in GC samples.

Results
Silencing of UBE2D1 inhibited cell migration and the levels of epithelial-mesenchymal transition makers (MMP2 and MMP9) in AGS and MKN45 cells. Silencing of UBE2D1 inhibited cell metastasis in mouse model. On the contrary, UBE2D1 overexpression increased cell migration and the levels of MMP2 and MMP9 in MGC-803 cells. Further, silencing of UBE2D1 decreased the ubiquitination level of mothers against decapentaplegic homolog 4 (SMAD4), and the increase of cell migration induced by UBE2D1 overexpression could be reversed by SMAD4.

Conclusion
Silencing of UBE2D1 inhibited cell migration through transforming growth factor β (TGF-β)/SMAD4 signaling pathway in GC.
N6-methyladenosine reader IMP2 stabilizes the ZFAS1/OLA1 axis and activates the Warburg effect: implication in colorectal cancer
Authors: Lu Senxu , Han Li , Hu Xiaoyun , Sun Tong , Xu Dongping , Li Yalun , Chen Qiuchen , Yao Weifan , He Miao , Wang Zhenning , Wu Huizhe , Wei Minjie 
Published: November 2021

Abstract
Background
Accumulating evidence shows that N6-methyladenine (m6A) modulators contribute to the etiology and progression of colorectal cancer (CRC). However, the exact mechanisms of m6A reader involved in glycolytic metabolism remain vague. This article aimed to crosstalk the m6A reader with glycolytic metabolism and reveal a new mechanism for the progression of CRC.

Methods
The relationship between candidate lncRNA and m6A reader was analyzed by bioinformatics, ISH and IHC assays. In vivo and in vitro studies (including MTT, CFA, trans-well, apoptosis, western blot, qRT-PCR and xenograft mouse models) were utilized to explore the biological functions of these indicators. Lactate detection, ATP activity detection and ECAR assays were used to verify the biological function of the downstream target. The bioinformatics, RNA stability, RIP experiments and RNA pull-down assays were used to explore the potential molecular mechanisms.

Results
We identified that the crosstalk of the m6A reader IMP2 with long-noncoding RNA (lncRNA) ZFAS1 in an m6A modulation-dependent manner, subsequently augmented the recruitment of Obg-like ATPase 1 (OLA1) and adenosine triphosphate (ATP) hydrolysis and glycolysis during CRC proliferation and progression. Specifically, IMP2 and ZFAS1 are significantly overexpressed with elevated m6A levels in CRC cells and paired CRC cohorts (n = 144). These indicators could be independent biomarkers for CRC prognostic prediction. Notably, IMP2 regulated ZFAS1 expression and enhanced CRC cell proliferation, colony formation, and apoptosis inhibition; thus, it was oncogenic. Mechanistically, ZFAS1 is modified at adenosine +843 within the RGGAC/RRACH element in an m6A-dependent manner. Thus, direct interaction between the KH3–4 domain of IMP2 and ZFAS1 where IMP2 serves as a reader for m6A-modified ZFAS1 and promotes the RNA stability of ZFAS1 is critical for CRC development. More importantly, stabilized ZFAS1 recognizes the OBG-type functional domain of OLA1, which facilitated the exposure of ATP-binding sites (NVGKST, 32–37), enhanced its protein activity, and ultimately accelerated ATP hydrolysis and the Warburg effect.

Conclusions
Our findings reveal a new cancer-promoting mechanism, that is, the critical modulation network underlying m6A readers stabilizes lncRNAs, and they jointly promote mitochondrial energy metabolism in the pathogenesis of CRC.