bluuebunny/crossref_metadata_2025_split huggingface dataset:
Improving CRISPR–Cas9 directed faithful transgene integration outcomes by reducing unwanted random DNA integration
Authors: Hermantara Rio , Richmond Laura , Taqi Aqeel Faisal , Chilaka Sabari , Jeantet Valentine , Guerrini Ileana , West Katherine , West Adam 
Published: March 2024

Abstract
Background
The field of genome editing has been revolutionized by the development of an easily programmable editing tool, the CRISPR–Cas9. Despite its promise, off-target activity of Cas9 posed a great disadvantage for genome editing purposes by causing DNA double strand breaks at off-target locations and causing unwanted editing outcomes. Furthermore, for gene integration applications, which introduce transgene sequences, integration of transgenes to off-target sites could be harmful, hard to detect, and reduce faithful genome editing efficiency.

Method
Here we report the development of a multicolour fluorescence assay for studying CRISPR–Cas9-directed gene integration at an endogenous locus in human cell lines. We examine genetic integration of reporter genes in transiently transfected cells as well as puromycin-selected stable cell lines to determine the fidelity of multiple CRISPR–Cas9 strategies.

Result
We found that there is a high occurrence of unwanted DNA integration which tarnished faithful knock-in efficiency. Integration outcomes are influenced by the type of DNA DSBs, donor design, the use of enhanced specificity Cas9 variants, with S-phase regulated Cas9 activity. Moreover, restricting Cas9 expression with a self-cleaving system greatly improves knock-in outcomes by substantially reducing the percentage of cells with unwanted DNA integration.

Conclusion
Our results highlight the need for a more stringent assessment of CRISPR–Cas9-mediated knock-in outcomes, and the importance of careful strategy design to maximise efficient and faithful transgene integration.
Providing medication for opioid use disorder and HIV pre-exposure prophylaxis at syringe services programs via telemedicine: a pilot study
Authors: McKellar Mehri S. , Des Marais Andrea C. , Chen Hillary , Choi Yujung , Lilly Rebecca , Ayers Denae , Bennett Jesse , Kestner Lauren , Perry Brian , Poley Stephanie , Corneli Amy , Meade Christina S. , Sachdeva Nidhi 
Published: March 2024

Abstract
Background
People who inject drugs (PWID) are at high risk for opioid overdose and infectious diseases including HIV. We piloted PARTNER UP, a telemedicine-based program to provide PWID with medication for opioid use disorder (MOUD) with buprenorphine/naloxone (bup/nx) and oral pre-exposure prophylaxis (PrEP) with tenofovir disoproxil fumarate/emtricitabine through two syringe services programs (SSP) in North Carolina. We present overall results from this project, including participant retention rates and self-reported medication adherence.

Methods
Study participants met with a provider for an initial in-person visit at the SSP, followed by weekly telemedicine visits in month 1 and then monthly until program end at month 6. Participants were asked to start both MOUD and PrEP at initiation but could choose to discontinue either at any point during the study. Demographics and health history including substance use, sexual behaviors, and prior use of MOUD/PrEP were collected at baseline. Follow-up surveys were conducted at 3- and 6-months to assess attitudes towards MOUD and PrEP, change in opioid use and sexual behaviors, and for self-reported medication adherence. Participant retention was measured by completion of visits; provider notes were used to assess whether the participant reported continuation of medication.

Results
Overall, 17 persons were enrolled and started on both bup/nx and PrEP; the majority self-identified as white and male. At 3 months, 13 (76%) remained on study; 10 (77%) reported continuing with both MOUD and PrEP, 2 (15%) with bup/nx only, and 1 (8%) with PrEP only. At 6 months, 12 (71%) remained on study; 8 (67%) reported taking both bup/nx and PrEP, and 4 (33%) bup/nx only. Among survey participants, opioid use and HIV risk behaviors decreased. Nearly all reported taking bup/nx daily; however, self-reported daily adherence to PrEP was lower and declined over time. The most common reason for not continuing PrEP was feeling not at risk for acquiring HIV.

Conclusions
Our study results show that MOUD and PrEP can be successfully administered via telemedicine in SSPs. PrEP appears to be a lower priority for participants with decreased continuation and adherence. Low perception of HIV risk was a reason for not continuing PrEP, possibly mitigated by MOUD use. Future studies including helping identify PWID at highest need for PrEP are needed.

Trial registration

Providing Suboxone and PrEP Using Telemedicine, NCT04521920. Registered 18 August 2020. https://clinicaltrials.gov/study/NCT04521920?term=mehri%20mckellar&rank=2.
Acceptability and usefulness of the EORTC ‘Write In three Symptoms/Problems’ (WISP): a brief open-ended instrument for symptom assessment in cancer patients
Authors: Rojas-Concha Leslye , Arrarrás Juan Ignacio , Conroy Thierry , Chalk Tara , Guberti Monica , Holzner Bernhard , Husson Olga , Kuliś Dagmara , Shamieh Omar , Piccinin Claire , Puga María José , Rohde Gudrun , Groenvold Mogens ,   on behalf the EORTC Quality of Life Group
Published: March 2024

Abstract
Background
The use of open-ended questions supplementing static questionnaires with closed questions may facilitate the recognition of symptoms and toxicities. The open-ended ‘Write In three Symptoms/Problems (WISP)’ instrument permits patients to report additional symptoms/problems not covered by selected EORTC questionnaires. We evaluated the acceptability and usefulness of WISP with cancer patients receiving active and palliative care/treatment in Austria, Chile, France, Jordan, the Netherlands, Norway, Spain and the United Kingdom.

Methods
We conducted a literature search on validated instruments for cancer patients including open-ended questions and analyzing their responses. WISP was translated into eight languages and pilot tested. WISP translations were pre-tested together with EORTC QLQ-C30, QLQ-C15-PAL and relevant modules, followed by patient interviews to evaluate their understanding about WISP. Proportions were used to summarize patient responses obtained from interviews and WISP.

Results
From the seven instruments identified in the literature, only the free text collected from the PRO-CTAE has been analyzed previously. In our study, 161 cancer patients participated in the pre-testing and interviews (50% in active treatment). Qualitative interviews showed high acceptability of WISP. Among the 295 symptoms/problems reported using WISP, skin problems, sore mouth and bleeding were more prevalent in patients in active treatment, whereas numbness/tingling, dry mouth and existential problems were more prevalent in patients in palliative care/treatment.

Conclusions
The EORTC WISP instrument was found to be acceptable and useful for symptom assessment in cancer patients. WISP improves the identification of symptoms/problems not assessed by cancer-generic questionnaires and therefore, we recommend its use alongside the EORTC questionnaires.
Exosomes from senescent epithelial cells activate pulmonary fibroblasts via the miR-217-5p/Sirt1 axis in paraquat-induced pulmonary fibrosis
Authors: Zhang Min , Xue Xiang , Lou Zhenshuai , Lin Yanhong , Li Qian , Huang Changbao 
Published: March 2024

Abstract
Background
Paraquat (PQ) is a widely used and highly toxic herbicide that poses a significant risk to human health. The main consequence of PQ poisoning is pulmonary fibrosis, which can result in respiratory failure and potentially death. Our research aims to uncover a crucial mechanism in which PQ poisoning induces senescence in epithelial cells, ultimately regulating the activation of pulmonary fibroblasts through the exosomal pathway.

Methods
Cellular senescence was determined by immunohistochemistry and SA-β-Gal staining. The expression of miRNAs was measured by qPCR. Pulmonary fibroblasts treated with specific siRNA of SIRT1 or LV-SIRT1 were used to analysis senescent exosomes-mediated fibroblasts activation. Luciferase reporter assay and western blot were performed to elucidated the underlying molecular mechanisms. The effects of miR-217-5p antagomir on pulmonary fibrosis were assessed in PQ-poisoned mice models.

Results
Impairing the secretion of exosomes effectively mitigates the harmful effects of senescent epithelial cells on pulmonary fibroblasts, offering protection against PQ-induced pulmonary fibrosis in mice. Additionally, we have identified a remarkable elevation of miR-217-5p expression in the exosomes of PQ-treated epithelial cells, which specifically contributes to fibroblasts activation via targeted inhibition of SIRT1, a protein involved in cellular stress response. Remarkably, suppression of miR-217-5p effectively impaired senescent epithelial cells-induced fibroblasts activation. Further investigation has revealed that miR-217-5p attenuated SIRT1 expression and subsequently resulted in enhanced acetylation of β-catenin and Wnt signaling activation.

Conclusion
These findings highlight a potential strategy for the treatment of pulmonary fibrosis induced by PQ poisoning. Disrupting the communication between senescent epithelial cells and pulmonary fibroblasts, particularly by targeting the miR-217-5p/SIRT1/β-catenin axis, may be able to alleviate the effects of PQ poisoning on the lungs.
Recent advances in endothelial colony-forming cells: from the transcriptomic perspective
Authors: Liu Yaqiong , Lyons Caomhán J. , Ayu Christine , O’Brien Timothy 
Published: March 2024

AbstractEndothelial colony-forming cells (ECFCs) are progenitors of endothelial cells with significant proliferative and angiogenic ability. ECFCs are a promising treatment option for various diseases, such as ischemic heart disease and peripheral artery disease. However, some barriers hinder the clinical application of ECFC therapeutics. One of the current obstacles is that ECFCs are dysfunctional due to the underlying disease states. ECFCs exhibit dysfunctional phenotypes in pathologic states, which include but are not limited to the following: premature neonates and pregnancy-related diseases, diabetes mellitus, cancers, haematological system diseases, hypoxia, pulmonary arterial hypertension, coronary artery diseases, and other vascular diseases. Besides, ECFCs are heterogeneous among donors, tissue sources, and within cell subpopulations. Therefore, it is important to elucidate the underlying mechanisms of ECFC dysfunction and characterize their heterogeneity to enable clinical application. In this review, we summarize the current and potential application of transcriptomic analysis in the field of ECFC biology. Transcriptomic analysis is a powerful tool for exploring the key molecules and pathways involved in health and disease and can be used to characterize ECFC heterogeneity.
Wnt5a/β-catenin-mediated epithelial-mesenchymal transition: a key driver of subretinal fibrosis in neovascular age-related macular degeneration
Authors: Liu Dandan , Du Jingxiao , Xie Hai , Tian Haibin , Lu Lixia , Zhang Chaoyang , Xu Guo-Tong , Zhang Jingfa 
Published: March 2024

Abstract
Background
Neovascular age-related macular degeneration (nAMD), accounts for up to 90% of AMD-associated vision loss, ultimately resulting in the formation of fibrotic scar in the macular region. The pathogenesis of subretinal fibrosis in nAMD involves the process of epithelial–mesenchymal transition (EMT) occurring in retinal pigment epithelium (RPE). Here, we aim to investigate the underlying mechanisms involved in the Wnt signaling during the EMT of RPE cells and in the pathological process of subretinal fibrosis secondary to nAMD.

Methods
In vivo, the induction of subretinal fibrosis was performed in male C57BL/6J mice through laser photocoagulation. Either FH535 (a β-catenin inhibitor) or Box5 (a Wnt5a inhibitor) was intravitreally administered on the same day or 14 days following laser induction. The RPE-Bruch's membrane-choriocapillaris complex (RBCC) tissues were collected and subjected to Western blot analysis and immunofluorescence to examine fibrovascular and Wnt-related markers. In vitro, transforming growth factor beta 1 (TGFβ1)-treated ARPE-19 cells were co-incubated with or without FH535, Foxy-5 (a Wnt5a-mimicking peptide), Box5, or Wnt5a shRNA, respectively. The changes in EMT- and Wnt-related signaling molecules, as well as cell functions were assessed using qRT-PCR, nuclear-cytoplasmic fractionation assay, Western blot, immunofluorescence, scratch assay or transwell migration assay. The cell viability of ARPE-19 cells was determined using Cell Counting Kit (CCK)-8.

Results
The in vivo analysis demonstrated Wnt5a/ROR1, but not Wnt3a, was upregulated in the RBCCs of the laser-induced CNV mice compared to the normal control group. Intravitreal injection of FH535 effectively reduced Wnt5a protein expression. Both FH535 and Box5 effectively attenuated subretinal fibrosis and EMT, as well as the activation of β-catenin in laser-induced CNV mice, as evidenced by the significant reduction in areas positive for fibronectin, alpha-smooth muscle actin (α-SMA), collagen I, and active β-catenin labeling. In vitro, Wnt5a/ROR1, active β-catenin, and some other Wnt signaling molecules were upregulated in the TGFβ1-induced EMT cell model using ARPE-19 cells. Co-treatment with FH535, Box5, or Wnt5a shRNA markedly suppressed the activation of Wnt5a, nuclear translocation of active β-catenin, as well as the EMT in TGFβ1-treated ARPE-19 cells. Conversely, treatment with Foxy-5 independently resulted in the activation of abovementioned molecules and subsequent induction of EMT in ARPE-19 cells.

Conclusions
Our study reveals a reciprocal activation between Wnt5a and β-catenin to mediate EMT as a pivotal driver of subretinal fibrosis in nAMD. This positive feedback loop provides valuable insights into potential therapeutic strategies to treat subretinal fibrosis in nAMD patients.
The effects of visual skills training on cognitive and executive functions in stroke patients: a systematic review with meta-analysis
Authors: Niering Marc , Seifert Johanna 
Published: March 2024

AbstractThe visual system and associated skills are of particular importance in stroke rehabilitation. The process of neuroplasticity involved in restoring cognitive function during this period is mainly based on anatomical and physiological mechanisms. However, there is little evidence-based knowledge about the effects of visual skills training that could be used to improve therapeutic outcomes in cognitive rehabilitation. A computerized systematic literature search was conducted in the PubMed, Medline, and Web of Science databases from 1 January 1960 to 11 Febuary 2024. 1,787 articles were identified, of which 24 articles were used for the calculation of weighted standardized mean differences (SMD) after screening and eligibility verification. The findings revealed moderate effects for global cognitive function (SMD = 0.62) and activities of daily living (SMD = 0.55) as well as small effects for executive function (SMD = 0.20) – all in favor of the intervention group. The analyses indicate that the results may not be entirely robust, and should therefore be treated with caution when applied in practice. Visual skills training shows positive effects in improving cognitive and executive functions, especially in combination with high cognitive load and in an early phase of rehabilitation. An improvement in activities of daily living can also be observed with this type of intervention. The high heterogeneity of the studies and different treatment conditions require the identification of a relationship between certain visual skills and executive functions in future research.
Neutrophil to lymphocyte ratio in odontogenic infection: a systematic review
Authors: Ghasemi Saeideh , Mortezagholi Bardia , Movahed Emad , Sanjarian Sahar , Ghaedi Arshin , Mallahi Amirhossein , Bazrgar Aida , Khanzadeh Monireh , Lucke-Wold Brandon , Khanzadeh Shokoufeh 
Published: March 2024

Abstract
Background
We conducted this systematic review to compile the evidence for the role of neutrophil to lymphocyte ratio (NLR) in odontogenic infection (OI) and to determine whether NLR is elevated in patients with OI. This was done to aid physicians in better understanding this condition for clinical management.

Methods
The search was conducted on PubMed, Scopus, and Web of Science libraries on March 30, 2023. Two reviewers independently screened the studies using Endnote software. The Newcastle-Ottawa Scale (NOS) was used to evaluate the quality of the studies.

Results
A total of nine studies were included in the review. Among patients with OI, positive and statistically significant correlations of NLR were seen with more severe disease, a prolonged hospital stay, postoperative requirement of antibiotics, and total antibiotic dose needed. In the receiver operating characteristics (ROC) analysis, the optimum cut–off level of NLR was 5.19 (specificity: 81, sensitivity: 51). In addition, NLR was correlated with preoperative fever (p = 0.001). Among patients with Ludwig’s Angina, NLR could predict disease severity and length of stay in the hospital (p = 0.032 and p = 0.033, respectively). In addition, the relationship between the NLR and mortality was statistically significant (p = 0.026, specificity of 55.5%, and sensitivity of 70.8%). Among patients with severe oral and maxillofacial space infection, a positive correlation was found between IL-6 and CRP with NLR (rs = 0.773, P = 0.005 and rs = 0.556, P = 0.020, respectively). Also, a higher NLR was considered an essential predictor of organ involvement (P = 0.027) and the number of complications (P = 0.001). However, among diabetes mellitus (DM) patients afflicted with submandibular abscesses, NLR had no association with therapeutic response.

Conclusions
Many people around the world suffer from OI, and a cheap and fast biomarker is needed for it. Interestingly, inflammation plays a role in this infection, and elevated NLR levels can be a good biomarker of inflammation and, as a result, for OI progression.
Sonographic characteristics of diffuse sclerosing variant of papillary thyroid carcinoma with histopathological correlation: a preliminary study
Authors: Li Wanying , Wang Ying , Gao Luying , Feng Ruie , Lv Ke , Wu Xining , Yang Xiao , Cai Sheng , Wang Hongyan , Li Jianchu 
Published: March 2024

Abstract
Background
Diffuse sclerosing variant of papillary thyroid carcinoma (DSVPTC) is a rare but high invasive subtype of papillary thyroid carcinoma, which mandates an aggressive clinical strategy. Few studies have focused on the sonographic characteristics of DSVPTC and the role of ultrasound in diagnosis and treatment of this variant remains unknown. This study aimed to identify and understand DSVPTC more accurately under ultrasound in correlation with pathology.

Methods
The ultrasound characteristics and histopathologic sections of 10 lesions in 10 DSVPTC patients who underwent thyroid surgery at our center between 2014 and 2020 were reviewed and compared with 184 lesions in 168 classic variant of papillary thyroid carcinoma (cPTC) patients.

Results
6 DSVPTC cases (60%) showed the “snowstorm” pattern on sonogram and 4 cases (40%) presented hypoechoic solid nodules only. Vague borders (100.0% vs. 18.5%, P = 0.019) and abundant microcalcifications (66.7% vs. 10.9%, P = 0.037) were more common in DSVPTC nodules than in cPTC nodules, corresponding to the infiltrating boundaries and numerous psammoma bodies under the microscope respectively. Most of the DSVPTC cases had a heterogeneous background (80%) and suspicious metastatic cervical lymph nodes (80%) on sonograms. All DSVPTC cases had histopathological metastatic cervical lymph nodes.

Conclusion
The sonographic “snowstorm” pattern indicated DSVPTC with whole-lobe occupation. Hypoechoic solid nodules with vague borders and abundant microcalcifications on sonogram suggested DSVPTC lesion with an ongoing invasion. Regardless of which of the two sonograms was shown, the corresponding DSVPTC lesions were aggressive and required the same attention from the surgeons.
Current usage of explainer animations in trials: a survey of the UKCRC registered clinical trial units in the UK
Authors: Barber Vicki S. , Calvert Clare , Appelbe Duncan , Sprange Kirsty , Nollett Claire , Tanner Samantha , Richards Duncan B. 
Published: March 2024

Abstract
Background
Explainer animations are a means to communicate aspects of clinical trials to participants in a more engaging and accessible way. Delivered well these have the potential to enhance recruitment and retention. The range of media technology used to deliver this material is expanding rapidly but is highly fragmented. Usage of explainer animations across the UK is unknown, the aim of this research was to determine current usage across the 52 registered UK Clinical Research Collaboration (UKCRC) Clinical Trials Units (CTUs) to understand the current landscape and any barriers that could be preventing wider uptake of this functionality.

Methods
A survey link was emailed to all UKCRC CTU Directors and Trial Management Leads to ascertain current usage of explainer animations within their CTU. The survey ran between 01 February 2023 and 07 March 2023.

Results
Responses were received from 35 CTUs—representing a response rate of 67%. 24 CTUs (69%) reported that they had created/used at least one explainer animation within their unit, although the usage, cost, length and production activities varied among the units.

Conclusions
The survey showed that a high proportion of the UKCRC CTUs have used explainer animations to provide information to participants about clinical studies. For those not using the technology yet, the most common reasons cited were a lack of expertise, lack of resources and costs to produce them. One of the desired outcomes of this project is the creation of a free-to-use library of animations to encourage wider uptake and avoid duplication.