bluuebunny/crossref_metadata_2025_split huggingface dataset:
A CRISPR-dCas13 RNA-editing tool to study alternative splicing
Authors: Núñez-Álvarez Yaiza , Espie-Caullet Tristan , Buhagiar Géraldine , Rubio-Zulaika Ane , Alonso-Marañón Josune , Luna-Pérez Elvira , Blazquez Lorea , Luco Reini F 
Published: August 2024

Abstract
Alternative splicing allows multiple transcripts to be generated from the same gene to diversify the protein repertoire and gain new functions despite a limited coding genome. It can impact a wide spectrum of biological processes, including disease. However, its significance has long been underestimated due to limitations in dissecting the precise role of each splicing isoform in a physiological context. Furthermore, identifying key regulatory elements to correct deleterious splicing isoforms has proven equally challenging, increasing the difficulty of tackling the role of alternative splicing in cell biology. In this work, we take advantage of dCasRx, a catalytically inactive RNA targeting CRISPR-dCas13 ortholog, to efficiently switch alternative splicing patterns of endogenous transcripts without affecting overall gene expression levels cost-effectively. Additionally, we demonstrate a new application for the dCasRx splice-editing system to identify key regulatory RNA elements of specific splicing events. With this approach, we are expanding the RNA toolkit to better understand the regulatory mechanisms underlying alternative splicing and its physiological impact in various biological processes, including pathological conditions.
Metabolic RNA labeling in non-engineered cells following spontaneous uptake of fluorescent nucleoside phosphate analogues
Authors: Pfeiffer Pauline , Nilsson Jesper R , Gallud Audrey , Baladi Tom , Le Hoang-Ngoan , Bood Mattias , Lemurell Malin , Dahlén Anders , Grøtli Morten , Esbjörner Elin K , Wilhelmsson L Marcus 
Published: August 2024

Abstract
RNA and its building blocks play central roles in biology and have become increasingly important as therapeutic agents and targets. Hence, probing and understanding their dynamics in cells is important. Fluorescence microscopy offers live-cell spatiotemporal monitoring but requires labels. We present two fluorescent adenine analogue nucleoside phosphates which show spontaneous uptake and accumulation in cultured human cells, likely via nucleoside transporters, and show their potential utilization as cellular RNA labels. Upon uptake, one nucleotide analogue, 2CNqAXP, localizes to the cytosol and the nucleus. We show that it could then be incorporated into de novo synthesized cellular RNA, i.e. it was possible to achieve metabolic fluorescence RNA labeling without using genetic engineering to enhance incorporation, uptake-promoting strategies, or post-labeling through bio-orthogonal chemistries. By contrast, another nucleotide analogue, pAXP, only accumulated outside of the nucleus and was rapidly excreted. Consequently, this analogue did not incorporate into RNA. This difference in subcellular accumulation and retention results from a minor change in nucleobase chemical structure. This demonstrates the importance of careful design of nucleoside-based drugs, e.g. antivirals to direct their subcellular localization, and shows the potential of fine-tuning fluorescent base analogue structures to enhance the understanding of the function of such drugs.
How Do Digital Advertising Auctions Impact Product Prices?
Authors: Bergemann Dirk , Bonatti Alessandro , Wu Nicholas 
Published: August 2024

Abstract
We present a model of digital advertising with three key features: (1) advertisers can reach consumers on and off a platform, (2) additional data enhances the value of advertiser–consumer matches, and (3) the allocation of advertisements follows an auction-like mechanism. We contrast data-augmented auctions, which leverage the platform’s data advantage to improve match quality, with managed-campaign mechanisms that automate match formation and price-setting. The platform-optimal mechanism is a managed campaign that conditions the on-platform prices for sponsored products on the off-platform prices set by all advertisers. This mechanism yields the efficient on-platform allocation but inefficiently high off-platform product prices. It attains the vertical integration profit for the platform and the advertisers, and it increases off-platform product prices while decreasing consumer surplus, relative to data-augmented auctions.
Racialising Refugees: The Global Colour Line in US Resettlement
Authors: Coen Alise 
Published: August 2024

Abstract
Following the 2021 Taliban takeover of Afghanistan and the 2022 Russian invasion of Ukraine, there were notable differences in access to resettlement and other pathways of humanitarian migration. Drawing on an analysis of statements by US policymakers, this article considers the global context and implications of the disparate language and approaches used in responses to Afghan and Ukrainian displacement. It shows how racialised and gendered narratives contributed to and were constituted within a broader international hierarchy and global colour line. The positioning of Ukrainians as possessing higher civilisational attributes deserving of solidarity and support, and their portrayal through prisms of strong agency, sovereignty, and kindred Western values, echoed across transnational constructions of collective white identity. In contrast, Afghan resettlement was rendered conditional on extensive security vetting and proof of loyal service to US and NATO missions in Afghanistan. Portrayals of Afghans as less assimilable, as potential terrorist infiltrators, as incapable of self-governance and unable to generate their own progress perpetuated features of the global colour line. Attending to the different logics used to construct refugee and parolee groups and policies broadens our understanding on how multilayered processes of Orientalism and racialisation shape resettlement and disparities in access to protection.
The actigraphic evaluation of daytime sleep in central disorders of hypersomnolence: comparison with polysomnography
Authors: Biscarini Francesco , Vandi Stefano , Riccio Caterina , Raggini Linda , Neccia Giulia , Plazzi Giuseppe , Pizza Fabio 
Published: August 2024

Abstract

Study Objectives
The role of actigraphy in central disorders of hypersomnolence (CDH) is expanding but evidence of reliability with polysomnography (PSG) is scarce and provided only during nighttime. We explored the agreement between actigraphy and continuous 24-hour PSG at CDH diagnosis.

Methods
Forty-four consecutive drug-naïve patients (28 narcolepsy and 16 idiopathic hypersomnia [IH]) underwent actigraphy during 24 hours of free-running PSG, during multiple sleep latency test (MSLT) and 13 of them also during maintenance of wakefulness test (MWT). Daytime and nighttime sleep features and MSLT and MWT mean sleep latencies (mSL) were estimated with the actigraphic algorithms by Cole-Kripke (CK), Sadeh (Sad), and University of California San Diego (UCSD). Agreement to corresponding PSG measures was assessed with Bland–Altman plots.

Results
Nighttime-total sleep time (TST) in narcolepsy was significantly underestimated with CK (bias 27.8 minutes, 95% CI 13.7 to 41.9) and Sad (bias 56.7 minutes, 95% CI 38.8/74.5). Daytime-TST was overestimated in IH and narcolepsy with all algorithms (CK: bias −42.2, 95% CI −67/−17.4; Sad: bias −30.2 minutes, 95% CI −52.7/−7.7; UCSD bias −86.9 minutes, 95% CI −118.2/−55.6). 24-hour-TST was overestimated by CK and UCSD in IH (CK: bias −58.5 minutes, 95% CI −105.5/−11.5; UCSD: bias −118.8 minutes, 95% CI −172.5/−65), and by UCSD in narcolepsy (bias −68.8 minutes, 95% CI −109.3/−38.2). In the entire cohort, actigraphy overestimated MSLT mSL but not MWT mSL.

Conclusions
Conventional actigraphic algorithms overestimate 24-hour TST in IH and underestimate nighttime TST in narcolepsy. These discrepancies call for the cautious application of actigraphy in the diagnostic process of CDH and the development of new quantitative signal analysis approaches.
A new theropod dinosaur from the Callovian Balabansai Formation of Kyrgyzstan
Authors: Rauhut Oliver W M , Bakirov Aizek A , Wings Oliver , Fernandes Alexandra E , Hübner Tom R 
Published: August 2024

AbstractRecent fieldwork in the late Middle Jurassic Balabansai Formation of Kyrgyzstan has yielded a partial skeleton of a large theropod dinosaur. The material includes a few bones of the skull (postorbital, quadratojugal), dorsal and sacral vertebrae, fragments of the pectoral girdle and forelimbs, and an almost complete pelvic girdle and hindlimbs, and is here made the type of a new theropod taxon, Alpkarakush kyrgyzicus gen. et sp. nov. Alpkarakush can be diagnosed by an extremely developed orbital brow on the postorbital, a pneumatic opening leading into cavities in the neural arch from the centroprezygodiapophyseal fossa in the posterior dorsal vertebrae, an almost enclosed ventral sulcus in manual phalanx II-1, a narrow and deep intercondylar groove on the anterior side of the distal femur, and an epicondylar crest on the distal femur that is offset from the distal end. A second, fragmentary, and smaller specimen from the same site represents the same taxon. Based on long bone histology, the type of Alpkarakush represents a late subadult individual, whereas the smaller specimen is a juvenile, possibly indicating gregarious behaviour. Phylogenetic analysis places Alpkarakush in the Metriacanthosauridae, underlining the diversity and wide distribution of this clade in the Jurassic of Asia.
Detection and Characterization of Potato Virus Y (PVY) Strains and Mixed Infections in San Luis Valley, Colorado
Authors: Rushton Jennifer , Larsen Brandon , Houser Andrew , Pitt W. Jacob , Charkowski Amy O. , Chikh-Ali M. , Nalam Vamsi J. 
Published: August 2024

Potato virus Y (PVY) is a major economic threat to potato production worldwide. Understanding the prevalent PVY strains and their dynamics is crucial for effective management. This study investigated PVY trends and diversity in the San Luis Valley (SLV), CO, U.S.A. We leveraged the Colorado Seed Potato Certification Program data (2017 to 2022), revealing a persistent problem with PVY incidence in certified seed lots that fluctuated between 2.6% (2017) and 6.5% (2022). PVYN-Wi was the dominant strain, with others such as PVYO also detected. A complementary field study (2021 to 2022) investigated PVY prevalence and diversity in 600 samples collected from 30 fields. PVYN-Wi was identified as the main strain, followed by PVYO and PVYNTN. Notably, the incidences of dual and triple infections, along with inconclusive samples, increased in both postharvest and field study samples. High-throughput sequencing (HTS) of the inconclusive samples identified from the field study samples determined PVYN-Wi as the predominant strain and identified polymorphisms that may hinder accurate identification by traditional strain typing methods. Beyond PVY, potato virus S (PVS) was the only other major potato-infecting virus detected. HTS revealed diverse nonplant-infecting viruses as well. This study provides valuable insights into the evolving PVY landscape and the complex potato virome in SLV. It highlights the importance of continued surveillance and improved diagnostics to mitigate the impact of viruses on potato production. [Formula: see text] Copyright © 2024 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license .
Heterogeneous Outcome Selection and Incomplete Prespecification of Outcomes in Systematic Reviews: A Case Study on Pressure Injury
Authors: Zhang Jun , Zhang Mingyue , Xu Caihua , Tian Jinhui , Yang Donghua , Wang Bo 
Published: August 2024

ABSTRACT

OBJECTIVE
To understand how reviewers select and prespecify outcomes for systematic reviews (SRs), the authors report on the outcomes used in SRs of pressure injury (PI) intervention and treatment and evaluate their completeness of prespecification.

DATA SOURCES
The authors searched four electronic databases for SRs involving PI prevention and/or treatments.

STUDY SELECTION
Inclusion criteria were SRs and meta-analyses evaluating interventions for preventing or treating PI. Studies without systematic search or risk-of-bias assessment, conference proceedings, and articles not in Chinese or English were excluded.

DATA EXTRACTION
Two reviewers extracted and categorized the outcomes in domains, assessing outcome prespecification using a five-element framework. Data items included study characteristics, target population, type of interventions, and outcome variables.

DATA SYNTHESIS
This review included 95 SRs that reported a total of 432 instances of 24 different outcome domains. An average of four outcome domains were reported per SR. The most frequently reported domains were PI healing, PI occurrence, and PI status. Of the 62 SRs that prespecified primary outcomes, 40 (64.52%) reported more than one primary outcome. Only 24 of the 432 instances (5.56%) were completely specified. Among the 24 outcome domains, 12 (50.00%) were listed as primary outcomes at least once. Primary outcomes were more completely specified than nonprimary outcomes.

CONCLUSIONS
Systematic reviews of PI prevention and/or treatment report diverse, incompletely prespecified outcomes, highlighting the need for a core outcome set to standardize key clinical outcomes.
Observation of the Therapeutic Effect of Hydrogel Combined with Alginate Dressings for a Patient with Grade 4 Acute Radiation Dermatitis: A Case Report
Authors: Cao Yongli , Zhu Changhui , Zhu Hongyu , Chen Xiumei , Luo Huiyu 
Published: August 2024

ABSTRACT
In this case report, the authors summarize their experience of using hydrogel combined with alginate dressings in the wound care of a patient with grade 4 acute radiation dermatitis. With the combination of hydrogel and alginate dressings, the authors achieved autolytic debridement of the wound and created a moist healing environment to facilitate wound closure. Hydrogel helps the dressing adhere better to the wound bed, ensuring that it does not easily detach during the wound healing process. It also eliminates the need for traditional adhesive tapes for fixation, thus avoiding damage to the fragile skin in the radiation field.
The wound gradually decreased in size from an area of 10 × 12 cm, and exudate decreased continuously. The wound completely healed in 20 days with a total of 17 dressing changes. As the wound gradually healed, the patient’s psychological burden decreased and comfort level increased. The patient expressed satisfaction and hope for the gradual healing of the wound.
Thus, the treatment of severe acute radiation dermatitis with hydrogel combined with alginate dressings yields remarkable results, aligning the noninvasive, low-adhesive, absorbent, conformable, and comfortable attributes of optimized wound care. This experience provides a practical foundation for wound management in acute radiation dermatitis and supports clinical application and promotion of the approach.
Project Extension for Community Healthcare Outcomes Intervention Evaluations: A Scoping Review of Research Methods
Authors: Maizel Jennifer , Filipp Stephanie L. , Zori Gaia , Yadav Sandhya , Avaiya Kishan , Figg Lauren , Hechavarria Melanie , Roque Xanadu , Anez-Zabala Claudia , Lal Rayhan , Addala Ananta , Haller Michael J. , Maahs David M. , Walker Ashby F. 
Published: August 2024

Introduction:
Since its inception in 2003, the Project Extension for Community Healthcare Outcomes (ECHO) tele-education model has reached and improved outcomes for patients, providers, and health centers through interventions in >180 countries. Utilization of this model has recently increased due to the COVID-19 pandemic and a higher demand for remote education. However, limited research has examined the methodologies used to evaluate Project ECHO interventions.

Methods:
We conducted a scoping review to determine the extent and types of research methods used to evaluate outcomes and implementation success of Project ECHO interventions and to identify gaps and opportunities for future investigation. Using Arksey and O'Malley's scoping review framework and the PRISMA-ScR checklist, we reviewed study designs, temporality, analysis methods, data sources, and levels and types of data in 121 articles evaluating Project ECHO interventions.

Results:
Most interventions addressed substance use disorders (24.8%, n = 30), infectious diseases (24%, n = 29), psychiatric and behavioral health conditions (21.5%, n = 26), and chronic diseases (19%, n = 23). The most frequently reported evaluation methods included cohort studies (86.8%, n = 105), longitudinal designs (74.4%, n = 90), mixed methods analysis (52.1%, n = 63), surveys (61.2%, n = 74), process evaluation measures (98.3%, n = 119), and provider-level outcome measures (84.3%, n = 102). Few evaluations used experimental designs (1.7%, n = 2), randomization (5.8%, n = 7), or comparison groups (14%, n = 17), indicating limited rigor.

Discussion:
This scoping review demonstrates the need for more rigorous evaluation methods to test the effectiveness of the Project ECHO model at improving outcomes and standardized reporting guidelines to enhance the dissemination of evaluation data from future Project ECHO interventions.
Efficacy evaluation and survival analysis of the combination of oxaliplatin plus Teysuno (SOX) with immune checkpoint inhibitors in the conversion therapy of locally advanced gastric cancer
Authors: Liu Shuai , Zhang Kai , Zhang Xiaoqing , Luan Wei 
Published: August 2024

Abstract

Background
The efficacy of combining immune checkpoint inhibitors (ICIs) with chemotherapy in neoadjuvant therapy for locally advanced gastric cancer has been explored. However, limited research exists on its effectiveness in conversion therapy, and its superiority over standalone chemotherapy remains to be elucidated. This study aims to investigate the efficacy and survival outcomes of patients treated with ICIs in combination with conversion therapy for locally advanced gastric cancer.

Methods
Retrospective data from patients with locally advanced gastric cancer treated with either oxaliplatin + S-1(SOX) alone or in combination with ICIs in conversion therapy were collected. Clinical and pathological characteristics, disease-free survival, and efficacy assessments in nonoperable patients were compared between the 2 treatment groups. Efficacy was further evaluated through dynamic changes in serum markers, and patients’ quality of life was assessed using the QLQ-STO22 (Gastric Cancer–Specific Quality of Life Questionnaire) quality-of-life measurement scale.

Results
A total of 140 patients underwent conversion therapy: 80 in the SOX alone group and 60 in the SOX combined with the ICIs group. There were no significant differences in baseline characteristics between the 2 groups. Compared with the SOX alone group, the SOX combined with ICIs group exhibited a higher conversion rate (83.3% vs 75%, P = 0.23), R0 resection rate (90.0% vs 83.3%, P = 0.31), pathological complete response (pCR) rate (18% vs 5%, P = 0.02), median disease-free survival (21.4 vs 16.9 months, P = 0.007), the objective response rate in nonoperable patients (60% vs 40%, P = 0.301), and median progression-free survival time (7.9 vs 5.7 months, P = 0.009). The QLQ-STO22 quality-of-life assessment revealed statistically significant improvements in pain, swallowing difficulties, and dietary restrictions in the combination therapy group compared with those in the monotherapy group. The enhanced efficacy of immune combination with SOX is evident, as demonstrated by the significantly prolonged surgical duration in operated patients (206.6 ± 26.6 min vs 197.8 ± 19.8 min, P = 0.35) and intraoperative blood loss (158.9 ± 21.2 mL vs 148.9 ± 25.1 mL, P = 0.59). No significant differences were observed in postoperative complications.

Conclusions
Compared with the SOX conversion therapy regimen, SOX combined with ICIs demonstrated higher conversion rates, R0 resection rates, pathological response rates, and disease-free survival without increasing surgical difficulty or complications. Nonoperable patients also experienced longer progression-free survival and objective response rates.
Nanomaterials for refining tumor microenvironment and enhancing therapy in head and neck squamous cell carcinoma: a review
Authors: Zheng Kaifeng , Song Ruibiao , Li Ruifeng , Liu Mengli , Ba Yunpeng , Jiang Wei , Fan Kelong 
Published: August 2024

Abstract
Head and neck squamous cell carcinoma (HNSCC) is a prevalent and lethal solid tumor with a high mortality rate. Conventional cancer treatments, including surgery, radiotherapy, and chemotherapy, primarily target cancer cell eradication. However, uncontrolled proliferation and metabolic activities of these cells result in abnormalities in nutrient levels, hypoxia, and immunosuppression within the tumor microenvironment (TME). These factors constrain the efficacy of traditional treatments by promoting drug resistance, recurrence, and metastasis. Nanomaterials (NMs), such as nanozymes, can exhibit enzymatic activity similar to that of natural enzymes and offer a promising avenue for the direct modification of the TME through catalytic oxidation-reduction processes. Moreover, they can serve as sensitizers or drug delivery carriers, enhancing the efficacy of traditional treatment methods. Recently, NMs have garnered significant attention from oncologists. This review begins with an overview of the composition and unique characteristics of the TME. Subsequently, we comprehensively explored the application of NMs in the treatment of HNSCC. Finally, we discuss the potential prospects and challenges associated with using NMs in biomedical research.
Exploring the connection between BRCA2 and thyroid cancer
Authors: Liu Xinjie , Wang Xueqin 
Published: August 2024

Abstract

Background
This study investigated the multifaceted role of BRCA2 (breast cancer 2) in various cancer types, with a specific focus on thyroid carcinoma (THCA).

Methods
Data sets were obtained from the University of California Santa Cruz database to analyze BRCA2 expression, genetic alterations, and clinical implications. Sample filtering criteria were applied, and immunohistochemistry from the Human Protein Atlas was used to validate protein expression. Correlation analyses were used to explore associations between immune-related genes, and immunological signatures were assessed using various tools. Genetic alterations in BRCA2 were analyzed using cBioPortal, and prognostic analysis involved evaluating gene expression differences at different clinical stages of THCA.

Results
In patients with THCA, differences in BRCA2 expression were observed at both the mRNA and protein levels when comparing tumor and normal tissues. Correlation studies revealed associations between BRCA2 and immune-related genes, emphasizing its potential role in modulating the tumor microenvironment. Immunological signature analyses indicated distinct frequencies of tumor-infiltrating immune cell subsets in BRCA2 high versus low tumors. Moreover, genetic alterations in BRCA2, particularly the A2738S mutation in exon 18, have been identified in patients with THCA. The prognostic analysis demonstrated a significant correlation between altered BRCA2 levels and improved overall survival in patients with THCA. Additionally, BRCA2 expression was associated with prognostic factors such as stage and N.

Conclusions
This study provides a holistic exploration of BRCA2 in cancer and highlights its diverse roles in expression, immune modulation, genetic alterations, and clinical prognosis. These findings underscore the potential significance of BRCA2 as a diagnostic and prognostic marker and offer valuable insights for future research and potential clinical applications in cancer management.