bluuebunny/crossref_metadata_2025_split huggingface dataset:
FUME-TCRseq Enables Sensitive and Accurate Sequencing of the T-cell Receptor from Limited Input of Degraded RNA
Authors: Baker Ann-Marie , Nageswaran Gayathri , Nenclares Pablo , Ronel Tahel , Smith Kane , Kimberley Christopher , Laclé Miangela M. , Bhide Shreerang , Harrington Kevin J. , Melcher Alan , Rodriguez-Justo Manuel , Chain Benny , Graham Trevor A. 
Published: March 2024

Abstract

Genomic analysis of the T-cell receptor (TCR) reveals the strength, breadth, and clonal dynamics of the adaptive immune response to pathogens or cancer. The diversity of the TCR repertoire, however, means that sequencing is technically challenging, particularly for samples with low-quality, degraded nucleic acids. Here, we developed and validated FUME-TCRseq, a robust and sensitive RNA-based TCR sequencing methodology that is suitable for formalin-fixed paraffin-embedded samples and low amounts of input material. FUME-TCRseq incorporates unique molecular identifiers into each molecule of cDNA, allowing correction for sequencing errors and PCR bias. Using RNA extracted from colorectal and head and neck cancers to benchmark the accuracy and sensitivity of FUME-TCRseq against existing methods demonstrated excellent concordance between the datasets. Furthermore, FUME-TCRseq detected more clonotypes than a commercial RNA-based alternative, with shorter library preparation time and significantly lower cost. The high sensitivity and the ability to sequence RNA of poor quality and limited amount enabled quantitative analysis of small numbers of cells from archival tissue sections, which is not possible with other methods. Spatially resolved FUME-TCRseq analysis of colorectal cancers using macrodissected archival samples revealed the shifting T-cell landscapes at the transition to an invasive phenotype and between tumor subclones containing distinct driver alterations. In summary, FUME-TCRseq represents an accurate, sensitive, and low-cost tool for the characterization of T-cell repertoires, particularly in samples with low-quality RNA that have not been accessible using existing methodology.

Significance:
FUME-TCRseq is a TCR sequencing methodology that supports sensitive and spatially resolved detection of TCR clones in archival clinical specimens, which can facilitate longitudinal tracking of immune responses through disease course and treatment.
Frauen in Furcht
Authors: Neumann Nils 
Published: March 2024

Abstract
Trembling with fear is a typically feminine phenomenon in the Gospel of Mark. The hermorrhaging woman as well as the women at the empty tomb tremble as they are afraid. Male characters, on the contrary, never tremble in Mark, although the male disciples frequently do exhibit fear. The present article explains these observations in the context of ancient medicine and philosophy of the body. Against this backdrop it is plausible that the women’s fearful trembling illustrates some form of embodied understanding of the divine presence that breaks into the earthly realm within the works of Jesus. This calls into question William Wrede’s contrasting juxtaposition of faith and fear in Mark.
The Western Mongol World in the Early Eighteenth Century: Kalmyks and Oirats in Vasilis Vatatzēs’s Periēgētikon and His 1732 Map of Central Asia
Authors: Kordosis Stefanos 
Published: March 2024

Abstract
The article revolves around the information on the Kalmyks and Oirats contained in Vasilis Vatatzēs’s Periēgētikon (Voyages). Vatatzēs, a Greek-Ottoman merchant who travelled in Central Asia in the first half of the eighteenth century, supplemented his text with a map (engraved and published in 1732 in London) and produced a biography of Shah Nader of Persia, the founder of the short-lived Afsharid dynasty. Vatatzēs travelled along the caravan routes connecting the cities of southern Siberia with the Khanates of Central Asia, as demonstrated by a reconstruction of his itineraries, reaching as far as Bukhara. Focusing on the nations of Central Asia, Vatatzēs’s accounts and map provide much information regarding western Mongolic nations, starting with the Kalmyks in the Volga region and reaching as far as the Oirats, to the NW of China.
Regional Sea Level Response to External Forcings from the Twentieth to the Twenty-First Century
Authors: Liu Zhen , Chen Changlin , Wang Guihua , Li Shouwei , Liu Shouhua 
Published: March 2024

Abstract
Using a range of Detection and Attribution Model Intercomparison Project (DAMIP) simulations from phase 6 of Coupled Model Intercomparison Project (CMIP6), we study the response of dynamic sea level (DSL) to external anthropogenic climate forcing [greenhouse gases (GHGs), aerosols, and stratospheric ozone] with a focus on the differences over the twentieth and twenty-first century. In the second half of the twentieth century, the DSL nonuniformity in the Northern Hemisphere (NH) was relatively small due to a cancellation between the effects of increasing GHGs and aerosols. In contrast, the DSL signal in the Southern Hemisphere (SH) over this period was large because stratospheric ozone depletion reinforced the effects of increasing GHGs. In the twenty-first century, the DSL response has been intensified in the NH because the warming effects of diminishing aerosols have acted to reinforce the effects of increasing GHGs. Meanwhile, the distribution of SH DSL has also become uneven although stratospheric ozone recovery has partially offset the effects of rising GHGs. Using a global ocean circulation model, we decompose the changes in the twenty-first century DSL into distinct responses to surface forcings including sea surface temperature, salinity, and wind stress. Our results show that the dipole-like pattern of DSL in the North Pacific can be attributed largely to sea surface warming, while the dipole-like pattern in the North Atlantic is attributed to subpolar surface salinity freshening. The belted pattern of DSL changes in the Southern Ocean is induced by both surface warming and intensifying/poleward-shifting westerly winds.
Repair of Inferior Alveolar Nerve in Orthognathic Surgery Simulator (RIANOS): A Novel, Open-Source, Combined 3D Printed, and Ex-Vivo Chicken Sciatic Nerve Training Model
Authors: Navia Alfonso , Tapia Sebastian , Rojas Maria Fernanda , Rojas Francisco , Vargas Alex , Guerra Claudio , Cuadra Alvaro , Searle Susana , Ramírez Hernan , Teuber Cristian 
Published: March 2024

Study Design Face and content validation of a surgical simulation model. Objective Accidental transection of the inferior alveolar nerve (IAN) during bilateral sagittal split osteotomies (BSSO) has a reported incidence of up to 7%, determining important sensory disturbances in patients. Proper repair demands the need of microsurgical anastomosis skills. No previous training models have been described to simulate this. Therefore, we present a validated simulation model for intraoral repair of transected IAN. Methods A CT scan of an orthognathic surgery patient was modified and a 3D model of a mandible with BSSO was printed. Chicken thigh anatomy was reviewed, and 2.5 mm sciatic nerves were dissected and mounted in the model. In order to simulate intraoral work depth, it was put inside a dental phantom or medical glove box. The model was tested by a group of experts (n = 12), simulating a transected IAN repair inside the mouth with both loupes and a double visor surgical training microscope. A survey was conducted to assess Face and Content validity. Results The model was named RIANOS after Repair of Inferior Alveolar Nerve in Orthognathic Surgery Simulator. The printing cost of each model was approximately US$3 and the design file is open-source and available for download. All experts “Strongly Agreed” that the model was useful for training inferior alveolar nerve microsurgical repair and would consider implementing it with their residents. Conclusions We developed a low cost, reproducible, open-source simulator for IAN injury repair training during BSSO. Face and Content validity was achieved through evaluation by a group of experts.
Clinical evaluation and treatment outcomes of caustic ingestion injuries in Syrian pediatric patients: A retrospective study: Short title: High-dose steroids for pediatric caustic ingestions in Syria
Authors: Nafiza Martini , Imad-Addin Almasri , Mohamad Moamen Almouallem , Raghad Khaled , Hussein Hamdar , Ali Alakbar Nahle , Jaber Mahmod ,   Data Collecting Group
Published: March 2024

Introduction: Accidental ingestion of caustic agents poses a significant concern in pediatric emergency departments globally. It is a growing public health concern in low-to-middle income countries, which often lack comprehensive data reporting. This study examines high doses of corticosteroid treatment outcomes of caustic ingestion injuries in Syrian pediatric patients, addressing clinical features, and associated variables. Methods and materials: A retrospective observational study was conducted at University Pediatric Hospital from January 2016 to January 2019. Medical records were reviewed for patients aged <10 years with esophagoscopy-confirmed grade IIa, IIb, or III burns. Data collected included sociodemographics, esophagoscopy results, treatment details, and outcomes. Results: Among 114 pediatric patients, 76 (67%) were males and 38 (33%) were females. Age groups included <1 year (11%), 1–3 years (39%), 3–5 years (29%), 5–7 years (11%), and >7 years (11%). Alkaline burns accounted for 54% of injuries, acidic for 32%, and other substances for 13%. Complications included bleeding (19%) and psychomotor disability (7%). The most common burn site was the entire esophagus (62%), with 81% having grade II burns. Healing was achieved in 71% of patients with high doses of corticosteroids treatment, and 29% required dilation, with final 92% healing rate. Conclusion: The use of corticosteroids for esophageal strictures remains inconclusive, demanding further robust research with larger sample sizes and control groups. While our study revealed that high doses of corticosteroids treatment followed by esophageal dilation had a 92% success rate. However, our study demonstrates promising results, methodological limitations and absence of a control group underscore the need for more definitive evidence. Both alkali and acidic ingestion contribute to stricture development.
MRE11A: a novel negative regulator of human DNA mismatch repair
Authors: Du Demin , Yang Yueyan , Zhang Yuanyuan , Wang Guanxiong , Chen Liying , Guan Xiaowei , Rasmussen Lene Juel , Liu Dekang 
Published: March 2024

Abstract
Background
DNA mismatch repair (MMR) is a highly conserved pathway that corrects DNA replication errors, the loss of which is attributed to the development of various types of cancers. Although well characterized, MMR factors remain to be identified. As a 3′–5′ exonuclease and endonuclease, meiotic recombination 11 homolog A (MRE11A) is implicated in multiple DNA repair pathways. However, the role of MRE11A in MMR is unclear.

Methods
Initially, short-term and long-term survival assays were used to measure the cells’ sensitivity to N-methyl-N′-nitro-N-nitrosoguanidine (MNNG). Meanwhile, the level of apoptosis was also determined by flow cytometry after MNNG treatment. Western blotting and immunofluorescence assays were used to evaluate the DNA damage within one cell cycle after MNNG treatment. Next, a GFP-heteroduplex repair assay and microsatellite stability test were used to measure the MMR activities in cells. To investigate the mechanisms, western blotting, the GFP-heteroduplex repair assay, and chromatin immunoprecipitation were used.

Results
We show that knockdown of MRE11A increased the sensitivity of HeLa cells to MNNG treatment, as well as the MNNG-induced DNA damage and apoptosis, implying a potential role of MRE11 in MMR. Moreover, we found that MRE11A was largely recruited to chromatin and negatively regulated the DNA damage signals within the first cell cycle after MNNG treatment. We also showed that knockdown of MRE11A increased, while overexpressing MRE11A decreased, MMR activity in HeLa cells, suggesting that MRE11A negatively regulates MMR activity. Furthermore, we show that recruitment of MRE11A to chromatin requires MLH1 and that MRE11A competes with PMS2 for binding to MLH1. This decreases PMS2 levels in whole cells and on chromatin, and consequently comprises MMR activity.

Conclusions
Our findings reveal that MRE11A is a negative regulator of human MMR.

Graphical Abstract
Complete chloroplast genome and comparison of herbicides toxicity on Aeschynomene indica (Leguminosae) in upland direct-seeding paddy field
Authors: Gao Yuan , Chen TianYu , Long Jiaqi , Shen Guohui , Tian Zhihui 
Published: March 2024

Abstract
Background
Indian jointvetch (Aeschynomene indica) is a common and pernicious weed found in the upland direct-seeding rice fields in the lower reaches of the Yangtze River in China. However, there are few reports on the degree of harm, genetic characteristics, and management methods of this weed. The purpose of this study is to clarify the harm of Indian jointvetch to upland direct-seeding rice, analyze the genetic characteristics of this weed based on chloroplast genomics and identify its related species, and screen herbicides that are effective in managing this weed in upland direct-seeding rice fields.

Results
In a field investigation in upland direct-seeding rice paddies in Shanghai and Jiangsu, we determined that the plant height and maximum lateral distance of Indian jointvetch reached approximately 134.2 cm and 57.9 cm, respectively. With Indian jointvetch present at a density of 4/m2 and 8/m2, the yield of rice decreased by approximately 50% and 70%, respectively. We further obtained the first assembly of the complete chloroplast (cp.) genome sequence of Indian jointvetch (163,613 bp). There were 161 simple sequence repeats, 166 long repeats, and 83 protein-encoding genes. The phylogenetic tree and inverted repeat region expansion and contraction analysis based on cp. genomes demonstrated that species with closer affinity to A. indica included Glycine soja, Glycine max, and Sesbania cannabina. Moreover, a total of 3281, 3840, and 3838 single nucleotide polymorphisms were detected in the coding sequence regions of the cp. genomes of S. cannabina voucher IBSC, G. soja, and G. max compared with the A. indica sequence, respectively. A greenhouse pot experiment indicated that two pre-emergence herbicides, saflufenacil and oxyfluorfen, and two post-emergence herbicides, florpyrauxifen-benzyl and penoxsulam, can more effectively manage Indian jointvetch than other common herbicides in paddy fields. The combination of these two types of herbicides is recommended for managing Indian jointvetch throughout the entire growth period of upland direct-seeding rice.

Conclusions
This study provides molecular resources for future research focusing on the identification of the infrageneric taxa, phylogenetic resolution, and biodiversity of Leguminosae plants, along with recommendations for reliable management methods to control Indian jointvetch.
Hybrid transformer convolutional neural network-based radiomics models for osteoporosis screening in routine CT
Authors: Liu Jiachen , Wang Huan , Shan Xiuqi , Zhang Lei , Cui Shaoqian , Shi Zelin , Liu Yunpeng , Zhang Yingdi , Wang Lanbo 
Published: March 2024

Abstract
Objective
Early diagnosis of osteoporosis is crucial to prevent osteoporotic vertebral fracture and complications of spine surgery. We aimed to conduct a hybrid transformer convolutional neural network (HTCNN)-based radiomics model for osteoporosis screening in routine CT.

Methods
To investigate the HTCNN algorithm for vertebrae and trabecular segmentation, 92 training subjects and 45 test subjects were employed. Furthermore, we included 283 vertebral bodies and randomly divided them into the training cohort (n = 204) and test cohort (n = 79) for radiomics analysis. Area receiver operating characteristic curves (AUCs) and decision curve analysis (DCA) were applied to compare the performance and clinical value between radiomics models and Hounsfield Unit (HU) values to detect dual-energy X-ray absorptiometry (DXA) based osteoporosis.

Results
HTCNN algorithm revealed high precision for the segmentation of the vertebral body and trabecular compartment. In test sets, the mean dice scores reach 0.968 and 0.961. 12 features from the trabecular compartment and 15 features from the entire vertebral body were used to calculate the radiomics score (rad score). Compared with HU values and trabecular rad-score, the vertebrae rad-score suggested the best efficacy for osteoporosis and non-osteoporosis discrimination (training group: AUC = 0.95, 95%CI 0.91–0.99; test group: AUC = 0.97, 95%CI 0.93–1.00) and the differences were significant in test group according to the DeLong test (p < 0.05).

Conclusions
This retrospective study demonstrated the superiority of the HTCNN-based vertebrae radiomics model for osteoporosis discrimination in routine CT.
Deep learning algorithms for predicting renal replacement therapy initiation in CKD patients: a retrospective cohort study
Authors: Leung Ka-Chun , Ng Wincy Wing-Sze , Siu Yui-Pong , Hau Anthony Kai-Ching , Lee Hoi-Kan 
Published: March 2024

Abstract
Background
Chronic kidney disease (CKD) requires accurate prediction of renal replacement therapy (RRT) initiation risk. This study developed deep learning algorithms (DLAs) to predict RRT risk in CKD patients by incorporating medical history and prescriptions in addition to biochemical investigations.

Methods
A multi-centre retrospective cohort study was conducted in three major hospitals in Hong Kong. CKD patients with an eGFR < 30ml/min/1.73m2 were included. DLAs of various structures were created and trained using patient data. Using a test set, the DLAs' predictive performance was compared to Kidney Failure Risk Equation (KFRE).

Results
DLAs outperformed KFRE in predicting RRT initiation risk (CNN + LSTM + ANN layers ROC-AUC = 0.90; CNN ROC-AUC = 0.91; 4-variable KFRE: ROC-AUC = 0.84; 8-variable KFRE: ROC-AUC = 0.84). DLAs accurately predicted uncoded renal transplants and patients requiring dialysis after 5 years, demonstrating their ability to capture non-linear relationships.

Conclusions
DLAs provide accurate predictions of RRT risk in CKD patients, surpassing traditional methods like KFRE. Incorporating medical history and prescriptions improves prediction performance. While our findings suggest that DLAs hold promise for improving patient care and resource allocation in CKD management, further prospective observational studies and randomized controlled trials are necessary to fully understand their impact, particularly regarding DLA interpretability, bias minimization, and overfitting reduction. Overall, our research underscores the emerging role of DLAs as potentially valuable tools in advancing the management of CKD and predicting RRT initiation risk.
Health literacy in the context of child health promotion: a scoping review of conceptualizations and descriptions
Authors: Van Boxtel Wieke , Jerković-Ćosić Katarina , Schoonmade Linda J. , Chinapaw Mai J. M. 
Published: March 2024

Abstract
Background
Increasing health literacy (HL) in children could be an opportunity for a more health literate future generation. The aim of this scoping review is to provide an overview of how HL is conceptualized and described in the context of health promotion in 9–12-year-old children.

Methods
A systematic and comprehensive search for ‘health literacy’ and ‘children’ and ‘measure’ was performed in accordance with PRISMA ScR in PubMed, Embase.com and via Ebsco in CINAHL, APA PsycInfo and ERIC. Two reviewers independently screened titles and abstracts and evaluated full-text publications regarding eligibility. Data was extracted systematically, and the extracted descriptions of HL were analyzed qualitatively using deductive analysis based on previously published HL definitions.

Results
The search provided 5,401 original titles, of which 26 eligible publications were included. We found a wide variation of descriptions of learning outcomes as well as competencies for HL. Most HL descriptions could be linked to commonly used definitions of HL in the literature, and some combined several HL dimensions. The descriptions varied between HL dimensions and were not always relevant to health promotion. The educational setting plays a prominent role in HL regarding health promotion.

Conclusion
The description of HL is truly diverse and complex encompassing a wide range of topics. We recommend adopting a comprehensive and integrated approach to describe HL dimensions, particularly in the context of health promotion for children. By considering the diverse dimensions of HL and its integration within educational programs, children can learn HL skills and competencies from an early age.
Lessons learned from health system rehabilitation preparedness and response for disasters in LMICs: a scoping review
Authors: Gosling Justine , Maritz Roxanne , Laplante-Lévesque Ariane , Sabariego Carla 
Published: March 2024

Abstract
Introduction
Disasters such as earthquakes, conflict, or landslides result in traumatic injuries creating surges in rehabilitation and assistive technology needs, exacerbating pre-existing unmet needs. Disasters frequently occur in countries where existing rehabilitation services are underdeveloped, hindering response to rehabilitation demand surge events.

Aims
The primary aim of this scoping review is therefore to synthesize the evidence on rehabilitation and assistive technology preparedness and response of health systems in LMICs to the demand associated with disasters and conflict situations. A secondary aim was to summarize related recommendations identified in the gathered literature.

Methodology
A scoping review was conducted using the Arksey and O’Malley framework to guide the methodological development. The results are reported in accordance with PRISMA-ScR. Four bibliographic databases were used: CINHAL, Cochrane, Pubmed, Scopus and. Key international organisations were also contacted. The search period was from 2010–2022. Eligible publications were categorized for analysis under the six World Health Organization health systems buildings blocks.

Results
The findings of this scoping review suggest that rehabilitation is poorly integrated into health systems disaster preparedness and response in LMICs. Of the 27 studies included in the scoping review, 14 focused on service delivery, 6 on health workforce, 4 on health information systems and 3 on the leadership and governance building block. No study focused on financing nor assistive technology. This review found the most frequently referenced recommendations for actions that should be taken to develop rehabilitation services in disasters to be: the provision early and multi-professional rehabilitation, including the provision of assistive technology and psychological support, integrated community services; disaster response specific training for rehabilitation professionals; advocacy efforts to create awareness of the importance of rehabilitation in disasters; and the integration of rehabilitation into disaster preparedness and response plans.

Conclusion
Findings of this scoping review suggest that rehabilitation is poorly integrated into health systems disaster preparedness and response in LMIC's, largely due to low awareness of rehabilitation, undeveloped rehabilitation health systems and a lack of rehabilitation professionals, and disaster specific training for them. The paucity of available evidence hinders advocacy efforts for rehabilitation in disaster settings and limits the sharing of experiences and lessons learnt to improve rehabilitation preparedness and response. Advocacy efforts need to be expanded.