bluuebunny/crossref_metadata_2025_split huggingface dataset:
GPT-4 as a Source of Patient Information for Anterior Cervical Discectomy and Fusion: A Comparative Analysis Against Google Web Search
Authors: Mastrokostas Paul G. , Mastrokostas Leonidas E. , Emara Ahmed K. , Wellington Ian J. , Ginalis Elizabeth , Houten John K. , Khalsa Amrit S. , Saleh Ahmed , Razi Afshin E. , Ng Mitchell K. 
Published: March 2024

Study Design Comparative study. Objectives This study aims to compare Google and GPT-4 in terms of (1) question types, (2) response readability, (3) source quality, and (4) numerical response accuracy for the top 10 most frequently asked questions (FAQs) about anterior cervical discectomy and fusion (ACDF). Methods “Anterior cervical discectomy and fusion” was searched on Google and GPT-4 on December 18, 2023. Top 10 FAQs were classified according to the Rothwell system. Source quality was evaluated using JAMA benchmark criteria and readability was assessed using Flesch Reading Ease and Flesch-Kincaid grade level. Differences in JAMA scores, Flesch-Kincaid grade level, Flesch Reading Ease, and word count between platforms were analyzed using Student’s t-tests. Statistical significance was set at the .05 level. Results Frequently asked questions from Google were varied, while GPT-4 focused on technical details and indications/management. GPT-4 showed a higher Flesch-Kincaid grade level (12.96 vs 9.28, P = .003), lower Flesch Reading Ease score (37.07 vs 54.85, P = .005), and higher JAMA scores for source quality (3.333 vs 1.800, P = .016). Numerically, 6 out of 10 responses varied between platforms, with GPT-4 providing broader recovery timelines for ACDF. Conclusions This study demonstrates GPT-4’s ability to elevate patient education by providing high-quality, diverse information tailored to those with advanced literacy levels. As AI technology evolves, refining these tools for accuracy and user-friendliness remains crucial, catering to patients’ varying literacy levels and information needs in spine surgery.
Are retention strategies used in National Institute for Health and Care Research, Health Technology Assessment trials supported by evidence for their effectiveness? A systematic mapping review
Authors: Way Rosalind , Parker Adwoa , Torgerson David J 
Published: March 2024

Background and Aims Poor retention of trial participants is common and can result in significant methodological, statistical, ethical, and financial challenges. To improve trial efficiency, we aimed to assess the extent to which commonly used strategies to retain participants within trials are supported by evidence for their effectiveness. Method A systematic methodological review was carried out to identify commonly used retention strategies in National Institute for Health and Care Research (NIHR) Health Technology Assessment (HTA) trials (January 2020–June 2022). Strategies were then mapped to evidence for their effectiveness from the most recent Cochrane retention review (published 2021), and a future Study Within A Trial (SWAT) priority list was created. Results Amongst 80 trials, the most frequently reported retention strategies were: flexibility with data collection method/location (53%); participant diaries (38%); use of routine data (29%); PPI input (26%); telephone reminders for participants (26%); postal reminders for participants (25%); monitoring approaches (21%); offering flexibility with timing of data collection (20%); pre-paid return postage (18%); prioritising collection of key outcomes (15%); and participant newsletters (15%). Out of the 56 identified strategies, mostly no, very low or low evidence for their effectiveness was identified (64%; 14%; 13% respectively). Discussion and Conclusions Commonly used retention strategies are lacking good quality evidence for their effectiveness. The findings support the need for more SWATs and help identify priority areas for future SWAT research. These priorities could be used with other priority lists to inform future SWAT conduct.
Landscape of driver mutations and their clinical effects on Down syndrome–related myeloid neoplasms
Authors: Sato Tomohiko , Yoshida Kenichi , Toki Tsutomu , Kanezaki Rika , Terui Kiminori , Saiki Ryunosuke , Ojima Masami , Ochi Yotaro , Mizuno Seiya , Yoshihara Masaharu , Uechi Tamayo , Kenmochi Naoya , Tanaka Shiro , Matsubayashi Jun , Kisai Kenta , Kudo Ko , Yuzawa Kentaro , Takahashi Yuka , Tanaka Tatsuhiko , Yamamoto Yohei , Kobayashi Akie , Kamio Takuya , Sasaki Shinya , Shiraishi Yuichi , Chiba Kenichi , Tanaka Hiroko , Muramatsu Hideki , Hama Asahito , Hasegawa Daisuke , Sato Atsushi , Koh Katsuyoshi , Karakawa Shuhei , Kobayashi Masao , Hara Junichi , Taneyama Yuichi , Imai Chihaya , Hasegawa Daiichiro , Fujita Naoto , Yoshitomi Masahiro , Iwamoto Shotaro , Yamato Genki , Saida Satoshi , Kiyokawa Nobutaka , Deguchi Takao , Ito Masafumi , Matsuo Hidemasa , Adachi Souichi , Hayashi Yasuhide , Taga Takashi , Saito Akiko M. , Horibe Keizo , Watanabe Kenichiro , Tomizawa Daisuke , Miyano Satoru , Takahashi Satoru , Ogawa Seishi , Ito Etsuro 
Published: March 2024

Abstract
Transient abnormal myelopoiesis (TAM) is a common complication in newborns with Down syndrome (DS). It commonly progresses to myeloid leukemia (ML-DS) after spontaneous regression. In contrast to the favorable prognosis of primary ML-DS, patients with refractory/relapsed ML-DS have poor outcomes. However, the molecular basis for refractoriness and relapse and the full spectrum of driver mutations in ML-DS remain largely unknown. We conducted a genomic profiling study of 143 TAM, 204 ML-DS, and 34 non-DS acute megakaryoblastic leukemia cases, including 39 ML-DS cases analyzed by exome sequencing. Sixteen novel mutational targets were identified in ML-DS samples. Of these, inactivations of IRX1 (16.2%) and ZBTB7A (13.2%) were commonly implicated in the upregulation of the MYC pathway and were potential targets for ML-DS treatment with bromodomain-containing protein 4 inhibitors. Partial tandem duplications of RUNX1 on chromosome 21 were also found, specifically in ML-DS samples (13.7%), presenting its essential role in DS leukemia progression. Finally, in 177 patients with ML-DS treated following the same ML-DS protocol (the Japanese Pediatric Leukemia and Lymphoma Study Group acute myeloid leukemia -D05/D11), CDKN2A, TP53, ZBTB7A, and JAK2 alterations were associated with a poor prognosis. Patients with CDKN2A deletions (n = 7) or TP53 mutations (n = 4) had substantially lower 3-year event-free survival (28.6% vs 90.5%; P &lt; .001; 25.0% vs 89.5%; P &lt; .001) than those without these mutations. These findings considerably change the mutational landscape of ML-DS, provide new insights into the mechanisms of progression from TAM to ML-DS, and help identify new therapeutic targets and strategies for ML-DS.
Therapy-related chronic myelomonocytic leukemia does not have the high-risk features of a therapy-related neoplasm
Authors: Bataller Alex , Gener-Ricos Georgina , Almanza-Huante Emmanuel , Chien Kelly S. , Urrutia Samuel , Bazinet Alexandre , Rodriguez-Sevilla Juan Jose , Hammond Danielle , Sasaki Koji , Takahashi Koichi , DiNardo Courtney D. , Ravandi Farhad , Borthakur Gautam , Kadia Tapan M. , Kanagal-Shamanna Rashmi , Kantarjian Hagop M. , Garcia-Manero Guillermo , Montalban-Bravo Guillermo 
Published: March 2024

Abstract
Therapy-related myeloid neoplasms (t-MNs) arise after exposure to cytotoxic therapies and are associated with high-risk genetic features and poor outcomes. We analyzed a cohort of patients with therapy-related chronic myelomonocytic leukemia (tCMML; n = 71) and compared its features to that of de novo CMML (dnCMML; n = 461). Median time from cytotoxic therapy to tCMML diagnosis was 6.5 years. Compared with dnCMML, chromosome-7 abnormalities (4% vs 13%; P = .005) but not complex karyotype (3% vs 7%; P = .15), were more frequent in tCMML. tCMML was characterized by higher TP53 mutation frequency (4% vs 12%; P = .04) and lower NRAS (6% vs 22%, P = .007) and CBL (4% vs 12%, P = .04) mutation frequency. Prior therapy with antimetabolites (odd ratio [OR], 1.22; 95% confidence interval [CI], 1.05-1.42; P = .01) and mitotic inhibitors (OR, 1.24; 95% CI, 1.06-1.44; P = .009) was associated with NF1 and SETBP1 mutations whereas prior mitotic inhibitor therapy was associated with lower TET2 mutation frequency (OR, 0.71; 95% CI, 0.55-0.92; P = .01). Although no differences in median overall survival (OS) were observed among tCMML and dnCMML (34.7 months vs 35.9 months, P = .26), multivariate analysis for OS revealed that prior chemotherapy was associated with increased risk of death (hazard ratio, 1.76; 95% CI, 1.07-2.89; P = .026). Compared with a cohort of therapy-related myelodysplastic syndrome, tCMML had lower TP53 mutation frequency (12% vs 44.4%, P &lt; .001) and less unfavorable outcomes. In summary, tCMML does not exhibit the high-risk features and poor outcomes of t-MNs.
Comparative study on chromatin loop callers using Hi-C data reveals their effectiveness
Authors: Chowdhury H. M. A. Mohit , Boult Terrance , Oluwadare Oluwatosin 
Published: March 2024

Abstract
Background
Chromosome is one of the most fundamental part of cell biology where DNA holds the hierarchical information. DNA compacts its size by forming loops, and these regions house various protein particles, including CTCF, SMC3, H3 histone. Numerous sequencing methods, such as Hi-C, ChIP-seq, and Micro-C, have been developed to investigate these properties. Utilizing these data, scientists have developed a variety of loop prediction techniques that have greatly improved their methods for characterizing loop prediction and related aspects.

Results
In this study, we categorized 22 loop calling methods and conducted a comprehensive study of 11 of them. Additionally, we have provided detailed insights into the methodologies underlying these algorithms for loop detection, categorizing them into five distinct groups based on their fundamental approaches. Furthermore, we have included critical information such as resolution, input and output formats, and parameters. For this analysis, we utilized the GM12878 Hi-C datasets at 5 KB, 10 KB, 100 KB and 250 KB resolutions. Our evaluation criteria encompassed various factors, including memory usages, running time, sequencing depth, and recovery of protein-specific sites such as CTCF, H3K27ac, and RNAPII.

Conclusion
This analysis offers insights into the loop detection processes of each method, along with the strengths and weaknesses of each, enabling readers to effectively choose suitable methods for their datasets. We evaluate the capabilities of these tools and introduce a novel Biological, Consistency, and Computational robustness score ($$BCC_{score}$$

B
C

C

score

) to measure their overall robustness ensuring a comprehensive evaluation of their performance.
Cell4D: a general purpose spatial stochastic simulator for cellular pathways
Authors: Chan Donny , Cromar Graham L. , Taj Billy , Parkinson John 
Published: March 2024

Abstract
Background
With the generation of vast compendia of biological datasets, the challenge is how best to interpret ‘omics data alongside biochemical and other small-scale experiments to gain meaningful biological insights. Key to this challenge are computational methods that enable domain-users to generate novel hypotheses that can be used to guide future experiments. Of particular interest are flexible modeling platforms, capable of simulating a diverse range of biological systems with low barriers of adoption to those with limited computational expertise.

Results
We introduce Cell4D, a spatial-temporal modeling platform combining a robust simulation engine with integrated graphics visualization, a model design editor, and an underlying XML data model capable of capturing a variety of cellular functions. Cell4D provides an interactive visualization mode, allowing intuitive feedback on model behavior and exploration of novel hypotheses, together with a non-graphics mode, compatible with high performance cloud compute solutions, to facilitate generation of statistical data. To demonstrate the flexibility and effectiveness of Cell4D, we investigate the dynamics of CEACAM1 localization in T-cell activation. We confirm the importance of Ca2+ microdomains in activating calmodulin and highlight a key role of activated calmodulin on the surface expression of CEACAM1. We further show how lymphocyte-specific protein tyrosine kinase can help regulate this cell surface expression and exploit spatial modeling features of Cell4D to test the hypothesis that lipid rafts regulate clustering of CEACAM1 to promote trans-binding to neighbouring cells.

Conclusions
Through demonstrating its ability to test and generate hypotheses, Cell4D represents an effective tool to help integrate knowledge across diverse, large and small-scale datasets.
GNNMF: a multi-view graph neural network for ATAC-seq motif finding
Authors: Zhang Shuangquan , Wu Xiaotian , Lian Zhichao , Zuo Chunman , Wang Yan 
Published: March 2024

Abstract
Background
The Assay for Transposase-Accessible Chromatin using sequencing (ATAC-seq) utilizes the Transposase Tn5 to probe open chromatic, which simultaneously reveals multiple transcription factor binding sites (TFBSs) compared to traditional technologies. Deep learning (DL) technology, including convolutional neural networks (CNNs), has successfully found motifs from ATAC-seq data. Due to the limitation of the width of convolutional kernels, the existing models only find motifs with fixed lengths. A Graph neural network (GNN) can work on non-Euclidean data, which has the potential to find ATAC-seq motifs with different lengths. However, the existing GNN models ignored the relationships among ATAC-seq sequences, and their parameter settings should be improved.

Results
In this study, we proposed a novel GNN model named GNNMF to find ATAC-seq motifs via GNN and background coexisting probability. Our experiment has been conducted on 200 human datasets and 80 mouse datasets, demonstrated that GNNMF has improved the area of eight metrics radar scores of 4.92% and 6.81% respectively, and found more motifs than did the existing models.

Conclusions
In this study, we developed a novel model named GNNMF for finding multiple ATAC-seq motifs. GNNMF built a multi-view heterogeneous graph by using ATAC-seq sequences, and utilized background coexisting probability and the iterloss to find different lengths of ATAC-seq motifs and optimize the parameter sets. Compared to existing models, GNNMF achieved the best performance on TFBS prediction and ATAC-seq motif finding, which demonstrates that our improvement is available for ATAC-seq motif finding.
Identification and characterization of structural variants related to meat quality in pigs using chromosome-level genome assemblies
Authors: Kwon Daehong , Park Nayoung , Wy Suyeon , Lee Daehwan , Park Woncheoul , Chai Han-Ha , Cho In-Cheol , Lee Jongin , Kwon Kisang , Kim Heesun , Moon Youngbeen , Kim Juyeon , Kim Jaebum 
Published: March 2024

Abstract
Background
Many studies have been performed to identify various genomic loci and genes associated with the meat quality in pigs. However, the full genetic architecture of the trait still remains unclear in part because of the lack of accurate identification of related structural variations (SVs) which resulted from the shortage of target breeds, the limitations of sequencing data, and the incompleteness of genome assemblies. The recent generation of a new pig breed with superior meat quality, called Nanchukmacdon, and its chromosome-level genome assembly (the NCMD assembly) has provided new opportunities.

Results
By applying assembly-based SV calling approaches to various genome assemblies of pigs including Nanchukmacdon, the impact of SVs on meat quality was investigated. Especially, by checking the commonality of SVs with other pig breeds, a total of 13,819 Nanchukmacdon-specific SVs (NSVs) were identified, which have a potential effect on the unique meat quality of Nanchukmacdon. The regulatory potentials of NSVs for the expression of nearby genes were further examined using transcriptome- and epigenome-based analyses in different tissues.

Conclusions
Whole-genome comparisons based on chromosome-level genome assemblies have led to the discovery of SVs affecting meat quality in pigs, and their regulatory potentials were analyzed. The identified NSVs will provide new insights regarding genetic architectures underlying the meat quality in pigs. Finally, this study confirms the utility of chromosome-level genome assemblies and multi-omics analysis to enhance the understanding of unique phenotypes.
Overcoming barriers for left atrial appendage thrombus: a systematic review of left atrial appendage closure
Authors: Zhang Zixi , Zhou Jiabao , Lin Qiuzhen , Wang Cancan , Huang Yunying , Dai Yongguo , Zuo Wanyun , Liu Na , Xiao Yichao , Liu Qiming 
Published: March 2024

Abstract
Background
Approximately 90% of intracardial thrombi originate from the left atrial appendage in non-valvular atrial fibrillation patients. Even with anticoagulant therapy, left atrial appendage thrombus (LAAT) still occurs in 8% of patients. While left atrial appendage closure (LAAC) could be a promising alternative, the current consensus considers LAAT a contraindication to LAAC. However, the feasibility and safety of LAAC in patients with LAAT have yet to be determined.

Methods
This systematic review synthesizes published data to explore the feasibility and safety of LAAC for patients with LAAT.

Results
This study included a total of 136 patients with LAATs who underwent successful LAAC. The Amulet Amplatzer device was the most frequently utilized device (48.5%). Among these patients, 77 (56.6%) had absolute contraindications to anticoagulation therapy. Cerebral protection devices were utilized by 47 patients (34.6%). Transesophageal echocardiography (TEE) is the primary imaging technique used during the procedure. Warfarin and novel oral anticoagulants were the main anticoagulant medications used prior to the procedure, while dual antiplatelet therapy was primarily used post-procedure. During a mean follow-up period of 13.2 ± 11.5 months, there was 1 case of fatality, 1 case of stroke, 3 major bleeding events, 3 instances of device-related thrombus, and 8 cases of peri-device leakage.

Conclusions
This review highlights the preliminary effectiveness and safety of the LAAC procedure in patients with persistent LAAT. Future large-scale RCTs with varied LAAT characteristics and LAAC device types are essential for evidence-based decision-making in clinical practice.
Development of the multivariate administrative data cystectomy model and its impact on misclassification bias
Authors: Ross James , Lavallee Luke T. , Hickling Duane , van Walraven Carl 
Published: March 2024

Abstract
Background
Misclassification bias (MB) is the deviation of measured from true values due to incorrect case assignment. This study compared MB when cystectomy status was determined using administrative database codes vs. predicted cystectomy probability.

Methods
We identified every primary cystectomy-diversion type at a single hospital 2009–2019. We linked to claims data to measure true association of cystectomy with 30 patient and hospitalization factors. Associations were also measured when cystectomy status was assigned using billing codes and by cystectomy probability from multivariate logistic regression model with covariates from administrative data. MB was the difference between measured and true associations.

Results
500 people underwent cystectomy (0.12% of 428 677 hospitalizations). Sensitivity and positive predictive values for cystectomy codes were 97.1% and 58.6% for incontinent diversions and 100.0% and 48.4% for continent diversions, respectively. The model accurately predicted cystectomy-incontinent diversion (c-statistic [C] 0.999, Integrated Calibration Index [ICI] 0.000) and cystectomy-continent diversion (C:1.000, ICI 0.000) probabilities. MB was significantly lower when model-based predictions was used to impute cystectomy-diversion type status using for both incontinent cystectomy (F = 12.75; p < .0001) and continent cystectomy (F = 11.25; p < .0001).

Conclusions
A model using administrative data accurately returned the probability that cystectomy by diversion type occurred during a hospitalization. Using this model to impute cystectomy status minimized MB. Accuracy of administrative database research can be increased by using probabilistic imputation to determine case status instead of individual codes.
Perioperative outcomes of the surgical management of achalasia in two tertiary Cameroonian hospitals: a cohort study
Authors: Kamla Joël Igor , Bang Guy Aristide , Tochie Joel Noutakdie , Bwelle George Motto , Oumarou Blondel Nana , Nonga Bernadette Ngo 
Published: March 2024

Abstract
Introduction
Achalasia is a rare esophageal disease with potentially lethal complications. Knowledge of the outcomes of the different surgical treatment modalities for achalasia by Heller’s cardiomyotomy (HCM) helps to choose the safest and most effective option. However, data on the management of achalsia using a Heller myotomy is limited in Africa. Thus, our aim was to determine the perioperative morbidity, mortality and short-term functional outcomes of HCM in Cameroon.

Methodology
We conducted a cohort study throughout a 10-year chart review of patients who underwent HCM for achalasia and were followed up postoperatively for at least three months at two tertiary health centers in Cameroon. We analyzed demographic data, preoperative clinical and imaging data, treatment details, and outcomes at three to twelve months after HCM using the Eckardt score.

Results
We enrolled 29 patients with achalasia having a mean age of 24 ± 16 years and predominantly females (M/F of 1/3.8). The mean symptom duration was 51 ± 20 months. In 80% of cases, the diagnosis was made through a conventional x-ray contrast imaging or “barium swallow test” (93%) and/or an upper gastrointestinal endoscopy (86%). The gold standard diagnostic method via esophageal manometry was unavailable. Preoperatievly, all patients had symptoms suggestive of an active achalasia. HCM was performed via laparotomy in 75% as opposed to 25% laparoscopic HCM procedures. Dor’s anterior partial fundoplication was the main anti-reflux procedure performed (59%). Mucosal perforations were the only intraoperative complications in eight patients (2 during laparoscopy vs. 6 during laparotomy; p > 0.5) and were managed successfully by simple sutures. Postoperative complications were non-severe and occurred in 10% of patients all operated via laparotomy. The mean postoperative length of hospital stay was 7 ± 3 days for laparotomy vs. 5 ± 2 days for laparoscopy; p > 0.5. The perioperative mortality rate was nil. Overall, the short-term postoperative functional outcome was rated excellent; average Eckardt score of 1.5 ± 0.5 (vs. preoperative Eckardt Score of 9 ± 1; p < 0.0001).

Conclusion
Achalasia is diagnosed late in this resource-limited setting. HCM yields satisfactory outcomes, especially via laparoscopic management. An improvement in diagnostic esophageal manometry and mini-invasive surgical infrastructure and the required surgical training/skills are needed for optimal achalasia care.