bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparative efficacy of pharmacologic therapies for MASH in reducing liver fat content: Systematic review and network meta-analysis
Authors: Koh Benjamin , Xiao Jieling , Ng Cheng Han , Law Michelle , Gunalan Shyna Zhuoying , Danpanichkul Pojsakorn , Ramadoss Vijay , Sim Benedix Kuan Loon , Tan En Ying , Teo Chong Boon , Nah Benjamin , Teng Margaret , Wijarnpreecha Karn , Seko Yuya , Lim Mei Chin , Takahashi Hirokazu , Nakajima Atsushi , Noureddin Mazen , Muthiah Mark , Huang Daniel Q. , Loomba Rohit 
Published: July 2024

Background and Aims:
Metabolic dysfunction–associated steatohepatitis (MASH) is a leading cause of liver disease. Dynamic changes in MRI proton-density-fat fraction (PDFF) are associated with MASH resolution. We aimed to determine the relative efficacy of therapeutic agents for reducing hepatic fat, assessed by MRI-PDFF.

Approach and Results:
In this systematic review and network meta-analysis, we searched MEDLINE and Embase from inception until December 26, 2023, for published randomized controlled trials comparing pharmacological interventions in patients with MASH that assessed changes in MRI-PDFF. The primary outcome was the absolute change in MRI-PDFF. The secondary outcome was a ≥30% decline in MRI-PDFF. A surface under-the-curve cumulative ranking probabilities (SUCRA) analysis was performed. Of 1550 records, a total of 39 randomized controlled trials (3311 participants) met the inclusion criteria. For MRI-PDFF decline at 24 weeks, aldafermin (SUCRA: 83.65), pegozafermin (SUCRA: 83.46), and pioglitazone (SUCRA: 71.67) were ranked the most effective interventions. At 24 weeks, efinopegdutide (SUCRA: 67.02), semaglutide + firsocostat (SUCRA: 62.43), and pegbelfermin (SUCRA: 61.68) were ranked the most effective interventions for achieving a ≥30% decline in MRI-PDFF.

Conclusions:
This study provides an updated, relative rank-order efficacy of therapies for MASH in reducing hepatic fat. These data may help inform the design and sample size calculation of future clinical trials and assist in the selection of combination therapy.
Expert Consensus on the Prevention and Treatment of Chronic Hepatitis B in Children
Authors:   Chinese Society of Infectious Diseases, Chinese Medical Association,   Chinese Society of Hepatology, Chinese Medical Association,   Group of Infectious Diseases, Chinese Pediatric Society, Chinese Medical Association,   National Clinical Research Center for Infectious Diseases (Beijing)
Published: July 2024

Abstract
The aim of this consensus is to standardize the prevention, diagnosis, and treatment of chronic hepatitis B in children and to achieve the goal of “eliminating viral hepatitis as a major public health threat by 2030” issued by the World Health Organization. Formulated by organized experts of the Chinese Society of Infectious Diseases and Chinese Society of Hepatology, Chinese Medical Association; Group of Infectious Diseases, Chinese Pediatric Society, Chinese Medical Association; and the National Clinical Research Center for Infectious Diseases (Beijing), the consensus provides the latest evidence and recommendations for the prevention, diagnosis, and treatment of chronic hepatitis B in children.
The Effectiveness of a Human Trafficking Protocol in the Emergency Department
Authors: Bastien Danielle Jordan , Peters Rosalind M. 
Published: July 2024

Background:
Human trafficking affects nearly 1.1 million persons in the United States. Over 50% of victims will receive care in an emergency department (ED) during their exploitation.

Purpose:
The purpose of this study was to assess the effectiveness of a human trafficking protocol and electronic medical record screening and assessment tool in identifying victims of human trafficking in the ED.

Methods:
A 5-year, retrospective chart audit was conducted.

Results:
Over 2 million ED visits occurred during the 5-year study period. Less than 1% (n = 525) of those patients screened positive as potential victims, while 45 (8.6%) were confirmed trafficking victims. The number of victims identified dropped following the pandemic.

Conclusions:
Pandemic issues, staffing turnover, and lack of ongoing trafficking education impeded the identification of victims. Recommended changes to the protocol are presented.
Explantation with Lateral Pedicle Mastopexy
Authors: Macmillan R. Douglas , Bell Kara , Wilson Emma , Asgeirsson Kristjan S. 
Published: July 2024

Background:
Although breast explantation combined with mastopexy is an increasingly common procedure, it does present certain technical difficulties. The authors present a technique of explantation mastopexy with the use of an extended lateral pedicle for autoaugmentation.

Methods:
A consecutive series of 40 cases was reviewed retrospectively, with a patient-reported outcome questionnaire and photography at 3 and 12 months.

Results:
The mean patient age was 57 years (range, 40 to 70 years), and the mean duration of implantation was 20.4 years (range, 7 to 42 years). Twelve women had undergone previous mastopexy (30%). Minor wound complications requiring simple dressings were seen in 7 patients (17.5%). Major infected wound problems occurred in 1 patient, who was a smoker and had other comorbidities. All except 1 patient reported being satisfied or very satisfied with the outcome, with a mean patient-reported satisfaction score of 4.9 of 5. When the photographs were independently assessed by a cosmetic practitioner, all patients were rated as average, good, or very good, with a mean score of 4.1 of 5.

Conclusions:
The procedure is associated with low risk of postoperative complications, good cosmetic outcomes, and a high degree of patient satisfaction. The authors believe this technique provides a logical, reproducible method for combined explantation and mastopexy.

CLINICAL QUESTION/LEVEL OF EVIDENCE:
Therapeutic, IV.
Mastoid Fascia Tissue Graft as a Tip Camouflage Technique in Rhinoplasty: A Reliable Alternative to Soft Cartilage Grafts
Authors: Tugertimur Buğra , Datta Shaishav , Goote Paige , Hanna Steven A. , Morris Matthew , Mattos David , Reish Richard G. 
Published: July 2024

Background:
Traditional rhinoplasty tip grafts often lead to visibility issues, prompting patients to seek revision surgery. The mastoid fascia tissue graft (MFTG) provides a natural-appearing alternative with an acceptable risk of complication. The MFTG remains less visible through the skin and helps camouflage and conceal tip irregularities. This study of 193 patients examines the MFTG’s effectiveness in nasal tip refinement, evaluating revision and infection rates.

Methods:
A retrospective analysis of MFTG use for nasal tip appearance during open rhinoplasty in the senior author’s (R.G.R.) practice was conducted, covering the period from January of 2019 to June of 2022. Inclusion criteria encompassed open rhinoplasty cases using mastoid tissue for tip appearance with at least 12 months of follow-up. Among 2003 cases, 193 met these criteria and were evaluated for subsequent revision and infection rates.

Results:
The average patient age was 34.2 years (175 female patients and 18 male patients). Primary rhinoplasty was performed in 113 patients, with 80 receiving revision operations. The average follow-up was 14.8 months. Six patients (3.1%) overall needed extended antibiotics, including 1 primary rhinoplasty patient (0.9%) and 5 secondary rhinoplasty patients (6.3%). Overall, revision rhinoplasty was required in 6 patients (3.1%) (1 primary patient [0.9%] and 5 secondary rhinoplasty patients [6.3%]).

Conclusions:
MFTG use for an aesthetically pleasing nasal tip appearance is a safe, convenient, and effective technique for camouflaging and concealing nasal tip contour irregularities in both primary and revision rhinoplasty. Use of the MTFG is associated with minimal morbidity.

CLINICAL QUESTION/LEVEL OF EVIDENCE:
Therapeutic, IV.
Synoviocytes assist in modulating the effect of Ross River virus infection in micromass-cultured primary human chondrocytes
Authors: Freppel Wesley , Lim Elisa X.Y. , Rudd Penny A. , Herrero Lara J. 
Published: July 2024

Graphical abstract
A schematic representation of the study methodology. Human micromass-cultured chondrocytes were either directly infected with RRV or secondarily through co-culture with RRV-infected FLS. Micromass chondrocytes were analysed after 1, 3 and 5 days post-infection for gene expression using a PCR array and for viral load using genome copy number qPCR. FLS were analysed for viral load via qPCR, and supernatants were analysed for infectious viral particles using a plaque assay.
Inter-individual variability in motor learning due to differences in effective learning rates between generalist and specialist memory stores
Authors: Osu Rieko , Sugimoto Norikazu , Yoshioka Toshinori , Schweighofer Nicolas , Kawato Mitsuo 
Published: July 2024

AbstractHumans exhibit large interindividual differences in motor learning ability. However, most previous studies have examined properties common across populations, with less emphasis on interindividual differences. We hypothesized here, based on our previous experimental and computational motor adaptation studies, that individual differences in effective learning rates between a generalist memory module that assumes environmental continuity and specialist modules that are responsive to trial-by-trial environmental changes could explain both large population-wise and individual-wise differences in dual tasks adaptation under block and random schedules. Participants adapted to two opposing force fields, either sequentially with alternating training blocks or simultaneously with random sequences. As previously reported, in the block training schedule, all participants adapted to the force field presented in a block but showed large interference in the subsequent opposing force field blocks, such that adapting to the two force fields was impossible. In contrast, in the random training schedule, participants could adapt to the two conflicting tasks simultaneously as a group; however, large interindividual variability was observed. A modified MOSAIC computational model of motor learning equipped with one generalist module and two specialist modules explained the observed behavior and variability for wide parameter ranges: when the predictions errors were large and consistent as in block schedules, the generalist module was selected to adapt quickly. In contrast, the specialist modules were selected when they more accurately predicted the changing environment than the generalist, as during random schedules; this resulted in consolidated memory specialized to each environment, but only when the ratio of learning rates of the generalist to specialists was relatively small. This dynamic selection process plays a crucial role in explaining the individual differences observed in motor learning abilities.
Permissive and instructiveHoxcodes govern limb positioning
Authors: Wang Yajun , Hintze Maik , Wang Jinbao , Petzsch Patrick , Köhrer Karl , Tao Hengxun , Cheng Longfei , Zhou Peng , Wang Jianlin , Liao Zhaofu , Qi Xufeng , Cai Dongqing , Bartolomaeus Thomas , Schilling Karl , Wilting Joerg , Kuerten Stefanie , Koentges Georgy , Patel Ketan , Pu Qin , Huang Ruijin 
Published: July 2024

AbstractThe positioning of limbs along the anterior-posterior axis varies widely across vertebrates. The mechanisms controlling this feature remain to be fully understood. For over 30 years, it has been speculated thatHoxgenes play a key role in this process but evidence supporting this hypothesis has been largely indirect. In this study, we employed loss- and gain-of-functionHoxgene variants in chick embryos to address this issue. Using this approach, we found thatHox4/5genes are necessary but insufficient for forelimb formation. Within theHox4/5expression domain,Hox6/7genes are sufficient for reprogramming of neck lateral plate mesoderm to form an ectopic limb bud, thereby inducing forelimb formation anterior to the normal limb field. Our findings demonstrate that the forelimb program depends on the combinatorial actions of theseHoxgenes. We propose that during the evolutionary emergence of the neck,Hox4/5provide permissive cues for forelimb formation throughout the neck region, while the final position of the forelimb is determined by the instructive cues ofHox6/7in the lateral plate mesoderm.Impact statementElucidation of theHoxcode defining forelimb positioning provides novel insights in lateral plate mesoderm patterning and the integration of vertebrate column structure and limb positioning.ClassificationDevelopment --- developmental biology
A third kind of episodic memory: Context familiarity is distinct from item familiarity and recollection
Authors: Addante Richard J. , Clise Evan , Waechter Randall , Bengson Jesse , Drane Daniel L. , Perez-Caban Jahdiel 
Published: July 2024

AbstractEpisodic memory is accounted for with two processes: ‘familiarity’ when generally recognizing an item and ‘recollection’ when retrieving the full contextual details bound with the item. Paradoxically, people sometimes report contextual information as familiar but without recollecting details, which is not easily accounted for by existing theories. We tested a combination of item recognition confidence and source memory, focusing upon ‘item-only hits with source unknown’ (‘item familiarity’), ‘low-confidence hits with correct source memory’ (‘context familiarity’), and ‘high-confidence hits with correct source memory’ (‘recollection’). Results across multiple within-subjects (trial-wise) and between subjects (individual variability) levels indicated these were behaviorally and physiologically distinct. Behaviorally, a crossover interaction was evident in response times, with context familiarity being slower than each condition during item recognition, but faster during source memory. Electrophysiologically, a Condition x Time x Location triple dissociation was evident in event-related potentials (ERPs), which was then independently replicated. Context familiarity exhibited an independent negative central effect from 800-1200 ms, differentiated from positive ERPs for item-familiarity (400 to 600 ms) and recollection (600 to 900 ms). These three conditions thus reflect mutually exclusive, fundamentally different processes of episodic memory. Context familiarity is a third distinct process of episodic memory.SummaryMemory for past events is widely believed to operate through two different processes: one called ‘recollection’ when retrieving confident, specific details of a memory, and another called ‘familiarity’ when only having an unsure but conscious awareness that an item was experienced before. When people successfully retrieve details such as the source or context of a prior event, it has been assumed to reflect recollection. We demonstrate that familiarity of context is functionally distinct from familiarity of items and recollection and offer a new, tri-component model of memory. The three memory responses were differentiated across multiple behavioral and brain wave measures. What has traditionally been thought to be two kinds of memory processes are actually three, becoming evident when using sensitive enough multi-measures. Results are independently replicated across studies from different labs. These data reveal that context familiarity is a third process of human episodic memory.Graphical Abstract
SmartImpute: A Targeted Imputation Framework for Single-cell Transcriptome Data
Authors: Yao Sijie , Yu Xiaoqing , Wang Xuefeng 
Published: July 2024

ABSTRACTSingle-cell RNA sequencing (scRNA-seq) has revolutionized our understanding of cellular heterogeneity and tissue transcriptomic complexity. However, the high frequency of dropout events in scRNA-seq data complicates downstream analyses such as cell type identification and trajectory inference. Existing imputation methods address the dropout problem but face limitations such as high computational cost and risk of over-imputation. We present SmartImpute, a novel computational framework designed for targeted imputation of scRNA-seq data. SmartImpute focuses on a predefined set of marker genes, enhancing the biological relevance and computational efficiency of the imputation process while minimizing the risk of model misspecification. Utilizing a modified Generative Adversarial Imputation Network architecture, SmartImpute accurately imputes the missing gene expression and distinguishes between true biological zeros and missing values, preventing overfitting and preserving biologically relevant zeros. To ensure reproducibility, we also provide a function based on the GPT4 model to create target gene panels depending on the tissue types and research context. Our results, based on scRNA-seq data from head and neck squamous cell carcinoma and human bone marrow, demonstrate that SmartImpute significantly enhances cell type annotation and clustering accuracy while reducing computational burden. Benchmarking against other imputation methods highlights SmartImpute’s superior performance in terms of both accuracy and efficiency. Overall, SmartImpute provides a lightweight, efficient, and biologically relevant solution for addressing dropout events in scRNA-seq data, facilitating deeper insights into cellular heterogeneity and disease progression. Furthermore, SmartImpute’s targeted approach can be extended to spatial omics data, which also contain many missing values.
TRGT-denovo: accurate detection ofde novotandem repeat mutations
Authors: Mokveld T. , Dolzhenko E. , Dashnow H. , Nicholas T. J. , Sasani T. , van der Sanden B. , Jadhav B. , Pedersen B. , Kronenberg Z. , Tucci A. , Sharp A. J. , Quinlan A. R. , Gilissen C. , Hoischen A. , Eberle M. A. 
Published: July 2024

AbstractMotivationIdentifyingde novotandem repeat (TR) mutations on a genome-wide scale is essential for understanding genetic variability and its implications in rare diseases. While PacBio HiFi sequencing data enhances the accessibility of the genome’s TR regions for genotyping, simplede novocalling strategies often generate an excess of likely false positives, which can obscure true positive findings, particularly as the number of surveyed genomic regions increases.ResultsWe developed TRGT-denovo, a computational method designed to accurately identify all types ofde novoTR mutations—including expansions, contractions, and compositional changes— within family trios. TRGT-denovo directly interrogates read evidence, allowing for the detection of subtle variations often overlooked in variant call format (VCF) files. TRGT-denovo improves the precision and specificity ofde novomutation (DNM) identification, reducing the number ofde novocandidates by an order of magnitude compared to genotype-based approaches. In our experiments involving eight rare disease trios previously studied TRGT-denovo correctly reclassified all false positive DNM candidates as true negatives. Using an expanded repeat catalog, it identified new candidates, of which 95% (19/20) were experimentally validated, demonstrating its effectiveness in minimizing likely false positives while maintaining high sensitivity for true discoveries.Availability and implementationBuilt in Rust, TRGT-denovo is available as source code and a pre-compiled Linux binary along with a user guide at:https://github.com/PacificBiosciences/trgt-denovo.
Transcriptome-wide alternative mRNA splicing analysis reveals post-transcriptional regulation of neuronal differentiation
Authors: Zhou Yuan , Rashad Sherif , Niizuma Kuniyasu 
Published: July 2024

AbstractAlternative splicing (AS) plays important roles in neuronal development, function, and diseases. Efforts to analyze AS transcriptome-wide in neurons remain limited. We characterized the transcriptome-wide AS changes in SH-SY5Y neuronal differentiation model, which is widely used to study neuronal function and disorders. Our analysis revealed global changes in five AS programs that drive neuronal differentiation. Motif analysis revealed the contribution of RNA binding proteins (RBPs) to the regulation of AS during neuronal development. We focused on the predominant AS program during differentiation, exon skipping (SE) events. Motif analysis revealed motifs for PTB and HuR/ELAVL1 to be the top enriched in SE events, and their protein levels were downregulated after differentiation. shRNA Knockdown of either PTB and HuR were associated with enhanced neuronal differentiation and transcriptome-wide exon skipping events driving the process of differentiation. At the level of gene expression, we observed only modest changes, indicating predominant post-transcriptional effects of PTB and HuR. We also observed that both RBPs altered cellular responses to oxidative stress, in line with the differentiated phenotype observed after KD. Our work characterizes the AS changes in a widely used and important model of neuronal development and neuroscience research and reveals intricate post-transcriptional regulation of neuronal differentiation.
Tbx1stabilizes differentiation of the cardiopharyngeal mesoderm and drives morphogenesis in the pharyngeal apparatus
Authors: Lanzetta Olga , Bilio Marchesa , Liebig Johannes , Jechow Katharina , Ten Foo Wei , Ferrentino Rosa , Aurigemma Ilaria , Illingworth Elizabeth , Conrad Christian , Lukassen Soeren , Angelini Claudia , Baldini Antonio 
Published: July 2024

ABSTRACTBackgroundTBX1 is required for the development of the pharyngeal apparatus. In the mouse, fish, and ascidian,Tbx1is a marker of cardiopharyngeal mesoderm (CPM), a cell population that provides progenitors to the heart and branchiomeric muscles. However, in mammals: a) the molecular cascade that drives the diversification of this multipotent cell population, and b) the role ofTbx1therein, are not well defined.Material and methodsWe usedin vitrodifferentiation of WT andTbx1−/−mouse embryonic stem cells into precardiac mesoderm, and performed single cell RNA-seq and ATAC-seq at two differentiation stages. We then used WT andTbx1−/−mouse embryos forin vivovalidation of the key findings.Results and conclusionsWe found that the response to loss of TBX1 is cell sub-population-specific, both in terms of gene expression and chromatin remodeling. We show thatTbx1regulates chromatin accessibility and gene expression of an ancient transcriptional module that orchestrates the development of the trunk, pharynx and heart across evolution. This module is co-regulated and includes genes encoding the conserved transcription factor families of Tea Shirt (Tshz), Sine Oculis (Six), Eye absent (Eya), and Ebf/Collier. Analysis of putative regulatory regions of these genes, which were selected using a machine-learning computational procedure, predicted a feed-forward regulatory relationship between TBX1 and SIX factors that drives or stabilizes the module. Most surprisingly, we found a drift in the differentiation trajectory of theTbx1mutant CPM that led to a relative expansion of cells with epithelial-like transcriptional features in the cell culture model and in mouse embryos. We conclude that TBX1 is a critical factor for maintaining the transcriptional profile of the CPM.