bluuebunny/crossref_metadata_2025_split huggingface dataset:
Cosmological foundations revisited with Pantheon+
Authors: Lane Zachary G , Seifert Antonia , Ridden-Harper Ryan , Wiltshire David L 
Published: November 2024

Abstract
We reanalyse the Pantheon+ supernova catalogue to compare a cosmology with non-FLRW evolution, the timescape cosmology, with the standard ΛCDM cosmology. To this end, we analyse the Pantheon+ for a geometric comparison between the two models. We construct a covariance matrix to be as independent of cosmology as possible, including independence from the FLRW geometry and peculiar velocity with respect to FLRW average evolution. This framework goes far beyond most other definitions of model independence. We introduce new statistics to refine Type Ia supernova (SNe Ia) light-curve analysis. In addition to conventional galaxy correlation functions used to define the scale of statistical homogeneity we introduce empirical statistics which enables refined analysis of the distribution biases of SNe Ia light-curve parameters βc and $\alpha {x_{\lower2pt\hbox{$\scriptstyle 1$}}}$. For lower redshifts, the Bayesian analysis highlights important features attributable to the increased number of low-redshift supernovae, the artefacts of model-dependent light-curve fitting and the cosmic structure through which we observe supernovae. This indicates the need for cosmology-independent data reduction to conduct a stronger investigation of the emergence of statistical homogeneity and to compare alternative cosmologies in light of recent challenges to the standard model. Dark energy is generally invoked as a place-holder for new physics. For the first time, we find evidence that the timescape cosmology may provide a better overall fit than ΛCDM and that its phenomenology may help disentangle other astrophysical puzzles. Our from-first-principles reanalysis of Pantheon+ supports future deeper studies between the interplay of matter and nonlinear spacetime geometry in a data-driven setting.
Constrain spatial curvature and dark energy with strong lenses and complementary probes: a forecast for next-generation surveys
Authors: Hu Yang , Dhawan Suhail 
Published: November 2024

ABSTRACT
Inferring spatial curvature of the Universe with high fidelity is a longstanding interest in cosmology. However, the strong degeneracy between dark energy equation-of-state parameter $w$ and curvature density parameter $\Omega _{\rm K}$ has always been a hurdle for precision measurements of curvature from late-Universe probes. With the imminent commissioning of Vera C. Rubin Observatory’s Legacy Survey of Space and Time (LSST), we demonstrate for the first time, using simulations of stage-IV surveys, the crucial role of time-delay distances from strong gravitational lenses in breaking this degeneracy. Our findings suggest that in non-flat $ow$CDM model, while strong lensing data alone only yield a $\Omega _{\rm K}$ constraint at $\sim \mathcal {O}(10^{-1})$ level, the integration with type Ia supernova and baryon acoustic oscillation data breaks the $w$–$\Omega _{\rm K}$ degeneracy and refines the $\Omega _{\rm K}$ constraint to $\sim \mathcal {O}(10^{-2})$. This surpasses the constraints typically derived from type Ia supernova Hubble diagrams and baryon acoustic oscillation data and is comparable to the constraints obtained from Planck primary cosmic microwave background data. Additionally, we present a non-parametric approach using Gaussian process to avoid parameter-dependence of the expansion history $H(z)$ and achieve similar $\mathcal {O}(10^{-2})$ level constraint on $\Omega _{\rm K}$. This study demonstrates the significant potential of strong gravitational lenses and Stage-IV surveys like LSST to achieve high-fidelity, independent constraints on $\Omega _{\rm K}$, contributing to our understanding of the Universe’s geometry and the dynamics of dark energy.
FunCoup 6: advancing functional association networks across species with directed links and improved user experience
Authors: Buzzao Davide , Persson Emma , Guala Dimitri , Sonnhammer Erik L L 
Published: November 2024

Abstract
FunCoup 6 (https://funcoup.org) represents a significant advancement in global functional association networks, aiming to provide researchers with a comprehensive view of the functional coupling interactome. This update introduces novel methodologies and integrated tools for improved network inference and analysis. Major new developments in FunCoup 6 include vastly expanding the coverage of gene regulatory links, a new framework for bin-free Bayesian training and a new website. FunCoup 6 integrates a new tool for disease and drug target module identification using the TOPAS algorithm. To expand the utility of the resource for biomedical research, it incorporates pathway enrichment analysis using the ANUBIX and EASE algorithms. The unique comparative interactomics analysis in FunCoup provides insights of network conservation, now allowing users to align orthologs only or query each species network independently. Bin-free training was applied to 23 primary species, and in addition, networks were generated for all remaining 618 species in InParanoiDB 9. Accompanying these advancements, FunCoup 6 features a new redesigned website, together with updated API functionalities, and represents a pivotal step forward in functional genomics research, offering unique capabilities for exploring the complex landscape of protein interactions.
TransmiR v3.0: an updated transcription factor-microRNA regulation database
Authors: Liang Maodi , Zhang Chenhao , Yang Yang , Cui Qinghua , Zhang Jun , Cui Chunmei 
Published: November 2024

Abstract
microRNAs (miRNAs) are active in various biological processes by mediating gene expression, and the full investigation of miRNA transcription is crucial for understanding the mechanisms underlying miRNA deregulation in pathological conditions. Here an updated TransmiR v3.0 database is presented with more comprehensive miRNA transcription regulation information, which contains 5095 transcription factor (TF) -miRNA regulations curated from 2285 papers and &gt;6 million TF–miRNA regulations derived from ChIP-seq data. Currently, TransmiR v3.0 covers 3260 TFs, 4253 miRNAs and 514 433 TF–miRNA regulation pairs across 29 organisms. Additionally, motif scanning of TF loci on promoter sequences of miRNAs from multiple species is employed to predict TF–miRNA regulations, generating 284 527 predicted TF–miRNA regulations. Besides the significant growth of data volume, we also improve the annotations for TFs and miRNAs by introducing the TF family, TFBS motif, and expression profiles for several species. Moreover, the functionality of the TransmiR v3.0 online database is enhanced, including allowing batch search for flexible queries and offering more extensive disease-specific, as well as newly sex-specific TF–miRNA regulation networks in the ‘Network’ module. TransmiR v3.0 provides a useful resource for studying miRNA biogenesis regulation and can be freely accessed at http://www.cuilab.cn/transmir.
Single-molecule visualization of sequence-specific RNA binding by a designer PPR protein
Authors: Marzano Nicholas , Johnston Brady , Paudel Bishnu P , Schmidberger Jason , Jergic Slobodan , Böcking Till , Agostino Mark , Small Ian , van Oijen Antoine M , Bond Charles S 
Published: November 2024

Abstract
Pentatricopeptide repeat proteins (PPR) are a large family of modular RNA-binding proteins, whereby each module can be modified to bind to a specific ssRNA nucleobase. As such, there is interest in developing ‘designer’ PPRs (dPPRs) for a range of biotechnology applications, including diagnostics or in vivo localization of ssRNA species; however, the mechanistic details regarding how PPRs search for and bind to target sequences is unclear. To address this, we determined the structure of a dPPR bound to its target sequence and used two- and three-color single-molecule fluorescence resonance energy transfer to interrogate the mechanism of ssRNA binding to individual dPPRs in real time. We demonstrate that dPPRs are slower to bind longer ssRNA sequences (or could not bind at all) and that this is, in part, due to their propensity to form stable secondary structures that sequester the target sequence from dPPR. Importantly, dPPR binds only to its target sequence (i.e. it does not associate with non-target ssRNA sequences) and does not ‘scan’ longer ssRNA oligonucleotides for the target sequence. The kinetic constraints imposed by random 3D diffusion may explain the long-standing conundrum of why PPR proteins are abundant in organelles, but almost unknown outside them (i.e. in the cytosol and nucleus).
The impact of timing of temozolomide chemoradiotherapy for newly diagnosed glioblastoma on patient overall survival: A multicenter retrospective study
Authors: Lau Arthur C K , Chan Brandon L H , Yeung Carly S K , Li Lai-Fung , Chan Danny T M , Lee Michael W Y , Chan Tony K T , Ho Jason M K , Cheung Ka-Man , Tse Teresa P K , Lau Sarah S N , Chow Joyce S W , Ko Natalie M W , Loong Herbert H F , El-Helali Aya , Poon Wai-Sang , Woo Peter Y M 
Published: November 2024

Abstract

Background
The optimal timing of initiating adjuvant temozolomide (TMZ) chemoradiotherapy after surgery in patients with glioblastoma is contentious. This study aimed to determine whether the timing of adjuvant treatment affects their overall survival (OS).

Methods
Consecutive adult patients with histologically-confirmed newly diagnosed glioblastoma treated with adjuvant TMZ chemoradiotherapy across all neurosurgical centers in Hong Kong between 2006 and 2020 were analyzed. The surgery-to-chemoradiotherapy (S-CRT) interval was defined as the date of the first surgery to the date of initiation of adjuvant TMZ chemoradiotherapy.

Results
Four hundred and forty-one patients were reviewed. The median S-CRT interval was 40 days (interquartile range [IQR]: 33–47) and the median overall survival (mOS) was 16.7 months (95% CI: 15.9–18.2). The median age was 58 years (IQR: 50–63). Multivariable Cox regression with restricted cubic splines identified a nonlinear relationship between the S-CRT interval and mOS. Post hoc analysis-derived S-CRT intervals revealed that early CRT (&lt;5 weeks; adjusted hazard ratio [aHR]: 1.11; 95% CI 0.90–1.37) or late CRT (&gt;9–12 weeks; aHR 1.07; 95% CI 0.67–1.71) were not significantly associated with OS. Subgroup analyses for the extent of resection (EOR) and pMGMT methylation status revealed no significant difference in treatment timing on OS.

Conclusion
The timing of adjuvant TMZ chemoradiotherapy, if commenced within 12 weeks after glioblastoma diagnosis, did not influence OS regardless of EOR or pMGMT methylation status. Clinical judgment should be exercised in optimizing the timing of initiating adjuvant therapy.
A Chinese Doctor in Eighteenth-Century Naples and the Practice of Pulse Diagnosis
Authors: Harrison Henrietta 
Published: November 2024

Abstract
Diagnosing a patient on the basis of their pulse alone is an impressive demonstration of medical ability for which early modern Chinese doctors were famous. This article looks at the early history of Chinese medicine in Europe by examining the encounter between Xu Shizhi, who travelled to Naples to study for the Catholic priesthood but became a sensation as a doctor, and Domenico Cirillo, a prominent physician who met him through a patient and became interested in Chinese medicine. Although Chinese pulse manuals had been translated into European languages, the sense of touch is impossible to convey in words, but when Xu met Cirillo, he was able to demonstrate how to feel the pulse. Cirillo then combined elements of Chinese medicine and new vitalist theories of the nervous system to produce a system of his own, published as the Tractatus de pulsibus, which he taught to his students and which became widespread across southern Italy. Recent work on the global circulation of medical ideas in the early modern period has focused on texts and pharmaceuticals, and on encounters in colonial spaces. Xu and Cirillo’s story suggests the importance of personal interactions in conveying tacit knowledge as a key part of this circulation.
CovTransformer: A transformer model for SARS-CoV-2 lineage frequency forecasting
Authors: Feng Yinan , Goldberg Emma E , Kupperman Michael , Zhang Xitong , Lin Youzuo , Ke Ruian 
Published: November 2024

Abstract
With hundreds of SARS-CoV-2 lineages circulating in the global population, there is an ongoing need for predicting and forecasting lineage frequencies and thus identifying rapidly expanding lineages. Accurate prediction would allow for more focused experimental efforts to understand pathogenicity of future dominating lineages and characterize the extent of their immune escape. Here, we first show that the inherent noise and biases in lineage frequency data make a commonly-used regression-based approach unreliable. To address this weakness, we constructed a machine learning model for SARS-CoV-2 lineage frequency forecasting, called CovTransformer, based on the transformer architecture. We designed our model to navigate challenges such as a limited amount of data with high levels of noise and bias. We first trained and tested the model using data from the UK and the USA, and then tested the generalization ability of the model to many other countries and US states. Remarkably, the trained model makes accurate predictions two months into the future with high levels of accuracy both globally (in 31 countries with high levels of sequencing effort) and at the US-state level. Our model performed substantially better than a widely used forecasting tool, the multinomial regression model implemented in Nextstrain, demonstrating its utility in SARS-CoV-2 monitoring. Assuming a newly emerged lineage is identified and assigned, our test using retrospective data shows that our model is able to identify the dominating lineages 7 weeks in advance on average before they became dominant. Overall, our work demonstrates that transformer models represent a promising approach for SARS-CoV-2 forecasting and pandemic monitoring.
Postoperative Complications and Readmission Rates in Robotic-Assisted and Manual Total Hip Arthroplasty
Authors: Howell Cole , Witvoet Sietske , Scholl Laura , Coppolecchia Andrea , Bhowmik-Stoker Manoshi , Chen Antonia F. 
Published: November 2024

Objective:
This study aims to compare 90-day postoperative complications, readmissions, and emergency department (ED) visits between robotic-assisted (RA-THA) and manual (M-THA) total hip arthroplasty.

Methods:
A retrospective review of a multi-hospital database identified primary total hip arthroplasty patients between January 2016 and December 2021. The cohorts were 1-to-1 matched based on patient sex, age, and body mass index resulting in 8033 patients in each cohort (N = 16,066). Odds of 90-day revisits, readmission with >23 hours of observation, and ED visits were compared between cohorts. Complications reported during revisits and readmission were classified according to the Clinical Classification Software schema, using the International Classification of Diseases, 10th Revision codes, and compared using mixed-effect models.

Results:
This study found an overall 90-day revisit rate of 8.3%. RA-THA was associated with significantly reduced odds of revisit within 90 days [odds ratio (OR): 0.71, 95% CI: 0.58–0.89, P = 0.002] and readmissions with >23 hours of observation (OR: 0.61, 95% CI: 0.48–0.77, P < 0.001). RA-THA patients had fewer readmissions with >23 hours of observation due to dislocations (RA-THA: 0.09%; M-THA: 0.39%, P < 0.001), surgical site infections (RA-THA: 0.04%; M-THA: 0.20%, P = 0.004), and wound infections/cellulitis (RA-THA: 0.01%; M-THA: 0.11%, P = 0.021). No difference in ED visits was observed between cohorts (OR: 0.92, 95% CI: 0.77–1.09, P = 0.3). RA-THA patients had more ED visits for dyspnea without pulmonary embolism (RA-THA: 0.20%; M-THA: 0.06%, P = 0.03).

Conclusion:
RA-THA showed significantly lower odds of overall 90-day revisit rates and readmissions with >23 hours of observation, most notably for readmissions due to dislocation and surgical site infection/wound infections. There was no significant difference in the odds of ED visits between cohorts.
Anaphylactic shock reaction caused by the anesthetic drug cyclopofol during general anesthesia: case report and literature review
Authors: Xia Guang , Cui Xiaoyu , Zhou Songhua 
Published: November 2024

Introduction:
Cyclopofol, as an alternative to propofol, is theoretically known as a safe drug and is widely used as a sedative. However, it is important to note that the short history of clinical application of cyclopofol and the rarity of systemic anaphylaxis, there is a lack of understanding that cyclopofol can cause systemic anaphylaxis. To our knowledge, there have been no reported allergic reactions associated with cyclopofol, but we should always be aware of this risk.

Case presentation:
A 47-year-old male patient developed severe hypotension, high airway pressure, decreased oxygen saturation, and rash after intravenous and pump administration of cyclopofol during general anesthesia, and a diagnosis of anaphylactic shock was made based on a skin test 6 weeks later.

Discussion:
This case serves as a reminder that although allergic reactions to cyclopofol are rare, it is important to be aware of such incidents. Therefore, the possibility of an allergic reaction caused by cyclopofol should be considered and always prepared for treatment.

Conclusion:
As a new drug substitute for propofol, cyclopofol should still be used with caution in people with a history of allergies or the possibility of allergies or other uncertain situations on patients.
Clinical Features of Conduction Block in Ulnar Neuropathy at the Elbow: The Surgery of the Ulnar Nerve (SUN) Multicenter Clinical Trial
Authors: Chung Kevin C. , Florczynski Matthew M. , Hearn Sandra L. , Kim Hyungjin M. , Burns Patricia B. , Malay Sunitha ,   For the SUN study group
Published: November 2024

Background:
In ulnar neuropathy at the elbow, weakness is classically a sign of severe disease. Weakness is associated with motor axonal loss as measured by decreased distal compound muscle action potential (CMAP) amplitude. Conduction block, a demyelinating phenomenon that recovers readily, can also cause weakness, creating ambiguity for the treating clinician.

Methods:
This cross-sectional study evaluated baseline blinded data collected from 2020-2023 from the Surgery of the Ulnar Nerve randomized controlled trial comparing in-situ decompression versus transposition procedures. Adult patients underwent electrodiagnostic testing, clinical motor and sensory testing, and completed the Michigan Hand Questionnaire and Carpal Tunnel Questionnaire.

Results:
177 patients were categorized into 3 distinct groups based on normal distal CMAP amplitudes (77 patients), presence of conduction block with or without distal CMAP amplitude loss (37 patients), or pure axonal loss with distal CMAP amplitude loss in the absence of conduction block (63 patients). Compared to the normal group, patients with conduction block had significantly decreased pinch strength and worse function domain scores on the Michigan Hand Questionnaire and Carpal Tunnel Questionnaire, but shorter duration of disease. Patients with pure axonal loss had decreased pinch strength, worse 2-point discrimination, and worse overall, function and aesthetics domain scores on the Michigan Hand Questionnaire. There was a significant interaction between the effects of conduction block and distal CMAP amplitude on pinch strength, indicating that higher degrees of conduction block resulted in more pronounced loss of pinch strength in patients with relatively preserved distal CMAP amplitude.

Conclusions:
Our findings support the paradigm that ulnar neuropathy at the elbow presenting with conduction block represents a distinct and intermediate pathophysiology, distinguished by quicker onset with less advanced neurological deficits.

Level of evidence:
Prognostic Level II
Utilization of Text-to-Image Artificial Intelligence Model in Preoperative Counseling for Lip Lift Procedures
Authors: Huang Ryan S. , Balas Michael , Yan Flora , Wulc Allan E. 
Published: November 2024

Summary:
Text-to-image models powered by artificial intelligence (AI) offer a promising tool for enhancing patients' comprehension of cosmetic surgery outcomes and providing personalized visual forecasts of their appearance after the procedure. This study explores the efficacy of text-to-image AI models, specifically DALL·E2, in improving preoperative counseling for patients undergoing lip lift procedures. Preoperative photographs of four patients, who had given their consent, were processed using DALL·E2, which allows users to modify specific areas of an image and input text descriptions to visualize anticipated changes. We successfully demonstrated the ability of DALL·E2 to generate accurate visual predictions within a short timeframe of two minutes. Selected images provided realistic expectations of the postoperative appearance, aiding in better patient understanding and expectation management.
Experimental Study on Video Discharge Instructions for Pediatric Fever in an Emergency Department
Authors: Luna-Arana Carmen , Castro-Rodríguez Cristina , Jové-Blanco Ana , Mora-Capín Andrea , Ferrero García-Loygorri Clara , Vázquez-López Paula 
Published: November 2024

Background and Objectives:
Fever is a frequent cause of consultation in the pediatric emergency department (PED). Adequate discharge instructions are essential to guarantee good management at home and can reduce caregivers’ anxiety and re-consultations. This study compares the improvement of caregivers’ knowledge regarding fever between verbal discharge instructions and the addition of a video to verbal information. As a secondary outcome, we compared the rate of return visits.

Methods:
An experimental, prospective, single-center study was conducted in a tertiary hospital PED. Patients between 3 months and 5 years old with febrile syndrome were enrolled. Patients with comorbidities or SARS-COV2 infection were excluded. First, caregivers answered a written test concerning fever characteristics, management, and warning signs. Patients were assigned by simple randomization to a control group (standard verbal and written instructions) or to an intervention group (which additionally received video instructions). After discharge, investigators contacted caregivers by telephone. Caregivers were asked to answer the same questions as in the written test in addition to the need for subsequent visits (at the PED or any other healthcare facility) after discharge.

Results:
Seventy-three patients were randomized to the intervention group and 77 to the control group (2 were lost during follow-up). There were no differences in the acquisition of caregiver’s knowledge, with a median score improvement of 2 points in both groups (control group interquartile range (IQR) 1-2; intervention group IQR 1-3) (P = .389). In the intervention group, we observed a significant increase of correct answers in 4 out of 7 questions compared to 3 out of 7 questions in the control group. In the control group, 18.7% reconsulted compared to 10.9% in the intervention group (P = .188).

Conclusions:
Video instructions were not superior to verbal instructions at improving caregivers’ knowledge of fever overall. However, more questions obtained a significant score increase in those that received video and verbal instructions. Our results suggest that the addition of video instructions could help reduce return visits.