bluuebunny/crossref_metadata_2025_split huggingface dataset:
Expertise-informed Generative AI Enables Ultra-High Data Efficiency for Building Generalist Medical Foundation Model
Authors: Yan Bo , Sun Yuqi , Tan Weimin , Gu Zhuoyao , He Ruian , Chen Siyuan , Pang Miao 
Published: January 2024

Abstract
Generalist medical foundation models, pre-trained on massive medical datasets, have shown great potential as the next generation of medical artificial intelligence (AI). However, collecting millions of medical data is extremely expensive, time-consuming, and raises concerns over the high-risk leakage of sensitive private patient information. Here, we present a general framework that enables ultra-high data efficiency in building medical foundation models by leveraging expertise-informed generative AI to scale the limited pre-training dataset. Specifically, we follow this framework and propose a new foundation model DERETFound in ophthalmology, using only 16.7% (150,786 images) of the real-world colour fundus photography images required in the latest retinal foundation model RETFound (904,170 images, Y. Zhou et al, Nature 2023). By integrating expert insights into generative AI, we generate approximately one million synthetic data that are consistent with real retinal images in terms of physiological structures and feature distribution. DERETFound achieves comparable or even superior performance to RETFound on nine public datasets across four downstream tasks, including diabetic retinopathy grading, glaucoma diagnosis, age-related macular degeneration grading, multi-disease classification, and challenging external evaluation. In addition, DERETFound demonstrates competitively high label efficiency, saving over 50% of expert-annotated training data compared to RETFound on datasets for diabetic retinopathy grading. Our data-efficient framework challenges the classic view that building medical foundation models requires the collection of large amounts of real-world medical data as a prerequisite. The framework also provides an effective solution for any other diseases that were once discouraged from building foundation models due to limited data, which has profound significance for medical AI.
Investigating topological valley disclinations using multiple scattering and null-field theories
Authors: Pernas René , Gao Penglin , Zhang Zhiwang , Chistensen Johan 
Published: January 2024

Abstract

Surprisingly, topological metamaterials became a frontier topic in wave physics. What began as a curiosity driven undertaking in condensed matter physics, evolved in serious possibilities to provide topologically resilient guiding of light, sound and vibrations. Topological defects, in the form of disclinations, dislocations, vortices, etc., have capitalized on man-made structures to demonstrate their wave-confining capabilities. In this report, we discuss topological edge and disclination states in valley hall sonic lattices. A prime meta-constituent is the three-legged rod or tripod as its mere rotation enables spatial symmetry breaking. For the most part, this complicated unit is numerically treated with commercially available finite element solvers. Here, we derive the structure factor for plane wave expansions and a null-field method in combination with a multiple scattering theory to study both valley edge and disclination states. We showcase how this method enables rapid evaluation of both spatial and spectral properties related to valley topological sound wave physics.
Climate variability shifts the vertical structure of phytoplankton in the Sargasso Sea
Authors: Viljoen Johannes , Sun Xuerong , Brewin Robert 
Published: January 2024

Abstract

Marine phytoplankton are essential to ocean biogeochemical cycles. Yet, how climate variability is impacting phytoplankton vertical structure remains unclear. Here, we apply a conceptual model that partitions a profile of phytoplankton into two communities – one in the surface mixed layer and one in the subsurface below – to 33 years of data in the Sargasso Sea. Seasonally, the surface community alters their carbon-to-chlorophyll ratio without changing their carbon biomass, whereas the chlorophyll-a and carbon of the subsurface community covaries with no change in their carbon-to-chlorophyll ratio. At the multidecadal scale, climate variability influences these two communities differently. Over the last decade, subsurface phytoplankton biomass has increased in response to warming. In contrast, the surface phytoplankton has altered their carbon-to-chlorophyll without modifying their carbon biomass. Given that satellites can only view the surface ocean, sustained subsurface monitoring is required to understand fully how phytoplankton are responding to climate change.
Comparison between a single dose of PEG G-CSF and multiple doses of non-PEG G-CSF: A systematic review and meta-analysis from Clinical Practice Guidelines for the Use of G-CSF 2022
Authors: Yoshinami Tetsuhiro , Nozawa Kazuki , Yokoe Takamichi , Ozaki Yukinori , Nishio Hiroshi , Tsuchihashi Kenji , Ichihara Eiki , Miura Yuji , Endo Makoto , Yano Shingo , Maruyama Dai , Susumu Nobuyuki , Takekuma Munetaka , Motohashi Takashi , Ito Mamoru , Baba Eishi , Ochi Nobuaki , Kubo Toshio , Uchino Keita , Kimura Takahiro , Kamiyama Yutaro , Nakao Shinji , Nishimoto Hitomi , Kato Yasuhisa , Sato Atsushi , Takano Toshimi 
Published: January 2024

Abstract

Granulocyte colony-stimulating factor (G-CSF) is widely used for the primary prophylaxis of febrile neutropenia (FN). Two types of G-CSF are available in Japan, namely G-CSF chemically bound to polyethylene glycol (PEG G-CSF), which provides long-lasting effects with a single dose, and non-polyethylene glycol-bound G-CSF (non-PEG G-CSF), which must be sequentially administrated for several days. This current study investigated the utility of these treatments for the primary prophylaxis of FN through a systematic review of the literature. A detailed literature search for related studies was performed using PubMed, Ichushi-Web, and the Cochrane Library. Data were independently extracted and assessed by two reviewers. A qualitative analysis or meta-analysis was conducted to evaluate six outcomes. Through the first and second screenings, 23 and 18 articles were extracted for qualitative synthesis and meta-analysis, respectively. The incidence of FN was significantly lower in the PEG G-CSF group than in the non-PEG G-CSF group with a strong quality/certainty of evidence. The differences in other outcomes, such as overall survival, infection-related mortality, the duration of neutropenia (less than 500/µL), quality of life, and pain, were not apparent. Therefore, a single dose of PEG G-CSF is strongly recommended over multiple-dose non-PEG G-CSF therapy for the primary prophylaxis of FN.
A new day 4 embryo evaluation system to predict the formation of transferable blastocyst
Authors: Dai Fangfang , Geng Yasong , Tao Linlin , Li Guozhen , Dai Haoyang , Wang Shusong , Zheng Bo 
Published: January 2024

Abstract
Purpose To explore a day 4 embryo evaluation system based on the potential for the embryo to develop into a transferable blastocyst.
Methods We observed the outcome of blastocyst culture for 1235 embryos from 199 patients. We considered the developmental stage, fragmentation, whether it was in a stage-specific cleavage pattern, and normal fertilization to formulate scoring criteria, based on whether they developed into transferable blastocysts. The receiver operative characteristics(ROC) curve was used to compare the predictive abilities of four criteria for day 4 evaluation to develop into transferable blastocysts and high-quality blastocysts.
Results The developmental stage, fragmentation, normal fertilization and stage-specific cleavage pattern had the greatest impact on the formation of transferable blastocysts. There were significant differences in the formation rates of transferable blastocysts and high-quality blastocysts among different embryo grades. The areas under ROC curves of the day 4 embryo evaluation criteria constructed in this study was the highest in predicting transferable blastocyst formation, relative to the other three evaluation criteria.
Conclusion This study observed the presence of pseudo-compacted embryos similar to cleavage-stage embryos. The Day 4 embryo evaluation criteria constructed in this study can effectively predict the formation of transferable blastocysts.
Lead isotopes of prehistoric copper tools define metallurgical phases in Eneolithic Italy
Authors: Artioli Gilberto , Angelini Ivana , Canovaro Caterina , Kaufmann Guenther , Villa Igor 
Published: January 2024

Abstract
The diffuse presence of small copper ore deposits in the Alpine area, mostly exploited since Late Medieval times, led most scholars to assume that these deposits may actually be active much earlier and that many of the circulating prehistoric metal objects found in the area were produced with local copper sources. This assumption was recently validated for the Recent Bronze Age through the use of lead isotope tracers, and well supported by the archaeometallurgical evidences found in the South-Eastern Alps. However, the scarcity of available lead isotope data for pre-Bronze Age metals precluded to date the reconstruction of the metal flow through the Eneolithic (or Copper Age). Based on 49 new artefact analyses, here we show that the Northern Italian Copper Age (approximately 3500 − 2200 BC) includes three major periods of metal production, each related to specific ore sources. The Alpine copper was massively used only starting from the middle of the 3rd millennium BC, in connection or slightly earlier than the Beaker event.
Engineered Treg Donor Cell Therapy to Prevent Graft-Versus-Host Disease
Authors: Meyer Everett , Pavlova Anna , Muffly Lori , Sutherland Katherine , Bader Cameron , Bharawaj Sushma , Dahiya Saurabh , Frank Matthew , Arai Sally , Johnston Laura , Miklos David , Rezvani Andrew , Shiraz Parveen , Sidana Surbhi , Shizuru Judith , Weng Wen-kai , Agrawal Vaibhav , Putnam Amy , Ferhnoff Nathaniel , Tamaresis John , Lu Ying , McClellan Scott , Lowsky Robert , Negrin Robert , error error ,   error2 error2,   error3 error3
Published: January 2024

Abstract

Allogeneic hematopoietic cell transplantation (HCT) is a curative therapy limited by graft-versus-host disease (GVHD). Donor regulatory T cells (Tregs) appear to prevent GVHD and promote healthy immunity. We have developed a high-precision Treg cell therapy manufactured from donor mobilized peripheral blood. We conducted an open-label, single-center, phase 2 efficacy study investigating if the use of a precision engineered donor Treg cell therapy improves one-year GVHD-free relapse free survival (GRFS) after myeloablative transplantation. Thirty-three patients with HLA-matched donors were enrolled. All donor Treg cell products were successfully manufactured and administered fresh within 72 hours. One-year incidence of acute grade III-IV GVHD of 6%, moderate to severe chronic GVHD of 7% and non-relapse mortality rate of 6%. The primary endpoint of significantly improved one-year GRFS was achieved at 67% for HLA-matched patients compared to a predicted 40% (p < 0.002). Trial participants had a reduced incidence of GVHD and improved GRFS, as compared to rates common to highly variable unmanipulated donor grafts and multi-agent immune suppression.
Detailed mechanisms for unintended large DNA deletions with CRISPR, base editors, and prime editors
Authors: Bae Sangsu , Hwang Gue-Ho , Lee Seok-Hoon , Oh Minsik , Kim Segi , Habib Omer , Jang Hyeon-Ki , Kim Heon Seok , Kim Chan Hyuk , Kim ﻿Sun 
Published: January 2024

Abstract

CRISPR-Cas9 nucleases are versatile tools for genetic engineering cells and function by producing targeted double-strand breaks (DSBs) in the DNA sequence. However, the unintended production of large deletions (> 100 bp) represents a challenge to the effective application of this genome-editing system. We optimized a long-range amplicon sequencing system and developed a k-mer sequence-alignment algorithm to simultaneously detect small DNA alteration events and large DNA deletions. With this workflow, we determined that CRISPR-Cas9 induced large deletions at varying frequencies in cancer cell lines, stem cells, and primary T cells. With CRISPR interference screening, we determined that end resection and the subsequent TMEJ [DNA polymerase theta-mediated end joining] repair process produce most large deletions. Furthermore, base editors and prime editors also generated large deletions despite employing mutated Cas9 “nickases” that produce single-strand breaks. Our findings reveal an important limitation of current genome-editing tools and identify strategies for mitigating unwanted large deletion events.
Non-zero sum stochastic differential game between two insurance companies under the variance premium principle
Authors: Mwigilwa Winfrida 
Published: January 2024

Abstract
This paper considers a non-zero-sum stochastic differential game between two competitive companies where both companies aim to seek the optimal investment and reinsurance strategies. Furthermore, these two companies are allowed to purchase proportional reinsurance to mitigate the company's claim risks and, at the same time, invest in one risk-free asset and one risky asset whose price dynamics follow the geometric Brownian motion and take dividend payments into account. In particular, under the proportional reinsurance contract, the reinsurance premium is assumed to be calculated via the variance value principle instead of the expected value principle. The optimal reinsurance and investment strategies of both companies can be determined by solving the Fleming-Bellman-Isaacs equations for an exponential utility function. In the end, several numerical simulations were conducted to show how model parameters affect equilibrium reinsurance and investment strategies, and some conclusions about economics from these findings were deduced.
JEL Classification: C73 , D53 , G11 , G22
MSC Classification: 91A15 , 93E20 , 91G15 , 97M30
A systems biology-based study to assess the effects of TNF-α ± apigenin in triple-negative breast cancer cell line
Authors: Amjad Elham , Asnaashari Solmaz , Sokouti Babak , Dastmalchi Siavoush 
Published: January 2024

Abstract
Background: Triple-negative breast cancer (TNBC) refers to the type of breast cancer with no estrogen, progesterone, and HER2 receptors. Various methods can be applied to treating patients with BC, among which the therapeutic-based ones without toxic side effects are extremely important. In this study, we computationally investigated the impact of apigenin on the TNBC cell line as traditional Chinese medicine.
Materials and methods: We retrieved the GSE120550 dataset from the NCBI-GEO database. The BRB-array tools employed pre- and post-processing approaches to identify significant differentially expressed genes. Additionally, the DAVID web server was applicable to analyze the three main components, including the "biological process," "cellular component," and "molecular function," as well as the KEGG signaling pathway. Finally, using the Venn diagram, we thoroughly investigated the number of shared genes among fifteen groups constructed from six compared sample sets.
Results: The primary analysis of six pairs of samples reveals significant DEGs, which are prone to be ranked in the TOPPGene web server in terms of priority. The identified genes that play vital roles in inhibiting the progression of BC enrich various signaling pathways. Then, protein-protein interaction network analysis revealed the involved biomarkers and the inhibitory effect of apigenin among fifteen possible sets constructed from the six groups in pairs. Conclusion: The outcomes of the current study showed and confirmed the inhibitory effect of apigenin with no toxic side effects on patients with TNBC. This natural product can also target future therapeutics and novel drug designs.
Dataset of hospital admissions authorizations in Brazil
Authors: Souto Gabriel , Kreischer Vinicius , Saldanha Raphael , Cardoso Carlos , Paixão Balthazar , Ribeiro Victor , Gritz Raquel , Carraro Lucas , Cruz Sérgio , Bonifácio Carmen , Miloski Matheus , Alencar Gizelton , Marques Aline , Alves Ariane , Neto Nelson , Salles Rebecca , Lima Jefferson , Pedroso Marcel 
Published: January 2024

Abstract
Objective: Hospital admissions data is an important source of information for health surveillance and health policy makers. The Brazilian Health Ministry offers access to this data in scattered files using a legacy format, justifying the effort of this work to present this data in a unique, coherent and comprehensible format and infrastructure, suitable to its big data dimension and importance.
Data Description: The produced dataset covers hospital admissions in the Brazilian Universal Health System as a whole, keeping the characteristics of the original files and additional new variables with valuable enrichments to understand the data better.
Exploring Rules Engines as an Artificial Intelligence Application in Medicine: A Scoping Review
Authors: Alnattah Ashraf , Jajroudi Mahdie , Eslami Saeid 
Published: January 2024

Abstract
Background
The past decade has witnessed significant efforts toward optimizing medical care through the incorporation of technology and artificial intelligence (AI) tools. Rules engines have emerged as key applications in this transformative process, aiming to enhance the quality and efficiency of healthcare systems.
Objective
This scoping review aims to provide a comprehensive overview of the research conducted on rules engines within the medical literature, focusing on their functionalities, the types of tasks they can perform, the evaluated clinical outcomes, and the technologies employed in clinical practice.
Methods
This review adhered to the Arksey and O'Malley framework and followed the PRISMA-ScR checklist (Preferred Reporting Items for Systematic Reviews and Meta-Analyses Extension for Scoping Reviews). A systematic search of the PubMed and Scopus databases was conducted, using specific eligibility criteria. The study included English publications that focused on the utilization of rules engines in medicine.
Results
Nineteen studies met the inclusion and exclusion criteria. The articles exhibited heterogeneity in scope and employed various types of rules engines, encompassing a limited range of medical domains. Several types of rules engines were identified, each contributing to the improvement of clinical outcomes. Descriptive formative designs were employed in ten out of nineteen (53%) articles. The studies primarily targeted chronic diseases and medical practices requiring special attention, such as diabetes mellitus (DM), adverse drug events (ADEs), and pediatric intensive care unit (ICU) settings. The most frequently utilized rules engine was Drools.
Conclusions
The scarcity of published studies on the potential utilization of rules engines in medicine is evident. However, all included studies in this review demonstrated the advantages of incorporating rules engines into medical care, resulting in positive clinical outcomes across various domains. We recommend the adoption of rules engines in healthcare centers, integrating them into daily workflows to deliver convenient, scalable, and effective clinical care. This review serves as a valuable resource for healthcare managers, providers, and patients, facilitating the achievement of more efficient and error-free healthcare environments.
Evaluation of the Pathological Complete Response (pCR) as a Surrogate Endpoint of Neoadjuvant Chemotherapy: Real-World Evidence
Authors: Antonini Marcelo , Mattar Andre , Richter Fernanda Grace Bauk , Pannain Gabriel Duque , Ramos Marcellus do Nascimento Moreira , Teixeira Marina Diogenes , Amorim Andressa Gonçalves , Pinheiro Denise Joffily Pereira da Costa , Ferraro Odair , Lopes Reginaldo Guedes Coelho , Gebrim Luiz Henrique , Real Juliana Monte 
Published: January 2024

Abstract
Purpose
Neoadjuvant chemotherapy (NAC), which in the past was only used only in for locally advanced disease, is currently being used upfront, especially in to treat aggressive breast cancer (BC). Real-world data (RWD) can address important research questions based on daily routine daily cancer care. The objective of this study was to characterize the pathological complete response (pCR) and its relationship with overall survival (OS) and disease-free survival (DFS) in BC patients with BC who received NAC at a Brazilian public reference center, a. And also to characterize the relationship between pCR and the BC subtypes, of BC and DFS and OS.
Methods
This was a retrospective cohort study based on a large BC database from a women’s health reference center for women’s health in Brazil. Patients with BC diagnosed between 2011 and 2020 were included if they received NAC. Data on regarding demographics, cancer-related information, treatment-related information, pCR, OS and DFS were collected. Survival analyses were performed using the semiparametric Kaplan‒Meier method to assess OS and DFS by using pCR status, considering BC diagnosis as the index date.
Results
A total of 1601 patients were included. BC patients were on average 49 years old and presented with stage IIIa disease (35%). Most patients had invasive nonspecial- type (NST) disease (94%);, and 86.7% of patients had a the Ki-67 index was ≥ 14 in 86.7% of patients. The overall pCR rate was 22.7%;, and pCR was observed more frequently in triple-negative and luminal B subtypes. A significant proportion of pCR patients were alive (89% vs. 61%, log-rank p < 0.0001) and had a greater DFS status (90% vs. 66%, log-rank p < 0.0001). Only Luminal A patients did not have a association of better worse OS and DFS associated with pCR.
Conclusions
Updated real-world data on for BC patients who received NAC in this Brazilian cohort have showedn that a 22.7%the pCR rate was 22.7% for all cancer subtypes and stages. Only Luminal A patients’ pCR status was not didn’t have associatedion of with a better OS and or DFS with pCR.