bluuebunny/crossref_metadata_2025_split huggingface dataset:
From Voxels to Prognosis: AI-Driven Quantitative Chest CT Analysis Forecasts ICU Requirements in 78 COVID-19 Cases
Authors: Bumm Rudolf , Zaffino Paolo , Lasso Andras , Estépar Raúl San José , Pieper Steven , Wasserthal Jakob , Spadea Maria Francesca , Latshang Tsogyal , Kawel-Böhm Nadine , Wäckerlin Adrian , Werner Raphael , Hässig Gabriela , Furrer Markus , Kikinis Ron 
Published: July 2023

Abstract
Background: The current study aimed to investigate the distribution and extent of lung involvement in patients with COVID-19, assess the relationship between lung involvement and the need for intensive care unit (ICU) admission and compare the performance of computer analysis with the judgment of radiological experts.
Methods: A total of 81 patients from an open-source COVID database with confirmed COVID-19 infection were included in the study. Three patients were excluded. Lung involvement was assessed in 78 patients using computed tomography (CT) scans, and the extent of infiltration and collapse was quantified across various lung lobes and regions. The associations between lung involvement and ICU admission were analyzed. Additionally, the computer analysis of COVID-19 involvement was compared against the expert rating provided by a radiological expert.
Results: The results showed a higher degree of infiltration and collapse in the left lower lobe compared to the upper lobe (p < 0.05) and a similar pattern in the right lower lobes (p < 0.05). No significant difference was detected in the COVID-19-related involvement of the left and right lower lobes. The right middle lobes demonstrated lower involvement compared to the right lower lobes (p < 0.05). When examining the regions, no significant difference in COVID-19 involvement was found when comparing the anterior and posterior lungs. The middle third displayed greater COVID-19 involvement than the upper and lower thirds. Patients requiring ICU admission during their inpatient treatment exhibited significantly higher COVID-19 involvement in their lung parenchyma according to computer analysis, compared to patients who remained in general wards. Patients with more than 40% COVID-19 involvement were almost exclusively treated in intensive care. A high correlation was observed between computer detection of COVID-19 affections and expert rating by radiological experts.
Conclusion: The findings suggest that the extent of lung involvement, particularly in the lower lobes and middle third, may be associated with the need for ICU admission in patients with COVID-19. Computer analysis showed a high correlation with expert rating, highlighting its potential utility in clinical settings for assessing lung involvement. This information may help guide clinical decision-making and resource allocation during ongoing or future pandemics. Further studies with larger sample sizes are warranted to validate these findings.
Long-term trends of nasopharyngeal carcinoma mortality in China from 2006 to 2020 by region and sex: An age-period-cohort analysis
Authors: Guo Xinru , Cui Jiameng , Yuan Xin , Gao Zibo , Yu Ge , Wu Hao , Kou Changgui 
Published: July 2023

Abstract
Background: China has a high mortality from nasopharyngeal carcinoma (NPC). The NPC mortality trends in China from 2006 to 2020 were described and analyzed to understand its epidemiological characteristics by region and sexand to explore age, period, and cohort effects.
Methods: A joinpoint regression model was used to fit the standardized NPC mortality and age-specific mortality. The age-period-cohort model was used to investigate age, period, and cohort effects on the NPC mortality risk.
Results: The results showed that the NPC mortality rate in China has been declining steadily. From 2006 to 2020, the standardized NPC mortality rate in most age groups showed a significant downward trend. The annual percentage change was smaller in rural areas than in urban areas. The mortality risks of rural malesand rural females from 2016 to 2020 were 1.139 times and 1.080 times those from 2011 to 2015, respectively. The risk of NPC death in urban males born in 1984-1988 and in rural males born in 1979-1983 both showed an increasing trend.
Conclusions: The strategies for preventing and treating NPC in China were effective from 2006 to 2020, but the findings indicate that people in rural areas need more targeted interventions to reduce NPC deaths.
Menstrual blood-derived mesenchymal stem cells combined with collagen I gel as a regenerative therapeutic strategy for degenerated disc after discectomy
Authors: Yu Li , Wu Honghao , Hu Xiaojian , Wu Yuxu , Zhou Jinhong , Zeng Shumei , Yuan Li , Xiang Charlie , Feng Zhiyun 
Published: July 2023

Abstract
Background:
Annulus fibrosis (AF) defects have been identified as the primary cause of disc herniation relapse and subsequent disc degeneration following discectomy. Stem cell-based tissue engineering offers a promising approach for structural repair. Menstrual blood-derived mesenchymal stem cells (MenSCs), a type of adult stem cell, have gained attention as an appealing source for clinical applications due to their potential for structure regeneration, ease of acquisition, and low immunogenicity.
Methods:
The differential potential of MenSCs cocultured with AF cells was examined by the expression of collagen I, SCX, and CD146 using immunofluorescence. Western blot and ELISA were used to examine the expression of TGF-β and IGF-I in coculture system. An injectable gel containing MenSCs was fabricated and its repairment properties was evaluated in a discectomy animal model (Sprague-Dawley rats, males, 8 weeks old). Disc degeneration was assessed via magnetic resonance (MR) imaging and histological staining. Immunohistochemical analysis was performed to assess the expression of aggrecan, MMP13, TGF-β and IGF-I in disc. Apoptosis in the disc was evaluated using TUNEL staining.
Results:
Coculturing MenSCs with AF cells demonstrated their ability to express collagen I and biomarkers of AF cells. Moreover, the coculture system led to upregulation of the growth factors TGF-β and IGF-I. After 12 weeks, discs treated with MenSCs gel exhibited significantly lower Pffirrmann scores (2.29 ± 0.18), compared to discs treated with MenSCs (3.43 ± 0.37, p < 0.05) or gel (3.71 ± 0.29, p < 0.01) alone. There is significant higher MR index in disc treated with MenSCs gel than that treated with MenSCs (0.51 ± 0.05 vs 0.24 ± 0.04, p < 0.01) or gel (0.51 ± 0.05 vs 0.26 ± 0.06, p < 0.01) alone. Additionally, MenSCs gel demonstrated preservation of the structure of degenerated discs as indicated by histological scoring (5.43 ± 0.43 vs 9.71 ± 1.04 in MenSCs group and 10.86 ± 0.63 in gel group, both p < 0.01), increased aggrecan expression, and decreased MMP13 expression in vivo. Furthermore, the percentage of TUNEL-positive cells in the disc treated with MenSCs Gel (26.59%) was significantly lower than those treated with gel alone (55.77%, p < 0.01) and MenSCs alone (50.95%, p < 0.01). The expression of TGF-β and IGF-I was higher in discs treated with MenSCs gel or MenSCs alone than in those treated with gel alone.
Conclusion:
MenSCs embedded in collagen I gel has the potential to preserve the disc structure and prevent disc degeneration after discectomy, which was probably attributed to the paracrine of growth factors of MenSCs.
Improving Information Extraction from Pathology Reports using Named Entity Recognition
Authors: Zeng Ken G. , Dutt Tarun , Witowski Jan , GV Kranthi Kiran , Yeung Frank , Kim Michelle , Kim Jesi , Pleasure Mitchell , Moczulski Christopher , Lopez L. Julian Lechuga , Zhang Hao , Harbi Mariam Al , Shamout Farah E. , Major Vincent J. , Heacock Laura , Moy Linda , Schnabel Freya , Pak Linda M. , Shen Yiqiu , Geras Krzysztof J. 
Published: July 2023

Abstract
Pathology reports are considered the gold standard in medical research due to their comprehensive and accurate diagnostic information. Natural language processing (NLP) techniques have been developed to automate information extraction from pathology reports. However, existing studies suffer from two significant limitations. First, they typically frame their tasks as report classification, which restricts the granularity of extracted information. Second, they often fail to generalize to unseen reports due to variations in language, negation, and human error. To overcome these challenges, we propose a BERT (bidirectional encoder representations from transformers) named entity recognition (NER) system to extract key diagnostic elements from pathology reports. We also introduce four data augmentation methods to improve the robustness of our model. Trained and evaluated on 1438 annotated breast pathology reports, acquired from a large medical center in the United States, our BERT model trained with data augmentation achieves an entity F1-score of 0.916 on an internal test set, surpassing the BERT baseline (0.843). We further assessed the model's generalizability using an external validation dataset from the United Arab Emirates, where our model maintained satisfactory performance (F1-score 0.860). Our findings demonstrate that our NER systems can effectively extract fine-grained information from widely diverse medical reports, offering the potential for large-scale information extraction in a wide range of medical and AI research. We publish our code at https://github.com/nyukat/pathology_extraction.
Patient's punctuality in an outpatient clinic: the role of age, medical branch and geographical factors
Authors: Cerruti Benedetta , Garavaldi Davide , Lerario Alberto 
Published: July 2023

Abstract
Background
The efficiency of the management of an outpatient clinic largely depends on the administration of patient flows and waiting times increase costs and affect clinical quality. In this study, we verify if the visit acceptance times are influenced by demographic or geographical factors in a large cohort of patients referred to a city and suburban private outpatient multidisciplinary clinic.
Methods
We included all scheduled visits of patients aged from 18 to 75 years who arrived in 2021, 2022 and 2023 in our private outpatient clinics, consisting of 34 medical clinics scattered in Milan metropolitan city and hinterland. The variables collected were age, visit time, check-in time, address of the medical clinic and its distance from the closest underground station, patient typology (new business vs. follow-up patient), and the medical branch of the visit. Outcome is ’punctuality’, defined as visit time minus check-in time (in minutes).
Results
We considered a sample of 410.808 visits from January 2021 to April 2023. The majority of patients check-in early (84.4%) and we found that the percentage of punctual patients increases linearly with age. Earlier hours in the morning show the worst punctuality pattern as well as blood draws in the analysis of different medical branches. We also observed that patients who already had some activity recorded in our systems show the worst pattern of punctuality. No particular differences emerged considering the geographical location of the clinics.
Conclusions
Younger patients have worse punctuality than older patients. Moreover, earlier hour slots are the most disadvantaged and the medical specialty has an influence on the arrival habits. This data should be considered for better clinical quality and efficiency.
Recruitment Strategies and Consent Rates in a National Prospective Colorectal Cancer Screening Cohort: Results from Year 1 of the Voyage Study
Authors: Yost Kathleen J. , Carlson Rachel E. , Kirt Christine R. , Kirsch Emily J. , Kneedler Bonny , Laffin Jennifer J. , Sauver Jennifer L. St. , Rutten Lila J. Finney , Grimm Jessica A. , Olson Janet 
Published: July 2023

Abstract
Background: Adherence to recommended colorectal cancer (CRC) screening among US adults is below the public health target of 80%. The multi-target stool DNA assay (mt-sDNA) is a self-administered CRC screening test that may remove barriers to adherence. To improve understanding of long-term outcomes and the real-world impact of mt-sDNA screening, Mayo Clinic and Exact Sciences Laboratories are collaborating on a prospective cohort study of CRC incidence and mortality outcomes in individuals screened with mt-sDNA. We conducted an embedded experiment to identify the optimal incentive protocol for maximizing participation while managing study costs.
Methods: A subset of the opt-in cohort was randomized to receive postage stamps as a pre-consent incentive, or as a post-consent incentive after completion of the consent and questionnaire. Descriptive statistics from year one of recruitment, as well as the incentive experiment, are reported.
Results: During year 1 of the Voyage trial, a total of 600,258 individuals with mt-sDNA orders received at Exact Sciences Laboratories were randomly selected and invited to participate. Of those, 26,429 (4.4%) opted in, 14,365 of whom (54.3%) consented. The opt-in and consent samples were similar to the target population with respect to sex but differed by geographic residence and age (p<0.001). For the embedded incentive experiment, 2,333 were randomized to the pre-incentive arm while 2,342 were randomized to the post-incentive arm. Overall consent rate in the incentive trial was 56.4% (60.9% for the pre-consent incentive arm (1421/2333) vs. 52.0% for the post-consent incentive arm (1217/2432), p<0.001). A cost reduction was observed for the pre-consent incentive group. Higher response rates were seen among older vs. younger individuals, reflecting a common pattern in healthcare-related survey research participation. Age adjusted incidence rates for CRC have been shown to vary regionally; thus, adjustment for differential response by region will be important to ensure representativeness.
Conclusions: CRC incidence and mortality vary with age; thus, adjusting for differential participation by age will be important in analyses of Voyage data. Pre-consent incentive option was associated with a higher participation rate and lower costs, and will be used for the remainder of the study recruitment.
Trial Registration: NCT04124406; October 11th, 2019
NCOA4 mediated ferritinophagy induced ferroptosis regulates radiosensitivity and prognosis of glioma
Authors: Gao Lianxuan , Ren Chen , Hu Shushu , zeng Yingying , Tang Nan , Chen Chen , Feng Wenqing , Zhang Qinghua , Xie Dehuan , Tan Peixin , Liu Yantan , Du Shasha 
Published: July 2023

Abstract
Aims
Gliomas are generally resistant to ionizing radiation. Ferroptosis is an important cause of cancer cell death caused by ionizing radiation. However, it is not clear how ferroptosis regulates the radiosensitivity of glioma.
Methods
In vitro, we verified the effect of ferroptosis on radiosensitivity of glioma cells, and tested the effect of NCOA4-mediated ferritinophagy on ferroptosis. The effect of NCOA4 on the prognosis of glioma patients treated with radiotherapy was analyzed using public databases, and the possible action pathways of NCOA4 were analyzed by bioinformatics. In vivo experiments, we again verified the effect of ferroptosis on radiosensitivity of glioma and the radiosensitivity change of glioma after knocking down NCOA4.
Results
We have demonstrated through experiments that both ferroptosis and autophagy promote the radiosensitivity of glioma cells. Bioinformatics analysis shows that ferritinophagy selective cargo receptor NCOA4 is highly expressed in gliomas with good prognosis, while patients with low expression of NCOA4 have poor prognosis after radiotherapy. Meanwhile, through experimental verification, low expression of NCOA4 is associated with poor prognosis in gliomas, while high expression is associated with good prognosis. Through analysis of the NCOA4 related pathways, we demonstrate that NCOA4 regulates the radiosensitivity and prognosis of gliomas by regulating the key gene ACSL4 for ferroptosis sensitivity. Ferroptosis promotes radiosensitivity in gliomas and is dependent on NCOA4 mediated ferritinophagy.
Navigating relationship dynamics, pregnancy and fatherhood in the Bukhali trial: a qualitative study with men in Soweto, South Africa
Authors: Draper Catherine E , Motlhatlhedi Molebogeng , Mabasa Jackson , Headman Tshepang , Klingberg Sonja , Pentecost Michelle , Lye Stephen J , Norris Shane A , Nyati Lukhanyo H 
Published: July 2023

Abstract
Background: South Africa has a complex range of historical, social, political, and economic factors that have shaped fatherhood. In the context of the Bukhali randomised controlled trial with young women in Soweto, South Africa, a qualitative study was conducted with the male partners of young women who had become pregnant during the trial. This exploratory study aimed to explore individual perceptions around relationship dynamics, their partner’s pregnancy, and fatherhood of partners of young women in Soweto, South Africa.
Methods: Individual, in-depth interviews were conducted with male partners (fathers, n=19, 25-46 years old) of Bukhali participants. A thematic approach was taken to the descriptive and exploratory process of analysis, and three final themes and subthemes were identified: 1) relationship dynamics (nature of relationship, relationship challenges); 2) pregnancy (feelings about the pregnancy, effect of the pregnancy on their relationship, providing support during pregnancy; and 3) fatherhood (view of fatherhood, roles of fathers, influences on views and motivation, challenges of fatherhood).
Results: While most male participants were in a committed (“serious”) relationship with their female partner, less than half of them were cohabiting. Most reported that their partner’s pregnancy was not planned, and shared mixed feelings about the pregnancy (e.g., happy, excited, shocked, nervous), although their views about fatherhood were overwhelmingly positive. Many were concerned about how they would economically provide for their child and partner, particularly those who were unemployed. Participants identified both general and specific ways in which they provided support for their partner, e.g., being present, co-attending antenatal check-ups, providing material resources. For many, the most challenging aspect of fatherhood was having to provide financially. They seemed to understand the level of responsibility expected of them as a father, and that their involvement and presence related to love for and connection with their child. Participants’ responses indicated that there were some changes in the norms around fatherhood, suggesting that there is a possibility for a shift in the fatherhood narrative in their context.
Conclusions: These findings suggest that the complex array of factors influencing fatherhood in South Africa continue to play out in this generation, although promising changes are evident.
Purification Scheduling Control for Throughput Maximization in Quantum Networks
Authors: Xue Kaiping , Xiao Zirui , Li Jian , Yu Nenghai , Li Ruidong , Sun Qibin , Lu Jun 
Published: July 2023

Abstract

Quantum networks can establish End-to-End (E2E) entanglement connections between two arbitrary nodes for various quantum applications through entanglement swapping. To support quantum applications reliably, quantum networks should establish E2E entanglement connections with desired entanglement fidelity by performing entanglement purification. The existing works provide mechanisms for link-level purification, which, however, leads to low throughput because of lacking consideration on purifications at network-level. (That is, efficiently allocating scarce resources to jointly purify entanglements under the situation with multiple concurrent requests in a network remains a critical but unsolved problem.) To address this problem, we analyze the cost of purification, design the E2E fidelity calculation method in detail, and propose a novel approach called Purification Scheduling Control (PSC). The basic idea of PSC is to determine the appropriate purification through jointly optimizing purification and resource allocation processes based on conflict avoidance. We conduct extensive experiments showing that PSC can maximize throughput under the fidelity requirement. This solution should spur the development of more applied reliable routing designs for quantum networks, combining quantum error correction, quantum applications, and computer network theory.
Causes of death after first time venous thromboembolism
Authors: Lonnberg Frida , Roos Andreas , Farm Maria , Heurlin André , Okas Mantas , Gigante Bruna , Siddiqui Anwar J 
Published: July 2023

Abstract

Background: Causes of death after first time community-acquired venous thromboembolism (VTE) diagnosed in unselected patients at the emergency department (ED) was investigated.
Material and Methods: The study consists of all patients>18 years of age who had a visit for any medical reason to any of 5 different ED in Stockholm County, Sweden from 1st January 2016 to 31st December 2017. We have identified all patients with a first registered incident VTE; deep vein thrombosis (DVT) and/or pulmonary embolism (PE) during the study period.
Cox regression models were used to estimate hazards ratios (HR) with 95% confidence intervals (CIs) for all-cause mortality and cause-specific death in patients with DVT or PE using all other patients as the reference group.
Results: In total, 409,971 patients had an ED visit during the study period of whom 2% were diagnosed with VTE (DVT= 4,817, PE= 3,147). During a mean follow up of 2.6 years, 1265 (16%) and 25,191 (6.3%) patients died within the VTE and reference group, respectively. The adjusted risk of all-cause mortality was nearly double in patients with DVT (HR 1.7; 95% CI, 1.5-1.8) and 3-fold in patients with PE (HR 2.8; 95% CI, 2.6-3.0). While the risk of cancer related death was nearly 3-fold in patient with DVT (HR 2.7; 95% CI, 2.4-3.1), and 5-fold in PE (HR 4.6; 95% CI, 4.1-5.1 respectively). A diagnosis of PE at the ED visit was associated with a 50% increased risk of cardiovascular death (HR 1.50; 95% CI, 1.2-1.9).
Conclusion: Patients with VTE have a high risk of all-cause mortality including cardiovascular death. The study findings indicate that cardiovascular preventive measures have to be improved in patients with VTE.
Osteoprotegerin and Vascular Dysfunction in Patients With Stage 3 Chronic Kidney Disease and Those Without Renal Dysfunction: a Case-control Study (Nefrovasc Study)
Authors: Matos Thalita Oliveira , Vitorino Priscila Valverde Oliveira , Orlow Rogério , Melo Átila Oliveira , Amorim Diogo Silva , Sousa Gleidson Junio Oliveira , Jorgetti Vanda , Sousa Ana Luiza Lima , Bezerra Rodrigo , Barroso Weimar Sebba Kunz 
Published: July 2023

Abstract
Background: Osteoprotegerin (OPG) is a marker of vascular calcification and cardiovascular (CV) risk in patients with chronic kidney disease (CKD). The study aimed to compare OPG values with flow-mediated dilation (FMD) and pulse wave velocity (PWV) and to evaluate the correlation between these measures in patients in stage 3 CKD and those without renal dysfunction.
Methods: This case-control study was conducted in a specialized hypertension clinic in 2022. A total of 79 patients over 18 years of age participated in the study. The case group consisted of 30 patients who had moderate renal dysfunction (CKD stage 3a and 3b) and the control group included 49 individuals with GFR ≥60 ml/min/1.73 m2. For the comparative analysis between patients with and without renal dysfunction, qualitative variables were analyzed using the chi-square test, while quantitative variables were evaluated using the independent t-test or Mann-Whitney test. The linear correlation between OPG and the other variables was analyzed using Pearson's or Spearman's correlation tests.
Results: Central pulse pressure (cPP), PWV, and augmentation index (AIx) were higher in patients with renal dysfunction. The serum OPG level positively correlated with peripheral and central systolic blood pressure (BP), PPc, PWV, and AIx. Conversely, the serum OPG did not correlate with FMD.
Conclusions: OPG and PWV are possible biomarkers of vascular dysfunction that are altered in patients with moderate renal dysfunction. This study is has limitations: is a case-control study conducted at a single center with a small number of patients with CKD.