bluuebunny/crossref_metadata_2025_split huggingface dataset:
Sctensor detects many-to-many cell–cell interactions from single cell RNA-sequencing data
Authors: Tsuyuzaki Koki , Ishii Manabu , Nikaido Itoshi 
Published: November 2023

Abstract
Background
Complex biological systems are described as a multitude of cell–cell interactions (CCIs). Recent single-cell RNA-sequencing studies focus on CCIs based on ligand–receptor (L–R) gene co-expression but the analytical methods are not appropriate to detect many-to-many CCIs.

Results
In this work, we propose , a novel method for extracting representative triadic relationships (or hypergraphs), which include ligand-expression, receptor-expression, and related L–R pairs.

Conclusions
Through extensive studies with simulated and empirical datasets, we have shown that can detect some hypergraphs that cannot be detected using conventional CCI detection methods, especially when they include many-to-many relationships. is implemented as a freely available R/Bioconductor package.
DNA methylation on C5-Cytosine and N6-Adenine in the Bursaphelenchus xylophilus genome
Authors: Liu Zhenkai , Li Yongxia , Zhang Xingyao 
Published: November 2023

Abstract
Background
The pinewood nematode is the causal agent of the pine wilt disease, which causes severe ecological and economic losses in coniferous forests. The invasion of pine wood nematode has undergone various rapid adaptations to a wide range of temperatures and to new hosts and vector insects. DNA methylation may play crucial roles in the rapid adaptation of PWN during invasion. However, whether the PWN genome contins functional DNA modifications remains elusive.

Results
Here, we detected the extensive presence of 5-methylcytosine (5mC) and N6-methyladenine (6mA) in the B. xylophilus genome, with low methylation levels at most positions. Cytosines were methylated in the CpG, CHG. and CHH sequence contexts, with the lowest methylation levels at CpG sites. The methylation levels of CpG and 6mA in gene regions showed opposite trends. The changes in the abundance of 5mC and 6mA showed the same trends in response to temperature change, but opposite trends during development. Sequence and phylogenetic analyses showed that the proteins BxDAMT and BxNMAD have typical characteristics of a methylase and demethylase, respectively, and are conserved among species.

Conclusions
These findings shed light on the epigenetic modifications present in the genome of PWN, and will improve our understanding of its invasiveness and evolution.
A shorter distal resection margin is a surrogate marker of nodal metastasis and poor prognosis in distal gastrectomy for advanced gastric cancer
Authors: Takashima Yusuke , Komatsu Shuhei , Nishibeppu Keiji , Ohashi Takuma , Kosuga Toshiyuki , Konishi Hirotaka , Shiozaki Atsushi , Kubota Takeshi , Fujiwara Hitoshi , Otsuji Eigo 
Published: November 2023

Abstract
Background
Although a 3–5 cm surgical margin distance is recommended for advanced gastric cancer (GC) in Japanese guidelines, little is known about the clinical effects of the surgical margin, especially the distal resection margin (DM). This study aims to clarify the clinical significance of DM in GC.

Methods
A total of 415 GC patients who underwent curative distal gastrectomy between 2008 and 2018 were analyzed retrospectively.

Results
The DM significantly stratified recurrence-free survival (P = 0.002), and a DM < 30 mm was an independent factor of a poor prognosis (P = 0.023, hazard ratio: 1.91). Lymphatic recurrence occurred significantly more frequently in the DM < 30 mm group than in the DM ≥ 30 mm group (P = 0.019, 6.9% vs. 1.9%). Regarding the station No.6 lymph node metastases in advanced GC (DM < 30 mm vs. 30 mm ≤ DM ≤ 50 mm vs. DM > 50 mm), the number (P < 0.001, 1.42 ± 1.69 vs. 1.18 ± 1.80 vs. 0.18 ± 0.64), the positive rate (P < 0.001, 59.0% vs. 46.7% vs. 11.3%) and therapeutic value index (43.3 vs. 14.5 vs. 8.0) were significantly higher in the DM < 30 mm group. By subdivision using the DM distance of 30 mm, more segmented prognostic stratifications were possible (P < 0.001).

Conclusions
A DM of less than 30 mm could be a surrogate marker of poor RFS, especially increasing nodal recurrence. More intensive treatment strategies, including lymphadenectomy and chemotherapy, are needed for patients with this condition.
Exploring how members of the public access and use health research and information: a scoping review
Authors: Heaton-Shrestha Celayne , Hanson Kristin , Quirke-McFarlane Sophia , Delaney Nancy , Vandrevala Tushna , Bearne Lindsay 
Published: November 2023

AbstractBackgroundMaking high-quality health and care information available to members of the general public is crucial to support populations with self-care and improve health outcomes. While attention has been paid to how the public accesses and uses health information generally (including personal records, commercial product information or reviews on healthcare practitioners and organisations) and how practitioners and policy-makers access health research evidence, no overview exists of the way that the public accesses and uses high quality health and care information.PurposeThis scoping review aimed to map research evidence on how the public accesses and uses a specific type of health information, namely health research and information that does not include personal, product and organisational information.MethodsElectronic database searches [CINAHL Plus, MEDLINE, PsycInfo, Social Sciences Full Text, Web of Science and SCOPUS] for English language studies of any research design published between 2010–2022 on the public’s access and use of health research or information (as defined above). Data extraction and analysis was informed by the Joanna Briggs Institute protocol for scoping reviews, and reported in accordance with the PRISMA extension for scoping reviews.ResultsThe search identified 4410 records. Following screening of 234 full text studies, 130 studies were included. One-hundred-and-twenty-nine studies reported on the public’s sources of health-research or information; 56 reported the reasons for accessing health research or information and 14 reported on the use of this research and information. The scoping exercise identified a substantial literature on the broader concept of ‘health information’ but a lack of reporting of the general public’s access to and use of health research. It found that ‘traditional’ sources of information are still relevant alongside newer sources; knowledge of barriers to accessing information focused on personal barriers and on independent searching, while less attention had been paid to barriers to access through other people and settings, people’s lived experiences, and the cultural knowledge required.ConclusionsThe review identified areas where future primary and secondary research would enhance current understanding of how the public accesses and utilises health research or information, and contribute to emerging areas of research.
Estimating the effect of timing of earned income tax credit refunds on perinatal outcomes: a quasi-experimental study of California births
Authors: Karasek Deborah , Batra Akansha , Baer Rebecca J. , Butcher Brittany D. Chambers , Feuer Sky , Fuchs Jonathan D. , Kuppermann Miriam , Gomez Anu Manchikanti , Prather Aric A. , Pantell Matt , Rogers Elizabeth , Snowden Jonathan M. , Torres Jacqueline , Rand Larry , Jelliffe-Pawlowski Laura , Hamad Rita 
Published: November 2023

Abstract
Background
The largest poverty alleviation program in the US is the earned income tax credit (EITC), providing $60 billion to over 25 million families annually. While research has shown positive impacts of EITC receipt in pregnancy, there is little evidence on whether the timing of receipt may lead to differences in pregnancy outcomes. We used a quasi-experimental difference-in-differences design, taking advantage of EITC tax disbursement each spring to examine whether trimester of receipt was associated with perinatal outcomes.

Methods
We conducted a difference-in-differences analysis of California linked birth certificate and hospital discharge records. The sample was drawn from the linked CA birth certificate and discharge records from 2007–2012 (N = 2,740,707). To predict eligibility, we created a probabilistic algorithm in the Panel Study of Income Dynamics and applied it to the CA data. Primary outcome measures included preterm birth, small-for-gestational age (SGA), gestational diabetes, and gestational hypertension/preeclampsia.

Results
Eligibility for EITC receipt during the third trimester was associated with a lower risk of preterm birth compared with preconception. Eligibility for receipt in the preconception period resulted in improved gestational hypertension and SGA.

Conclusion
This analysis offers a novel method to impute EITC eligibility using a probabilistic algorithm in a data set with richer sociodemographic information relative to the clinical and administrative data sets from which outcomes are drawn. These results could be used to determine the optimal intervention time point for future income supplementation policies. Future work should examine frequent income supplementation such as the minimum wage or basic income programs.
Introduction and acceptability of the Surveillance Outbreak Response Management and Analysis System (SORMAS) during the COVID-19 pandemic in Côte d’Ivoire
Authors: Barth-Jaeggi Tanja , Houngbedji Clarisse A. , Palmeirim Marta S. , Coulibaly Daouda , Krouman Aboubakar , Ressing Cordula , Wyss Kaspar 
Published: November 2023

Abstract
Background
The Surveillance Outbreak Response Management and Analysis System (SORMAS) has been implemented for various infectious diseases since 2015. 2020, at the beginning of the COVID-19 pandemic, SORMAS was adapted to SARS-CoV2.

Methods
We assessed the acceptability and usability of SORMAS and accompanied its implementation in two pilot regions of Côte d’Ivoire (Abidjan 2 and Gbêkê) from July/August 2021 to March 2022. We conducted 136 semi-structured interviews to cover knowledge on COVID-19, information on conventional surveillance systems for disease monitoring including COVID-19, acceptability of SORMAS, and impact of SORMAS on epidemic preparedness and surveillance. Scores before and 6–8 months after implementation were compared.

Results
SORMAS was implemented in two pilot regions in Côte d’Ivoire. The conventional software for the surveillance of the COVID-19 pandemic by the company MAGPI was maintained in parallel; the additional time needs to enter and manage the data in SORMAS were the main concern. SORMAS acceptance and satisfaction scores were high after the user training, which was prior to implementation, and after 6–8 months of use. The ability of SORMAS to improve COVID-19 preparedness and early detection of cases and contacts was widely acknowledged. To keep the understanding and skills of users up-to-date, regular refresher trainings were requested. The expectation to be able to make decisions based on data produced by SORMAS was high at baseline and the perceived experience after several months of use of the software was very positive. Unfortunately, the link with the laboratories could not be established in the pilot regions, but it is an existing feature of SORMAS that many users were asking for. Following the positive experience using SORMAS for COVID-19, the pilot regions expanded its use for monitoring and management of measles, yellow fever, meningitis, and cholera.

Conclusion
SORMAS was very well accepted by users and decision makers in the two pilot regions of Côte d’Ivoire and its ability to improve epidemic preparedness and surveillance was acknowledged. If the hurdles of maintenance (tablets, server, and maintaining user skills) are handled sustainably, it can serve as a valid tool to identify, surveil and manage future outbreaks of various infectious diseases in Côte d’Ivoire.
Socioeconomic inequality in teenage pregnancy in Papua New Guinea: a decomposition analysis
Authors: Li Hao , Pu Yiran , Li Zhen , Jin Ziyang , Jiang Yi 
Published: November 2023

Abstract
Background
Teenage pregnancy is a global public health issue, and it poses a serious threat to the health and socioeconomic status of mothers and their newborn children. Although Papua New Guinea has recorded one of the highest teenage pregnancy rates among Asia-Pacific countries, few studies have conducted research on the related inequality in the country. Therefore, this study aimed to assess socioeconomic inequality in teenage pregnancy and its contributing factors in Papua New Guinea.

Methods
Data for this cross-sectional study were obtained from the 2016–2018 Papua New Guinea Demographic and Health Survey. The analytical sample consisted of 2,864 girls aged 15–19 years. We employed Erreygers normalized concentration index (ECI) and concentration curves to measure and depict socioeconomic inequality in teenage pregnancy. Decomposition analysis was likewise performed to identify the contributions of determinants to the observed inequality.

Results
Weighted ECI for teenage pregnancy was − 0.0582 (P < 0.001), thereby indicating that teenage pregnancy in Papua New Guinea is disproportionately concentrated among poor girls. Decomposition analysis suggested that education level (65.2%), wealth index (55.2%), early sexual debut (25.1%), region (8.5%), and sex of household head (4.1%) are the main determinants explaining the pro-poor socioeconomic inequality in teenage pregnancy.

Conclusions
A pro-poor socioeconomic inequality of teenage pregnancy was present in Papua New Guinea. This inequality may be alleviated by such interventions as ensuring that teenage girls receive education; implementing poverty alleviation projects, eliminating child, early, and forced marriages; strengthening promotion for household head to support teenagers in accessing sexual and reproductive health education; improving geographical accessibility to health facilities on contraceptive services, and taking necessary precautions and responses to sexual misconduct.
Self-rated health impact of COVID 19 confinement on inmates in Southeastern of Europe: a qualitative study
Authors: Sánchez-Recio Raquel , Samper-Pardo Mario , Llopis-Lambán Rebeca , Oliván-Blázquez Bárbara , Cerdan-Bernad Marta , Magallón-Botaya Rosa 
Published: November 2023

Abstract
Introduction
The COVID-19 pandemic necessitated the implementation of various measures within closed institutions like prisons to control the spread of the virus. Analyzing the impact of these measures on the health of inmates is crucial from a public health perspective. This study aimed to explore inmates’ subjective perception of the COVID-19 lockdown, the implemented measures, their physical self-perception, and their views on the vaccination process.

Method
Between April 2021 and January 2022, 27 semi-structured individual interviews and 1 focus group were conducted with inmates in a prison located in northwest Spain. The interviews were conducted in person and audio-recorded. Thematic content analysis was employed, utilizing methodological triangulation to enhance the coherence and rigor of the results.

Results
The analysis revealed two main themes and nine subthemes. The first theme focused on inmates’ perception of the implementation of protective measures against COVID-19 within the prison and its impact on their well-being. The second theme explored the pandemic’s emotional impact on inmates. All participants reported negative consequences on their health resulting from the measures implemented by the institution to contain the pandemic. However, they acknowledged that measures like lockdowns and mass vaccination helped mitigate the spread of the virus within the prison, contrary to initial expectations.

Conclusion
COVID-19 and related measures have directly affected the health of inmates. To improve their health and minimize the impact of pandemic-induced changes, community participation and empowerment of individuals are essential tools, particularly within closed institutions such as prisons.
Complications analysis of Ilizarov bone transport technique in the treatment of tibial bone defects–a retrospective study of 199 cases
Authors: Feng Dongwei , Zhang Yaxin , Jia Heping , Xu Guogang , Wu Weize , Yang Fan , Ding Jianan , Li Dong , Wang Kang , Luo Yongjie , Liu Xin , Guo Qi , Zong Zhiguo 
Published: November 2023

Abstract
Background
The clinical treatment of long bone defets in the extremities caused by trauma, infection, tumours, and nonunion has been a challenge for orthopaedic surgeons. Bone transport techniques have become the only way to treat such bone defects. However, inevitable difficulties and complications related to bone transport techniques have been reported in many studies.

Aim
The purpose of this study was to investigate the risk factors for complications and the effectiveness of the Ilizarov bone transport technique in the treatment of tibial bone defects.

Methods
The study was conducted in 199 patients who underwent treatment with the Ilizarov bone transport technique at our institution from May 2012 to September 2019. Patient demographic data, complications and clinical outcomes after a minimum of 2 years of follow-up were collected and retrospectively analysed. Additionally, a risk factor analysis was performed for the top three major complications. The clinical outcomes were evaluated using the Association for the Study and Application of the Method of Ilizarov (ASAMI) criteria at the last clinical follow-up.

Results
A total of 199 patients underwent follow-up for 12–40 months, with an average of 23.5 months, and all achieved bone healing. A total of 310 complications occurred, with an average of 1.04 minor complications and 0.48 major complications per patient. The top three complications were pin tract infection in 48 cases (61.3%), axial deviation in 86 cases (43.2%), and delayed union in 50 cases (25.13%). Multivariate analysis showed that the bone defect length (P = 0.02, OR = 5.489), the number of previous surgeries (P = 0.003, OR = 2.204), and the external fixation index (P = 0.01, OR = 1.202) were significantly correlated with pin tract infection. Bone defects of the middle 1/3 (P < 0.001, OR = 23.769), the bone defect length (P < 0.001, OR = 2.776), and the external fixation index (P < 0.001, OR = 1.154) were significantly correlated with axial deviation. The bone defect length (P = 0.003, OR = 1.242), soft tissue defects (P = 0.013, OR = 0.312) and bone defects of the distal 1/3 (P = 0.023, OR = 4.257) were significantly correlated with delayed healing. The ASAMI bone score at the last follow-up showed a rate of excellent and good bone results of 95.48% and a rate of excellent functional results of 87.94%.

Conclusion
The Ilizarov bone transfer technique is an effective method for treating tibial bone defects, and shortening the treatment period can reduce the incidence of complications. Older patients and those with longer bone defects, a higher external fixation index, more previous operations, and defects of the middle and distal 1/3 had a higher incidence of complications.
Pullout strength of different pedicle screws after primary and revision insertion: an in vitro study on polyurethane foam
Authors: Wu Lien-Chen , Hsieh Yueh-Ying , Tsuang Fon-Yih , Kuo Yi-Jie , Chen Chia-Hsien , Chiang Chang-Jung 
Published: November 2023

Abstract
Background
Surgeons are routinely required to remove loose or failed pedicle screws and insert a new screw in their place. However, inserting a new screw into an existing hole may compromise the holding capacity of the pedicle screw. The purpose of this study is to evaluate the pullout strength of pedicle screws with different thread designs after the primary insertion and revision surgery in a synthetic bone model.

Methods
Four pedicle screws with different thread designs (single-lead-thread (SLT) screw, dual-lead-thread (DLT) screw, mixed-single-lead-thread (MSLT) screw, and proximal-unthreaded-dual-thread (PUDL) screw) were inserted into pre-drilled, untapped holes (ø 4.2 mm, length 35 mm) in Sawbone blocks of density 20 pcf. In the first sequence, a 6.0 mm screw was inserted into the predrilled foam block and the primary pullout strength of the screw was measured according to ASTM F543. In the second sequence, a 6.0 mm screw was inserted and removed, and then either a 6.5 mm screw of the same design or a different screw design was inserted into the same hole and the pullout strength recorded.

Results
In the first sequence, the mean pullout strength of the MSLT screw was significantly (p < 0.05) greater than all other screw designs. In the second sequence, when the MSLT screw was the primary screw, using a larger MSLT screw (6.5 mm) as the revision screw did not lead to a higher pullout strength than if a 6.0 mm diameter PUDL screw was used for the revision. Using a larger DLT screw (6.5 mm) as the revision screw resulted in a significantly (p < 0.05) greater pullout strength than a 6.0 mm STL, DLT, MSLT, or PUDL screw.

Conclusions
Our results indicate that employing classic oversizing of the same screw design is a safe choice for maintaining screw purchase in the bone after revision. In cases where oversizing with the same screw design is not practical, opting for a PUDL screw with the same original diameter can provide enough purchase in the bone to maintain stability.
Super pulsed thulium fiber laser outcomes in retrograde intrarenal surgery for ureteral and renal stones: a systematic review and meta-analysis
Authors: Almasoud Nazal A. , Safar Omar , Elatreisy Adel , Alshahrani Saad Thamer , Libdah Saud Bin , Alkhaldi Sulaiman M. , Alsoliman Nezar F. , Alderaan Abdulrahman M. , Abdel-Al Ibrahim , Abouelgreed Tamer A. , Alabeedi Mohammed , Al-Aown Abdulrahman 
Published: November 2023

Abstract
Background
Laser lithotripsy using a thulium fiber laser (TFL) has become an effective treatment option for small renal stones with low complication rates. TFL has a higher absorption coefficient, smaller fibers, and better pulse rate capability.

Methods
We conducted a systematic review and meta-analysis to evaluate the published evidence regarding TFL's lithotripsy performance in retrograde intrarenal surgery (RIRS), for which we primarily assessed the outcomes of stone-free rate, operation time, and complications. We searched different databases from inception to April 2023. We assessed the methodological quality and risk of bias using the Cochrane Risk of Bias tool for randomized trials and the ROBINS-I tool for non-randomized studies. We used a random-effects model for meta-analysis and assessed heterogeneity using the I2 statistic.

Results
Twelve published studies evaluated the efficacy of RIRS using a TFL for treating renal and ureteral stones. The meta-analysis revealed a predicted stone-free rate of 89.37% (95% CI: 83.93% to 93.12%), indicating that, on average, approximately 89.37% of patients achieved a stone-free state after treatment. The substantial heterogeneity among the studies was evident, as shown by a Q-value of 33.1174 and a p-value of 0.0003. The I2 value of 69.80% (95% CI: 25.91% to 92.02%) highlighted the proportion of variability attributed to genuine heterogeneity across the studies. Moreover, the H2 value 3.31 (95% CI: 1.35 to 12.53) indicated significant heterogeneity beyond random chance. The estimated overall effect size (logit-transformed) of 2.1289 was highly statistically significant (z = 8.7648, p < 0.0001) with a confidence interval of 1.6528 to 2.6049. The reported complications varied across studies, encompassing Clavien grade I–II complications in most cases, with a subset experiencing more severe Clavien grade III–V complications. Additionally, other studies noted a range of complications, such as haematuria, fever, transient creatinine elevation, and postoperative issues like bleeding, pain, and sepsis.

Conclusion
This meta-analysis suggests that RIRS using TFL is an effective and safe treatment option for renal and ureteral stones, with high stone-free and low complication rates. The included studies exhibited a low risk of bias and were of high quality. However, more extensive randomized controlled trials with extended follow-up periods are needed to investigate this technique's efficacy and safety.