bluuebunny/crossref_metadata_2025_split huggingface dataset:
Prognostic impact of R1 resection margin in synchronous and simultaneous colorectal liver metastasis resection: a retrospective cohort study
Authors: Kim Na Reum , Alhothaifi Essam Dhafer , Han Dai Hoon , Choi Jin Sub , Choi Gi Hong 
Published: June 2023

Abstract
Background
A margin ≥ 1 mm is considered a standard resection margin for colorectal liver metastasis (CRLM). However, microscopic incomplete resection (R1) is not rare since aggressive surgical resection has been attempted in multiple and bilobar CRLM. This study aimed to investigate the prognostic impact of resection margins and perioperative chemotherapy in patients with CRLM.

Methods
A total of 368 of 371 patients who underwent simultaneous colorectal and liver resection for synchronous CRLM between 2006 and June 2017, excluding three R2 resections, were included in this study. R1 resection was defined as either abutting tumor on the resection line or involved margin in the pathological report. The patients were divided into R0 (n = 304) and R1 (n = 64) groups. The clinicopathological characteristics, overall survival, and intrahepatic recurrence-free survival were compared between the two groups using propensity score matching.

Results
The R1 group had more patients with ≥ 4 liver lesions (27.3 vs. 50.0%, P < 0.001), higher mean tumor burden score (4.4 vs. 5.8%, P = 0.003), and more bilobar disease (38.8 vs. 67.2%, P < 0.001) than the R0 group. Both R0 and R1 groups showed similar long-term outcomes in the total cohort (OS, P = 0.149; RFS, P = 0.414) and after matching (OS, P = 0.097, RFS: P = 0.924). However, the marginal recurrence rate was higher in the R1 group than in the R0 group (26.6 vs. 16.1%, P = 0.048). Furthermore, the resection margin did not have a significant impact on OS and RFS, regardless of preoperative chemotherapy. Poorly differentiated, N-positive stage colorectal cancer, liver lesion number ≥ 4, and size ≥ 5 cm were poor prognostic factors, and adjuvant chemotherapy had a positive impact on survival.

Conclusions
The R1 group was associated with aggressive tumor characteristics; however, no effect on the OS and intrahepatic RFS with or without preoperative chemotherapy was observed in this study. Tumor biological characteristics, rather than resection margin status, determine long-term prognosis. Therefore, aggressive surgical resection should be considered in patients with CRLM expected to undergo R1 resection in this multidisciplinary approach era.
Evaluating the distinct pleiotropic effects of omega-3 fatty acids on type 2 diabetes mellitus: a mendelian randomization study
Authors: Hu Chunyan , Zhou Yulin , Wu Xueyan , Jia Xiaojing , Zhu Yuanyue , Zheng Ruizhi , Wang Shuangyuan , Lin Lin , Qi Hongyan , Lin Hong , Li Mian , Wang Tiange , Zhao Zhiyun , Xu Min , Xu Yu , Chen Yuhong , Ning Guang , Borges Maria-Carolina , Wang Weiqing , Zheng Jie , Bi Yufang , Lu Jieli 
Published: June 2023

Abstract
Background
Observational studies and conventional Mendelian randomization (MR) studies showed inconclusive evidence to support the association between omega-3 fatty acids and type 2 diabetes. We aim to evaluate the causal effect of omega-3 fatty acids on type 2 diabetes mellitus (T2DM), and the distinct intermediate phenotypes linking the two.

Methods
Two-sample MR was performed using genetic instruments derived from a recent genome-wide association study (GWAS) of omega-3 fatty acids (N = 114,999) from UK Biobank and outcome data obtained from a large-scale T2DM GWAS (62,892 cases and 596,424 controls) in European ancestry. MR-Clust was applied to determine clustered genetic instruments of omega-3 fatty acids that influences T2DM. Two-step MR analysis was used to identify potential intermediate phenotypes (e.g. glycemic traits) that linking omega-3 fatty acids with T2DM.

Results
Univariate MR showed heterogenous effect of omega-3 fatty acids on T2DM. At least two pleiotropic effects between omega-3 fatty acids and T2DM were identified using MR-Clust. For cluster 1 with seven instruments, increasing omega-3 fatty acids reduced T2DM risk (OR: 0.52, 95%CI 0.45–0.59), and decreased HOMA-IR (β = − 0.13, SE = 0.05, P = 0.02). On the contrary, MR analysis using 10 instruments in cluster 2 showed that increasing omega-3 fatty acids increased T2DM risk (OR:1.10; 95%CI 1.06–1.15), and decreased HOMA-B (β = − 0.04, SE = 0.01, P = 4.52 × 10–5). Two-step MR indicated that increasing omega-3 fatty acid levels decreased T2DM risk via decreasing HOMA-IR in cluster 1, while increased T2DM risk via decreasing HOMA-B in cluster 2.

Conclusions
This study provides evidence to support two distinct pleiotropic effects of omega-3 fatty acids on T2DM risk influenced by different gene clusters, which could be partially explained by distinct effects of omega-3 fatty acids on insulin resistance and beta cell dysfunction. The pleiotropic feature of omega-3 fatty acids variants and its complex relationships with T2DM need to be carefully considered in future genetic and clinical studies.
Re-evaluating the risk factors for radiation pneumonitis in the era of immunotherapy
Authors: Chen Feihu , Niu Jiling , Wang Min , Zhu Hui , Guo Zhijun 
Published: June 2023

AbstractAs one of the common complications of radiotherapy, radiation pneumonia (RP) limits the prognosis of patients. Therefore, better identifying the high-risk factors that lead to RP is essential to effectively prevent its occurrence. However, as lung cancer treatment modalities are being replaced and the era of immunotherapy has arrived, literature that reviews the parameters and mode of radiotherapy, chemotherapy drugs, targeted drugs and current hot immune checkpoint inhibitors related to RP is lacking. This paper summarizes the risk factors for radiation pneumonia by retrieving and analysing previously published literature and the results of large clinical trials. The literature primarily included retrospective analyses, including clinical trials in different periods and a part of the literature review. A systematic literature search of Embase, PubMed, Web of Science, and Clinicaltrials.gov was performed for relevant publications up to 6 Dec. 2022. Search keywords include, but are not limited to, “radiation pneumonia”, “pneumonia”, “risk factors”, “immunotherapy”, etc. The factors related to RP in this paper include physical parameters of radiotherapy, including V5, V20, and MLD; chemoradiotherapy mode and chemotherapy drugs, including paclitaxel and gemcitabine; EGFR-TKI; ALK inhibitors; antiangiogenic drugs; immune drugs and the underlying disease of the patient. We also introduce the possible mechanism of RP. In the future, we hope that this article not only sounds the alarm for clinicians but also helps to identify a method that can effectively intervene and reduce the occurrence of RP, significantly improve the quality of life and prognosis of patients, and more effectively improve the therapeutic effect of radiation therapy.
The interplay between noncoding RNAs and drug resistance in hepatocellular carcinoma: the big impact of little things
Authors: Fang Yuan , Zhang XiaoLi , Huang HanFei , Zeng Zhong 
Published: June 2023

AbstractHepatocellular carcinoma (HCC) is the leading cause of cancer-related death in people, and a common primary liver cancer. Lacking early diagnosis and a high recurrence rate after surgical resection, systemic treatment is still an important treatment method for advanced HCC. Different drugs have distinct curative effects, side effects and drug resistance due to different properties. At present, conventional molecular drugs for HCC have displayed some limitations, such as adverse drug reactions, insensitivity to some medicines, and drug resistance. Noncoding RNAs (ncRNAs), including microRNAs (miRNAs), long noncoding RNAs (lncRNAs) and circular RNAs (circRNAs), have been well documented to be involved in the occurrence and progression of cancer. Novel biomarkers and therapeutic targets, as well as research into the molecular basis of drug resistance, are urgently needed for the management of HCC. We review current research on ncRNAs and consolidate the known roles regulating drug resistance in HCC and examine the potential clinical applications of ncRNAs in overcoming drug resistance barriers in HCC based on targeted therapy, cell cycle non-specific chemotherapy and cell cycle specific chemotherapy.
Mental health and adherence to antiretroviral therapy among Mexican people living with HIV during the COVID-19 pandemic
Authors: Gutiérrez-Velilla Ester , Barrientos-Casarrubias Vania , Gómez-Palacio Schjetnan María , Perrusquia-Ortiz Lydia E. , Cruz-Maycott Rosa , Alvarado-de la Barrera Claudia , Ávila-Ríos Santiago , Caballero-Suárez Nancy Patricia 
Published: June 2023

Abstract
Background
The mental health and medical follow-up of people living with HIV (PLWH) have been disrupted by the COVID-19 pandemic. The objectives of this study were to assess anxiety, depression and substance use in Mexican PLWH during the pandemic; to explore the association of these symptoms with adherence to antiretroviral therapy (ART), and to compare patients with and without vulnerability factors (low socioeconomic level, previous psychological and/or psychiatric treatment).

Methods
We studied 1259 participants in a cross-sectional study, PLWH receiving care at the HIV clinic in Mexico City were contacted by telephone and invited to participate in the study. We included PLWH were receiving ART; answered a structured interview on sociodemographic data and adherence to ART; and completed the psychological instruments to assess depressive and anxiety symptoms and substance use risk. Data collection was performed from June 2020 to October 2021.

Results
84.7% were men, 8% had inadequate ART adherence, 11% had moderate-severe symptoms of depression, and 13% had moderate-severe symptoms of anxiety. Adherence was related to psychological symptoms (p < 0.001). Vulnerable patients were more likely to be women, with low educational level and unemployed (p < 0.001).

Conclusions
It is important to address mental health of PLWH during the COVID-19 pandemic, with special attention to the most vulnerable individuals. Future studies are needed to understand the relationship between mental health and ART adherence.
The POP (Permanent Supportive Housing Overdose Prevention) Study: protocol for a hybrid type 3 stepped-wedge cluster randomized controlled trial
Authors: Doran Kelly M. , Torsiglieri Allison , Blaufarb Stephanie , Hernandez Patricia , Melnick Emily , Velez Lauren , Cleland Charles M. , Neighbors Charles , O’Grady Megan A. , Shelley Donna 
Published: June 2023

Abstract
Background
Permanent supportive housing (PSH)—subsidized housing paired with support services such as case management—is a key part of national strategic plans to end homelessness. PSH tenants face high overdose risk due to a confluence of individual and environmental risk factors, yet little research has examined overdose prevention in PSH.

Methods
We describe the protocol for a hybrid type 3 stepped-wedge cluster randomized controlled trial (RCT) of overdose prevention practice implementation in PSH. We adapted evidence-based overdose prevention practices and implementation strategies for PSH using input from stakeholder focus groups. The trial will include 20 PSH buildings (with building size ranging from 20 to over 150 tenants) across New York City and New York’s Capital Region. Buildings will be randomized to one of four 6-month intervention waves during which they will receive a package of implementation support including training in using a PSH Overdose Prevention (POP) Toolkit, time-limited practice facilitation, and learning collaboratives delivered to staff and tenant implementation champions appointed by each building. The primary outcome is building-level fidelity to a defined list of overdose prevention practices. Secondary and exploratory implementation and effectiveness outcomes will be examined using PSH staff and tenant survey questionnaires, and analysis of tenant Medicaid data. We will explore factors related to implementation success, including barriers and facilitators, using qualitative interviews with key stakeholders. The project is being conducted through an academic-community partnership, and an Advisory Board including PSH tenants and other key stakeholders will be engaged in all stages of the project.

Discussion
We describe the protocol for a hybrid type 3 stepped-wedge cluster RCT of overdose prevention practice implementation in PSH. This study will be the first controlled trial of overdose prevention implementation in PSH settings. The research will make a significant impact by testing and informing future implementation strategies to prevent overdose for a population at particularly high risk for overdose mortality. Findings from this PSH-focused research are expected to be broadly applicable to other housing settings and settings serving people experiencing homelessness.

Trial registration
ClinicalTrials.gov, NCT05786222, registered 27 March 2023.
A systematic review of radiomics in giant cell tumor of bone (GCTB): the potential of analysis on individual radiomics feature for identifying genuine promising imaging biomarkers
Authors: Zhong Jingyu , Xing Yue , Zhang Guangcheng , Hu Yangfan , Ding Defang , Ge Xiang , Pan Zhen , Yin Qian , Zhang Huizhen , Yang Qingcheng , Zhang Huan , Yao Weiwu 
Published: June 2023

Abstract
Purpose
To systematically assess the quality of radiomics research in giant cell tumor of bone (GCTB) and to test the feasibility of analysis at the level of radiomics feature.

Methods
We searched PubMed, Embase, Web of Science, China National Knowledge Infrastructure, and Wanfang Data to identify articles of GCTB radiomics until 31 July 2022. The studies were assessed by radiomics quality score (RQS), transparent reporting of a multivariable prediction model for individual prognosis or diagnosis (TRIPOD) statement, checklist for artificial intelligence in medical imaging (CLAIM), and modified quality assessment of diagnostic accuracy studies (QUADAS-2) tool. The radiomic features selected for model development were documented.

Results
Nine articles were included. The average of the ideal percentage of RQS, the TRIPOD adherence rate and the CLAIM adherence rate were 26%, 56%, and 57%, respectively. The risk of bias and applicability concerns were mainly related to the index test. The shortness in external validation and open science were repeatedly emphasized. In GCTB radiomics models, the gray level co-occurrence matrix features (40%), first order features (28%), and gray-level run-length matrix features (18%) were most selected features out of all reported features. However, none of the individual feature has appeared repeatably in multiple studies. It is not possible to meta-analyze radiomics features at present.

Conclusion
The quality of GCTB radiomics studies is suboptimal. The reporting of individual radiomics feature data is encouraged. The analysis at the level of radiomics feature has potential to generate more practicable evidence for translating radiomics into clinical application.
Type 2 diabetes has a protective causal association with thoracic aortic aneurysm: a Mendelian randomization study
Authors: Zhang Yiran , Li Yongxin , Dai Xiaoyi , Lin Haokai , Ma Liang 
Published: June 2023

Abstract
Background
Observational studies have reported an inverse association of type 2 diabetes (T2D) with thoracic aortic aneurysm (TAA). However, the causality of the association has not been established yet. The present study aims to clarify the causal relationship between T2D and TAA via a Mendelian randomization (MR) approach.

Methods
Causality of associations were assessed using a two-sample MR framework. Genome-wide association study (GWAS) summary statistics were obtained for T2D, glycated hemoglobin (HbA1c), fasting glucose (FG) and fasting insulin (FI) as exposures, and TAA, ascending aortic diameter (AAoD) and descending aortic diameter (DAoD) as outcomes. Four different methods (inverse variance weighted [IVW], weight median, MR-Egger and MR-PRESSO) were used to calculate causal estimates. Heterogeneity and horizontal pleiotropy were assessed using Cochran Q test and MR-Egger regression intercept, respectively.

Results
Genetically predicted T2D was inversely associated with the risk of TAA (OR: 0.931, 95% CI 0.870 to 0.997, p = 0.040, IVW method) and AAoD (Beta: -0.065, 95%CI −0.099 to  − 0.031, p = 1.7e−04, IVW method), but not with DAoD (p > 0.05). Genetically predicted FG level was inversely associated with AAoD (Beta: −0.273, 95% CI −0.396 to –0.150, p = 1.41e−05, IVW method) and DAoD (Beta: −0.166, 95% CI −0.281 to −0.051, p = 0.005, IVW method), but not with TAA (p > 0.05). The effect of genetically predicted HbA1c and FI on TAA, AAoD and DAoD did not reach statistical significance (p > 0.05).

Conclusions
Genetic predisposition to T2D decreases the risk of TAA. Genetically predicted T2D is inversely associated with AAoD, but not with DAoD. Genetically predicted FG level was inversely associated with AAoD and DAoD.
Tora3D: an autoregressive torsion angle prediction model for molecular 3D conformation generation
Authors: Zhang Zimei , Wang Gang , Li Rui , Ni Lin , Zhang RunZe , Cheng Kaiyang , Ren Qun , Kong Xiangtai , Ni Shengkun , Tong Xiaochu , Luo Li , Wang Dingyan , Lu Xiaojie , Zheng Mingyue , Li Xutong 
Published: June 2023

AbstractThree-dimensional (3D) conformations of a small molecule profoundly affect its binding to the target of interest, the resulting biological effects, and its disposition in living organisms, but it is challenging to accurately characterize the conformational ensemble experimentally. Here, we proposed an autoregressive torsion angle prediction model Tora3D for molecular 3D conformer generation. Rather than directly predicting the conformations in an end-to-end way, Tora3D predicts a set of torsion angles of rotatable bonds by an interpretable autoregressive method and reconstructs the 3D conformations from them, which keeps structural validity during reconstruction. Another advancement of our method over other conformational generation methods is the ability to use energy to guide the conformation generation. In addition, we propose a new message-passing mechanism that applies the Transformer to the graph to solve the difficulty of remote message passing. Tora3D shows superior performance to prior computational models in the trade-off between accuracy and efficiency, and ensures conformational validity, accuracy, and diversity in an interpretable way. Overall, Tora3D can be used for the quick generation of diverse molecular conformations and 3D-based molecular representation, contributing to a wide range of downstream drug design tasks.
Graphical Abstract
Hydrophobic surface for direct PEGDA micro-pattern fabrication
Authors: Danielak Anna , Ko Juhee , Islam Aminul , Pedersen David Bue , Lee Jungchul 
Published: June 2023

AbstractPhotopolymerization of hydrogels films has gained interest in many biomedical and industrial fields. Hydrogel micro-patterns fabricated directly on a device are used as filtering barriers, however, due to weak mechanical properties, these parts require a stable support but deposition of hydrogel in non-polymerized state brings a risk of sinking inside the structure. These limitations can be overcome by applying a hydrophobic surface. This paper presents a novel two-step method, in which a hydrophobic surface was designed and manufactured using mask-projection vat photopolymerization additive manufacturing (VPP). Afterwards, PEGDA-based hydrogel photopolymers were deposited on the surface and a micro-scale patterns were cured. The parts were subjected to water immersion and heating in order to evaluate the swelling and shrinking behaviour of hydrogel. The parts remained stable on the substrate and maintained the properties and the results revealed the shape retention over 97%. This work shows that VPP can be applied in the manufacturing of hydrophobic surfaces for hydrogel photopolymer deposition and curing without sacrificing critical properties.
Graphical Abstract
Abdominal wall defect repair with component separation technique for giant omphalocele with previous relaxing incisions on the abdominal skin
Authors: Matsukubo Makoto , Muto Mitsuru , Yamada Koji , Nishida Nanako , Kedoin Chihiro , Matsui Mayu , Nagano Ayaka , Murakami Masakazu , Sugita Koshiro , Yano Keisuke , Onishi Shun , Harumatsu Toshio , Yamada Waka , Kawano Takafumi , Kaji Tatsuru , Ieiri Satoshi 
Published: June 2023

Abstract
Background
The repair of large abdominal wall defects that cannot be closed primarily is quite challenging. The component separation technique (CST) is a surgical approach using autologous tissue to close large abdominal wall defects. The CST requires extensive dissection between the abdominal skin and the anterior sheath of the rectus abdominis muscle. Subsequently, incisions are made at both sides of the external oblique aponeurosis, releasing the external oblique muscle from the internal oblique muscle, and then the right and left rectus abdominis muscles are brought together in the midline for defect closure. However, impairment of blood flow in the abdominal wall skin and necrotic changes are recognized as potential complications.

Case presentation
The CST was performed in a 4-year-old boy with a large ventral hernia who had undergone skin closure with abdominal wall relaxing incisions for the primary treatment of giant omphalocele in the neonatal period. Given his history of incisions on the abdominal wall, he was speculated to be at high risk for postoperative skin ischemia. Dissection was therefore kept to a minimum to preserve the blood supply from the superior and inferior epigastric arteries and perforating branches of those arteries through the rectus abdominis muscle. In addition, care was taken to adjust the muscle relaxant dosage while monitoring the intravesical pressure, ensuring that it did not exceed 20 mmHg to avoid impaired circulation in the abdominal wall caused by abdominal compartment syndrome. He was discharged 23 days after the surgery without any complications, and neither recurrence of the ventral hernia nor bowel obstruction was observed in 4 years.

Conclusions
A giant omphalocele with primary skin closure was treated by applying the CST. The procedure can be performed safely while preserving the blood flow to the abdominal wall, even in patients with a history of relaxing incisions on the abdominal skin. The CST is expected to be effective for repairing the large abdominal wall defects seen in giant omphalocele when primary closure is not possible.