bluuebunny/crossref_metadata_2025_split huggingface dataset:
Risk factors for metachronous colorectal cancer and advanced neoplasia following primary colorectal cancer: A systematic review and meta-analysis
Authors: Zhang Ye , Karahalios Amalia , Aung Ye Kyaw , Win Aung Ko , Boussioutas Alex , Jenkins Mark A. 
Published: June 2023

Abstract
Background
Identifying risk factors for metachronous colorectal cancer (CRC) and metachronous advanced neoplasia could be useful for guiding surveillance and cancer prevention. We conducted a systematic review and meta-analysis to investigate the risk factors for metachronous CRC and advanced neoplasia.
Methods
Searches were conducted in MEDLINE, Embase, Web of Science and Cochrane Central Registry of Controlled Trials. Random effects models were fitted to estimate the association between the investigated risk factors and metachronous CRC or advanced neoplasia.
Results
22 articles were included in the systematic review. The risks of metachronous CRC or advanced neoplasia were higher if the first CRC was diagnosed in the presence of a synchronous advanced lesion (pooled risk ratio (RR) from 3 studies: 3.61, 95% confidence interval (CI): 1.44–9.05; and pooled RR from 8 studies: 2.77, 95% CI: 2.23–3.43, respectively). The risk of metachronous CRC was lower, but the risk of metachronous advanced neoplasia was higher if the first CRC was distal (compared with proximal) (pooled RR from 3 studies: 0.48, 95% CI: 0.23–0.98; and pooled RR from 2 studies: 2.99, 95% CI: 1.60–5.58 respectively). The risk of metachronous advanced neoplasia increased with age (pooled RR from 3 studies: 1.07 per year of age, 95% CI: 1.03–1.11). There was no evidence that any lifestyle risk factors studied were associated with the risk of metachronous CRC or advanced neoplasia.
Conclusions
Identified risk factors for metachronous CRC and advanced neoplasia might be useful to tailor the existing surveillance guidelines after the first CRC.
Integrating cfDNA Liquid Biopsy and Organoid-Based Drug Screening Reveals PI3K Signaling as a Promising Therapeutic Target in Colorectal Cancer
Authors: YANG HUAN , Xiao Xing , Zeng Leli , Zeng Haiteng , Wang Jingshu , Li Guanghua , Dai Weigang , He Yulong , Wang Suihai , Peng Jianjun , Chen Wei 
Published: June 2023

Abstract
Background The current model of precision medicine relay on biomarkers, which are mainly obtained through next generation sequencing (NGS). However, this model failed to find effective drugs for most cancer patients. The current study tried to combine liquid biopsy with functional drug test through organoid models to find potential drugs for cancer patients.Methods CRC patients were prospectively enrolled and blood samples were collected from patients start of treatment. Targeted deep sequencing of cfDNA samples was performed using a 14-gene panel. Gastrointestinal (GI) cancer organoids were established and PI3K and mTOR inhibitors were evaluated on organoid models.Results A total of 195 mutations were detected across 58 cfDNA samples. The most frequently mutated genes were KRAS, TP53, PIK3CA, and BRAF, all of which exhibited higher mutation rates than tissue biopsy. Although 81% of variants had an allele frequency of less than 1%, certain mutations in KRAS, TP53, and SMAD4 had high allele frequencies exceeding 10%. Notably, among the seven patients with high allele frequency mutations, six had metastatic tumors, indicating that a high allele frequency of ctDNA could potentially serve as a biomarker of later-stage cancer. A high rate of PIK3CA mutation (31 out of 67, or 46.3%) was discovered in CRC patients, suggesting possible tumor progression mechanisms and targeted therapy opportunities. To evaluate the value of anti PI3K strategy in GI cancer, different lines of GI cancer organoids were established. The organoids recapitulated the morphologies of the original tumors. Organoids were generally insensitive to PI3K inhibitors. However, CRC-3 and GC-4 showed response to mTOR inhibitor Everolimus, and GC-3 was sensitive to PI3Kδ inhibitor Idelalisib. The CRC organoid with a PIK3CA mutation showed greater sensitivity to the PI3K inhibitor Alpelisib than wildtype organoids, suggesting potential treatment options for the corresponding patients.Conclusion Liquid biopsy holds significant promise for improving precision treatment and tumor prognosis in colorectal cancer patients. The combination of biomarker-based drug prediction with organoid-based functional drug sensitivity assay may lead to more effective cancer treatment.
Exploratory biological coordinate analysis on 2,4-epi-brassinolide-induced the size change of leaf angle in tobacco seedlings
Authors: He Hui , Xiao Junchen , Zhang Yang , Dai Huawei , Dong Xiaowei , Ma Ruhui , Shi Yi , Sun Yanguo , Zhang Yan 
Published: June 2023

Abstract
Leaf angle (LA) is one of the most important agronomic trait of plant architecture for crop yield. 2,4-epibrassinolide (EBR) is a bioactive form of brassinosteroids (BRs) and plays a significant role in influencing plant architecture, including the regulation of LA. To investigate the effect of EBR on the size of LA in tobacco seedlings, we performed a histochemical and molecular characterization of LA by spraying differential concentrations of EBR, T1(1×10− 8mol/L), T2 (1×10− 5 mol/L) and CK (0 mol/L). The results showed that compared with CK, EBR could significantly enlarge the size of LA in T1 and T2, respectively (increased 38.6% and 37.3%), especially by promoting cell area (increased 95.2% and 185%) and inhibiting cell division (cell number in per unit area reduced 16.4% and 41.8%). The relative expression levels of NtBIN2, NtEXPA28, and NtCYCD1 was consistent correlation with the size of LA. Through detection the representative genes of IAA, GA, BR biosynthesis and signaling pathway, the coordinate relationship of these hormones were evaluated. It showed a positive correlation of EBR concentration with the genes of IAA biosynthesis (NtYUCCA8), GA biosynthesis (NtGA20), BR signaling pathway (NtBRI1, NtBES1), IAA signaling pathway (NtGH3.2 and NtLC3), and a negative correlation with cell cycle (NtCYCD2, NtCYCD3, and NtCYCD5). In conclusion, exogenously application of EBR enlarge the size of LA in tobacco seeding via increasing the cell area by modulating the IAA, GA biosynthesis and IAA, BR signaling and restraining the cell division by cell cycle regulation.
Lattice dynamics and carrier recombination in GaAs/GaAsBi nanowires
Authors: Jansson M. , Nosenko V. V. , Rudko G. Yu. , Ishikawa F. , Chen W. M. , Buyanova I. A. 
Published: June 2023

Abstract
GaAsBi nanowires represent a novel and promising material platform for future nano-photonics. However, the growth of high-quality GaAsBi nanowires and GaAsBi alloy is still a challenge due to a large miscibility gap between GaAs and GaBi. In this work we investigate effects of Bi incorporation on lattice dynamics and carrier recombination processes in GaAs/GaAsBi core/shell nanowires grown by molecular-beam epitaxy. By employing photoluminescence (PL), PL excitation, and Raman scattering spectroscopies complemented by scanning electron microscopy, we show that increasing Bi-beam equivalent pressure (BEP) during the growth does not necessarily result in a higher alloy composition but largely affects the carrier localization in GaAsBi. Specifically, it is found that under high BEP, bismuth tends either to be expelled from a nanowire shell towards its surface or to form larger clusters within the GaAsBi shell. Due to these two processes the bandgap of the Bi-containing shell remains practically independent of the Bi BEP, while the emission spectra of the NWs experience a significant red shift under increased Bi supply as a result of the localization effect.
Some like it burnt: species differences in small mammal assemblage in a Mediterranean-basin nearly 3 years after a major fire
Authors: Tomassini Orlando , Aghemo Anna , Baldeschi Benedetta , Bedini Gianni , Petroni Giulio , Giunchi Dimitri , Massolo Alessandro 
Published: June 2023

Abstract

The Habitat Accommodation Model (HAM) predicts wildlife community recovery based on vegetation structure. However, studies on HAM in the Mediterranean basin are scarce. Here, we described the assemblage of small mammals in a Mediterranean area ~ 3 years after a fire, specifically examining three functional small mammalian categories: ground-foraging insectivorous, ground-foraging herbivorous/granivorous and arboreal-foraging species. The study was conducted in Monte Pisano (Italy), where a September 2018 fire burned ~ 12 km2. A stratified random sampling was adopted, basing on burnt status and forest type. In each site, during late spring-summer 2021, hair-tube sampling was conducted, and collected hair were species-attributed. Distance-based redundancy analysis (db-RDA) explored assemblage composition, and single-species occupancy models tested hypotheses for the identified species.Crociduraspp. andApodemusspp. abundances were not significantly associated with any factor tested. Abundances of house mouseMus domesticusand Savi’s pine voleMicrotus saviiwere higher in the burnt area. Garden dormouseEliomys quercinushad higher abundance in pine forest, whereas red squirrelSciurus vulgariswas more abundant in chestnut forest. The overall greater abundance of ground-foraging herbivorous/granivorous in the burnt area, characterised by a dense undergrowth, could be related to anti-predatory strategies and food opportunities. Insectivorous could be in a recolonisation phase that would hide their earlier absence. Arboreal-foraging species were associated with forest type, regardless of burnt status. The HAM was overall confirmed also in Mediterranean basin ecosystems, probably due to their temperate climate. This may facilitate predictions about post-fire animal successions, which will be even more crucial in future.
Three-dimensional printed titanium mesh combined with iliac cancellous bone in the reconstruction of mandibular defects secondary to ameloblastoma resection
Authors: Zhao Zhiyang , Shen Shunyao , Yu Hongbo , Shen Guofang , Li Meng , Ding Guanrong 
Published: June 2023

Abstract
Background
The reconstruction of large mandibular defects is a challenge, and the free vascularized bone flaps are most commonly used. However, the precision and symmetry of this repair are deficient, and patients have a risk of vascular embolism, flap necrosis and donor site complications. Therefore, to explore an ideal alternative in mandibular reconstruction with high surgical accuracy and low complications is indispensable.
Methods
Seven patients with recurrent or large-scope ameloblastoma were enrolled in this study. All patients were provided with a fully digital treatment plan, including the design of osteotomy lines, surgical guides, and three-dimensional printed titanium mesh for implantation. With the assistance of a surgical guide, ameloblastomas were resected, and custom 3D printed titanium mesh combined with posterior iliac bone harvest was used in mandibular reconstruction. The surgical discrepancy between the surgical plan and the real result was compared. At the same time, the resorption rate of the implanted bone was evaluated.
Results
All patients completed the fully digital treatment process successfully without severe complications. Image fusion showed that the postoperative contour of the mandible was basically consistent with surgical planning, except for a slight increase in the inferior border of the affected side. The mean error between the intraoperative bone volume and the digital planning bone volume was 2.44%±2.10%. Furthermore, the bone resorption rates of the harvested graft 6 months later were 32.15%±6.95%.
Conclusions
The use of digital surgical planning and 3D-printed templates can assist surgeons in performing precise surgery, and the 3D-printed titanium mesh implant can improve the patient's facial symmetry. 3D printed titanium combined with posterior iliac cancellous bone graft can be regarded as an ideal alternative in extensive mandibular reconstruction.
Association between chronic obstructive pulmonary disease and 28-day mortality in patients with sepsis: a retrospective study based on the MIMIC-III database
Authors: Chen Yubiao , Lu Lifei , Li Xicong , Liu Baiyun , Zhang Yu , Zheng Yongxin , Zeng Yuan , Wang Ke , Pan Yaru , Liang Xiangning , Wu Zhongji , Fu Yutian , Huang Yongbo , Li Yimin 
Published: June 2023

Abstract
Background: Along with a variety of chronic co-morbid medical conditions, sepsis is a common cause of mortality in critically ill patients, and chronic obstructive pulmonary disease (COPD) is one of the most common comorbidities in septic patients. However, the impact of COPD on patients with sepsis is still unclear. Therefore, the purpose of this study was aimed to assess the effect of COPD on the prognosis of sepsis patients based on MIMIC-III database.
Methods: In this retrospective study based on the Medical Information Mart for Intensive Care (MIMIC)-III database version 1.4 (v1.4), we collected clinical data and 28-day all-cause mortality from sepsis patients in intensive care unit (ICU) who met the diagnostic criteria of Sepsis 3 on ICU admission between 2008 and 2012. ICD-9 code was used to identified COPD. We applied Kaplan-Meier analysis to compare difference between 28-day all-cause mortality of COPD and non-COPD patients. Univariate and multivariate cox proportional-hazards model was applied to explore the risk factor associated with 28-day all-cause mortality in patients with sepsis.
Results: 6257 patients with sepsis were included in this study, including 955 (15.3%) with COPD and 5302 without COPD (84.7%). Compared with sepsis patients without COPD, sepsis patients with COPD were older (median: 73.5 vs 65.8, P<0.001), had a higher simplified acute physiology score II (SAPSII) (median: 40.0 vs 38.0, P<0.001) and greater proportion of mechanical ventilatory support (MV) (55.0% vs 48.9%, P=0.001). In our study, patients with COPD had higher 28-day all-cause mortality (23.6% vs 16.4%, P < 0.001) than non-COPD patients. After adjusting the confounding factors, the results showed that COPD was an independent risk factor for the 28-day all-cause mortality in septic patients (HR 1.30, 95%CI: 1.12-1.51, P=0.001).
Conclusions: The comorbidity of COPD was an independent predictor of 28-day all-cause mortality in critical septic patients. Clinically, sepsis patients with COPD should be given additional care.
Prediction of metachronous gastric neoplasms after curative endoscopic submucosal dissection for early gastric cancer
Authors: Chen Na , Ge Jian , Shi Lei , Jia Ruzhen , Jiang Junmei 
Published: June 2023

Abstract
Background: As more early gastric cancer (EGC) patients are being treated with endoscopic submucosal dissection (ESD), it is important to find the risk factors which contribute to the occurrence of metachronous gastric neoplasms (MGN). This study aimed to analyze the characteristics of MGN and to generate useful tools for the prediction of MGN following ESD.
Methods: A total of 819 patients were retrospectively enrolled. The risk factors for MGN were analyzed using Cox hazard proportional model. Moreover, RStudiosoftware is used to build nomogram models, and evaluate the discrimination, consistency and decision curves.
Results: A total of 5.0% (41/819) of patients had MGN after ESD for EGC. The median interval between the discovery of MGN and the initial EGC was 23 months. Cox multivariable analysis found that history of drinking [HR:2.486(1.082-5.710), p=0.032], location of lesion (middle 1/3) [HR: 2.613(1.192-5.725), p=0.016], node metastasis [HR: 3.152(1.046-9.502), p=0.041] and whole lesion removal(not) [HR: 2.526(1.029-6.200), p=0.043] were independent risk factors for the development of MGN. In addition, we were developed and internally validated nomogram to predict the 3-, 5-, and 7-year probability of developing MGN after ESD for EGC (C index= 0.665). The calibration chart showed that the predicted probability of MGN after ESD for EGC was the similar to the actual observed result and the DCA decision curve analysis showed strong clinical practicability.
Conclusions: We constructed a nomogram for predicting the incidence of MGN after ESD in EGC patients and the performance of the model is excellent.
Falls, hospitalizations, and poor self-rated health in older people with diabetes and frailty: A secondary analysis of SABE-Colombia
Authors: Morros-González Elly , Chacón-Valenzuela Estephania , Vargas-Beltrán María Paula , Gómez Ana María , Chavarro-Carvajal Diego , Cano-Gutiérrez Carlos Alberto , Venegas-Sanabria Luis Carlos 
Published: June 2023

Abstract
Background
Diabetes and frailty, together, have been related to adverse events such as increased risk of hypoglycemia, functional decline, disability, hospital admissions, and worsening quality of life. We estimated the prevalence of diabetes and frailty and their association with hospitalization, poor self-rated health, recurrent falls, and fear of falling.
Methods
Data came from the “Salud, Bienestar y Envejecimiento” (SABE) Colombia Survey 2015, a cross-sectional study of 23694 community-dwelling adults aged 60 years or older living in rural or urban areas, a representative sample from the total population. A modified version created of the frailty phenotype proposed by Fried, was used to measure frailty. Diabetes prevalence was considered by self-report.
Results
3873 older people were analyzed, 16.2% had diabetes, were more likely to be women, younger age (≤ 69 years), lived in urban areas and had lower economic income. Geriatric syndromes, chronic illnesses, hospitalization in the last year and poor self-rated health were also significantly associated with diabetes. The prevalence of older adults having diabetes and frailty was 22.4%. Diabetes and frailty were associated with hospitalization in the last year, poor self-rated health, recurrent falls, and fear of falling, associations that were higher than analysis with diabetes or frailty.
Conclusions
Findings of our study provide additional evidence supporting association between older people with diabetes and frailty and unfavorable outcomes.
A possible expansion of the VISTA enhancer database
Authors: Ni Pengyu , Wu Siwen , Su Zhengchang 
Published: June 2023

Abstract
The VISTA enhancer database is a valuable resource for evaluating predicted enhancers in humans and mice. In addition to thousands of validated positive regions (VPRs) in the human and mouse genomes, the database also contains similar numbers of validated negative regions (VNRs). We have previously shown that the VPRs are on average half as long as predicted overlapping enhancers that are highly conserved, and hypothesize that the VPRs might be truncated forms of long bona fide enhancers. Here, we show that like the VPRs, the VNRs also are under strongly evolutionary constraints and overlap predicted enhancers in the genomes. Moreover, the VNRs are also on average half as long as predicted overlapping enhancers that are highly conserved. Thus, we hypothesize that like the VPRs, the VPRs might also be truncated forms of long bona fide enhancers.
Accelerated prime-and-trap vaccine regimen in mice using repRNA-based CSP malaria vaccine
Authors: MacMillen Zachary , Hatzakis Kiara , Simpson Adrian , Shears Melanie , Watson Felicia , Erasmus Jesse , Khandhar Amit , Wilder Brandon , Murphy Sean , Reed Steven , Davie James , AVRIL Marion 
Published: June 2023

Abstract
Malaria, caused by Plasmodium parasites, remains one of the most devastating infectious diseases worldwide, despite control efforts that have lowered morbidity and mortality. The only P. falciparum vaccine candidates to show field efficacy are those targeting the asymptomatic pre-erythrocytic (PE) stages of infection. The subunit (SU) RTS,S/AS01 vaccine, the only licensed malaria vaccine to date, is only modestly effective against clinical malaria. Both RTS,S/AS01 and the SU R21 vaccine candidate target the PE sporozoite (spz) circumsporozoite (CS) protein. These candidates elicit high-titer antibodies that provide short-term protection from disease, but do not induce the liver-resident memory CD8+ T cells (Trm) that confer strong PE immunity and long-term protection. In contrast, whole-organism (WO) vaccines, employing for example radiation-attenuated spz (RAS), elicit both high antibody titers and Trm, and have achieved high levels of sterilizing protection. However, they require multiple intravenous (IV) doses, which must be administered at intervals of several weeks, complicating mass administration in the field. Moreover, the quantities of spz required present production difficulties. To reduce reliance on WO while maintaining protection via both antibodies and Trm responses, we have developed an accelerated vaccination regimen that combines two distinct agents in a prime-and-trap strategy. While the priming dose is a self-replicating RNA encoding P. yoelii CS protein, delivered via an advanced cationic nanocarrier (LION™), the trapping dose consists of WO RAS. This accelerated regime confers sterile protection in the P. yoelii mouse model of malaria. Our approach presents a clear path to late-stage preclinical and clinical testing of dose-sparing, same-day regimens that can confer sterilizing protection against malaria.
RepID represses megakaryocytic differentiation by recruiting CRL4A-JARID1A at DAB2 promoter
Authors: Jo Jae-Hyun , Ok Seon-Mi , Kim Dong-Kyu , Kim Yeong-Mu , Park Jong-Uk , Jung Dong-Hyun , Kim Hye-Ji , Seong Hyun-A , Cho Hyo Je , Nah Jihoon , Kim Sangjune , Fu Haiqing , Redon Christophe E. , Aladjem Mirit I. , Jang Sang-Min 
Published: June 2023

Abstract
Background
Megakaryocytes (MKs) are platelet precursors, which arise from hematopoietic stem cells (HSCs). While MK lineage commitment and differentiation are accompanied by changes in gene expression, many factors that modulate megakaryopoiesis remain to be uncovered. Replication origin binding protein (RepID) which has multiple histone-code reader including bromodomain, cryptic Tudor domain and WD40 domains and Cullin 4-RING ubiquitin ligase complex (CRL4) recruited to chromatin mediated by RepID have potential roles in gene expression changes via epigenetic regulations. We aimed to investigate whether RepID-CRL4 participates in transcriptional changes required for MK differentiation.
Methods
The PCR array was performed using cDNAs derived from RepID-proficient or RepID-deficient K562 erythroleukemia cell lines. Correlation between RepID and DAB2 expression was examined in the Cancer Cell Line Encyclopedia (CCLE) through the CellMinerCDB portal. The acceleration of MK differentiation in RepID-deficient K562 cells was determined by estimating cell sizes as well as counting multinucleated cells known as MK phenotypes, and by qRT-PCR analysis to validate transcripts of MK markers using phorbol 12-myristate 13-acetate (PMA)-mediated MK differentiation condition. Interaction between CRL4 and histone methylation modifying enzymes were investigated using BioGRID database, immunoprecipitation and proximity ligation assay. Alterations of expression and chromatin binding affinities of RepID, CRL4 and histone methylation modifying enzymes were investigated using subcellular fractionation followed by immunoblotting. RepID-CRL4-JARID1A-based epigenetic changes on DAB2 promoter were analyzed by chromatin-immunoprecipitation and qPCR analysis.
Results
RepID-deficient K562 cells highly expressing MK markers showed accelerated MKs differentiation exhibiting increases in cell size, lobulated nuclei together with reaching maximum levels of MK marker expression earlier than RepID-proficient K562 cells. Recovery of WD40 domain-containing RepID constructs in RepID-deficient background repressed DAB2 expression. CRL4A formed complex with histone H3K4 demethylase JARID1A in soluble nucleus and loaded to the DAB2 promoter in a RepID-dependent manner during proliferation condition. RepID, CRL4A, and JARID1A were dissociated from the chromatin during MK differentiation, leading to euchromatinization of the DAB2 promoter.
Conclusion
This study uncovered a role for the RepID-CRL4A-JARID1A pathway in the regulation of gene expression for MK differentiation, which can form the basis for the new therapeutic approaches to induce platelet production.