bluuebunny/crossref_metadata_2025_split huggingface dataset:
Potential value of the homologous recombination deficiency signature we developed in the prognosis and drug sensitivity of gastric cancer
Authors: Wu Xin , Wang Qiong , Liu Peifa , Sun Linde , Wang Yu 
Published: November 2022

Background: Homologous recombination is an important DNA repair mechanism, which deficiency is a common feature of many cancers. Defining homologous recombination deficiency (HRD) status can provide information for treatment decisions of cancer patients. HRD score is a widely accepted method to evaluate HRD status. This study aimed to explored HRD in gastric cancer (GC) patients’ clinical outcomes with genes related to HRD score and HRD components score [HRD-loss of heterozygosity (LOH), large-scale state transitions (LST), and telomeric allelic imbalance (NtAI)].Methods: Based on LOH, NtAI scores, LST, and integrated HRD scores-related genes, a risk model for stratifying 346 TCGA GC cases were developed by Cox regression analysis and LASSO Cox regression. The risk scores of 33 cancers in TCGA were calculated to analyze the relationship between risk scores of each cancer and HRD scores and 3 HRD component scores. Relationship between the risk model and patient survival, BRCA1, BRCA2 mutation, response to Cisplatin and Talazoparib treatment was analyzed by generating Kaplan-Meier curve, mutations waterfall map and conducting Pearson correlation analysis.Results: An gene signature was constructed based on 11 HRD scores-related gene (BEX2, C1QL2, DKK1, DRC1, GLUD2, HCAR1, IGFBP1, NXPH1, PROC, SERPINA5, and SLCA1A2). Risk groups were stratified by risk score. Prognosis of the high-risk score group was worse than the low-risk ones. Risk score was associated with BRCA2 mutation, and patients grouped according to BRCA2 mutation status had distinguishable risk score, NtAI score, HRD-LOH, LST, and HRD scores. The low-score group showed higher sensitivity to Cisplatin and Talazoparib. The risk score of adrenocortical carcinoma (ACC), stomach adenocarcinoma (STAD), uterine corpus endometrial carcinoma (UCEC), kidney renal clear cell carcinoma (KIRC), sarcoma (SARC), prostate adenocarcinoma (PRAD), breast invasive carcinoma (BRCA) was significantly positively correlated with HRD score.Conclusion: We developed an 11 HRD scores-related genes risk model and revealed the potential association between HRD status and GC prognosis, gene mutations, patients’ sensitivity to therapeutic drugs.
Association of concomitant autoimmunity with the disease features and long-term treatment and health outcomes in Celiac disease
Authors: Tauschi Riku , Eurén Anna , Vuorela Nina , Koskimaa Sara , Huhtala Heini , Kaukinen Katri , Kivelä Laura , Kurppa Kalle 
Published: November 2022

BackgroundCeliac disease (CeD) is often accompanied by other autoimmune diseases (AID). However, the association of co-existing autoimmunity with the presentation and treatment success in CeD is unclear. We investigated these issues with a large and well-defined cohort of Finnish patients.MethodsAdult CeD patients (n = 806) were collected from multiple heath care sites via nationwide recruitment. They were interviewed, underwent measurement of CeD autoantibodies, and filled out questionnaires to ascertain quality of life (PGWB) and gastrointestinal symptoms (GSRS) after a median of 9.7 years on a gluten-free diet. Data were supplemented retrospectively from patient records. The results were compared between CeD patients with and without a coexisting AID.ResultsAltogether 185 patients had CeD+AID and 621 had CeD only. At CeD diagnosis, patients with CeD+AID were older (median 42 vs. 36 years, p = 0.010) and had more joint symptoms (9.1 vs. 4.2%, p = 0.011), whereas the groups were comparable in sex, family history of CeD, other presenting symptoms, proportion of screen-detected subjects, and severity of duodenal lesion. During follow-up on gluten-free diet, CeD+AID patients experienced poorer general health (median score 12 vs. 14, p &lt; 0.001) in PGWB, more overall gastrointestinal symptoms (2.1 vs. 1.9, p = 0.001), and constipation (2.0 vs. 1.7, p &lt; 0.001) in GSRS, whereas there was no difference in histological and serological recovery, dietary adherence, use of gluten-free oats, smoking, and presence of regular follow-up.ConclusionsCo-existing AID was not significantly associated with the baseline features or with most long-term outcomes in CeD. However, the increased prevalence of gastrointestinal symptoms and reduced poorer self-perceived health during treatment indicates these patients' need for special support.
No safe renal warm ischemia time—The molecular network characteristics and pathological features of mild to severe ischemia reperfusion kidney injury
Authors: Chen Ya-Lei , Li Huai-Kang , Wang Lei , Chen Jian-Wen , Ma Xin 
Published: November 2022

Ischemic acute kidney injury (AKI) has always been a hot and difficult research topic in the field of renal diseases. This study aims to illustrate the safe warm ischemia time of kidney and the molecular network characteristics and pathological features of mild to severe ischemia reperfusion kidney injury. We established varying degrees of renal injury due to different ischemia time (0 min, 16 min, 18 min, 20 min, 22 min, 24 min, 26 min, 28 min, and 30 min) on unilateral (left kidney) ischemia-reperfusion injury and contralateral (right kidney) resection (uIRIx) mouse model. Mice were sacrificed 24 h after uIRIx, blood samples were harvested to detect serum creatinine (Scr), and kidney tissue samples were harvested to perform Periodic Acid-Schiff (PAS) staining and RNA-Seq. Differentially expressed genes (DEGs) were identificated, time-dependent gene expression patterns and functional enrichment analysis were further performed. Finally, qPCR was performed to validated RNA-Seq results. Our results indicated that there was no absolute safe renal warm ischemia time, and every minute of ischemia increases kidney damage. Warm ischemia 26min or above in mice makes severe kidney injury, renal pathology and SCr were both significantly changed. Warm ischemia between 18 and 26 min makes mild kidney injury, with changes in pathology and renal molecular expression, while SCr did not change. No obvious pathological changes but significant differences in molecular expression were found less than 16min warm ischemia. There are two key time intervals in the process of renal ischemia injury, 0 min–16 min (short-term) and 26 min–28 min (long-term). Gene expression of immune-related pathways were most significantly down-regulated in short-term ischemia, while metabolism-related pathways were the mainly enriched pathway in long-term ischemia. Taken together, this study provides novel insights into safe renal artery occlusion time in partial nephrectomy, and is of great value for elucidating molecular network characteristics and pathological features of mild to severe ischemia reperfusion kidney injury, and key genes related to metabolism and immune found in this study also provide potential diagnostic and therapeutic biomarkers for AKI.
Structural network efficiency mediates the association between glymphatic function and cognition in mild VCI: a DTI-ALPS study
Authors: Song Hao , Ruan Zhao , Gao Lei , Lv Dongwei , Sun Dong , Li Zeng , Zhang Ran , Zhou Xiaoli , Xu Haibo , Zhang Junjian 
Published: November 2022

Background and objective: Vascular cognitive impairment (VCI) can be caused by multiple types of cerebrovascular pathology and is considered a network disconnection disorder. The heterogeneity hinders research progress in VCI. Glymphatic failure has been considered as a key common pathway to dementia recently. The emergence of a new method, Diffusion Tensor Image Analysis Along the Perivascular Space (DTI-ALPS), makes it possible to investigate the changes of the glymphatic function in humans non-invasively. We aimed to investigate alterations of glymphatic function in VCI and its potential impact on network connectivity.Methods: We recruited 79 patients with mild VCI, including 40 with cerebral small vessel disease cognitive impairment (SVCI) and 39 with post-stroke cognitive impairment (PSCI); and, 77 normal cognitive (NC) subjects were recruited. All subjects received neuropsychological assessments and multimodal magnetic resonance imaging scans. ALPS-index was calculated and structural networks were constructed by deterministic tractography, and then, the topological metrics of these structural connectivity were evaluated.Results: The ALPS-index of VCI patients was significantly lower than that of NC subjects (P &lt; 0.001). Multiple linear regression analysis showed that ALPS-index affects cognitive function independently (β = 0.411, P &lt; 0.001). The results of correlation analysis showed that the ALPS-index was correlated with overall vascular risk factor burden (r = −0.263, P = 0.001) and multiple cerebrovascular pathologies (P &lt; 0.05). In addition, global efficiency (Eg) of network was correlated with ALPS-index in both SVCI (r = 0.348, P = 0.028) and PSCI (r = 0.732, P &lt; 0.001) patients. Finally, the results of mediation analysis showed that Eg partially mediated in the impact of glymphatic dysfunction on cognitive impairment (indirect effect = 7.46, 95% CI 4.08–11.48).Conclusion: In both major subtypes of VCI, the ALPS-index was decreased, indicating impaired glymphatic function in VCI. Glymphatic dysfunction may affect cognitive function in VCI by disrupting network connectivity, and, may be a potential common pathological mechanism of VCI. ALPS-index is expected to become an emerging imaging marker for VCI.
Neural cue reactivity is not stronger in male than in female patients with alcohol use disorder
Authors: Gerhardt Sarah , Hoffmann Sabine , Tan Haoye , Gerchen Martin Fungisai , Kirsch Peter , Vollstädt-Klein Sabine , Kiefer Falk , Bach Patrick , Lenz Bernd 
Published: November 2022

BackgroundMales consume more alcohol than females, and alcohol use disorder (AUD) is more prevalent in males than females. However, females progress faster to AUD. Sex differences in neural alcohol cue reactivity were previously observed in young social drinkers, indicating a role of hypersensitivity to alcohol-related cues in very early stages of addiction. To our knowledge, this is the first study on patients diagnosed with AUD to test sex differences in neural reactivity to alcohol cues in order to widen previous findings.MethodsWe analyzed data from previous studies, using a well-established functional magnetic resonance imaging (fMRI) paradigm to compare neural reactivity to alcohol cues between 42 female and 124 male patients with AUD (mean age 45 and 46 years) in predefined regions of interest that were implicated by previous studies (ventral and dorsal striatum as well as caudate, putamen, amygdala, hippocampus, insula, anterior cingulate cortex, and medial prefrontal cortex) using independent samples t-tests. Post-hoc, effect size calculations were performed.ResultsThroughout all nine regions of interest, we found no statistically significant sex differences in neural reactivity toward alcoholic pictures alone or in comparison to neutral pictures (p &gt; 0.05, FDR-corrected). Post-hoc effect size estimates indicated a magnitude between 0.137 and 0.418 (Hedge’s g) on alcohol reactivity to alcohol cues compared to neutral cues and indicate very small to less than medium effect sizes in the direction of higher cue reactivity in female patients.ConclusionPrevious studies showed sex differences in neural alcohol cue reactivity in younger social and problematic alcohol drinkers, i.e., stronger striatal cue-reactivity in males. After correction for multiple comparisons, we did not observe significant sex differences in a cohort of middle-aged females and males with AUD. Sex differences that are present during early phases of addiction development might disappear at later stages of AUD and might thus be considered as clinically less relevant in patients with more severe AUD.
Effects of swift heavy ion irradiation and annealing on the microstructure and recrystallizationof SiC pre-implanted with Sr ions
Authors: Abdelbagi H. A. A. , Jafer T. A. O. , Skuratov V. A. , Njoroge E. G. , Mlambo M. , Hlatshwayo T. T. , Malherbe J. B. 
Published: November 2022

Polycrystalline SiC wafers were implanted with 360 keV strontium (Sr) ions at room temperature (RT)to a fluence of 2 × 1016 cm−2. Some of the implanted samples were irradiated with xenon (Xe) ions of 167 MeV to a fluence of 3.4 × 1014 cm−2 and 8.4 × 1014 cm−2at RT. The as-implanted and implanted then irradiated samples were vacuum annealed (isochronally) at temperatures ranging from 1,100 to 1,400°C in steps of 100°C for 5 h. Annealing induced modification of the microstructure of the implanted and swift heavy ions (SHIs) irradiated SiC was studied by Raman spectroscopy, scanning electron microscopy (SEM) and backscattering spectrometry (RBS). Sr ions bombardment caused formation of an amorphous layer in SiC, while irradiation by Xe ions led to partial recrystallization of the amorphized layer. After annealing at 1,100°C, the samples with low Sr retained ratio showed full recrystallization, while the samples with high Sr retained ratio showed poor recrystallization. This suggests that the presence of Sr within the implanted region inhibited the recrystallization of SiC. Annealing of the as-implanted samples at temperatures from 1,100°C and 1,200°Cresulted in larger average crystal size compared to the SHIsirradiated samples annealed in the same temperature range. The difference in the average crystal sizes between the as-implanted and SHIs irradiated samples was due to the differences in the nucleation rate per amorphous area in the two samples. Ramanspectroscopy results showedthat the intensity of the LO mode of SiC increases with increasing crystal size. However, several factors such as pores and defects in SiC play a role in the decrease of the LO mode intensity of SiC (even if the average crystal size is large).
Potential effect of dietary zinc intake on telomere length: A cross-sectional study of US adults
Authors: Shi Huanchen , Li Xiaoxuan , Yu Haihong , Shi Wanting , Lin Yue , Zhou Yunping 
Published: November 2022

BackgroundTelomere length, which is related to chronic diseases and premature mortality, is influenced by dietary factors. Zinc is known as a dietary antioxidant micronutrient, however, its impact on telomere length remains unclear.ObjectiveWe aimed to examine the potential effect of dietary zinc intake on telomere length among middle-aged and older individuals in the US.Materials and methodsOur study included 3,793 US participants aged 45 years and older from the 1999 to 2002 National Health and Nutrition Examination Survey (NHANES). 24-h dietary recall interviews were employed to evaluate zinc consumption. Leukocyte telomere length was assessed by real-time quantitative polymerase chain reaction (qPCR). We adopted generalized linear models to investigate the effect of dietary zinc intake on telomere length, and subgroup analyses were further applied. We further evaluated the dose-response relationship using restricted cubic spline analysis.ResultsAmong the 3,793 participants, the average telomere length was 0.926 ± 0.205 (T/S ratio) or 5509.5 ± 494.9 (bp). After adjusting for major confounders, every 5 mg increment in dietary zinc consumption was related to 0.64% (95% CI: 0.17%, 1.10%) longer telomere length. In the subgroup analyses, significant relationships were found in females (Percentage change: 1.11%; 95% CI: 0.48%, 1.75%), obese (Percentage change: 0.88%; 95% CI: 0.26%, 1.50%), and low energy intake individuals (Percentage change: 0.99%; 95% CI: 0.51%, 1.46%). Additionally, we revealed a positive linear relationship between dietary zinc intake and telomere length (P for non-linearity = 0.636).ConclusionOur study revealed that elevated dietary zinc intake was significantly related to longer telomere length among adults aged 45 years and older in the US. And the association was more pronounced in females, obese, and low energy intake individuals.
Prediction of outcomes by diffusion kurtosis imaging in patients with large (≥5 cm) hepatocellular carcinoma after liver resection: A retrospective study
Authors: Qin Yun-Long , Wang Shuai , Chen Fei , Liu Hong-Xiu , Yue Kui-Tao , Wang Xi-Zhen , Ning Hou-Fa , Dong Peng , Yu Xiang-Rong , Wang Guang-Zhi 
Published: November 2022

PurposeTo evaluate preoperative diffusion kurtosis imaging (DKI) in predicting the outcomes of large hepatocellular carcinoma (HCC) after liver resection (LR).Materials and methodsFrom January 2015 to December 2017, patients with a large (≥5cm) HCC who underwent preoperative DKI were retrospectively reviewed. The correlations of the mean kurtosis (MK), mean diffusivity (MD), and apparent diffusion coefficient (ADC) with microvascular invasion (MVI) or histological grade were analyzed. Cox regression analyses were performed to identify the predictors of recurrence-free survival (RFS) and overall survival (OS). A nomogram to predict RFS was established. P&lt;0.05 was considered as statistically significant.ResultsA total of 97 patients (59 males and 38 females, 56.0 ± 10.9 years) were included in this study. The MK, MD, and ADC values were correlated with MVI or histological grade (P&lt;0.01). With a median follow-up time of 41.2 months (range 12-69 months), 67 patients (69.1%) experienced recurrence and 41 patients (42.3%) were still alive. The median RFS and OS periods after LR were 29 and 45 months, respectively. The 1-, 3-, and 5-year RFS and OS rates were 88.7%, 41.2%, and 21.7% and 99.0%, 68.3%, and 25.6%, respectively. MK (P&lt;0.001), PVT (P&lt;0.001), and ADC (P=0.033) were identified as independent predictor factors for RFS. A nomogram including the MK value for RFS showed the best performance, and the C-index was 0.895.ConclusionThe MK value obtained from DKI is a potential predictive factor for recurrence and poor survival, which could provide valuable information for guiding the efficacy of LR in patients with large HCC.
Construction and validation of a prediction model of extrahepatic metastasis for hepatocellular carcinoma based on common clinically available data
Authors: Zhou Liuxin , Ren Li , Yu Wenhao , Qi Mengjian , Yuan Jiaqi , Wang Wen , Su Xiaoxia , Yin Fengjiao , Deng Manjun , Wang Haijiu , Long Hongmu , Zeng Jiangchao , Yu Jiajian , Fan Haining , Wang Zhixin 
Published: November 2022

ObjectiveThis study aimed to investigate the clinical characteristics and risk factors of patients with hepatocellular carcinoma (HCC) with extrahepatic metastases (EHM) and to establish an effective predictive nomogram.MethodsClinical and pathological data from 607 patients with hepatocellular carcinoma admitted to the Affiliated Hospital of Qinghai University between 1 January 2015 and 31 May 2018 were documented, as well as demographics, clinical pathological characteristics, and tumor-related parameters to clarify clinical risk factors for HCC EHM. These risks were selected to build an R-based clinical prediction model. The predictive accuracy and discriminating ability of the model were determined by the concordance index (C-index) and the calibration curve. The results were validated with a bootstrap resample and 151 patients from 1 June 2018 to 31 December 2019 at the same facility.ResultsIn multivariate analysis, independent factors for EHM were neutrophils, prothrombin time, tumor number, and size, all of which were selected in the model. The C-index in the EHM prediction model was 0.672 and in the validation cohort was 0.694. In the training cohort and the validation cohort, the calibration curve for the probability of EHM showed good agreement between the nomogram prediction and the actual observation.ConclusionThe extrahepatic metastasis prediction model of hepatocellular carcinoma constructed in this study has some evaluation capability.
Construction of a lactate-related prognostic signature for predicting prognosis after surgical repair for acute type a aortic dissection
Authors: Wang Zhigang , Li Kai , Xu Jingfang , Cheng Xiaofeng , Wang Dongjin 
Published: November 2022

Background: Serum lactate is commonly measured in the perioperative period in patients who have undergone surgery for an acute type A aortic dissection (ATAAD). However, conflicting data has been reported as to whether lactate elevation is associated with short-term prognosis. The aim of the current study was to determine the association between perioperative arterial lactate levels and postoperative 30-day mortality.Methods: Patients who underwent repair of a ATAAD at our institution were retrospectively screened and those with comprehensive measurements of serum lactate before surgery and at 0, 1, 3, 6, 12, and 24 h after surgery in the intensive care unit (ICU) were selected for the analysis. Patients’ demographic features and outcomes were reviewed to determine risk factors associated with 30-day mortality using logistic regression modeling. The association between serum lactate levels at different time points and 30-day mortality were analyzed by receiver-operating characteristic curves.Results: 513 patients were identified and retrospectively analyzed for this study including 66 patients (12.9%) who died within 30 days after surgery. Patients who died within 30 days after surgery had elevated lactate levels measured before surgery and at 0, 1, 3, 6, 12, and 24 h after their ICU stay. Lactate measured at 24 h post ICU admission (odds ratio, 2.131; 95% confidence interval, 1.346–3.374; p = 0.001) was a predictor of 30-day mortality. The area under the curve (AUC) for 30-day mortality with lactate levels at 12 h and 24 h post ICU stay were 0.820 and 0.805, respectively.Conclusion: Early elevation of lactate level is correlated with increased 30-day mortality in patients who received ATAAD surgical repair.
The metabolomic differential plasma profile between dialysates. Pursuing to understand the mechanisms of citrate dialysate clinical benefits
Authors: Broseta José Jesús , Roca Marta , Rodríguez-Espinosa Diana , López-Romero Luis Carlos , Gómez-Bori Aina , Cuadrado-Payán Elena , Bea-Granell Sergio , Devesa-Such Ramón , Soldevila Amparo , Sánchez-Pérez Pilar , Hernández-Jaras Julio 
Published: November 2022

Background: Currently, bicarbonate-based dialysate needs a buffer to prevent precipitation of bicarbonate salts with the bivalent cations, and acetate at 3–4 mmol/L is the most used. However, citrate is being postulated as a preferred option because of its association with better clinical results by poorly understood mechanisms. In that sense, this hypothesis-generating study aims to identify potential metabolites that could biologically explain these improvements found in patients using citrate dialysate.Methods: A unicentric, cross-over, prospective untargeted metabolomics study was designed to analyze the differences between two dialysates only differing in their buffer, one containing 4 mmol/L of acetate (AD) and the other 1 mmol/L of citrate (CD). Blood samples were collected in four moments (i.e., pre-, mid-, post-, and 30-min-post-dialysis) and analyzed in an untargeted metabolomics approach based on UPLC-Q-ToF mass spectrometry.Results: The 31 most discriminant metabolomic variables from the plasma samples of the 21 participants screened by their potential clinical implications show that, after dialysis with CD, some uremic toxins appear to be better cleared, the lysine degradation pathway is affected, and branched-chain amino acids post-dialysis levels are 9–10 times higher than with AD; and, on its part, dialysis with AD affects acylcarnitine clearance.Conclusion: Although most metabolic changes seen in this study could be attributable to the dialysis treatment itself, this study successfully identifies some metabolic variables that differ between CD and AD, which raise new hypotheses that may unveil the mechanisms involved in the clinical improvements observed with citrate in future research.