bluuebunny/crossref_metadata_2025_split huggingface dataset:
Prevalence of Breast Cancer Subtypes Among Different Ethnicities and Bangladeshi Women: Demographic, Clinicopathological, and Integrated Cancer Informatics Analysis
Authors: Islam Diganta , Islam Md. Shihabul , Dorin Sanjida Islam , Jesmin  
Published: January 2023

Background: The molecular subtyping of breast cancer is related to estrogen receptor (ER), progesterone receptor (PR), and human epidermal growth factor receptor 2 (HER2). The present study aimed to systematically analyze the expression, function, and prognostic value of ER, PR, HER2, and their prevalence in different ethnic groups and among Bangladeshi breast cancer (BC) patients. Method: This study included 25 BC patients and 25 healthy controls, aged between 25 and 70 years. The study characteristics were compared using the ANOVA and Chi-square tests. Also, the multi-Omics dataset of 775 BC patients from TCGA was analyzed for ER, PR, and HER2 in breast cancer subtypes and compared among different ethnicities. Results: For most BD breast cancer cases, the age at diagnosis was ⩾40 years, had only a histopathological diagnosis ( P-value .004), and no history of mammography or other pathological tests. For treatment, had only chemotherapy ( P-value .004) and no hormone therapy ( P-value <.001). The majority of patients (>60%) were of stage-II cancer and TNBC (40%) subtype. The BC ethnicity-stratified data of ER, PR, and HER2 indicated a strong correlation across all ethnicities ( P-value 4.99e−35; P-value 3.79e−18). The subtypes stratified data indicated a higher percentage of Luminal A (58.3%) in Caucasians whereas Luminal B (24.3%) and HER2 (25.2%) subtypes were found higher in Asians and TNBC (36.0%) were found in Africans. However, a significantly higher frequency of TNBC (52.2%) compared to Asians (14.8%) was found in BD patients ( P-value <.001). The overall survival analysis of BC subtypes demonstrated that Luminal B ( P-value .005) and HER2 enriched ( P-value .015) were significantly more aggressive and were dominant in the Asian population. Conclusion: A significant association was found between BC subtypes with different ethnicities and Bangladeshi women and these findings might aid in the prevention, management, and raising of awareness against risk factors in the near future.
Investigations of thickness effects on the acoustic characteristics of symmetric and asymmetric airfoils
Authors: Kumar Sujit , Mishra Priyanshu , Narayanan S 
Published: January 2023

The present paper provides a detailed acoustic characterization of symmetric and asymmetric NACA airfoils for various thickness ratios to determine the best thickness ratio and geometry which provide lower acoustic radiations with respect to the standard NACA0010 airfoil. The studies are conducted for various t/c values of 0.12, 0.15 and 0.21, where t is the airfoil thickness and c is the airfoil chord. The far-field acoustic emissions are observed to decrease with increase in t/c ratios for both the symmetric and asymmetric airfoils. For all the t/c values and jet velocities studied, the asymmetric airfoils show higher noise reductions from mid to high frequencies as compared to the symmetric ones, which might be due to the reduced transverse velocity fluctuations as a result of the large distortions imparted to oncoming turbulent gust by the formation of the larger stagnation pressure zone. The symmetric airfoils show a maximum reduction up to 3 dB from mid to high frequencies while asymmetric ones show a reduction up to about 5 dB. An empirical expression is developed for the ΔOAPWL as a function of t/c only for both the symmetric and asymmetric airfoils, where ΔOAPWL is the overall sound power reduction level in dB. It reveals that the ΔOAPWL follow a second order polynomial for both the symmetric and asymmetric airfoils at all jet velocities studied. It is observed that thicker (i.e., t/c = 0.21) symmetric and asymmetric airfoils show lower acoustic radiations as compared to the thinner ones for all the emission angles. In general, it is observed that the thinner airfoils show higher directivity as compared thicker ones, albeit they show a common trait of downstream directivity. Further the highest directivity is seen at an emission angle of 67.5° for both the symmetric and asymmetric airfoils. Thus, the present study clearly demonstrates that the airfoils with higher t/c ratios could be considered as the best passive means for achieving substantial reductions of airfoil broadband noise over a wide range of frequencies.
A Statistical Shape Model of Infrarenal Aortic Necks in Patients With and Without Late Type Ia Endoleak After Endovascular Aneurysm Repair
Authors: van Veldhuizen Willemina A. , Schuurmann Richte C. L. , Zuidema Roy , Geraedts Anna C. M. , IJpma Frank F. A. , Kropman Rogier H. J. , Antoniou George A. , van Sambeek Marc R. H. M. , Balm Ron , Wolterink Jelmer M. , de Vries Jean-Paul P. M. 
Published: January 2023

Purpose: Hostile aortic neck characteristics, including short length, severe suprarenal and infrarenal angulation, conicity, and large diameter, have been associated with increased risk for type Ia endoleak (T1aEL) after endovascular aneurysm repair (EVAR). This study investigates the mid-term discriminative ability of a statistical shape model (SSM) of the infrarenal aortic neck morphology compared with or in combination with conventional measurements in patients who developed T1aEL post-EVAR. Materials and Methods: The dataset composed of EVAR patients who developed a T1aEL during follow-up and a control group without T1aEL. Principal component (PC) analysis was performed using a parametrization to create an SSM. Three logistic regression models were created. To discriminate between patients with and without T1aEL, sensitivity, specificity, and the area under the receiver operating characteristic (ROC) curve (AUC) were calculated. Results: In total, 126 patients (84% male) were included. Median follow-up time in T1aEl group and control group was 52 (31, 78.5) and 51 (40, 62.5) months, respectively. Median follow-up time was not statistically different between the groups (p=0.72). A statistically significant difference between the median PC scores of the T1aEL and control groups was found for the first, eighth, and ninth PC. Sensitivity, specificity, and AUC values for the SSM-based versus the conventional measurements–based logistic regression models were 79%, 70%, and 0.82 versus 74%, 73%, and 0.85, respectively. The model of the SSM and conventional measurements combined resulted in sensitivity, specificity, and AUC of 81%, 81%, and 0.92. Conclusion: An SSM of the infrarenal aortic neck determines its 3-dimensional geometry. The SSM is a potential valuable tool for risk stratification and T1aEL prediction in EVAR. The SSM complements the conventional measurements of the individual preoperative infrarenal aortic neck geometry by increasing the predictive value for late type Ia endoleak after standard EVAR. Clinical Impact A statistical shape model (SSM) determines the 3-dimensional geometry of the infrarenal aortic neck. The SSM complements the conventional measurements of the individual pre-operative infrarenal aortic neck geometry by increasing the predictive value for late type Ia endoleaks post-EVAR. The SSM is a potential valuable tool for risk stratification and late T1aEL prediction in EVAR and it is a first step toward implementation of a treatment planning support tool in daily clinical practice.
Disappearance of a small unruptured intracranial aneurysm: A case report and brief literature review
Authors: Begley Sabrina L , White Timothy G , Khilji Hamza , Katz Jeffrey , Dehdashti Amir R 
Published: January 2023

Disappearing intracranial aneurysms are rare and have not been extensively reported in the literature. They are often small or partially thrombosed and carry a significant risk of recurrence. We discuss a unique case of a 65-year-old woman who presented in 2006 with a subarachnoid hemorrhage and was found to have a ruptured posterior communicating artery and an unruptured P1 aneurysm. Follow-up angiography and imaging showed no changes in the size of a left P1 aneurysm for 11 years (2006–2017). However, in 2021, 15 years after initial presentation, no aneurysm was seen on magnetic resonance angiography, and subsequent digital subtraction angiography in 2022 showed almost complete disappearance of the unruptured P1 aneurysm. Literature review reveals only six reported cases during which a small, unruptured anterior circulation aneurysm disappeared, or regressed on follow-up imaging and no reported cases in the posterior circulation.
Comparing ability and norm-referenced scores as clinical trial outcomes for neurodevelopmental disabilities: a simulation study
Authors: Farmer Cristan , Thurm Audrey , Troy Jesse D. , Kaat Aaron J. 
Published: January 2023

Abstract
Background
For genetic conditions associated with neurodevelopmental disorder (GCAND), developmental domains such as motor ability, thinking and learning, social abilities, and communication are potential intervention targets. Performance on measures of developmental concepts can be expressed using several types of scores. Norm-referenced scores are intended for the diagnostic context, allowing for the identification of impairment relative to age-based expectations, and can exhibit dramatic floor effects when used in individuals with more significant limitations. Person ability scores, which are derived via Rasch analysis or item response theory, are available on many standardized tests and are intended to measure within-person change. However, they have not been used or evaluated as primary endpoints in GCAND clinical trials. In this study, we simulated a series of parallel-arm clinical trials under several chronological age and impairment conditions, to compare empirically the power and type I error rate of operationalizing test performance using ability scores rather than norm-referenced scores.

Results
Using the Vineland Adaptive Behavior Scales as the example, we demonstrated an advantage in statistical power of ability scores over norm-referenced scores at extreme levels of impairment. This advantage was at least partially driven by floor effects in norm-referenced scores. For simulated conditions where impairment was less severe, ability scores outperformed norm-referenced scores, but they were more similar. The type I error rate closely approximated the nominal type I error rate of 5% for both scores.

Conclusion
The results of this simulation demonstrate a substantial power and interpretative advantage of ability scores over norm-referenced scores for studies of GCAND that will enroll participants with high levels of impairment. These results are expected to generalize to studies of developmental concepts, regardless of the etiology or specific test. However, the relative advantage of ability scores is expected to be even greater for tests with a higher floor than the Vineland.
Artificially Selected Grain Shape Gene Combinations in Guangdong Simiao Varieties of Rice (Oryza sativa L.)
Authors: Yang Tifeng , Gu Haiyong , Yang Wu , Liu Bin , Liang Shihu , Zhao Junliang 
Published: January 2023

Abstract
Background
Grain shape is a key trait in rice breeding. Although many QTLs and genes of grain shape have been identified, how different combinations of alleles of these genes affect grain shape is largely unknown. It is important to understand the effects of grain shape gene combinations for breeding by design. In the present study, we performed genetic dissection of the grain shapes in Guangdong Simiao varieties, a popular kind of rice in South China, to identify the effective alleles and their combination for breeding.

Results
We selected two hundred nineteen indica accessions with diverse grain shapes and fifty-two Guangdong Simiao varieties with long and slender grain shapes for genome-wide selection analysis. The results showed that four (GS3, GS5, GW5 and GL7) of the twenty grain shape genes fall into the regions selected for in Guangdong Simiao varieties. Allele analysis and frequency distribution of these four genes showed that GS3allele3 and GW5allele2 accounted for 96.2%, and GL7allele2 and GS5allele2 accounted for 76.9% and 74.5% of the Simiao varieties, respectively. Further analysis of the allelic combinations showed that 30 allelic combinations were identified in the whole panel, with 28 allelic combinations found in the international indica accessions and 6 allelic combinations found in Guangdong Simiao varieties. There were mainly three combinations (combinations 17, 18 and 19) in the Guangdong Simiao varieties, with combination 19 (GS3allele3 + GW5allele2 + GL7allele2 + GS5allele2) having the highest percentage (51.9%). All three combinations carried GS3allele3 + GW5allele2, while combinations 17 (GL7allele1) and 19 (GL7allele2) showed significant differences in both grain length and length/width ratio due to differences in GL7 alleles. Pedigree analysis of Guang8B, the maintainer of the first released Simiao male sterile line Guang8A, showed that the parent lines and Guang8B carried GS3allele3 + GW5allele2 + GS5allele2, while the GL7 allele differed, resulting in significant differences in grain size.

Conclusion
The results suggest that specific alleles of GS3, GS5, GW5 and GL7 are the key grain shape genes used in the Guangdong Simiao varieties and selected for grain shape improvement. Combination 19 is the predominant allelic combination in the Guangdong Simiao varieties. Our current study is the first to dissect the genetics of grain shape in Guangdong Simiao varieties, and the results will facilitate molecular breeding of Guangdong Simiao varieties.
PU.1-CD23 signaling mediates pulmonary innate immunity against Aspergillus fumigatus infection by driving inflammatory response
Authors: Wang Min , Zhang Ming , Qiu Jiayong , Liu Chenyang , Lou Yao , Wang Tongsheng , Zhang Yingmin , Mao Yimin 
Published: January 2023

Abstract
Background
Aspergillosis is a common cause of morbidity and mortality in immunocompromised populations. PU.1 is critical for innate immunity against Aspergillus fumigatus (AF) in macrophages. However, the molecular mechanism underlying PU.1 mediating immunity against AF infection in human alveolar macrophages (AMs) is still unclear.

Methods
In this study, we detected the expressions of PU.1, CD23, p-ERK, CCL20 and IL-8 and key inflammatory markers IL-1β, IL-6, TNF-α and IL-12 in human THP-1-derived macrophages (HTMs) or PU.1/CD23-overexpressed immunodeficient mice with AF infection. Moreover, we examined these expressions in PU.1-overexpressed/interfered HTMs. Additionally, we detected the phagocytosis of macrophages against AF infection with altered PU.1 expression. Dual luciferase, ChIP and EMSAs were performed to detect the interaction of PU.1 and CD23. And we invested the histological changes in mouse lung tissues transfected with PU.1/CD23-expressing adenoviruses in AF infection.

Results
The results showed that the expressions of PU.1, CD23, p-ERK, CCL20, IL-8, IL-1β, IL-6, TNF-α and IL-12 increased significantly with AF infection, and PU.1 regulated the later 8 gene expressions in HTMs. Moreover, CD23 was directly activated by PU.1, and overexpression of CD23 in PU.1-interfered HTMs upregulated IL-1β, IL-6, TNF-α and IL-12 levels which were downregulated by PU.1 interference. PU.1 overexpression strengthened the phagocytosis of the HTMs against AF. And injection of PU.1/CD23-expressing adenoviruses attenuated pathological defects in immunodeficient mouse lung tissues with AF infection. Adenovirus (Ad)-PU.1 increased the CD23, p-ERK, CCL20, IL-8 levels.

Conclusions
Our study concluded that PU.1-CD23 signaling mediates innate immunity against AF in lungs through regulating inflammatory response. Therefore, PU.1-CD23 may be a new anti-aspergillosis therapeutic for the treatment of invasive aspergillosis with the deepening of gene therapy and its wide application in the clinic.
Biochar and biofertilizer reduced nitrogen input and increased soybean yield in the maize soybean relay strip intercropping system
Authors: Luo Kai , Xie Chen , Yuan Xiaoting , Liu Shanshan , Chen Ping , Du Qing , Zheng Benchuan , Fu Zhidan , Wang Xiaochun , Yong Taiwen , Yang Wenyu 
Published: January 2023

AbstractApplying Biochar (BC) or biofertilizers (BF) are potential approaches to reduce the nitrogen input and mitigate soil degradation in the maize soybean relay strip intercropping system (IS). In 2019 and 2020, a two-factor experiment was carried out to examine the effects of BC and BF on soil productivity and yield production in IS. 4 N input levels (8.4, 22.5, 45 kg, and 67.5 kg ha − 1) referred to as N0, N1, N2, and N3 were paired with various organic treatments, including BC (150 kg ha − 1), BF (300 kg ha − 1), and without organic amendments (CK). The results demonstrated that, despite BF decreasing the biomass and N distribution into grains, BF performed better on improved soybean yield (5.2–8.5%) by increasing the accumulation of soybean biomass (7.2 ~ 11.6%) and N (7.7%). Even though BC and BF have a detrimental effect on soybean nitrogen fixation by reducing nodule number and weight, the values of soybean nitrogenase activity and nitrogen fixation potential in BF were higher than those in BC. Additionally, BF performs better at boosting the soil’s nitrogen content and nitrate reductase and urease activity. BF increased the concentration of total N, soil organic matter, Olsen-phosphorus, and alkaline hydrolyzable N in the soil by 13.0, 17.1, 22.0, and 7.4%, respectively, compared to CK. Above all, applying BF combination with N2 (45 kg ha − 1 N) is a feasible strategy to raise crop grain output and keep soil productivity over the long term in IS.
The risk factors of thrombus formation and the effect of catheter ablation on repetitive thrombus formation in patients with atrial fibrillation: a single center retrospective study in China
Authors: Liu Huiyu , Lin Mingjie , Han Wenqiang , Ge Junye , Maduray Kellina , Zhong Jingquan 
Published: January 2023

AbstractBackgroundAtrial fibrillation (AF) predisposes patients to the formation of atrial thrombi. The CHA2DS2-VASc score does not include all risk factors for atrial thrombosis. The present study is designed to explore the influencing factors of thrombus formation in patients with AF and to investigate the effect of catheter ablation (CA) on recurrent thrombosis in patients with a history of intracardiac thrombus.Methods(1) This study consisted of 1726 patients that underwent CA, among which 58 patients had a history of intracardiac thrombus prior to CA. The risk factors for thrombus formation were explored by comparing the baseline clinical characteristics of patients with and without atrial thrombus. (2) The left atrial appendage flow velocity (LAAFV) in patients with a history of intracardiac thrombus who were willing to undergo transesophageal echocardiography (TEE) at the latest follow-up were examined, and comparisons of the LAAFV was made before and after CA.ResultsThe median follow-up period is 13 months. Persistent AF was found to be the only independent risk factor affecting the formation of atrial thrombus among the investigated factors (OR 3.152; 95%CI 1.806–5.500;p < 0.001). Twenty-seven patients agreed to undergo TEE during follow-up, no clinical ischemic stroke events were recorded, no recurrent intracardiac thrombus formation was detected in patients, 15 patients maintained sinus rhythm (55.6%) during follow-up; successful CA significantly increased LAAFV (difference between latest evaluation prior to CA 17.46 ± 14.81 cm/s,p < 0.001).ConclusionsPersistent AF is the only independent risk factor for thrombus formation. Successful CA may improve the LAAFV and thereby decrease the risk of intracardiac thrombus formation.
3-Year outcomes after left atrial appendage closure in patients with nonvalvular atrial fibrillation: cardiomyopathy related with increased death and stroke rate
Authors: Chen Chunyu , Chen Yuyi , Qu Lulu , Su Xi , Chen Yanhong 
Published: January 2023

Abstract
Introduction
Left atrial appendage closure (LAAC) is a novel treatment for stroke prevention in high-risk patients with non-valvular atrial fibrillation (NVAF). However, the long-term outcomes after LAAC in Chinese NVAF patients are still lacking.

Methods
This was a single-center, bidirectional, nonrandomized registered study. Patients who underwent LAAC implantation from May 2014 to April 2021 in a large Chinese center were enrolled. The primary endpoint was combined all-cause death and stroke.

Results
From May 2014 to April 2021, a total of 673 NVAF patients were enrolled. The overall successful implantation rate was 97.62% (657 of 673). The rate of perioperative adverse events was 1.19% (8 of 673), including 3 cardiac tamponades, 2 ischemic strokes, one device-related thrombus (DRT) and 2 device dislocations. 604 (92.24%) patients completed the follow-up, the median follow-up period was 36.9 months (IQR 24.8–56.5 months). 16 stroke events occurred in 15 patients (one patient suffered from both hemorrhagic and ischemic strokes). 13 patients (2.15%) had ischemic stroke, and the fatal rate was 0.33% (2 of 604). 3 patients (0.15%) suffered from hemorrhagic stroke, and the fatal rate was 0.17% (1 of 604). The overall stroke rate was 0.74% per-year. The combined death and stroke rate was 1.93% per-year. In the multivariate Cox regression analysis, age ≥ 75 (hazard ratio 2.264, 95% CI 1.074–4.772, P = 0.032) and ventricular cardiomyopathy (hazard ratio 2.738, 95% CI 1.060–7.071, P = 0.037) were independent predictors of combined mortality and stroke.

Conclusion
The overall successful implantation rate of LAAC was 97.62% and the rate of perioperative adverse events was 1.19% in this study, and the stroke rate was 0.74% per year during the long-term follow-up. Age ≥ 75 years and ventricular cardiomyopathy were independent predictors of the primary endpoint.
Trial registration This study was retrospectively registered.
Comparing g-computation, propensity score-based weighting, and targeted maximum likelihood estimation for analyzing externally controlled trials with both measured and unmeasured confounders: a simulation study
Authors: Ren Jinma , Cislo Paul , Cappelleri Joseph C. , Hlavacek Patrick , DiBonaventura Marco 
Published: January 2023

Abstract
Objectives
To have confidence in one's interpretation of treatment effects assessed by comparing trial results to external controls, minimizing bias is a critical step. We sought to investigate different methods for causal inference in simulated data sets with measured and unmeasured confounders.

Methods
The simulated data included three types of outcomes (continuous, binary, and time-to-event), treatment assignment, two measured baseline confounders, and one unmeasured confounding factor. Three scenarios were set to create different intensities of confounding effect (e.g., small and blocked confounding paths, medium and blocked confounding paths, and one large unblocked confounding path for scenario 1 to 3, respectively) caused by the unmeasured confounder. The methods of g-computation (GC), inverse probability of treatment weighting (IPTW), overlap weighting (OW), standardized mortality/morbidity ratio (SMR), and targeted maximum likelihood estimation (TMLE) were used to estimate average treatment effects and reduce potential biases.

Results
The results with the greatest extent of biases were from the raw model that ignored all the potential confounders. In scenario 2, the unmeasured factor indirectly influenced the treatment assignment through a measured controlling factor and led to medium confounding. The methods of GC, IPTW, OW, SMR, and TMLE removed most of bias observed in average treatment effects for all three types of outcomes from the raw model. Similar results were found in scenario 1, but the results tended to be biased in scenario 3. GC had the best performance followed by OW.

Conclusions
The aforesaid methods can be used for causal inference in externally controlled studies when there is no large, unblockable confounding path for an unmeasured confounder. GC and OW are the preferable approaches.