bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genomic and transcriptomic analysis of breast cancer identifies novel signatures associated with response to neoadjuvant chemotherapy
Authors: Yin Gengshen , Liu Liyuan , Yu Ting , Yu Lixiang , Feng Man , Zhou Chengjun , Wang Xiaoying , Teng Guoxin , Ma Zhongbing , Zhou Wenzhong , Ye Chunmiao , Zhang Jialin , Ji Changhua , Zhao Linfeng , Zhou Peng , Guo Yaxun , Meng Xingchen , Fu Qinye , Zhang Qiang , Li Liang , Zhou Fei , Zheng Chao , Xiang Yujuan , Guo Mingming , Wang Yongjiu , Wang Fei , Huang Shuya , Yu Zhigang 
Published: January 2024

Abstract
Background
Neoadjuvant chemotherapy (NAC) has become a standard treatment strategy for breast cancer (BC). However, owing to the high heterogeneity of these tumors, it is unclear which patient population most likely benefit from NAC. Multi-omics offer an improved approach to uncovering genomic and transcriptomic changes before and after NAC in BC and to identifying molecular features associated with NAC sensitivity.

Methods
We performed whole-exome and RNA sequencing on 233 samples (including matched pre- and post-treatment tumors) from 50 BC patients with rigorously defined responses to NAC and analyzed changes in the multi-omics landscape. Molecular features associated with NAC response were identified and validated in a larger internal, and two external validation cohorts, as well as in vitro experiments.

Results
The most frequently altered genes were TP53, TTN, and MUC16 in both pre- and post-treatment tumors. In comparison with pre-treatment tumors, there was a significant decrease in C > A transversion mutations in post-treatment tumors (P = 0.020). NAC significantly decreased the mutation rate (P = 0.006) of the DNA repair pathway and gene expression levels (FDR = 0.007) in this pathway. NAC also significantly changed the expression level of immune checkpoint genes and the abundance of tumor-infiltrating immune and stroma cells, including B cells, activated dendritic cells, γδT cells, M2 macrophages and endothelial cells. Furthermore, there was a higher rate of C > T substitutions in NAC nonresponsive tumors than responsive ones, especially when the substitution site was flanked by C and G. Importantly, there was a unique amplified region at 8p11.23 (containing ADGRA2 and ADRB3) and a deleted region at 3p13 (harboring FOXP1) in NAC nonresponsive and responsive tumors, respectively. Particularly, the CDKAL1 missense variant P409L (p.Pro409Leu, c.1226C > T) decreased BC cell sensitivity to docetaxel, and ADGRA2 or ADRB3 gene amplifications were associated with worse NAC response and poor prognosis in BC patients.

Conclusions
Our study has revealed genomic and transcriptomic landscape changes following NAC in BC, and identified novel biomarkers (CDKAL1P409L, ADGRA2 and ADRB3) underlying chemotherapy resistance and poor prognosis, which could guide the development of personalized treatments for BC.
Insulin resistance-related features are associated with cognitive decline: a cross-sectional study in adult patients with type 1 diabetes
Authors: Ji Xiaolin , Zou Wenjing , Fan Li , Zhou Zhiguang , Zhu Xiongzhao , Li Xia 
Published: January 2024

Abstract
Background
To investigate the associations between insulin resistance (IR)-related features and cognitive function in type 1 diabetes (T1D).

Methods
A total of 117 adult patients with T1D were recruited in this cross-sectional study. IR-related features include overweight/obesity/central obesity, hypertension, atherogenic dyslipidemia, and decreased estimated insulin sensitivity (eIS). The Wechsler Memory Scale-Chinese Revision, Wisconsin Card Sorting Test, and Sustained Attention to Response Task was used to assess memory, executive function and sustained attention, respectively. A z-score was generated from each test, and a composite measure of global cognitive performance was calculated by averaging the z-scores of all tests. Cognitive differences were measured between T1D patients with and without IR-related features. The associations between IR-related features and and cognitive performance were analyzed using: logistic regression, partial correlation, and multivariate linear regression analysis.

Results
A total of 53 (45.3%) T1D patients were defined as having IR-related features. Individuals with IR-related features displayed worse overall cognitive scores compared to those without and had a 4-fold increase in the risk for having global cognitive z-score < 0. Among the IR-related features, higher triglyceride (TG) and lower eIS showed linear correlation with lower global cognitive performance. And the subsequent regression analysis identified eIS as the factor independently associated with global cognitive performance.

Conclusions
We have provided evidence linking IR-related features to deteriorated cognitive function in adult patients with T1D. And eIS showed an independent positive correlation with global cognitive performance. Although no causal relationship can be drawn, IR emerges as an important factor reflecting cognitive function.

Trial registration
ClinicalTrials.gov NCT03610984.
Sleep patterns and risks of incident cardiovascular disease and mortality among people with type 2 diabetes: a prospective study of the UK Biobank
Authors: Hu Jinxia , Wang Xuanyang , Cheng Licheng , Dang Keke , Ming Zhu , Tao Xinmiao , Xu Xiaoqing , Sarker Shuvan Kumar , Li Ying 
Published: January 2024

Abstract
Background
To explore the relationship between sleep patterns and cardiovascular disease (CVD) incidence and mortality risk in a population with type 2 diabetes through a UK Biobank sample.

Methods
A total of 6860 patients with type 2 diabetes were included in this study. Five sleep factors (including Chronotype, sleep duration, insomnia, daytime sleepiness, and snoring) were collected as a questionnaire. The calculation generates a sleep score of 0–5, and then three sleep patterns were defined based on the sleep scores: poor sleep pattern (0–2), Intermediate sleep pattern (3–4), and healthy sleep pattern (5). HRs and 95% confidence intervals were calculated by multivariate COX proportional risk model adjustment. Restricted cubic splines were used to validate linear associations between sleep scores CVD events.

Results
Our results found a reduced risk of CVD events in individuals with healthy sleep patterns compared to participants with poor sleep patterns. CVD Mortality (HR, 0.690; 95% CI 0.519–0.916), ASCVD (Atherosclerosis CVD) (HR, 0.784; 95% CI 0.671–0.915), CAD (Coronary Artery Disease) (HR, 0.737; 95% CI 0.618–0.879), PAD (Peripheral Arterial Disease) (HR, 0.612; 95% CI 0.418–0.896), Heart Failure (HR, 0.653; 95% CI 0.488–0.875). Restricted cubic spline responded to a negative linear correlation between sleep scores and CVD Mortality, ASCVD, CAD, PAD, and Heart Failure.

Conclusions
Healthy sleep patterns are significantly associated with a reduced risk of CVD Mortality, ASCVD, CAD, PAD, and Heart Failure in the diabetes population.
Effects of APOE2 and APOE4 on brain microstructure in older adults: modification by age, sex, and cognitive status
Authors: Reas Emilie T. , Triebswetter Curtis , Banks Sarah J. , McEvoy Linda K. 
Published: January 2024

AbstractBackgroundAPOE4is the strongest genetic risk factor for sporadic Alzheimer’s disease (AD), whereasAPOE2confers protection. However, effects ofAPOEon neurodegeneration in cognitively intact individuals, and how these associations evolve with cognitive decline, are unclear. Furthermore, few studies have evaluated whether effects ofAPOEon neurodegenerative changes are modified by other AD key risk factors including age and sex.MethodsParticipants included older adults (57% women; 77 ± 7 years) from the Rancho Bernardo Study of Health Aging and the University of California San Diego Alzheimer’s Disease Research Center, including 192 cognitively normal (CN) individuals and 33 with mild cognitive impairment. Participants underwent diffusion MRI, and multicompartment restriction spectrum imaging (RSI) metrics were computed in white matter, gray matter, and subcortical regions of interest. Participants were classified asAPOE4carriers,APOE2carriers, andAPOE3homozygotes. Analysis of covariance among CN (adjusting for age, sex, and scanner) assessed differences in brain microstructure byAPOE, as well as interactions betweenAPOEand sex. Analyses across all participants examined interactions betweenAPOE4and cognitive status. Linear regressions assessedAPOEby age interactions.ResultsAmong CN,APOE4carriers showed lower entorhinal cortex neurite density than non-carriers, whereasAPOE2carriers showed lower cingulum neurite density than non-carriers. Differences in entorhinal microstructure byAPOE4and in entorhinal and cingulum microstructure byAPOE2were present for women only. Age correlated with lower entorhinal restricted isotropic diffusion amongAPOE4non-carriers, whereas age correlated with lower putamen restricted isotropic diffusion amongAPOE4carriers. Differences in microstructure between cognitively normal and impaired participants were stronger forAPOE4-carriers in medial temporal regions, thalamus, and global gray matter, but stronger for non-carriers in caudate.ConclusionsThe entorhinal cortex may be an early target of neurodegenerative changes associated withAPOE4in presymptomatic individuals, whereasAPOE2may support beneficial white matter and entorhinal microstructure, with potential sex differences that warrant further investigation.APOEmodifies microstructural patterns associated with aging and cognitive impairment, which may advance the development of biomarkers to distinguish microstructural changes characteristic of normal brain aging,APOE-dependent pathways, and non-AD etiologies.
How Germany is phasing out lignite: insights from the Coal Commission and local communities
Authors: Radtke Jörg , David Martin 
Published: January 2024

Abstract
Background
This article asks the following question: how well are coal regions, affected by phase-out plans, represented in mediating commissions, to what extent do local communities participate in the decision-making process and how are the political negotiations perceived by the communities? We look at the case of the German lignite phase-out from a procedural justice perspective. Informed by literature on sociotechnical decline and procedural justice in energy transitions, we focus first on aspects of representation, participation and recognition within the German Commission on Growth, Structural Change and Employment (“Coal Commission”). Second, we analyze how to exnovate coal in two regions closely tied to the coal- and lignite-based energy history in Germany: Lusatia and the Rhenish Mining District.

Results
Based on interview series in both regions, we connect insights from local communities with strategies for structural change and participation programs in the regions. We find significant differences between the two regions, which is primarily an effect of the challenging historical experiences in Lusatia. Participation within existing arrangements is not sufficient to solve these problems; they require a comprehensive strategy for the future of the regions.

Conclusions
We conclude that the first phase-out process was a lost opportunity to initiate a community-inclusive sustainable transition process. As the phase-out process is not yet concluded, additional efforts and new strategies are needed to resolve the wicked problem of lignite phase-out.
Solar-assisted poultry production in small-scale farms: a case study in the Bekaa semi-arid region, Lebanon
Authors: Sleem Sara T. , Salam Darine A. , Ghaddar Nesreen , Abou Ghali Kamel , Chehab Ghassan , Daghir Nuhad , Doughan Youssef , Haddad Nicolas 
Published: January 2024

Abstract
Background
In Lebanon, poultry production is one of the major components of the agricultural sector; however, it suffers from increasing energy costs necessary to cover poultry heating requirements. This affects the profits of brooding farms, namely, small-scale farms in rural areas. Few studies have addressed the use of renewable energy in the poultry industry in Lebanon, with most having focused on modelling ventilation and air quality requirements in poultry houses. Therefore, there is a need to investigate the efficiency of renewable energy sources in providing heating requirements for poultry production. Accordingly, this study evaluates the performance of a solar-assisted, localized heating system in providing heat requirements for chicks in a renovated green poultry house in the Bekaa semi-arid rural region in Lebanon. For this aim, two brooding cycles were conducted during the warm and cold seasons in a greenhouse and were later replicated in a conventional poultry house.

Results
The energy inputs in the green and conventional houses, respectively, were 33,995.39 and 40,656.97 MJ (1000 birds)−1 in the warm season, and 37,058.25 and 45,770.05 MJ (1000 birds)−1 in the cold season. Calculated energy efficiency values for the green and conventional poultry houses were, respectively, 0.58 and 0.50 in the warm season, and 0.46 and 0.41 in the cold season. The net return was negative for both systems and the benefit-to-cost ratio from broiler production was calculated to be 0.49 and 0.50 in the green and conventional houses, respectively. Life cycle cost analysis showed that adopting the green heating system in the studied farm would entail an 18.89% increase in cost over a period of 20 years as compared to the conventional system.

Conclusion
It was concluded that poultry production is not profitable in small-scale farms in the studied area in Lebanon. The use of renewable energy might be more suited for large-scale broiler operations to achieve their purpose in reducing overall production costs. Optimization of the green system to fully satisfy the poultry energy requirements would render it more economically competitive.
Phytoplankton ecology in the early years of a boreal oil sands end pit lake
Authors: Furgason Chantel C. , Smirnova Angela V. , Dacks Joel B. , Dunfield Peter F. 
Published: January 2024

Abstract
Background
Base Mine Lake (BML) is the first full-scale end pit lake for the oil sands mining industry in Canada. BML sequesters oil sands tailings under a freshwater cap and is intended to develop into a functional ecosystem that can be integrated into the local watershed. The first stage of successful reclamation requires the development of a phytoplankton community supporting a typical boreal lake food web. To assess the diversity and dynamics of the phytoplankton community in BML at this reclamation stage and to set a baseline for future monitoring, we examined the phytoplankton community in BML from 2016 through 2021 using molecular methods (targeting the 23S, 18S, and 16S rRNA genes) and microscopic methods. Nearby water bodies were used as controls for a freshwater environment and an active tailings pond.

Results
The phytoplankton community was made up of diverse bacteria and eukaryotes typical of a boreal lake. Microscopy and molecular data both identified a phytoplankton community comparable at the phylum level to that of natural boreal lakes, dominated by Chlorophyta, Cryptophyta, and Cyanophyta, with some Bacillariophyta, Ochrophyta, and Euglenophyta. Although many of the same genera were prominent in both BML and the control freshwater reservoir, there were differences at the species or ASV level. Total diversity in BML was also consistently lower than the control freshwater site, but consistently higher than the control tailings pond. The phytoplankton community composition in BML changed over the 5-year study period. Some taxa present in 2016–2019 (e.g., Choricystis) were no longer detected in 2021, while some dinophytes and haptophytes became detectable in small quantities starting in 2019–2021. Different quantification methods (qPCR analysis of 23S rRNA genes, and microscopic estimates of populations and total biomass) did not show a consistent directional trend in total phytoplankton over the 5-year study, nor was there any consistent increase in phytoplankton species diversity. The 5-year period was likely an insufficient time frame for detecting community trends, as phytoplankton communities are highly variable at the genus and species level.

Conclusions
BML supports a phytoplankton community composition somewhat unique from control sites (active tailings and freshwater lake) and is still changing over time. However, the most abundant genera are typical of natural boreal lakes and have the potential to support a complex aquatic food web, with many of its identified major phytoplankton constituents known to be primary producers in boreal lake environments.
A hybrid neuro fuzzy decision-making approach to the participants of derivatives market for fintech investors in emerging economies
Authors: Rahadian Dadan , Firli Anisah , Dinçer Hasan , Yüksel Serhat , Mikhaylov Alexey , Ecer Fatih 
Published: January 2024

AbstractThe risk profiles of investors play an important role in the success of derivative products investments. It is also necessary to determine the appropriate investor profile according to the conditions of a country. This protects investors from major losses. Therefore, there is a strong need for a new study that analyzes the risk profiles of derivative products in emerging economies. This study aims to identify the most appropriate investor risk profile for derivative instruments in emerging economies. It constructs a novel decision-making model. In this model, the facial action coding system, quantum theory, spherical fuzzy sets, and multi-stepwise weight assessment ratio analysis (M-SWARA) methodology are integrated to minimize uncertainty in this process. First, three main participants of derivatives for financial technology investors are evaluated using the quantum spherical fuzzy M-SWARA technique. After that, seven emerging economies are ranked based on this performance using quantum spherical fuzzy technique for order of preference by similarity to ideal solution. The main contribution is that an appropriate investor profile is identified for financial derivative investments in emerging economies. One of the important originalities of this study is the development of a new technique called M-SWARA by making some improvements to the classical stepwise weight assessment ratio analysis method. It is concluded that hedging is the most appropriate purpose for making investments in derivative products in emerging economies. It is also identified that China has the greatest performance among the seven emerging economies regarding the appropriate purpose for making derivative investments. For the effective management of this problem in these countries, it is recommended to prevent the speculative use of derivative products with legal regulations.
Phenolic-rich fraction of green tea attenuates histamine-mediated cardiopulmonary toxicity by inhibiting Cox-2/NF-κB signaling pathway and regulating oxidant/antioxidant balance
Authors: Hassanen Eman I. , Kamel Shaimaa , Issa Marwa Y. , Mohamed Wafaa A. , Mansour Hayam A. , Mahmoud Mahmoud A. 
Published: January 2024

Abstract
Background
Histamine (HIS) has a substantial impact on the development of numerous allergic disorders including asthma. Antihistamines mostly target histamine receptor-1 alone, so it is not entirely effective in the treatment of allergic diseases. In the current investigation, we examine the growing evidence for novel therapeutic strategies that aim to treat histamine-mediated cardiopulmonary toxicity with the phenolic-rich fraction of green tea (PRFGT).

Results
Our findings demonstrated that weekly ingestion of HIS to rats induced oxidant/antioxidant imbalance in both lung and heart homogenates. The histopathological examination demonstrated extensive interstitial pneumonia with progressive alveolar and bronchial damage in HIS receiving groups. Heart sections showed severe myocardial necrosis and hemorrhage. All lesions were confirmed by the immunohistochemical staining that demonstrated strong caspase-3, cyclooxygenase-2 (Cox-2), and tumor necrosis factor-α (TNF-α) protein expressions along with upregulation of the pulmonary m-RNA expression of TNF-α, nuclear factor kappa-B (NF-κB), and interleukin-1β (IL-1β) genes and cardiac levels of many apoptotic genes. Otherwise, the pretreatment of rats with PRFGT had the ability to alleviate all the aforementioned toxicological parameters and return the microscopic picture of both lung and heart sections to normal histology.

Conclusions
We concluded that PRFGT’s powerful antioxidant, anti-inflammatory, and anti-apoptotic properties can reduce cardiopulmonary toxicity caused by HIS. We recommended daily intake of green tea as a beverage or adding it to foods containing elevated levels of HIS to prevent its possible toxicity.
In vitro and in vivo evaluation of nanoliposomes loading quercetin and 3-bromopyruvate against glioma
Authors: Soriano-Ursúa Marvin Antonio , Vega-García Angélica , Buzoianu-Anguiano Vinnitsa , Ocampo-Nestor Ana Lilia , Manjarrez-Marmolejo Joaquín , Feria-Romero Iris Angélica 
Published: January 2024

Abstract
Background
Diffuse astrocytoma (a type of glioma) and its prevalence are matters of concern worldwide. Patients with this type of tumour have a poor prognosis because after surgical treatment, radiotherapy and/or chemotherapy, these tumours eventually regrow or progress. To date, there is no effective treatment that can cure affected patients. Quercetin and 3-bromopyruvate are chemical compounds that have been proven to have antitumour effects alone or in combination with other compounds. Nevertheless, combination treatments including these agents are not used for treating diffuse astrocytoma.

Methods
The use of nanoliposomes loaded with quercetin and 3-bromopyruvate as combination therapy was evaluated by treating C6 cells in vitro and in vivo (in Sprague–Dawley rat brain).

Results
The 0.5 mg/mL quercetin + 0.75 mg/mL 3-bromopyruvate combination treatment decreased the expression of the biomarkers Annexin V and Caspase-3 and inhibited tumour growth; this was consistent with the in vivo results that revealed the administration of this treatment resulted in improved animal survival.

Conclusions
The observations in the present study support the further exploration of this combination of active agents in the treatment of high-grade diffuse astrocytoma, especially in cases for which wide resection is possible.