bluuebunny/crossref_metadata_2025_split huggingface dataset:
Identification of Immune-related Cuproptosis Genes in the Prognosis of Thyroid Cancer
Authors: Zeng Lin , Xiong Ni , Qu Xin , Wang Ximing , Zhao Hengxia , Li Huilin , Liu Deliang 
Published: July 2023

Abstract
Background: Thyroid cancer (THCA) has gradually become the highest incidence of endocrine tumors, but its immunotherapy is still in its infancy. Cuproptosis has been reported to be closely related to various tumors. However, the mechanism of cuproptosis in THCA remains obscure.
Methods: TCGA-THCA dataset was downloaded from TCGA GDC portal. We then conducted survival analysis based on the cuproptosis scores (CPs), and constructed the models of RF and LASSO. GSVA and ssGSEA was subsequently performed. CIBERSORT was used to assess immune infiltration. TIDE algorithm was used to predict the likelihood of response to immunotherapy. qRT-PCR was used to confirm the expression of cuproptosis-related differentially expressed genes (CRDEGs) in THCA cells.
Results: We extracted 14 cuproptosis-related genes (CRGs) from TCGA-THCA, and 11 CRGs (SLC25A3, DLD, LIAS, ATP7B, PDHA1, SLC31A1, FDX1, DBT, GCSH, LIPT1 and DLAT) were CRDEGs. Survival analysis showed that the THCA patients with low-CPs had a relatively good prognosis. No matter which model (RF model or LASSO model) was chosen, the survival rate of high-risk group was lower in both Training dataset and Testing dataset, and 5 CRDEGs was selected as potential prognostic genes for THCA. GSVA showed that there were four differentially expressed hallmark gene sets (“APICAL_JUNCTION”, “APOPTOSIS”, “ANGIOGENESIS” and “COAGULATION” ) between high- and low-risk group in RF model and LASSO model. ssGSEA showed that pathways including glycerophospholipid metabolism, carbon metabolism and so on was differentially expressed among THCA patients with high- and low-CPs. CIBERSORT showed that the infiltrations of CD8+ T cells, Tregs, M0 Macrophages and M2 Macrophages, etc. exhibited significant differences. The scores of TIDE was higher in the high-CPs group, indicating THCA patients with high-CPs might be more likely to response immune checkpoint inhibits. qRT-PCR showed the mRNA levels of the above 5 CRDEGs were significantly downregulated in FTC-133 cells and 8505C cells.
Conclusions: This study identified 5 CRDEGs (FDX1, LIAS, LIPT1, DLD and PDHA1) and some immune cells associated with THCA, suggesting the treatment feasibility combined with targeting cuproptosis and immunotherapy in THCA.
Detailed Audit of the Energy Efficiency in Water Systems: New Performance Indices
Authors: Morani Maria Cristina , Carravetta Armando , Fecarotta Oreste , Montillo Renato 
Published: July 2023

Abstract

The proposed work aims at developing a new set of indices to carry out the energy audit of water systems. The new set consists of both supply and distribution indices and results from a global energy balance applied to a reference network. In this study, the energy audit of two case study networks is presented by the aid of the new proposed indices. Moreover, for each network, different scenarios are considered, differing in the management strategy proposed to increase the energy efficiency of the system. The comparison of the scenarios in terms of indices has allowed for evaluating the most efficient strategy to reduce the pressure exceeding within the network, among different solutions. According to the results, with reference to the case study distribution network, installing both pumps as turbines and pressure reducing valves represent the most efficient strategy, containing the excess pressure and also offering possibility for energy recovery. Moreover, with reference to the water supply system assumed as further case study network, the strategy exhibiting better values in terms of indices is represented by a direct pumping towards the downstream distribution network, instead of pumping towards an upper reservoir and using a valve or a turbine to dissipate the excess pressure. In this work, the proposed indices are demonstrated to be a useful tool for water managers to identify, among different solutions, the most effective intervention to increase the energy efficiency of water systems.
Cognitive Impairment and Associated Factors in Middle-aged and Elderly Individuals in Anhui Province, China
Authors: Cui Can , Zhai Yujia , Yu Tianyun , Zhang Shan , Su Zengfeng 
Published: July 2023

Abstract
Background The prevalence rate of CI among middle-aged and elderly individuals in Anhui Province was 12.6%. Female sex, elderly age, family history, low educational status, current smoking status, sleep disorders, hypertension, stroke, and diabetes were shown to be risk factors for CI, while exercise was shown to be a protective factor.
Methods From May to June 2022, a multistage, stratified cluster-sampling method was used to select 3200 middle-aged and elderly people over 45 years old in Anhui Province for a questionnaire survey, and the Chinese version of the Mini-Mental State Examination (MMSE) was used to assess cognitive function. SPSS 25.0 was used for univariate and multivariate analyses, and R software was used to establish and validate the nomogram.
Results A total of 3059 valid questionnaires were included, of which 384 were from participants who were diagnosed with CI, and the prevalence rate was 12.6%. Multivariate logistic analysis showed that female sex, advanced age, family history, etc., were closely related to the occurrence of CI. The AUC values in the modeling and validation groups were 0.845 (95% CI: 0.822-0.868) and 0.868 (95% CI: 0.835-0.902), respectively, indicating that the predictive ability of the model was good. The Hosmer‒Lemeshow test suggested that the model had good goodness-of-fit, and the decision-curve evaluation nomogram had a high benefit within the threshold, which had a certain clinical importance.
Cross inoculation study using the potential yeast strains isolated from starter cakes of traditional rice beer and different indigenous rice varieties of Tripura
Authors: Nath Nandita , Sharma Bipin Kumar 
Published: July 2023

Abstract

Tripura is a small hilly state of Northeast India, inhabited by several ethnic tribes having the tradition of preparation and consumption of traditional rice beer. The present study aimed to isolate and identify the potential yeast strains from starter culture cakes of different rice beers of Tripura and evaluate its fermentation ability by cross inoculation study with traditional rice varieties of this region. The yeast species were studied using culture-dependent methods, and they were identified as Saccharomyces cerevisiae, Saccharomycopsis fibuligera, and Wickerhamomyces anomalus. This identification was further supported by molecular analysis utilising partial 5.8S-ITS gene sequencing. To determine the most effective mixture for alcohol production, three traditional rice varieties—Tipra Binni, Kali Khasa, and Mula Sail and five potential yeast isolates were used in a cross-inoculation investigation. According to the findings of this study, Saccharomyces cerevisiae (NN/BKS/R4) and Tripra Binni have the highest prospect for producing alcohol. Additionally, it was also determined that using traditional rice varieties on a larger scale will enhance the quality of traditional beer and provide ample opportunity for scientific advancement for social acceptance and commercialization.
Assessment of the health risks associated with the consumption of bivalve molluscs potentially contaminated with phycotoxins, from a coastal ecosystem, the Ebrié lagoon, Côte d'Ivoire
Authors: Mel Hayo Vianney , Ouffoué Koffi Sébastien , Bamba Kafoumba , Diabagaté Dangui , Kouadio Olivier 
Published: July 2023

Abstract
This work focuses on the assessment of the risk associated with the consumption of bivalve molluscs, potentially contaminated with phycotoxins. The studied phycotoxins are saxitoxin (STX), okadaic acid (OA) and dinophysistoxins (DTX), yessotoxins (YTX), pectenotoxins (PTX), azaspiracids (AZA) and domoic acid (AD). They were sought in three species of bivalve molluscs (Anadara senilis, Crassostrea gasar and Perna perna), originating from the Ebrié lagoon. The quantifications were carried out by chromatography. The concentrations of OA and DTX, STX and AD were, respectively, 4.2 µg/kg; 9.6 µg/kg and 0.17 mg/kg. That of PTX, AZA and YTX were 3.3 µg/kg, respectively; 3.3 µg/kg and 0.003 mg/kg. The daily dose exposure DDE was 0.007 µg/kg bw for OA and DTX; 0.029 mg/kg bw for AD; 0.006 µg/kg bw for PTX; 0.017µg/kg bw for STX; 0.005 µg/kg bw for YTX and 0.006 µg/kg bw for AZA for the Crassostrea gasar oyster. These estimated values are lower than the acute reference doses (ARfD) of each phycotoxin promulgated by the European Food Safety Agency (EFSA). The risk of harmful effects is acceptable for the coastal populations, therefore a fortiori for the Ivorian population.
An extramedullary bone model to study metastatic dormancy reveals a piecemeal model for metastatic reactivation.
Authors: Malanchi Ilaria , Blasio Stefania Di , Rizou Tatiana , Gay Laurie , Rabas Nicolas , Chakravarty Probir , Snoeks Thomas , Karoutas Adam , Rodrigues Felipe , Bridgeman Victoria , Fan Xuanxuan , Bonnet Dominique , Abarrategi Ander 
Published: July 2023

Abstract

Metastatic relapse can occur months to years after the cancer is first diagnosed, and it relies on the reactivation of disseminated tumour cells (DTCs) that have lied dormant in secondary organs. The acquisition and maintenance of a dormancy phenotype are tightly regulated by the interaction of DTCs with their microenvironment. In the bone, the dormant program activated in metastatic competent cells and how their reactivation is induced are largely unknown. We here present a strategy to engineer a mouse-to-mouse extramedullary (EM) bone, which faithfully recapitulates endogenous bone and that can induce the acquisition of dormancy in highly metastatic breast cancer cells. By characterising the dormant state of metastatic cells, we found that they persist in two distinct transcriptional states: a more abundant quiescent and a less abundant proliferative state. The local environment influences the ratio between the two states. We found that an inflammatory mediator expressed by neutrophils progenitors, HMGB2, can contribute to nudging DTCs into an increased proliferation. Indeed, waves of emergency granulopoiesis expanding the neutrophils pool caused by inflammatory events such as intestinal colitis, expanded the proliferative pool of DTCs without resulting in a direct outgrowth. However, these events, progressively augmented the amount of DTCs in the bone, increasing the chance of overt metastasis. Therefore, this study proposes a piecemeal model of metastatic reactivation, where subsequent inflammatory events challenging the bone environment progressively increase the likelihood of outgrowth over time as opposed to a sudden switch from dormancy to metastasis.
Artificial intelligence reveals human biases in sustainability research
Authors: Varelas Panagiotis , Larosa Francesca , Hoyas Sergio , Conejero J. Alberto , Contino Francesco , Fuso-Nerini Francesco , García-Martínez Javier , Garibo-i-Orts Òscar , Parente Alessandro , Vinuesa Ricardo 
Published: July 2023

Abstract
To achieve sustainability, it is essential that all sustainable development goals (SDGs) receive adequate funding and that their interlinkages are supported in proposals. We use an artificial-intelligence-based approach to survey funding proposals in the European Union and the United States. We reveal that while some SDGs are widely covered by research projects, others receive less attention. Furthermore, we uncover persistent gender imbalances of the main applicant across almost all SDGs.
Leveraging Established Machine Learning Methodology to Tackle Viral Infections in Emergency Departments: A Retrospective Analysis using Hemocytometric Data to detect SARS-CoV-2
Authors: CURIER R. Lyana , Brouwer Calvin , wardak Hilda , Twist Daan van , Bromuri Stefano , Martens Remy , Leers Mathie 
Published: July 2023

Abstract
During the COVID-19 pandemic, the healthcare system faced significant strain. This study aimed to achieve two objectives: developing a machine learning model using only haemocytometric data to accurately identify COVID-19 positive patients in Emergency Departments (EDs) and empowering non-technical healthcare professionals to assess model performance and make informed decisions about implementing machine learning models in healthcare settings. This study utilized data from suspected COVID-19 admissions at Zuyderland Medical Center and employed principal component analysis, agglomerative hierarchical clustering, followed by Random Forest to build and evaluate the prediction model. Model validation was conducted using a separate dataset. The resulting model, based on 14 haemocytometric parameters, achieved an overall weighted accuracy of 0.88, with specificity, sensitivity, positive predictive values, and negative predictive values of 0.93, 0.78, 0.86, and 0.89, respectively. Concentrations of highly fluorescent lymphocytes, basophils, and eosinophils had the most significant impact on the model's output. This study demonstrates the potential of a well-trained machine learning model to predict COVID-19 infection within one hour using easily accessible laboratory data. Implementing this model in Emergency Departments could provide valuable support and alleviate staff workload.
Can we support mourning older adults in their grief process with an e-mental health intervention?
Authors: Hurmuz Marian Z. M. , Brandl Lena , Siderakis Eva , Schokking Lotte , Jacinto Sofia , Verdam Mandy , Jansen-Kosterink Stephanie M. 
Published: July 2023

Abstract

Purpose
To ensure a sustainable and safe implementation of e-mental health interventions for mourning older adults, we need to know how these interventions are used and whether the target group accepts them. Consequently, this research investigates the user experience of an e-mental health intervention supporting mourning older adults, called LEAVES.
Methods
We conducted a crossover pilot study in the Netherlands among older adults who lost their spouse: one group started with using the e-mental health intervention, the other group started with a waiting period and then used the e-mental health intervention. For both groups, a follow-up period was scheduled after using the intervention. Participants completed several questionnaires during the study and were invited to join a focus group session.
Results
We started with a total of 96 older adults: 45 in the intervention group and 51 in the waitlist group. The mean age of the total group was 67.9 (SD = 8.5) years old and the group consisted of slightly more females (52.1%). Participants used LEAVES on average around five times during the ten week period. The participants had positive attitudes towards their experience with LEAVES, and on an individual level we noticed that for the majority LEAVES was helpful in decreasing their grief symptoms, depression or loneliness.
Conclusions
Implementing an e-mental health intervention for supporting older adults while processing the loss of their spouse is promising. In our paper, we propose several recommendations for future e-mental health interventions which are important to take into account to ensure their sustainable implementation.
CYP5122A1 encodes an essential sterol C4-methyl oxidase in Leishmania donovani and determines the antileishmanial activity of antifungal azoles
Authors: Wang Michael , Jin Yiru , Basu Somrita , Feng Mei , Ning Yu , Munasinghe Indeewara , Joachim Arline , Li Junan , Madden Robert , Burks Hannah , Gao Philip , Perera Chamani , Werbovetz Karl , Zhang Kai 
Published: July 2023

Abstract

Visceral leishmaniasis, caused by Leishmania donovani, is a life-threatening parasitic disease, but current antileishmanial drugs are limited and have severe drawbacks. There have been efforts to repurpose antifungal azole drugs for the treatment of Leishmania infection. Antifungal azoles are known to potently inhibit the activity of cytochrome P450 (CYP) 51 enzymes which are responsible for removing the C14α-methyl group of lanosterol, a key step in ergosterol biosynthesis in Leishmania. However, they exhibit varying degrees of antileishmanial activities in culture, suggesting the existence of unrecognized molecular targets for these compounds. Our previous study reveals that, in Leishmania, lanosterol undergoes parallel C4- and C14-demethylation reactions to form 4α,14α-dimethylzymosterol and T-MAS, respectively. In the current study, CYP5122A1 is identified as a sterol C4-methyl oxidase that catalyzes the sequential oxidation of lanosterol to form C4-oxidation metabolites. CYP5122A1 is essential for both L. donovani promastigotes in culture and intracellular amastigotes in infected mice. Overexpression of CYP5122A1 results in growth delay, differentiation defects, increased tolerance to stress, and altered expression of lipophosphoglycan and proteophosphoglycan. CYP5122A1 also helps to determine the antileishmanial effect of antifungal azoles in vitro. Dual inhibitors of CYP51 and CYP5122A1, e.g., clotrimazole and posaconazole, possess superior antileishmanial activity against L. donovani promastigotes whereas CYP51-selective inhibitors, e.g., fluconazole and voriconazole, have little effect on promastigote growth. Our findings uncover the critical biochemical and biological role of CYP5122A1 in L. donovani and provide an important foundation for developing new antileishmanial drugs by targeting both CYP enzymes.
Bright and stable monomeric fluorescent proteins derived from StayGold
Authors: Piatkevich Kiryl , Lesnov Gleb , Zhang Hanbin , Subach Oksana , Vlaskina Anna , Samygina Valeriya , Nikolaeva Alena , Gabdulkhakov Azat , Qin Wenming , Borshchevskiy Valentin , Perfilov Maxim , Mishin Alexander , Subach Fedor 
Published: July 2023

Abstract
High brightness and photostability of StayGold make it a particularly attractive probe for long-term live cell imaging. However, its dimeric nature precludes its application as a fluorescent tag for proteins. Here, we report the development and X-ray structures of a monomeric variant of StayGold (mStayGold), which preserves the beneficial properties of its precursor while serving as a tag for structural proteins and membranes. We compare mStayGold to other state-of-art GFPs and utilize it for super-resolution long-term live cell imaging.
Essential oil production, chemical composition, bioactive compounds, and antioxidant activity of Thymus vulgaris as affected by harvesting season and drying conditions
Authors: Tohidi-Nejad Zahra , Khajoei-Nejad Gholamreza , Tohidi-Nejad Enayatollah , Ghanbari Jalal 
Published: July 2023

Abstract

In this study, the effects of seven distinct drying methods (sun, shade, freeze-drying [FD], oven drying at 40°C [OV40] and 70°C [OV70], and microwave 360 W [MW360] and 720 W [MW720]) were assessed in two harvesting seasons (spring and autumn) on the essential oil (EO) content, total phenolic content (TPC), total flavonoid content (TFC), antioxidant activity, and volatile compounds of thyme (Thymus vulgaris L.). The analysis of essential oils facilitated the identification of numerous compounds, 18 of which accounted for approximately 67.84–64.94% of the total thyme EO compounds. Six significant compounds were investigated, including thymol, p-cymene, γ-terpinene, carvacrol, linalool, and borneol. The results demonstrated that the thyme samples harvested in spring possessed higher amounts of γ-terpinene, thymol, carvacrol, EO content, and TFC, while samples harvested in autumn exhibited the highest amounts of borneol, p-cymene, TPC, and higher antioxidant activity. Principal component analysis (PCA) findings revealed that thyme samples harvested in spring, dried in the sun, shade, and FD conditions were rich in EO content, γ-terpinene and samples dried in MW720, OV40, and FD conditions possessed the highest amounts of thymol, carvacrol, and TFC. Drying the samples under MW360, OV40, and FD indicated significantly higher TPC and linalool. Drying the autumn-harvested samples under the sun and shade also exhibited higher linalool and TFC than other methods. Overall, the results conclusively indicated that the harvesting season and drying conditions significantly affected bioactive compounds, antioxidant activity, and EO production and quality.
Occult Squamous Cell Carcinoma in Lichenoid Dermatitis of the Glans Penis: a Potentially Life Threatning Entity Identified by Immunohistochemistry
Authors: Alomary Simona , Shah Rohan , Bova Emma , Swearingen Alyssa , Schwartz Robert , Lambert W. Clark 
Published: July 2023

Abstract
We have recently reported a series of three cases initially diagnosed histopathologically as lichenoid dermatitis subsequently revealed to be occult squamous cell carcinoma using immunohistochemistry. We now report a fourth case in the glans penis.
Development of gene-based InDel markers on putative drought stress responsive genes and genetic diversity of durian (Durio zibethinus)
Authors: Sathapondecha Ponsit , Suksri Phassorn , Nuanpirom Jirathchaya , Nakkanong Korakot , Nualsri Charassri , Whankaew Sukhuman 
Published: July 2023

Abstract
Insertion-deletion (InDel) markers are co-dominant, relatively abundant and practical for agarose gel genotyping. InDel polymorphism usually affects gene functions. Nucleotide sequences of durian (Durio zibethinus) are available, but InDel makers have not been well established. This study aimed to develop drought-related gene-based InDel markers for durian through bioinformatic analysis of RNA-Seq datasets. The polymorphism of the markers was verified in 24 durian genotypes local to Thailand. Bioinformatic analysis indicated 497 InDel loci having lengths more than 9 bp. To evaluate these InDel markers, 15 InDel loci were selected. Nine markers were successfully amplified a clear polymorphic band pattern on 2% agarose gel. The polymorphic information content (PIC) of these nine markers ranged from 0.1103 to 0.5808. The genetic distance between the 24 genotypes ranged from 0.222 to 0.889. The phylogeny based on the nine InDel loci distinguished the 24 genotypes, and divided samples into four groups. This set of gene-based InDel markers on putative drought responsive genes will be useful for genetic studies.
Analysis of the Brucella melitensis epidemic in Xinjiang: Genotyping, polymorphism, antibiotic resistance and tracing
Authors: Yang Xiaowen , Liu Yan , Li Na , Peng Xiaowei , Zhang Yinghui , Zhang Xiaoqian , Liang Lin , Bian Zengjie , Jiang Hui , Ding Jiabo 
Published: July 2023

Abstract

Brucella spp. are facultative intracellular pathogens that cause the zoonosis- brucellosis worldwide. There has been a trend of the re-emergence of brucellosis worldwide in recent years. Xinjiang is located in northwestern China and in the hinterland of the Eurasian continent. The epidemic situation of brucellosis is serious in Xinjiang. To analyze the epidemic situation of Brucella spp. in Xinjiang among humans and animals, this study used 16S rRNA amplification to identify 144 isolates of Brucella and their biovars. MLVA, drug resistance testing, and wgSNP detection were also performed. At the same time, analysis based on the published data of Brucella isolates worldwide was conducted. The results showed that the dominant species was B. melitensis biovar 3 and the correlation among isolates was high, whether in humans or animals. Since 2010, the polymorphism of isolates in Xinjiang has been increasing each year. No reported amikacin/kanamycin-resistant strains were found, but 6 rifampicin-intermediate isolates were found without rpoB gene variation. The NJ tree of the wgSNP results indicated that there were three main complexes of the B. melitensis epidemic in Xinjiang. In conclusion, the dominant Brucella species has greatest genetic variation in Xinjiang than other location in China, and the rifampicin-resistant trend has been existed in Xinjiang. This study analyzes the prevalence, genotyping, diversity, drug resistance, and tracing of B. melitensis in Xinjiang. The results provide basic data for the prevention and control of brucellosis in Xinjiang and China.