bluuebunny/crossref_metadata_2025_split huggingface dataset:
Engineering a marine microalga Chlorella sp. as the cell factory
Authors: Gu Xinping , Deng Ying , Wang Aoqi , Gan Qinhua , Xin Yi , Paithoonrangsarid Kalyanee , Lu Yandu 
Published: September 2023

AbstractThe use of marine microalgae in industrial systems is attractive for converting CO2 into value-added products using saline water and sunlight. The plant nature and demonstrated industrial potential facilitate Chlorella spp. as excellent model organisms for both basic research and commercial application. However, the transformation method has not been developed in marine Chlorella spp., thus genetic engineering is hindered in exploiting the industrial potentialities of these strains. In this study, we provided a transformation protocol for the marine Chlorella strain MEM25, which showed robust characteristics, including high production of proteins and polyunsaturated fatty acids in multiple cultivation systems over various spatial–temporal scales. We showed that transformants could be obtained in a dramatically time-saving manner (comparable to Saccharomyces cerevisiae) with four functional proteins expressed properly. The transgenes are integrated into the genome and can be successfully inherited for more than two years. The development of a marine Chlorella transformation method, in combination with the complete genome, will greatly facilitate more comprehensive mechanism studies and provide possibilities to use this species as chassis for synthetic biology to produce value-added compounds with mutual advantage in neutralization of CO2 in commercial scales.
Waist circumference is independently associated with liver steatosis and fibrosis in LMNA-related and unrelated Familial Partial Lipodystrophy women
Authors: Viola Luiz F. , Valerio Cynthia M. , Araujo-Neto João M. , Santos Fabio F. , Matsuura Felipe , Moreira Rodrigo O. , Godoy-Matos Amélio F. 
Published: September 2023

Abstract
Background
Lipodystrophies are a heterogeneous group of diseases characterized by the selective loss of subcutaneous adipose tissue and ectopic fat deposition in different organs, including the liver. This study aimed to determine the frequencies of liver steatosis (LS) and liver fibrosis (LF) in a sample of individuals with LMNA-related and unrelated Familial Partial Lipodystrophy.

Methods
This cross-sectional study included 17 women with LMNA-related FPLD and 15 women with unrelated FPLD. LS and LF were assessed using transient elastography (TE) with FibroScan®. Anthropometric and biochemical variables were included in a multiple linear regression analysis to identify the variables that were independently related to liver disease.

Results
Regarding the presence of LF, 22 (68.2%) women were classified as having non-significant fibrosis, and 10 (31.8%) were classified as having significant or severe fibrosis. Regarding LS, only six women (20.7%) were classified as having an absence of steatosis, and 23 (79.3%) had mild to severe steatosis. After multiple linear regression, waist circumference (but not age, body mass index, or waist-to-hip ratio) was found to be independently related to LS and LF. Among the biochemical variables, only triglyceride levels were independently related to LS but not LF.

Conclusions
In women with FPLD, visceral fat accumulation appears to be the most important determinant of liver disease, including LF, rather than fat scarcity in the lower limbs.
Machine learning-identified stemness features and constructed stemness-related subtype with prognosis, chemotherapy, and immunotherapy responses for non-small cell lung cancer patients
Authors: Liu Mingshan , Zhou Ruihao , Zou Wei , Yang Zhuofan , Li Quanjin , Chen Zhiguo , jiang Lei , Zhang Jingtao 
Published: September 2023

Abstract
Aim
This study aimed to explore a novel subtype classification method based on the stemness characteristics of patients with non-small cell lung cancer (NSCLC).

Methods
Based on the Cancer Genome Atlas database to calculate the stemness index (mRNAsi) of NSCLC patients, an unsupervised consensus clustering method was used to classify patients into two subtypes and analyze the survival differences, somatic mutational load, copy number variation, and immune characteristics differences between them. Subsequently, four machine learning methods were used to construct and validate a stemness subtype classification model, and cell function experiments were performed to verify the effect of the signature gene ARTN on NSCLC.

Results
Patients with Stemness Subtype I had better PFS and a higher somatic mutational burden and copy number alteration than patients with Stemness Subtype II. In addition, the two stemness subtypes have different patterns of tumor immune microenvironment. The immune score and stromal score and overall score of Stemness Subtype II were higher than those of Stemness Subtype I, suggesting a relatively small benefit to immune checkpoints. Four machine learning methods constructed and validated classification model for stemness subtypes and obtained multiple logistic regression equations for 22 characteristic genes. The results of cell function experiments showed that ARTN can promote the proliferation, invasion, and migration of NSCLC and is closely related to cancer stem cell properties.

Conclusion
This new classification method based on stemness characteristics can effectively distinguish patients' characteristics and thus provide possible directions for the selection and optimization of clinical treatment plans.
Mature human induced pluripotent stem cell-derived cardiomyocytes promote angiogenesis through alpha-B crystallin
Authors: Tanaka Yuki , Kadota Shin , Zhao Jian , Kobayashi Hideki , Okano Satomi , Izumi Masaki , Honda Yusuke , Ichimura Hajime , Shiba Naoko , Uemura Takeshi , Wada Yuko , Chuma Shinichiro , Nakada Tsutomu , Tohyama Shugo , Fukuda Keiichi , Yamada Mitsuhiko , Seto Tatsuichiro , Kuwahara Koichiro , Shiba Yuji 
Published: September 2023

Abstract
Background
Human induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CMs) can be used to treat heart diseases; however, the optimal maturity of hiPSC-CMs for effective regenerative medicine remains unclear. We aimed to investigate the benefits of long-term cultured mature hiPSC-CMs in injured rat hearts.

Methods
Cardiomyocytes were differentiated from hiPSCs via monolayer culturing, and the cells were harvested on day 28 or 56 (D28-CMs or D56-CMs, respectively) after differentiation. We transplanted D28-CMs or D56-CMs into the hearts of rat myocardial infarction models and examined cell retention and engraftment via in vivo bioluminescence imaging and histological analysis. We performed transcriptomic sequencing analysis to elucidate the genetic profiles before and after hiPSC-CM transplantation.

Results
Upregulated expression of mature sarcomere genes in vitro was observed in D56-CMs compared with D28-CMs. In vivo bioluminescence imaging studies revealed increased bioluminescence intensity of D56-CMs at 8 and 12 weeks post-transplantation. Histological and immunohistochemical analyses showed that D56-CMs promoted engraftment and maturation in the graft area at 12 weeks post-transplantation. Notably, D56-CMs consistently promoted microvessel formation in the graft area from 1 to 12 weeks post-transplantation. Transcriptomic sequencing analysis revealed that compared with the engrafted D28-CMs, the engrafted D56-CMs enriched genes related to blood vessel regulation at 12 weeks post-transplantation. As shown by transcriptomic and western blot analyses, the expression of a small heat shock protein, alpha-B crystallin (CRYAB), was significantly upregulated in D56-CMs compared with D28-CMs. Endothelial cell migration was inhibited by small interfering RNA-mediated knockdown of CRYAB when co-cultured with D56-CMs in vitro. Furthermore, CRYAB overexpression enhanced angiogenesis in the D28-CM grafts at 4 weeks post-transplantation.

Conclusions
Long-term cultured mature hiPSC-CMs promoted engraftment, maturation and angiogenesis post-transplantation in infarcted rat hearts. CRYAB, which was highly expressed in D56-CMs, was identified as an angiogenic factor from mature hiPSC-CMs. This study revealed the benefits of long-term culture, which may enhance the therapeutic potential of hiPSC-CMs.
Infodemic: Challenges and solutions in topic discovery and data process
Authors: Zhang Jinjin , Pan Yang , Lin Han , Sun Zhoubao , Wu Pingping , Tu Juan 
Published: September 2023

Abstract
Background
The Coronavirus Disease 2019 (COVID-19) pandemic was a huge shock to society, and the ensuing information problems had a huge impact on society at the same time. The urgent need to understand the Infodemic, i.e., the importance of the spread of false information related to the epidemic, has been highlighted. However, while there is a growing interest in this phenomenon, studies on the topic discovery, data collection, and data preparation phases of the information analysis process have been lacking.

Objective
Since the epidemic is unprecedented and has not ended to this day, we aimed to examine the existing Infodemic-related literature from January 2019 to December 2022.

Methods
We have systematically searched ScienceDirect and IEEE Xplore databases with some search limitations. From the searched literature we selected titles, abstracts and keywords, and limitations sections. We conducted an extensive structured literature search and analysis by filtering the literature and sorting out the available information.

Results
A total of 47 papers ended up meeting the requirements of this review. Researchers in all of these literatures encountered different challenges, most of which were focused on the data collection step, with few challenges encountered in the data preparation phase and almost none in the topic discovery section. The challenges were mainly divided into the points of how to collect data quickly, how to get the required data samples, how to filter the data, what to do if the data set is too small, how to pick the right classifier and how to deal with topic drift and diversity. In addition, researchers have proposed partial solutions to the challenges, and we have also proposed possible solutions.

Conclusions
This review found that Infodemic is a rapidly growing research area that attracts the interest of researchers from different disciplines. The number of studies in this field has increased significantly in recent years, with researchers from different countries, including the United States, India, and China. Infodemic topic discovery, data collection, and data preparation are not easy, and each step faces different challenges. While there is some research in this emerging field, there are still many challenges that need to be addressed. These findings highlight the need for more articles to address these issues and fill these gaps.
Hand hygiene knowledge, attitude, barriers and improvement measures among healthcare workers in the Republic of Korea: a cross-sectional survey exploring interprofessional differences
Authors: Kim Jaewoong , Yu Shi Nae , Jeong Yeon Su , Kim Jin Hwa , Jeon Min Hyok , Kim Tark , Choo Eun Ju , Lee Eunjung , Kim Tae Hyong , Park Se Yoon 
Published: September 2023

Abstract
Background
Hand hygiene (HH) is a fundamental component of infection prevention and control in healthcare settings. This study aimed to identify knowledge, attitude, and barriers to HH according to occupational groups and strategies to increase the rate of HH compliance among healthcare workers (HCWs).

Methods
This cross-sectional survey was conducted in July 2018 at four university-affiliated hospitals. The survey comprised seven parts with 49 items, including self-reported HH compliance, knowledge, attitudes, behaviours, barriers to HH, and improvement strategies.

Results
A total of 1046 HCWs participated in the survey. The nursing group’s self-reported HH compliance rate was the highest, followed by other HCWs and physicians. The scores regarding knowledge, attitudes, and behaviours regarding HH were the highest in the nursing group. The nursing group also had higher internal and emotional motivation scores. Physicians and nurses found HH the most challenging in emergencies, while other HCWs considered skin problems caused by HH products the most significant barrier. Among 12 improvement measures, approximately 20% of the respondents ranked “diversify types of hand sanitisers,“ “install soap and paper towels in each hospital room,“ and “change perception through various HH campaigns” as the top three priorities. The physician group deemed the timely reminder of HH compliance as the second most critical improvement measure.

Conclusion
Differences in knowledge, attitude and barriers hindering HH compliance and improvement plans were identified for each group. The findings suggest that targeted interventions tailored to the specific needs of different occupational groups may effectively improve HH compliance in healthcare settings.
Exosomal NOX1 promotes tumor-associated macrophage M2 polarization-mediated cancer progression by stimulating ROS production in cervical cancer: a preliminary study
Authors: Gu Liying , Feng Chunyang , Li Meng , Hong Zubei , Di Wen , Qiu Lihua 
Published: September 2023

Abstract
Background
Cervical cancer the fourth most frequently diagnosed cancer and the fourth leading cause of cancer death in women, with an estimated 604,000 new cases and 342,000 deaths worldwide in 2020 for high rates of recurrence and metastasis. Identification of novel targets could aid in the prediction and treatment of cervical cancer. NADPH oxidase 1 (NOX1) gene-mediated production of reactive oxygen species (ROS) could induce migration and invasion of cervical cancer cells. Tumor-associated macrophages (TAMs) play important roles in cervical cancer. Tumor cell-derived exosomes mediate signal transduction between the tumor and tumor microenvironment. Elucidation of the mechanisms of NOX1-carrying exosomes involved in the regulation of TAMs may provide valuable insights into the progression of cervical cancer.

Methods
Uniformly standardized mRNA data of pan-carcinoma from the UCSC database were downloaded. Expression of NOX1 in tumor and adjacent normal tissues for each tumor type was calculated using R language software and significant differences were analyzed. SNP data set were downloaded for all TCGA samples processed using MuTect2 software from GDC. Cell experiment and animal tumor formation experiment were used to evaluate whether exosomal NOX1 stimulating ROS production to promote M2 polarization of TAM in cervical cancer.

Results
NOX1 is highly expressed with a low mutational frequency in pan-carcinoma. Upregulation of NOX1 may be associated with infiltration of M2-type macrophages in cervical cancer tissues, and NOX1 promotes malignant features of cervical cancer cells by stimulating ROS production. Exosomal NOX1 promotes M2 polarization of by stimulating ROS production. Exosomal NOX1 enhances progression of cervical cancer and M2 polarization in vivo by stimulating ROS production.

Conclusion
Exosomal NOX1 promotes TAM M2 polarization-mediated cancer progression through stimulating ROS production in cervical cancer.
The cause and effect of gut microbiota in development of inflammatory disorders of the breast
Authors: Gu Yibo , Hou Muye , Chu Jinyu , Wan Li , Yang Muyi , Shen Jiemiao , Ji Minghui 
Published: September 2023

Abstract
Background
Inflammatory disorders of the breast (IDB) damages the interests of women and children and hinders the progress of global health seriously. Several studies had offered clues between gut microbiota (GM) and inflammatory disorders of the breast (IDB). The gut–mammary gland axis also implied a possible contribution of the GM to IDB. However, the causality between them is still elusive.

Methods
The data of two-sample Mendelian randomization (MR) study related to the composition of GM (n = 18,340) and IDB (n = 177,446) were accessed from openly available genome-wide association studies (GWAS) database. As the major analytical method, inverse variance weighted (IVW) was introduced and several sensitive analytical methods were conducted to verify results.

Results
Inverse variance weighted revealed Eubacterium rectale group (OR = 1.87, 95% CI: 1.02–3.43, p = 4.20E−02), Olsenella (OR = 1.29, 95% CI: 1.02–1.64, p = 3.30E−02), Ruminiclostridium-6 (OR = 1.53, 95% CI: 1.08–2.14, p = 1.60E−02) had an anti-protective effect on IDB. Peptococcus (OR = 0.75, 95% CI: 0.60–0.94, p = 1.30E−02) had a protective effect on IDB. The results were credible through a series of test.

Conclusions
We revealed causality between IDB and GM taxa, exactly including Ruminiclostridium-6, Eubacterium rectale group, Olsenella and Peptococcus. These genera may become novel biomarkers and supply new viewpoint for probiotic treatment. However, these findings warrant further test owing to the insufficient evidences.
Effects of others’ gaze and facial expression on an observer’s microsaccades and their association with ADHD tendencies
Authors: Motomura Yuki , Hayashi Sayuri , Kurose Ryousei , Yoshida Hiroki , Okada Takashi , Higuchi Shigekazu 
Published: September 2023

Abstract
Background
The aim of this study was to examine the effect of others’ gaze on an observer’s microsaccades. We also aimed to conduct preliminary investigations on the relationship between the microsaccadic response to a gaze and a gazer’s facial expression and attention-deficit/hyperactivity disorder (ADHD) tendencies.

Methods
Twenty healthy undergraduate and graduate students performed a peripheral target detection task by using unpredictable gaze cues. During the task, the participants’ eye movements, along with changes in pupil size and response times for target detection, were recorded. ADHD tendencies were determined using an ADHD questionnaire.

Results
We found that consciously perceiving the gaze of another person induced the observer’s attention; moreover, microsaccades were biased in the direction opposite to the gaze. Furthermore, these microsaccade biases were differentially modulated, based on the cognitive processing of the facial expressions of the gaze. Exploratory correlation analysis indicated that microsaccade biases toward gazes with fearful expressions may specifically be correlated with participant characteristics, including inattention.

Conclusions
Our findings support that microsaccades reflect spatial attention processing and social cognitive processing. Moreover, the exploratory correlation analysis results suggested the potential benefit of using microsaccade bias toward spatial attention to assess pathophysiological responses associated with ADHD tendencies.
Fast adaptive multimodal feature registration (FAMFR): an effective high-resolution point clouds registration workflow for cultural heritage interiors
Authors: Foryś Piotr , Sitnik Robert , Markiewicz Jakub , Bunsch Eryk 
Published: September 2023

Abstract
Accurate registration of 3D scans is crucial in creating precise and detailed 3D models for various applications in cultural heritage. The dataset used in this study comprised numerous point clouds collected from different rooms in the Museum of King Jan III’s Palace in Warsaw using a structured light scanner. Point clouds from three relatively small rooms at Wilanow Palace: The King’s Chinese Cabinet, The King’s Wardrobe, and The Queen’s Antecabinet exhibit intricate geometric and decorative surfaces with diverse colour and reflective properties. As a result, creating a high-resolution full 3D model require a complex and time-consuming registration process. This process often consists of several steps: data preparation, registering point clouds, final relaxation, and evaluation of the resulting model. Registering two-point clouds is the most fundamental part of this process; therefore, an effective registration workflow capable of precisely registering two-point clouds representing various cultural heritage interiors is proposed in this paper. Fast Adaptive Multimodal Feature Registration (FAMFR) workflow is based on two different handcrafted features, utilising the colour and shape of the object to accurately register point clouds with extensive surface geometry details or geometrically deficient but with rich colour decorations. Furthermore, this work emphasises the challenges associated with high-resolution point clouds registration, providing an overview of various registration techniques ranging from feature-based classic approaches to new ones based on deep learning. A comparison shows that the algorithm explicitly created for this data achieved much better results than traditional feature-based or deep learning methods by at least 35%.
Validity, acceptability, and procedural issues of selection methods for graduate study admissions in the fields of science, technology, engineering, and mathematics: a mapping review
Authors: Kurysheva Anastasia , van Rijen Harold V. M. , Stolte Cecily , Dilaver Gönül 
Published: September 2023

AbstractThis review presents the first comprehensive synthesis of available research on selection methods for STEM graduate study admissions. Ten categories of graduate selection methods emerged. Each category was critically appraised against the following evaluative quality principles: predictive validity and reliability, acceptability, procedural issues, and cost-effectiveness. The findings advance the field of graduate selective admissions by (a) detecting selection methods and study success dimensions that are specific for STEM admissions, (b) including research evidence both on cognitive and noncognitive selection methods, and (c) showing the importance of accounting for all four evaluative quality principles in practice. Overall, this synthesis allows admissions committees to choose which selection methods to use and which essential aspects of their implementation to account for.
Preoperative CT-based radiomics combined with tumour spread through air spaces can accurately predict early recurrence of stage I lung adenocarcinoma: a multicentre retrospective cohort study
Authors: Wang Yuhang , Ding Yun , Liu Xin , Li Xin , Jia Xiaoteng , Li Jiuzhen , Zhang Han , Song Zhenchun , Xu Meilin , Ren Jie , Sun Daqiang 
Published: September 2023

Abstract
Objective
To develop and validate a prediction model for early recurrence of stage I lung adenocarcinoma (LUAD) that combines radiomics features based on preoperative CT with tumour spread through air spaces (STAS).

Materials and methods
The most recent preoperative thin-section chest CT scans and postoperative pathological haematoxylin and eosin-stained sections were retrospectively collected from patients with a postoperative pathological diagnosis of stage I LUAD. Regions of interest were manually segmented, and radiomics features were extracted from the tumour and peritumoral regions extended by 3 voxel units, 6 voxel units, and 12 voxel units, and 2D and 3D deep learning image features were extracted by convolutional neural networks. Then, the RAdiomics Integrated with STAS model (RAISm) was constructed. The performance of RAISm was then evaluated in a development cohort and validation cohort.

Results
A total of 226 patients from two medical centres from January 2015 to December 2018 were retrospectively included as the development cohort for the model and were randomly split into a training set (72.6%, n = 164) and a test set (27.4%, n = 62). From June 2019 to December 2019, 51 patients were included in the validation cohort. RAISm had excellent discrimination in predicting the early recurrence of stage I LUAD in the training cohort (AUC = 0.847, 95% CI 0.762–0.932) and validation cohort (AUC = 0.817, 95% CI 0.625–1.000). RAISm outperformed single modality signatures and other combinations of signatures in terms of discrimination and clinical net benefits.

Conclusion
We pioneered combining preoperative CT-based radiomics with STAS to predict stage I LUAD recurrence postoperatively and confirmed the superior effect of the model in validation cohorts, showing its potential to assist in postoperative treatment strategies.