bluuebunny/crossref_metadata_2025_split huggingface dataset:
Transcriptomic analysis of glucosidase II beta subunit (GluIIß) knockout A549 cells reveals its roles in regulation of cell adhesion molecules (CAMs) and anti-tumor immunity
Authors: Khaodee Worapong , Xiyuan Guo , Han Moe Thi Thi , Tayapiwatana Chatchai , Chiampanichayakul Sawitree , Anuchapreeda Songyot , Cressey Ratchada 
Published: January 2024

AbstractGlucosidase II beta subunit (GluIIß), encoded from PRKCSH, is a subunit of the glucosidase II enzyme responsible for quality control of N-linked glycoprotein folding and suppression of GluIIß led to inhibitory effect of the receptor tyrosine kinase (RTKs) activities known to be critical for survival and development of cancer. In this study, we investigated the effect of GluIIß knockout on the global gene expression of cancer cells and its impact on functions of immune cells. GluIIß knockout lung adenocarcinoma A549 cell line was generated using CRISPR/Cas9-based genome editing system and subjected to transcriptomic analysis. Among 23,502 expressed transcripts, 1068 genes were significantly up-regulated and 807 genes greatly down-regulated. The KEGG enrichment analysis showed significant down-regulation of genes related extracellular matrix (ECM), ECM-receptor interaction, cytokine-cytokine receptor interaction and cell adhesion molecules (CAMs) in GluIIß knockout cells. Of 9 CAMs encoded DEG identified by KEGG enrichment analysis, real time RT-PCR confirmed 8 genes to be significantly down-regulated in all 3 different GluIIß knockout clones, which includes cadherin 4 (CDH4), cadherin 2 (CDH2), versican (VCAN), integrin subunit alpha 4 (ITGA4), endothelial cell-selective adhesion molecule (ESAM), CD274 (program death ligand-1 (PD-L1)), Cell Adhesion Molecule 1 (CADM1), and Nectin Cell Adhesion Molecule 3 (NECTIN3). Whereas PTPRF (Protein Tyrosine Phosphatase Receptor Type F) was significantly decreased only in 1 out of 3 knockout clones. Microscopic analysis revealed distinctively different cell morphology of GluIIβ knockout cells with lesser cytoplasmic and cell surface area compared to parental A549 cells and non-targeted transfected cells.Further investigations revealed that Jurkat E6.1 T cells or human peripheral blood mononuclear cells (PBMCs) co-cultured with GluIIß knockout A549 exhibited significantly increased viability and tumor cell killing activity compared to those co-cultured with non-target transfected cells. Analysis of cytokine released from Jurkat E6.1 T cells co-cultured with GluIIß knockout A549 cells showed significant increased level of angiogenin and significant decreased level of ENA-78. In conclusion, knockout of GluIIß from cancer cells induced altered gene expression profile that improved anti-tumor activities of co-cultured T lymphocytes and PBMCs thus suppression of GluIIß may represent a novel approach of boosting anti-tumor immunity.
Computational dissection of genetic variation modulating the response of multiple photosynthetic phenotypes to the light environment
Authors: Gong Huiying , Zhou Ziyang , Bu Chenhao , Zhang Deqiang , Fang Qing , Zhang Xiao-Yu , Song Yuepeng 
Published: January 2024

Abstract
Background
The expression of biological traits is modulated by genetics as well as the environment, and the level of influence exerted by the latter may vary across characteristics. Photosynthetic traits in plants are complex quantitative traits that are regulated by both endogenous genetic factors and external environmental factors such as light intensity and CO2 concentration. The specific processes impacted occur dynamically and continuously as the growth of plants changes. Although studies have been conducted to explore the genetic regulatory mechanisms of individual photosynthetic traits or to evaluate the effects of certain environmental variables on photosynthetic traits, the systematic impact of environmental variables on the dynamic process of integrated plant growth and development has not been fully elucidated.

Results
In this paper, we proposed a research framework to investigate the genetic mechanism of high-dimensional complex photosynthetic traits in response to the light environment at the genome level. We established a set of high-dimensional equations incorporating environmental regulators to integrate functional mapping and dynamic screening of gene‒environment complex systems to elucidate the process and pattern of intrinsic genetic regulatory mechanisms of three types of photosynthetic phenotypes of Populus simonii that varied with light intensity. Furthermore, a network structure was established to elucidate the crosstalk among significant QTLs that regulate photosynthetic phenotypic systems. Additionally, the detection of key QTLs governing the response of multiple phenotypes to the light environment, coupled with the intrinsic differences in genotype expression, provides valuable insights into the regulatory mechanisms that drive the transition of photosynthetic activity and photoprotection in the face of varying light intensity gradients.

Conclusions
This paper offers a comprehensive approach to unraveling the genetic architecture of multidimensional variations in photosynthetic phenotypes, considering the combined impact of integrated environmental factors from multiple perspectives.
Development and validation of a long-read metabarcoding platform for the detection of filarial worm pathogens of animals and humans
Authors: Huggins Lucas G. , Atapattu Ushani , Young Neil D. , Traub Rebecca J. , Colella Vito 
Published: January 2024

Abstract
Background
Filarial worms are important vector-borne pathogens of a large range of animal hosts, including humans, and are responsible for numerous debilitating neglected tropical diseases such as, lymphatic filariasis caused by Wuchereria bancrofti and Brugia spp., as well as loiasis caused by Loa loa. Moreover, some emerging or difficult-to-eliminate filarioid pathogens are zoonotic using animals like canines as reservoir hosts, for example Dirofilaria sp. ‘hongkongensis’. Diagnosis of filariasis through commonly available methods, like microscopy, can be challenging as microfilaremia may wane below the limit of detection. In contrast, conventional PCR methods are more sensitive and specific but may show limited ability to detect coinfections as well as emerging and/or novel pathogens. Use of deep-sequencing technologies obviate these challenges, providing sensitive detection of entire parasite communities, whilst also being better suited for the characterisation of rare or novel pathogens. Therefore, we developed a novel long-read metabarcoding assay for deep-sequencing the filarial nematode cytochrome c oxidase subunit I gene on Oxford Nanopore Technologies’ (ONT) MinION™ sequencer. We assessed the overall performance of our assay using kappa statistics to compare it to commonly used diagnostic methods for filarial worm detection, such as conventional PCR (cPCR) with Sanger sequencing and the microscopy-based modified Knott’s test (MKT).

Results
We confirmed our metabarcoding assay can characterise filarial parasites from a diverse range of genera, including, Breinlia, Brugia, Cercopithifilaria, Dipetalonema, Dirofilaria, Onchocerca, Setaria, Stephanofilaria and Wuchereria. We demonstrated proof-of-concept for this assay by using blood samples from Sri Lankan dogs, whereby we identified infections with the filarioids Acanthocheilonema reconditum, Brugia sp. Sri Lanka genotype and zoonotic Dirofilaria sp. ‘hongkongensis’. When compared to traditionally used diagnostics, such as the MKT and cPCR with Sanger sequencing, we identified an additional filarioid species and over 15% more mono- and coinfections.

Conclusions
Our developed metabarcoding assay may show broad applicability for the metabarcoding and diagnosis of the full spectrum of filarioids from a wide range of animal hosts, including mammals and vectors, whilst the utilisation of ONT’ small and portable MinION™ means that such methods could be deployed for field use.
Clinical characteristics of congenital heart defects in mild congenital anorectal malformation: single-centre experience
Authors: Feng Wei , Zhang Minjie , Hou Jinping , Die Xiaohong , Wang Yi , Liu Rong 
Published: January 2024

Abstract
Objective
To analyze the clinical characteristics and types of congenital heart defect (CHD) in mild congenital anorectal malformation (CARM), namely the rectoperineal and rectovestibular fistulas.

Methods
The retrospective study of 183 patients with mild CARM was conducted with assessments of demographic information, color Doppler echocardiography results, and follow-up data. We performed an analysis of the clinical characteristics of CHD, grouping them based on sex and type of mild CARM.

Results
Of the 183 patients, rectoperineal fistula occurred in 133 patients (72.7%), while the frequency of CHD was 79.8% (146/183). Ventricular septal defects (VSDs) occur more frequently in patients with rectoperineal fistula compared to those with rectovestibular fistula (1.5% vs. 10%), while the opposite trend was observed for patent ductus arteriosus (PDAs) (39.8% vs. 22.0%). Additionally, males presented higher frequency of PDA (42.7% vs. 26.4%) and self-healing (6 months: 87.2% vs. 42.6%; 12 months: 91.0% vs. 63.2%) than females. However, males had a lower rate of undergoing cardiac surgery (6.4% vs. 17.6%) and a younger median diagnosis age (1 day vs. 9 days).

Conclusion
Our study indicates that there is a necessity for meticulous cardiac assessment and follow-up in neonates diagnosed with mild CARM.
The impact of China's universal two-child policy on total, preterm, and multiple births: a nationwide interrupted time-series analysis
Authors: Geng Yuehang , Zhuo Lin , Zhang Rui , Zhao Houyu , Hou Xinlin , Chen Hu , Liu Lili 
Published: January 2024

Abstract
Background
Although years have passed since the implementation of China’s universal two-child policy, the effectiveness of this policy remains unclear. To address this knowledge gap, we, here, assessed the impact of the two-child policy on total live births, preterm births, and multiple live births.

Methods
Data identifying pregnancies resulting in at least one live birth between April 1 2013 and December 31 2018 were collected from the Hospital Quality Monitoring System database. Using an interrupted time-series analysis, we estimated immediate level changes and long-term trends in total, preterm (birth before 37 weeks’ gestation), and multiple live births that had occurred after July 2016, when the universal two-child policy had taken effect.

Results
A total of 8,273,622 live births were reported during the study time frame. The number of live births (p = 0.277), preterm births (p = 0.052), and multiple births (p = 0.856) per month slightly increased immediately after July 2016, but these increases did not meet statistical significance. Further, all three outcomes showed a significant downward trend that lasted until the end of 2018 (p < 0.0001 for all). Among all live births, the percentage of preterm births remained stable (p = 0.101), while the percentage of multiple live births that were preterm significantly increased (trend change = 0.21% per month, 95% CI 0.14 to 0.28, p < 0.0001). The percentage of live multiple births among all live births significantly decreased (p for trend = 0.0039).

Conclusions
Overall, our data reveal a transient baby boom, as well as an increase in the proportion of live multiple births that were preterm, after China’s two-child policy took effect. The latter should be noted by healthcare professionals due to the high risk of complications and special medical care required by preterm babies.
Reducing risk for chronic disease: evaluation of a collective community approach to sustainable evidence-based health programming
Authors: Oestman Katherine , Rechis Ruth , Williams Pamela A. , Brown Jill A. , Treiman Katherine , Zulkiewicz Brittany , Walsh Michael T. , Basen-Engquist Karen , Rodriguez Trina , Chennisi Catherine , Macneish Amber , Neff Alise , Pomeroy Mike , Bhojani Faiyaz A. , Hawk Ernest 
Published: January 2024

Abstract
Background
Community initiatives can shape health behaviors, such as physical activity and dietary habits, across a population and help reduce the risk of developing chronic disease. To achieve this goal and impact health outcomes, Pasadena Vibrant Community aimed to engage communities in an ongoing dialogue about the importance of healthy behaviors, implement and advance community-based strategies to promote health, and improve diet and physical activity behaviors. The initiative was centered around a collaboration between a backbone organization, steering committee, and 7 collaborating organizations funded to implement multicomponent, evidence-based programs.. The common agenda was detailed in a community action plan, which included 19 interventions targeting healthy eating and active living among adults and youth in Pasadena, Texas.

Methods
A mixed methods evaluation of the initiative was conducted over 4 years. Data sources included document reviews of quarterly progress reports (n = 86) and supplemental data reports (n = 16) provided by collaborating organizations, annual Steering Committee surveys (n = 4), and interviews conducted with staff from a subset of Collaborating Organizations (n = 4).

Results
The initiative reached over 50,000 community members per year through 19 evidence-based interventions and impacted health outcomes, including knowledge and adoption of healthy eating practices and increased physical activity. Thirty-one systems-level changes were implemented during the initiative, including 16 environmental changes. Steering Committee meetings and shared goals enabled connections, communication, and cooperation, which allowed Collaborating Organizations to address challenges and combine resources to deliver their programs.

Conclusions
Community initiatives can effectively permeate the community by reaching individuals, improving physical activity and dietary habits, and ensuring sustainability. Based on the experience reported here, the success of a community initiative can be facilitated if collaborating organizations come together to implement evidence-based interventions and tailor them to the community, and if they are empowered by significant leadership and supportive collaboration and aligned by a common agenda.
Validity across four common street-crossing distraction indicators to predict pedestrian safety
Authors: Ning Peishan , Xie Cifu , Cheng Peixia , Li Li , Schwebel David C. , Yang Yang , He Jieyi , Li Jie , Hu Guoqing 
Published: January 2024

Abstract
Background
Multiple distraction indicators have been applied to measure street-crossing distraction but their validities in predicting pedestrian safety are poorly understood.

Methods
Based on a video-based observational study, we compared the validity of four commonly used distraction indicators (total duration of distraction while crossing a street, proportion of distracted time over total street-crossing time, duration of the longest distraction time, and total number of distractions) in predicting three pedestrian safety outcomes (near-crash incidence, frequency of looking left and right, and speed crossing the street) across three types of distraction (mobile phone use, talking to other pedestrians, eating/drinking/smoking). Change in Harrell’s C statistic was calculated to assess the validity of each distraction indicator based on multivariable regression models including only covariates and including both covariates and the distraction indicator.

Results
Heterogeneous capacities in predicting the three safety outcomes across the four distraction indicators were observed: 1) duration of the longest distraction time was most predictive for the occurrence of near-crashes and looks left and right among pedestrians with all three types of distraction combined and talking with other pedestrians (Harrell’s C statistic changes ranged from 0.0310 to 0.0335, P < 0.05), and for the occurrence of near-crashes for pedestrians involving mobile phone use (Harrell’s C statistic change: 0.0053); 2) total duration of distraction was most predictive for speed crossing the street among pedestrians with the combination and each of the three types of distraction (Harrell’s C statistic changes ranged from 0.0037 to 0.0111, P < 0.05), frequency of looking left and right among pedestrians distracted by mobile phone use (Harrell’s C statistic change: 0.0115), and the occurrence of near-crash among pedestrians eating, drinking, or smoking (Harrell’s C statistic change: 0.0119); and 3) the total number of distractions was the most predictive indicator of frequency of looking left and right among pedestrians eating, drinking, or smoking (Harrell’s C statistic change: 0.0013). Sensitivity analyses showed the results were robust to change in grouping criteria of the four distraction indicators.

Conclusions
Future research should consider the pedestrian safety outcomes and type of distractions to select the best distraction indicator.
Effect of lower limb alignment on outcome after lateral unicompartmental knee arthroplasty: a retrospective study
Authors: Zheng Tong , Liu Dehua , Chu Ziyue , Luo Yange , Lu Qunshan , Zhang Baoqing , Liu Peilai 
Published: January 2024

Abstract
Purpose
The objective of this study was to investigate the correlation between lower limb alignment and patient outcomes after lateral unicompartmental knee arthroplasty (LUKA).

Methods
In this retrospective study, the information of 51 patients who underwent lateral UKA was collected after an average of 27months of follow-up (13 to 60 months). Evaluation indicators include the AKS and WOMAC score. The Kellgren-Lawrence grade is used to evaluate the severity of osteoarthritis, while the hip-knee-ankle (HKA) angle is utilized to measure the valgus angle of lower limb alignment.

Result
Patients with postoperative valgus (≥ 3°) alignment had the best outcomes, while those with varus (≤-3°) alignment had the worst outcomes (p < 0.001). Furthermore, it was noted that patients with preoperative mild valgus (≤ 4°) alignment had worse postoperative outcomes than those with severe valgus (≥ 7°) alignment (p < 0.05). The study also revealed a positive correlation between postoperative valgus and WOMAC scores (p < 0.001), whereas a negative correlation was observed between the change in valgus angle and WOMAC scores (p = 0.005).

Conclusion
During follow-ups, we found that lower limb alignment seems to be an independent predictor of postoperative outcomes. It is recommended that more than 3° of valgus alignment should be maintained after LUKA. Surgeons performing lateral UKA should be cautious of overcorrecting alignment, particularly in patients with preoperative mild valgus alignment.
No-ozone cold plasma induces apoptosis in human neuroblastoma cell line via increased intracellular reactive oxygen species (ROS)
Authors: Lee Jung-Han , Jaiswal M Shriya , Jang Yoon-Seo , Choi Jeong-Hae , Kim Gyoo-Cheon , Hong Jin-Woo , Hwang Dae-Seok 
Published: January 2024

Abstract
Background
This study aimed to evaluate the effect of argon-based No-ozone Cold Plasma (NCP) on neuroblastoma cancer cell apoptosis.

Methods
Experiments were performed with SK-N-SH and HS 68. Cell cultures were treated with NCP for 1, 3, and 5 min. NCP was applied using three different strategies: direct NCP application to cell cultures, to only media, and to only cells. Evaluation of cell viability and the level of the reactive oxygen species (ROS) was performed. N-acetyl-L-cysteine (NAC) was also used to antagonize intracellular ROS. Cleaved caspase 3, PARP, aquaporin (AQP) 3 and 8 were detected.

Results
NCP induced a gradual decrease in the SK-N-SH cell viability. In contrast, the viability of HS 68 cells did not change. SK-N-SH cells viability was reduced the most when the only media-NCP application strategy was employed. Intracellular ROS levels were significantly increased with time. Cleaved caspase 3 and PARP were increased at 6 h after NCP application. SK-N-SH cells remained viable with NAC after NCP application. AQP 3 and 8 were over-expressed in SK-N-SH cells.

Conclusion
These findings demonstrate the anti-cancer effect of NCP on neuroblastoma cells. NCP enhanced the selective apoptosis of neuroblastoma cells due to the increased intracellular ROS.
From master’s thesis to research publication: a mixed-methods study of medical student publishing and experiences with the publishing process
Authors: Björklund Maria , Massoumi Ramin , Ohlsson Bodil 
Published: January 2024

AbstractBackgroundMedical student master’s theses are often carried out as research projects, and some are published as research papers in journals. We investigated the percentage of master’s theses conducted by 5th -year students at the Medical Degree Program at Lund University, Sweden, that subsequently served as the basis for research publications. In addition, we explored both student and supervisor experiences with the publishing process.MethodsA cohort of four semesters of student data covering the period from 2019 to 2020 (n = 446) was searched in PubMed, Embase and the Web of Science to assess whether they had been published as research papers. Surveys were sent to students (n = 121) and supervisors (n = 77) to explore their experiences with the publishing process.ResultsWe found that 33% (149 of 446) of the students in the 2019–2020 cohort subsequently published their theses, and 50% of these students were listed as first authors. Most students published original research. Students (n = 21) and supervisors (n = 44) reported that the publishing process was time-consuming and that students needed multilevel support from supervisors to achieve successful publication. The publishing process was reported by 79% of the students to have led to additional learning. Most of the papers (126 of 149, 85%) had a clinical or patient-oriented focus.ConclusionA high percentage of the student publications in which students are listed as first authors require engagement from both students and supervisors. Supervisors play an essential role in supporting students in a successful publication process. Most of the published papers were either clinical or patient-oriented research.
Oncology nurses’ experiences of providing emotional support for cancer patients: a qualitative study
Authors: Lyu Xiao-Chen , Jiang Hai-Jiao , Lee Li-Hung , Yang Cheng-I. , Sun Xiang-Yun 
Published: January 2024

AbstractBackgroundA high percentage of cancer patients may experience emotional distress. Oncology nurses are expected to play an important role in recognizing emotional distress and planning and delivering care that meets the individual needs of each patient. However, few studies have focused on the experiences of clinical nurses in such cases. This study adopted a qualitative research method to gain an in-depth understanding of the experience of nursing staff in caring for cancer patients with emotional distress.MethodsA qualitative descriptive design and semi-structured interviews were used in this study. Twenty-one oncology nurses were interviewed, and the qualitative content analysis suggested by Graneheim & Lundman (2004) was used to interpret the data.ResultsSix themes were identified, as follows: (1) dictating the abnormality of emotion, (2) soothing and comforting patients, (3) a lack of psychology knowledge and communication skills, (4) negative impacts of a lack of time, (5) managing emotional labor, and (6) reflecting on the experiences.ConclusionHospital administrators should arrange pre-employment education and training as well as on-the-job education to help nurses in caring for cancer patients with emotional distress. They should also focus attention on the personal emotional states of nursing staff in a timely manner and provide psychological support and emotional counseling as necessary.