bluuebunny/crossref_metadata_2025_split huggingface dataset:
Microbiome single cell atlases generated with a commercial instrument
Authors: Abate Adam , Li Xiangpeng , Xu Linfeng , Demaree Benjamin , Noecker Cecilia , Bisanz Jordan , Weisgerber Daniel , Modavi Cyrus , Turnbaugh Peter 
Published: September 2023

Abstract
Single cell sequencing is useful for resolving complex systems into their composite cell types and computationally mining them for unique features that are masked in pooled sequencing. However, while commercial instruments have made single cell analysis widespread for mammalian cells, analogous tools for microbes are limited. Here, we present EASi-seq (Easily Accessible Single microbe sequencing). By adapting the single cell workflow of the commercial Mission Bio Tapestri instrument, this method allows for efficient sequencing of individual microbes’ genomes. EASi-seq allows thousands of microbes to be sequenced per run and, as we show, can generate detailed atlases of human and environmental microbiomes. The ability to capture large shotgun genome datasets from thousands of single microbes provides new opportunities in discovering and analyzing species subpopulations. To facilitate this, we develop a companion bioinformatic pipeline that clusters microbes by similarity, improving whole genome assembly, strain identification, taxonomic classification, and gene annotation. In addition, we demonstrate integration of metagenomic contigs with the EASi-seq datasets to reduce capture bias and increase coverage. Overall, EASi-seq enables high quality single cell genomic data for microbiome samples using an accessible workflow that can be run on a commercially available platform.
A Comprehensive Survival Analysis of Oral Squamous Cell Carcinoma Patients Undergoing Initial Radical Surgery
Authors: Dong LINSHENG , Xue lINGLI , Cheng WEI , TANG JING , Ran JINGXUAN , LI YADONG 
Published: September 2023

Abstract

Objective
This study aims to evaluate the five-year overall survival (OS) rate and postoperative survival duration in patients diagnosed with oral squamous cell carcinoma (OSCC). Additionally, it seeks to scrutinize the clinical and pathological determinants influencing the survival outcomes in OSCC patients.
Methods
We meticulously gathered data from OSCC patients who underwent their first radical surgical intervention in the Department of Maxillofacial Surgery at the First Affiliated Hospital of Chongqing Medical University between April 2014 and December 2016. Follow-up was diligently conducted until March 2022.
Results
The study encompassed a total of 162 patients. The observed 5-year OS rate was 59.3%. Approximately 45.7% of OSCC patients experienced recurrence and metastasis post-surgery, with the 5-year overall disease-free survival rate being 49.4%. Univariate analysis revealed that clinical stage, tumor size, lymph node metastasis (pN), pathological differentiation, and recurrence and metastasis were significant factors influencing survival duration (p < 0.05). Multivariate analysis further indicated that pathological differentiation and recurrence and metastasis were independent determinants of survival duration (P < 0.05). An intriguing observation was that 11 OSCC patients were diagnosed with esophageal squamous cell carcinoma (ESCC) within 1–4 years following surgery.
Conclusion
The survival prognosis of OSCC patients is significantly associated with clinical stage, tumor size, lymph node metastasis (pN), pathological differentiation, and recurrence and metastasis. Pathological differentiation and recurrence and metastasis are independent determinants affecting survival duration. Routine clinical screening for esophageal squamous cell carcinoma may be recommended for OSCC patients with a history of alcohol and tobacco consumption.
Evaluation of polymethyl-methacrylate and acetal denture base resins processed by two different techniques before and after nano-chlorohexidine surface treatment
Authors: Fathy Salma , Abdel-halim Mohmoud , El-Safty Samy , El-Ganiny Amira 
Published: September 2023

Abstract
Background
This study aimed to evaluate surface roughness and biofilm formation tendency of two types of denture base resins manufactured with two techniques before and after surface coating with chlorohexidine (CHX) NPs and release of these NPs from coated resins.
Materials and methods
Acetal (AC) and Polymethyl-methacrylate (PMMA) resins manufactured by conventional and CAD/CAM methods were shaped into disk (10 X 10 X 1 mm). They were dipped for 8h and 24h in colloidal suspension prepared by mixing aqueous solutions of CHX digluconate and hexa-metaphosphate (0.01 M). Surface roughness, optical density (OD) of microbial growth media and biofilm formation tendency were evaluated directly after coating. Elutes concentrations of released CHX were evaluated for 19 days using spectrophotometer and then OD after release was evaluated again. Three way ANOVA and Tukey’s post-hoc statistical analysis were used.
Results
AC CAD/CAM groups showed statistically significant highest roughness before and after coating (54.703 ± 4.32 and 77.58 ± 6.07 nm, respectively). All groups showed significant reduction in OD and biofilm formation tendency after surface coating even after 19 days of CHX NPs release.
Conclusions
Biofilm formation tendency was highly relevant to surface roughness of tested resins before coating. After CHX NPs coating all tested groups showed significant impact on microbial growth and reduction in biofilm formation tendency with no relation to surface roughness. Significant antimicrobial effect remained even after 19 days of NPs release and specimens storage.
Retrospective analysis of the efficacy of epidural labour analgesia on early breastfeeding after vaginal delivery
Authors: Hu Xudong , Xiong Dongqin , Luo Meifang , Ling Chen , Liu Xingqing , Wen Xianjie 
Published: September 2023

Abstract
Background
The breast feeding is important for infant and mother .The epidural labour analgesia is used frequently to alleviate the pain during the vaginal delivery . Studies found that epidural labor analgesia may have a negative effect on postpartum breastfeeding. But the efficacy of epidural labour analgesia on breastfeeding early after vaginal delivery was unclear . So this retrospective analysis was made to illuminate the efficacy of epidural labour analgesia on postpartum breast feeding.
Methods
392 women who received vaginal delivery in the Second People's Hospital of Foshan from July 2022 to June 2023 were selected in this studyand all women received the epidural labour analgesia were divide into three group according to the efficacy of labour analgesia. Women with VAS score 4-6 were divided into Group M(n=127) and women with VAS score﹥7 were divided into Group P (n=73).The lactation initiation time and the incidenceof delayed onset of lactation were analyzed .The lactation volume and times and the LATCH score at 24,48 and 72 hours after vaginal delivery were also analyzed.
Results
The lactation initiation time in Group M was shorter than those in Group E and Group P with statistical significance (All P﹤0.05);There was no significant difference of lactation initiation time after vaginal delivery between Group E and Group P (P﹥0.05). The incidence of delayed onset of lactation in Group M were lower than those in Group E and Group P with statistical significance(All P﹤0.05);There was no statistical significance of the incidence of delayed onset of lactation between Group E and Group P(P﹥0.05).The lactation volume at 24 , 48 and 72 hours after vaginal delivery in Group M were higher than those in Group E and Group P with statistical significance (All P ﹤0.05); There wasno significant difference of lactation volume at 24,48 and 72 hours after vaginal delivery between Group E and Group P(P﹥0.05). The lactation times at 24 , 48 and 72 hours after vaginal delivery in Group M were higher than those in Group E and Group Pwith statistical significance (All,P﹤0.05); There wasno significant difference of lactation times at 24,48 and 72 hours after vaginal delivery between Group E and Group P(P﹥0.05).There was no significant difference of LATCH scores at 24,48 and 72 hours after vaginal delivery among the three groups (All P﹥0.05).
Conclusions
Compared with labour analgesia with excellent and poor analgesia efficacy, the labouranalgesia with moderate analgesia efficacy has less cases of prolatin using,morelactation volume and times, shorter lactation initiation time, lessincidence of delayed onset of lactation and no effect on the LATCH score of breastfeeding.
Evaluation of disease knowledge and attitude with selected self-care and sociodemographic factors among outpatients with hypertension – a multicenter study
Authors: Aje Akinniyi A. , Fakeye Titilayo O. 
Published: September 2023

Abstract

Background:There are lots of interplays between many patient-related factors which may influence disease progression among patients with hypertension.This study evaluated disease knowledge and attitude, as well as selected self-care and sociodemographic factors among patients with hypertension.Methods:A cross-sectional study was carried out among outpatients with hypertension in a multicenter study involving three tertiary hospitals. An interviewer-administered semi-structured questionnaire was administered for data collection. Data was summarized with descriptive and inferential statistics with the level of significance set at p<0.05.Results:Self-reported medication adherence revealed that majority, 180 (60.4%), had high medication adherence out of 298 that participated. Medication discrepancy was observed among 153 (51.3%) patients, while 131 (44.0%) had high health literacy. Average hypertension knowledge assessment score was 10.89 ± 1.79 out of a maximum obtainable score of 13. Average hypertension attitude score was 52.60 ± 5.49, out of the maximum obtainable of 60. Significant associations observed with patients’ hypertension knowledge were with level of formal education (p<0.001), health literacy (p<0.001) and disease attitude (p<0.001); while patients’ age (p=0.002), level of formal education (p=0.005), and health literacy (p<0.001) had significant associations with disease attitude. Significant associations were also observed between patients’ age and medication discrepancy (p=0.047), medication adherence and age (p=0.046), level of formal education and health literacy (p<0.001). No significant associations were observed between medication discrepancy and health literacy (p=0.192), medication adherence and health literacy (p=0.499), medication adherence and medication discrepancy (p=0.435).ConclusionsDisease knowledge and attitude among the patients were satisfactory, and the majority were medication adherent. Health literacy level was average, and a positive association was observed when disease knowledge and attitude was compared with health literacy and educational level.
Metallothionein 3 promotes osteoclast differentiation and survival by regulating the intracellular Zn2+ concentration and NRF2 pathway
Authors: Fujiwara Toshifumi , Arisumi Shinkichi , Yasumoto Keitaro , Tsutsui Tomoko , Saiwai Hirokazu , Kobayakawa Kazu , Okada Seiji , Zhao Haibo , Nakashima Yasuharu 
Published: September 2023

Abstract
In osteoclastogenesis, the metabolism of metal ions plays an essential role in controlling reactive oxygen species (ROS) production, mitochondrial biogenesis, and survival, and differentiation. However, the mechanism regulating metal ions during osteoclast differentiation remains unclear. The metal-binding protein metallothionein (MT) detoxifies heavy metals, maintains metal ion homeostasis, especially zinc, and manages cellular redox levels. We carried out tests using murine osteoclast precursors to examine the function of MT in osteoclastogenesis and evaluated their potential as targets for future osteoporosis treatments. MT genes were significantly upregulated upon differentiation from osteoclast precursors to mature osteoclasts in response to receptor activators of nuclear factor-κB (NF-κB) ligand (RANKL) stimulation, and MT3 expression was particularly pronounced in mature osteoclasts among MT genes. The knockdown of MT3 in osteoclast precursors demonstrated a remarkable inhibition of differentiation into mature osteoclasts. In preosteoclasts, MT3 knockdown suppressed the activity of mitogen-activated protein kinase (MAPK) and NF-κB signaling pathways upon RANKL stimulation, leading to increased apoptosis through elevated cleaved Caspase 3 and poly (ADP-ribose) polymerase (PARP) levels. Additionally, ROS levels were decreased, and nuclear factor erythroid 2-related factor 2 (NRF2) (a suppressor of ROS) and the downstream antioxidant proteins, such as catalase (CAT) and heme oxygenase 1 (HO-1), were more highly expressed in the MT3 preosteoclast knockdowns. mitochondrial ROS, which is involved in mitochondrial biogenesis and the production of reactive oxygen species, were similarly decreased because cAMP response element-binding (CREB) and peroxisome proliferator-activated receptor γ coactivator 1β (PGC-1β) were less activated due to MT3 depletion. Thus, by modulating ROS through the NRF2 pathway, MT3 plays a crucial role in regulating osteoclast growth and survival, acting as a metabolic modulator of intracellular zinc ions.
Construction and validation of a hypoxia-related gene signature to predict the prognosis of invasive ductal breast carcinoma
Authors: Qiu Chaoran , Wang Wenjun , Xu Shengshan , Li Yong , Zhu Jingtao , Zhang Yiwen , Lei Chuqian , Li Weiwen , Li Hongsheng , Li Xiaoping 
Published: September 2023

Abstract
Background: Invasive ductal carcinoma (IDC), the most common type of breast cancer, was known for its aggressive nature. Recent research revealeda lack of oxygen, known as hypoxia, wascrucial in forming breast cancer. This research aimed to create a robustsignature with hypoxia-related genes to predict the prognosis of IDC patients. The function of hypoxia genes was further studied through cell line experiments.
Materials and Methods: In the bioinformatic part, transcriptome and clinical information of breast IDC were obtained from The Cancer Genome Atlas. Hypoxia-related genes were downloaded from the Genecards Platform. Differentially expressed hypoxia-related genes (DEHRGs) were identified. Training and test sets were defined with a 1:1 ratio. Prognostic-related DEHRGs were identified through Cox regression; then the signature was established and validated. The nomogram was created by incorporating the signature and clinicopathological characteristics. The predictive value of the nomogram was evaluated by C-index and receiver operating characteristic cure. Immune microenvironment and mutation burden were also examined. In the experiment part, the function of the two most significant hypoxia-related genes were further explored by cell-line experiments.
Results: In the bioinformatic part, 37 up-regulated and 55 down-regulated DEHRGs were screened out. A prognostic signature was constructed containing nine hypoxia genes (ALOX15B, CA9, CD24, CHEK1, FOXM1, HOTAIR, KCNJ11, NEDD9, PSME2) in the training set. Low-risk patients exhibited a much more favorable prognosis tthan higher-risk ones(P<0.001). The signature was double-validated in the test set and GSE131769 (P=0.006 and P=0.001). The nomogram showed excellent predictive value with 1-year OS AUC: 0.788, 3-year OS AUC: 0.783, and 5-year OS AUC: 0.817. Patients in the high-risk group had a higher tumor mutation burden when compared to the low-risk group. In the experiment part, the down-regulation of PSME2 inhibited cell growth ability and clone formation capability of breast cancercells, while the down-regulation of KCNJ11 did not have any functions.
Conclusion: Based on 9 DEHRGs, a reliable signature was established through the bioinformatic method. It could accurately predict the prognosis of breast IDC patients. Cell line experiment indicated that PSME2 played a protective role. Summarily, we provided a new insight to predict the prognosis of breast IDC by hypoxia-related genes.
Strategies and resources used by public health units to encourage COVID-19 vaccination among priority groups: a behavioural science-informed review of three urban centres in Canada
Authors: Langmuir Tori , Wilson Mackenzie , McCleary Nicola , Patey Andrea M , Mekki Karim , Ghazal Hanan , Noad Elizabeth Estey , Buchan Judy , Dubey Vinita , Galley Jana , Gibson Emily , Fontaine Guillaume , Smith Maureen , Alghamyan Amjad , Thompson Kimberly , Crawshaw Jacob , Grimshaw Jeremy M , Arnason Trevor , Brehaut Jamie , Michie Susan , Brouwers Melissa , Presseau Justin 
Published: September 2023

Abstract

Background: Ensuring widespread COVID-19 vaccine uptake is a public health priority in Canada and globally, particularly within communities that exhibit lower uptake rates and are at a higher risk of infection. Public health units (PHUs) have leveraged many resources to promote the uptake of recommended COVID-19 vaccine doses. Understanding barriers and enablers to vaccine uptake, and which strategies/resources have been used to address them to date, may help identify areas where further support could be provided. We sought to identify the strategies/resources used by PHUs to promote the uptake of the first and third doses of the COVID-19 vaccine among priority groups in their jurisdictions. We examined the alignment of these existing strategies/resources with behavioral science principles, to inform potential complementary strategies/resources.
Methods: We reviewed the online and in-person strategies/resources used by three PHUs in Ontario, Canada to promote COVID-19 vaccine uptake among priority groups (Black and Eastern European populations, and/or neighbourhoods with low vaccine uptake or socioeconomic status). Strategies/resources were identified from PHU websites, social media, and member-checking. We used the Behaviour Change Techniques (BCT) Taxonomy – which describes 93 different ways of supporting behaviour change – to categorise the types of strategies/resources used, and the Theoretical Domains Framework – which synthesises 14 factors that can be barriers or enablers to decisions and actions – to categorise the barriers and enablers addressed by each strategy/resource.
Results: PHUs operationalised 21 out of 93 BCTs, ranging from 15–20 BCTs per PHU. The most frequently operationalised BCTs were found in PHU strategies/resources that provided information about COVID-19 infection and vaccines, increased access to COVID-19 vaccination, and integrated social supports such as community ambassadors and engagement sessions with healthcare professionals. Identified BCTs aligned most frequently with addressing barriers and enablers related to Knowledge, Environmental context and resources, and Beliefs about consequences domains.
Conclusion: PHUs have used several BCTs to address different barriers and enablers to COVID-19 vaccine uptake for priority groups. Opportunities should be pursued to broaden the scope of BCTs used in strategies/resources and barriers/enablers addressed in general and for prioritised populations to support ongoing and future efforts supporting uptake of COVID-19 vaccine doses.
Genetic background of FHLH in Qatar: Registry data and population study
Authors: Elgaali Elkhansa , Mezzavilla Massimo , Ahmed Ikhlak , Elanbari Mohammed , Ali Aesha , Abdelaziz Ghada , Fakhro Khalid , Saleh Ayman , Ben-Omran Tawfeg , Almulla Naima , Cugno Chiara 
Published: September 2023

Abstract
Background
Familial Hemophagocytic Lymphohistiocytosis (FHLH) is an inherited life-threatening disease. Five types are identified with the addition of congenital immunodeficiency syndromes in which HLH is a typical manifestation. The literature on this disease is very scarce in the Middle East, with only a few scattered reports.
Methods:
We report detailed demographic, clinical, and genomic data from 28 patients diagnosed with FHLH and Griscelli syndrome type 2 over the last decade in Qatar.
Evaluation of allele frequencies of deleterious variants from 12 FHLH causative genes was performed on the Qatar Genome Programme (QGP) cohort of 14,669 Qatari individuals.
Results
The genetic diagnosis was obtained in 15 patients and 4 novel mutations in PRF1, UNC13D, LYST and RAB27A genes were identified.
We identified 22,945 low/high/moderate impact variants significantly enriched in the QGP in those 12 genes. The variants rs1271079313 in PRF1 and rs753966933 in RAB27A found in our patients’ cohort were significantly more prevalent in QGP compared to the gnomAD database, with a high carrier frequency in the Qatari population.
Conclusions
We established the first FHLH Registry in the Gulf Region and identified novel pathogenic variants present at higher frequency in the Qatari population, which could be used for screening purposes. Raising awareness about FHLH and implementing screening activities in the Qatari highly inbred population could stem into more comprehensive pre-marital and prenatal evaluations and faster diagnosis.
Application of neurally adjusted ventilatory assist in preterm infants after patent ductus arteriosus ligation: a retrospective cohort study
Authors: Lin Hui-Zi , Lin Yun-Feng , Zheng Yi-Rong 
Published: September 2023

Abstract
Objective
This study aimed to compare the efficacy and safety of neurally adjusted ventilatory assist (NAVA) and synchronized intermittent mandatory ventilation (SIMV) in preterm infants requiring mechanical ventilation after patent ductus arteriosus (PDA) ligation.
Methods
A retrospective analysis was conducted on intubated preterm infants who underwent PDA ligation at our hospital from July 2021 to January 2023. Infants were divided into NAVA or SIMV groups based on the ventilation mode after surgery.
Results
Forty-eight preterm infants were included. During treatment, peak inspiratory pressure (PIP) and mean airway pressure (MAP) were lower with NAVA than SIMV (PIP: 19.0 ± 3.0 vs. 22.4 ± 3.6 cmH2O, P = 0.001; MAP: 9.2 ± 1.9 vs. 10.9 ± 2.7 cmH2O, P = 0.008). PaO2 and PaO2/FiO2 were higher with NAVA (PaO2: 94.2 ± 12.1 vs. 84.8 ± 15.8 mmHg, P = 0.022; PaO2/FiO2: 267 [220–322] vs. 232 [186–290] mmHg, P = 0.023). Less sedation was required with NAVA (midazolam: 1.5 ± 0.5 vs. 1.0 ± 0.3 µg/kg/min, P < 0.001).
Conclusion
Compared with SIMV, early NAVA after PDA ligation in preterm infants significantly decreased PIP and MAP, required less sedation, and improved oxygenation.