bluuebunny/crossref_metadata_2025_split huggingface dataset:
Cyclophosphamide for interstitial lung disease-associated acute respiratory failure: mortality, clinical response and radiological characteristics
Authors: van Gemert Johanna P. , van den Berk Inge A. H. , Nossent Esther J. , Heunks Leo M. A. , Jonkers Rene E. , Vlaar Alexander P. , Bonta Peter I. 
Published: July 2021

Abstract
Background
Treatment for interstitial lung disease (ILD) patients with acute respiratory failure (ARF) is challenging, and literature to guide such treatment is scarce. The reported in-hospital mortality rates of ILD patients with ARF are high (62–66%). Cyclophosphamide is considered a second-line treatment in steroid-refractory ILD-associated ARF. The first aim of this study was to evaluate the in-hospital mortality in patients with ILD-associated ARF treated with cyclophosphamide. The second aim was to compare computed tomographic (CT) patterns and physiological and ventilator parameters between survivors and non-survivors.

Methods
Retrospective analysis of patients with ILD-associated ARF treated with cyclophosphamide between February 2016 and October 2017. Patients were categorized into three subgroups: connective tissue disease (CTD)-associated ILD, other ILD or vasculitis. In-hospital mortality was evaluated in the whole cohort and in these subgroups. Clinical response was determined using physiological and ventilator parameters: Sequential Organ Failure Assessment Score (SOFA), PaO2/FiO2 (P/F) ratio and dynamic compliance (Cdyn) before and after cyclophosphamide treatment. The following CT features were quantified: ground-glass opacification (GGO) proportion, reticulation proportion, overall extent of parenchymal disease and fibrosis coarseness score.

Results
Fifteen patients were included. The overall in-hospital mortality rate was 40%. In-hospital mortality rates for CTD-associated ILD, other ILD and vasculitis were 20, 57, and 33%, respectively. The GGO proportion (71% vs 45%) was higher in non-survivors. There were no significant differences in the SOFA score, P/F ratio or Cdyn between survivors and non-survivors. However, in survivors the P/F ratio increased from 129 to 220 mmHg and Cdyn from 75 to 92 mL/cmH2O 3 days after cyclophosphamide treatment. In non-survivors the P/F ratio hardly changed (113–114 mmHg) and Cdyn even decreased (27–20 mL/cmH2O).

Conclusion
In this study, we found a mortality rate of 40% in patients treated with cyclophosphamide for ILD-associated ARF. Connective tissue disease-associated ILD and vasculitis were associated with a lower risk of death. In non-survivors, the CT GGO proportion was significantly higher. The P/F ratio and Cdyn in survivors increased after 3 days of cyclophosphamide treatment.
The relation between incisal guidance angle and the growth and development of temporomandibular joint: a multi-cross-sectional retrospective study
Authors: Li Ying , Zhou Wenwen , Wu Yan , Dai Hongwei , Zhou Jianping 
Published: July 2021

Abstract
Background
The incisal guidance angle (IGA) is related to temporomandibular joint (TMJ), and changes to the IGA are often involved in the prosthetic and orthodontic treatment of anterior teeth. However, the influence of incisal guidance on the growth, development and remodelling of the TMJ is not yet clear. The aim of this study was to investigate age-related morphological differences in the TMJ in subjects with different IGAs.

Methods
Cone-beam computed tomography (CBCT) images of 274 patients were included (group 1, IGA < 45°; group 2, 45° ≤ IGA ≤ 60°; group 3, IGA > 60°). Each group was then divided into 4 age groups (group a, 6–12 years; group b, 13–16 years; group c, 17–25 years; group d, 26–33 years). TMJ morphology was assessed by linear measurements, angular measurements, and subjective evaluations. The IGA and occlusal plane angle were also measured.

Results
Anterior inclination of condyle (AIC) increased with age in the three IGA groups but decreased from 17 years onward in group 2 (P < 0.05). In the age groups analysis, the AIC in group 1 was smaller than that in group 3 but larger than that in group 2 (P > 0.05). Articular eminence inclination (AEI) decreased with age in group 1 (P = 0.027) but increased with age in group 3 (P = 0.053). The AEI in group 2 was larger than that in group 1 at 17–25 years (P = 0.046), and it was larger in group 3 than in group 1 at 26–33 years (P = 0.047). The IGA had a weak correlation with AEI (P < 0.05).

Conclusion
The articular fossa of patients with shallower incisal guidance changed to a flatter shape with age, whereas the condylar anterior slope and articular eminence of patients with steeper incisal guidance changed towards a steeper alignment. There was a correlation between IGA and TMJ shape.
Chiropractic students’ experiences on the use of virtual radiography simulation: a pilot observational study
Authors: Shanahan Madeleine , Molyneux Tom , Vindigni Dein 
Published: July 2021

Abstract
Background
Virtual radiography provides students with an opportunity to practise their clinical skills in patient positioning and evaluating radiographic images. The purpose of this pilot study was to introduce Projection VR™, a software radiography simulation program, into a student chiropractic program and evaluate its potential application as a teaching and learning tool.

Methods
Undergraduate chiropractic students, enrolled in a radiographic course (unit within the chiropractic program), were invited to attend a scheduled laboratory where they were introduced to, and undertook purposefully designed activities using the radiography simulation. At the end of this activity, students were asked to complete an online survey (see Virtual Radiography Survey) to describe their experiences of the educational value of the software program. Descriptive statistics were used to evaluate outcomes. Content analysis was performed for free-text comments provided by respondents with key themes provided by the predetermined quantitative categories of the questionnaire.

Results
Responses were received from 44 out of the 47 students who attended the scheduled laboratory (response rate 92%). Overall students were positive about this simulation identifying that it was easy to use (95%) and that they could control the equipment as needed (95%). The main reported benefits included students being enabled to repeat tasks until they were satisfied with the results (98%) and being able to quickly assess images and determine if changes needed to be made (98%). Participants reported improvement in their understanding of the effect of exposure factors on patient radiation dose (93%) as well as their technical image evaluation (84%) and problem-solving skills (80%).

Conclusions
The results of this study suggest that virtual radiography is a valuable complementary resource in providing chiropractic students with radiographic knowledge and skills.
Intra- and inter-rater reliability of an electronic health record audit used in a chiropractic teaching clinic system: an observational study
Authors: Injeyan H. Stephen , Hogg-Johnson Sheilah , Abdulla Sean , Chow Ngai , Cox Jocelyn , Ridding Anthony , Jacobs Craig 
Published: July 2021

AbstractBackgroundThere is a dearth of information about health education clinical file audits in the context of completeness of records and demonstrating program-wide competency achievement. We report on the reliability of an audit instrument used for electronic health record (EHR) audits in the clinics of a chiropractic college in Canada.MethodsThe instrument is a checklist built within an electronic software application designed to pull data automatically from the EHR. It consists of a combination of 61 objective (n = 20) and subjective (n = 41) elements, representing domains of standards of practice, accreditation and in-house educational standards. Trained auditors provide responses to the elements and the software yields scores indicating the quality of clinical record per file.A convenience sample of 24 files, drawn randomly from the roster of 22 clinicians, were divided into three groups of eight to be completed by one of three auditors in the span of 1 week, at the end of which they were transferred to another auditor. There were four audit cycles; audits from cycles 1 and 4 were used to assess intra-rater (test-retest) reliability and audits from cycles 1, 2 and 3 were used to assess inter-rater reliability. Percent agreement (PA) and Kappa statistics (K) were used as outcomes. Scatter plots and intraclass correlation (ICC) coefficients were used to assess standards of practice, accreditation, and overall audit scores.ResultsAcross all 3 auditors test-retest reliability for objective items was PA 89% and K 0.75, and for subjective items PA 82% and K 0.63. In contrast, inter-rater reliability was moderate at PA 82% and K 0.59, and PA 70% and K 0.44 for objective and subjective items, respectively. Element analysis indicated a wide range of PA and K values inter-rater reliability of many elements being rated as poor. ICC coefficient calculations indicated moderate reliability for the domains of standards of practice, accreditation, and overall file scores.ConclusionThe file audit process has substantial test-retest reliability and moderate inter-rater reliability. Recommendations are made to improve reliability outcomes. These include modifying the audit checklist with a view of improving clarity of elements, and enhancing uniformity of auditor responses by increased training aided by preparation of an audit guidebook.
Both Conifer II and Gnetales are characterized by a high frequency of ancient mitochondrial gene transfer to the nuclear genome
Authors: Kan Sheng-Long , Shen Ting-Ting , Ran Jin-Hua , Wang Xiao-Quan 
Published: July 2021

Abstract
Background
Mitochondrial gene transfer/loss is common in land plants, and therefore the fate of missing mitochondrial genes has attracted more and more attention. The gene content of gymnosperm mitochondria varies greatly, supplying a system for studying the evolutionary fate of missing mitochondrial genes.

Results
Here, we studied the tempo and pattern of mitochondrial gene transfer/loss in gymnosperms represented by all 13 families, using high-throughput sequencing of both DNA and cDNA. All 41 mitochondrial protein-coding genes were found in cycads, Ginkgo and Pinaceae, whereas multiple mitochondrial genes were absent in Conifer II and Gnetales. In Conifer II, gene transfer from mitochondria to the nucleus followed by loss of the mitochondrial copy was common, but complete loss of a gene in both mitochondrial and nuclear genomes was rare. In contrast, both gene transfer and loss were commonly found in Gnetales. Notably, in Conifer II and Gnetales, the same five mitochondrial genes were transferred to the nuclear genome, and these gene transfer events occurred, respectively, in ancestors of the two lineages. A two-step transfer mechanism (retroprocessing and subsequent DNA-mediated gene transfer) may be responsible for mitochondrial gene transfer in Conifer II and Gnetales. Moreover, the mitochondrial gene content variation is correlated with gene length, GC content, hydrophobicity, and nucleotide substitution rates in land plants.

Conclusions
This study reveals a complete evolutionary scenario for variations of mitochondrial gene transferring in gymnosperms, and the factors responsible for mitochondrial gene content variation in land plants.
Fine-tuning the expression of pathway gene in yeast using a regulatory library formed by fusing a synthetic minimal promoter with different Kozak variants
Authors: Xu Liping , Liu Pingping , Dai Zhubo , Fan Feiyu , Zhang Xueli 
Published: July 2021

AbstractBackgroundTailoring gene expression to balance metabolic fluxes is critical for the overproduction of metabolites in yeast hosts, and its implementation requires coordinated regulation at both transcriptional and translational levels. Although synthetic minimal yeast promoters have shown many advantages compared to natural promoters, their transcriptional strength is still limited, which restricts their applications in pathway engineering.ResultsIn this work, we sought to expand the application scope of synthetic minimal yeast promoters by enhancing the corresponding translation levels using specific Kozak sequence variants. Firstly, we chose the reported UASF-E-C-Core1 minimal promoter as a library template and determined its Kozak motif (K0). Next, we randomly mutated the K0to generate a chimeric promoter library, which was able to drive green fluorescent protein (GFP) expression with translational strengths spanning a 500-fold range. A total of 14 chimeric promoters showed at least two-fold differences in GFP expression strength compared to the K0control. The best one named K528even showed 8.5- and 3.3-fold increases in fluorescence intensity compared with UASF-E-C-Core1 and the strong native constitutive promoter PTDH3, respectively. Subsequently, we chose three representative strong chimeric promoters (K540, K536, and K528) from this library to regulate pathway gene expression. In conjunction with thetHMG1gene for squalene production, the K528variant produced the best squalene titer of 32.1 mg/L in shake flasks, which represents a more than 10-fold increase compared to the parental K0control (3.1 mg/L).ConclusionsAll these results demonstrate that this chimeric promoter library developed in this study is an effective tool for pathway engineering in yeast.
LncRNA HOTAIR promotes proliferation and inhibits apoptosis by sponging miR-214-3p in HPV16 positive cervical cancer cells
Authors: Zhou Yu , Wang Yuqing , Lin Mingying , Wu Daiqian , Zhao Min 
Published: July 2021

Abstract
Background
Cervical cancer (CC) is one of the most common gynaecological malignancies all around the world. The mechanisms of cervical carcinoma formation remain under close scrutiny. The long non-coding RNAs (lncRNA) and microRNAs (miRNAs) play important roles in controlling gene expression and promoting the development and progression of cervical cancer by acting as competitive endogenous RNA (ceRNA). However, the roles of lncRNA associated with ceRNAs in cervical carcinogenesis remains unknown. In this study, the expression of long non-coding RNA HOTAIR was investigated in HPV16 positive cervical cancer cells, the candidate miRNAs and target genes were identified to clarify putative ceRNAs of HOTAIR/miRNA in cervical cancer cells.

Methods
The proliferation ability of cells was measured by CCK8 and EdU incorporation assays and cell apoptosis was analyzed by flow cytometry. The expression of HOTAIR, miR-214-3p, HPV16 E7 mRNA were detected by qRT-PCR. As for searching for the interaction between miR-214-3p and HOTAIR, the binding sites for miR-214-3p on HOTAIR was predicted by starbase v2.0 database, then dual-luciferase assay was used to verify the binding sites. In addition, Gene Ontology (GO) and protein–protein interaction (PPI) network analysis of target genes of miR-214-3p were performed with bioinformatics analysis. The potential signal pathway regulated by HOTAIR/miR-214-3p was predicted by KEGG enrichment analysis and confirmed by qPCR and WB analysis in cervical cancer cells.

Results
Our results showed that expression of HOTAIR was up-regulated, while that of miR-214-3p was down-regulated in HPV16-positive cervical cancer cells. The expression status of HPV16 E7 played an important role in regulating expression of HOTAIR or miR-214-3p in cervical cancer cells. HOTAIR knockdown could significantly inhibited cell proliferate ability and promote cellular apoptosis, whereas the inhibition of miR-214-3p expression partially reversed such results. Bioinformatics analysis identified 1451 genes as target genes of miR-214-3p. The Gene ontology (GO) and KEGG Pathway enrichment analysis showed that these target genes were mainly related to regulation of cell communication, protein binding, enzyme binding and transferase activity, and Wnt ligand biogenesis. Pathway enrichment analysis results showed that the predicted target genes were significantly enriched in Wnt/β-catenin signaling pathway. Finally, our results confirmed that miR-214-3p could significantly inhibit β-catenin expression in HPV16 positive cancer cells by qPCR and WB analysis.

Conclusion
HOTAIR could act as a ceRNA through binding to miR-214-3p, promote cell proliferation and inhibit the apoptosis of HPV16 positive cervical cancer. HOTAIR/miR-214-3p/Wnt/β-catenin signal pathway might played important regulated roles in HPV16 positive cervical cancer. Our results provided new insight into defining novel biomarkers for cervical cancer.
Decreased prevalence of the Plasmodium falciparum Pfcrt K76T and Pfmdr1 and N86Y mutations post-chloroquine treatment withdrawal in Katete District, Eastern Zambia
Authors: Mulenga Mwenda C. , Sitali Lungowe , Ciubotariu Ilinca I. , Hawela Moonga B. , Hamainza Busiku , Chipeta James , Mharakurwa Sungano 
Published: July 2021

Abstract
Background
In 2002, Zambia withdrew chloroquine as first-line treatment for Plasmodium falciparum malaria due to increased treatment failure and worldwide spread of chloroquine resistance. The artemisinin combination regimen, artemether–lumefantrine, replaced chloroquine (CQ) as first choice malaria treatment. The present study determined the prevalence of CQ resistance molecular markers in the Pfcrt and Pfmdr1 genes in Eastern Zambia at 9 and 13 years after the removal of drug pressure.

Methods
Samples collected from Katete District during the drug therapeutic efficacy assessments conducted in 2012 and 2016 were assayed by polymerase chain reaction (PCR) and restriction fragment length polymorphisms (RFLP) to determine the prevalence of genetic mutations, K76T on the Pfcrt gene and N86Y on the Pfmdr1 gene. A total of 204 P. falciparum-positive DBS samples collected at these two time points were further analysed.

Results
Among the samples analysed for Pfcrt K76T and Pfmdr1 N86Y in the present study, 112 (82.4%) P. falciparum-infected samples collected in 2012 were successfully amplified for Pfcrt and 94 (69.1%) for Pfmdr1, while 69 (65.7%) and 72 (68.6%) samples from 2016 were successfully amplified for Pfcrt and Pfmdr1, respectively. In 2012, the prevalence of Pfcrt 76K (sensitive) was 97.3%, 76T (resistant) was 1.8%, and 0.8% had both 76K and 76T codons (mixed). Similarly in 2012, the prevalence of Pfmdr1 86N (sensitive) was 97.9% and 86Y (resistant) was 2.1%. In the 2016 samples, the prevalence of the respective samples was 100% Pfcrt 76K and Pfmdr1 86N.

Conclusion
This study shows that there was a complete recovery of chloroquine-sensitive parasites by 2016 in Katete District, Eastern Zambia, 13 years following the withdrawal of CQ in the country. These findings add to the body of evidence for a fitness cost in CQ-resistant P. falciparum in Zambia and elsewhere. Further studies are recommended to monitor resistance countrywide and explore the feasibility of integration of the former best anti-malarial in combination therapy in the future.
Endocrine disrupting chemical-associated hair product use during pregnancy and gestational age at delivery: a pilot study
Authors: Preston Emma V. , Fruh Victoria , Quinn Marlee R. , Hacker Michele R. , Wylie Blair J. , O’Brien Karen , Mahalingaiah Shruthi , James-Todd Tamarra 
Published: July 2021

Abstract
Background
Prenatal endocrine disrupting chemical (EDC) exposure has been associated with increased risk of preterm birth. Non-Hispanic Black women have higher incidence of preterm birth compared to other racial/ethnic groups and may be disproportionately exposed to EDCs through EDC-containing hair products. However, research on the use of EDC-associated hair products during pregnancy and risk of preterm birth is lacking. Therefore, the objective of this pilot study was to estimate associations of prenatal hair product use with gestational age at delivery in a Boston, Massachusetts area pregnancy cohort.

Methods
The study population consisted of a subset of participants enrolled in the Environmental Reproductive and Glucose Outcomes (ERGO) Study between 2018 and 2020. We collected self-reported data on demographics and hair product use using a previously validated questionnaire at four prenatal visits (median: 12, 19, 26, 36 weeks’ gestation) and abstracted gestational age at delivery from medical records. We compared gestational age and hair product use by race/ethnicity and used linear regression to estimate covariate-adjusted associations of product use and frequency of use at each study visit with gestational age at delivery. Primary models were adjusted for maternal age at enrollment and delivery method.

Results
Of the 154 study participants, 7% delivered preterm. Non-Hispanic Black participants had lower mean gestational age at delivery compared to non-Hispanic White participants (38.2 vs. 39.2 weeks) and were more likely to report ever and more frequent use of hair products. In regression models, participants reporting daily use of hair oils at visit 4 had lower mean gestational age at delivery compared to non-users (β: -8.3 days; 95% confidence interval: -14.9, -1.6). We did not find evidence of associations at earlier visits or with other products.

Conclusions
Frequent use of hair oils during late pregnancy may be associated with shorter gestational duration. As hair oils are more commonly used by non-Hispanic Black women and represent potentially modifiable EDC exposure sources, this may have important implications for the known racial disparity in preterm birth.
Role of CRISPR-Cas system on antibiotic resistance patterns of Enterococcus faecalis
Authors: Gholizadeh Pourya , Aghazadeh Mohammad , Ghotaslou Reza , Rezaee Mohammad Ahangarzadeh , Pirzadeh Tahereh , Cui Longzhu , Watanabe Shinya , Feizi Hadi , Kadkhoda Hiva , Kafil Hossein Samadi 
Published: July 2021

AbstractClustered regularly interspaced short palindromic repeat (CRISPR)-Cas systems are one of the factors which can contribute to limiting the development and evolution of antibiotic resistance in bacteria. There are three genomic loci of CRISPR-Cas in Enterococcus faecalis. In this study, we aimed to assess correlation of the CRISPR-Cas system distribution with the acquisition of antibiotic resistance among E. faecalis isolates. A total of 151 isolates of E. faecalis were collected from urinary tract infections (UTI) and dental-root canal (DRC). All isolates were screened for phenotypic antibiotic resistance. In addition, antibiotic resistance genes and CRISPR loci were screened by using polymerase chain reaction. Genomic background of the isolates was identified by random amplified polymorphic DNA (RAPD)-PCR. The number of multidrug-resistant E. faecalis strains were higher in UTI isolates than in DRC isolates. RAPD-PCR confirmed that genomic background was diverse in UTI and DRC isolates used in this study. CRISPR loci were highly accumulated in gentamycin-, teicoplanin-, erythromycin-, and tetracycline-susceptible strains. In concordance with drug susceptibility, smaller number of CRISPR loci were identified in vanA, tetM, ermB, aac6’-aph(2”), aadE, and ant(6) positive strains. These data indicate a negative correlation between CRISPR-cas loci and antibiotic resistance, as well as, carriage of antibiotic resistant genes in both of UTI and DRC isolates.