bluuebunny/crossref_metadata_2025_split huggingface dataset:
De novo full length transcriptome analysis and gene expression profiling to identify genes involved in phenylethanol glycosides biosynthesis in Cistanche tubulosa
Authors: Hou Lei , Li Guanghui , Chen Qingliang , Zhao JinJin , Pan Jiaowen , Lin Ruxia , Zhu Xiujin , Wang Pengfei , Wang Xingjun 
Published: October 2022

Abstract
Background
The dried stem of Cistanche, is a famous Chinese traditional medicine. The main active pharmacodynamic components are phenylethanol glycosides (PhGs). Cistanche tubulosa produces higher level of PhGs in its stems than that of Cistanche deserticola. However, the key genes in the PhGs biosynthesis pathway is not clear in C. tubulosa.

Results
In this study, we performed the full-length transcriptome sequencing and gene expression profiling of C. tubulosa using PacBio combined with BGISEQ-500 RNA-seq technology. Totally, 237,772 unique transcripts were obtained, ranging from 199 bp to 31,857 bp. Among the unique transcripts, 188,135 (79.12%) transcripts were annotated. Interestingly, 1080 transcripts were annotated as 22 enzymes related to PhGs biosynthesis. We measured the content of echinacoside, acteoside and total PhGs at two development stages, and found that the content of PhGs was 46.74% of dry matter in young fleshy stem (YS1) and then decreased to 31.22% at the harvest stage (HS2). To compare with YS1, 13,631 genes were up-regulated, and 15,521 genes were down regulated in HS2. Many differentially expressed genes (DEGs) were identified to be involved in phenylpropanoid biosynthesis pathway, phenylalanine metabolism pathway, and tyrosine metabolism pathway.

Conclusions
This is the first report of transcriptome study of C. tubulosa which provided the foundation for understanding of PhGs biosynthesis. Based on these results, we proposed a potential model for PhGs biosynthesis in C. tubulosa.
Occurrence of waterborne pathogens and antibiotic resistance in water supply systems in a small town in Mozambique
Authors: Taviani Elisa , van den Berg Harold , Nhassengo Fernando , Nguluve Eugenia , Paulo Jussa , Pedro Olivia , Ferrero Giuliana 
Published: October 2022

Abstract
Background
. Microbiological quality of drinking water supplied in Moamba, a small town in southern Mozambique, was assessed by collecting and analyzing 91 water sample from 5 sampling sites: raw or inlet water, treated water and 3 household taps along the water distribution system. The presence of Escherichia coli as indicator fecal contamination, three bacterial pathogens, Vibrio cholerae, Salmonella and Campylobacter spp., and Cefotaximee resistant E. coli as antibiotic resistance determinant, was assessed.

Results
. The results showed fecal contamination in all types of water samples: E. coli was found in 100% of inlet water samples, in 21% of treated water samples, and in 22% of tap water samples. No Salmonella spp. was detected during the study. The presence of V. cholerae was detected in 42% of all water samples tested: 100% of inlet water samples, in 16% of treated water samples, and in 23% household tap water samples. All V. cholerae confirmed isolates where genotyped by PCR as non-O1/non-O139; however, 9 isolates showed the presence of the genes encoding for cholera toxin. The presence of Campylobacter spp. was detected in 36% of the water samples tested: in 95% of inlet water samples, in 10% of treated water samples and in 23% household tap water samples. Cefotaxime resistant E. coli was detected in 63% of inlet water, 16% of treated water, and in 9% of tap water samples, these isolates were also resistant to multiple other antibiotics: ampicillin, streptomycin, tetracycline chloramphenicol. All 70 V. cholerae non-O1/non-O139 confirmed isolated were resistant to ampicillin, 51% to streptomycin, 13% to gentamycin, and 1 isolate was resistant to tetracycline; 13% showed a multi-drug resistant profile, being resistant to at least three antibiotics.

Conclusion
. The presence of fecal contamination and pathogens in the water treatment system and household taps in Moamba indicates a health risk for the population. This burden increases by the presence of bacterial pathogens showing multidrug resistance.
Comparative transcriptomic responses of European and Japanese larches to infection by Phytophthora ramorum
Authors: Dun Heather F. , Hung Tin Hang , Green Sarah , MacKay John J. 
Published: October 2022

AbstractBackground and objectivesPhytophthora ramorumseverely affects both European larch (EL) and Japanese larch (JL) trees as indicated by high levels of mortality particularly in the UK. Field observations suggested that EL is less severely affected and so may be less susceptible toP. ramorumthan JL; however, controlled inoculations have produced inconsistent or non-statistically significant differences. The present study aimed to compare RNA transcript accumulation profiles in EL and JL in response to inoculation withP. ramorumto improve our understanding of their defence responses.MethodologyRNA-sequencing was carried out on bark tissues following the inoculation withP. ramorumof potted saplings in both EL and JL carried out under controlled environment conditions, with sampling at 1, 3, 10, and 25 days post inoculation in infected and control plants.ResultsAll of the inoculated trees rapidly developed lesions but no statistically significant differences were found in lesion lengths between EL and JL. RNA-Sequencing comparing control and inoculate saplings identified key differences in differentially expressed genes (DEGs) between the two larch species. European larch had rapid induction of defence genes within 24 hours of infection followed by sustained expression until 25 days after inoculation. Results in JL were more varied; upregulation was stronger but more transient and represented fewer defence pathways. Gene enrichment analyses highlighted differences in jasmonate signalling and regulation including NPR1 upregulation in EL only, and specific aspects of secondary metabolism. Some DEGs were represented by multiple responsive copies including lipoxygenase, chalcone synthase and nucleotide-binding, leucine-rich-repeat genes.ConclusionThe variations between EL and JL in responsive DEGs of interest as potentially related to differences seen in the field and should be considered in the selection of trees for planting and future breeding.
Joint analysis of PK and immunogenicity outcomes using factorization model − a powerful approach for PK similarity study
Authors: Haliduola Halimu N. , Berti Fausto , Stroissnig Heimo , Guenzi Eric , Otto Hendrik , Sattar Abid , Mansmann Ulrich 
Published: October 2022

AbstractBiological products, whether they are innovator products or biosimilars, can incite an immunogenic response ensuing in the development of anti-drug antibodies (ADA). The presence of ADA’s often affects the drug clearance, resulting in an increase in the variability of pharmacokinetic (PK) analysis and challenges in the design and analysis of PK similarity studies. Immunogenic response is a complex process which may be manifested by product and non-product-related factors. Potential imbalances in non-product-related factors between treatment groups may lead to differences in antibodies formation and thus in PK outcome. The current standard statistical approaches dismiss any associations between immunogenicity and PK outcomes. However, we consider PK and immunogenicity as the two correlated outcomes of the study treatment. In this research, we propose a factorization model for the simultaneous analysis of PK parameters (normal variable after taking log-transformation) and immunogenic response subgroup (binary variable). The central principle of the factorization model is to describe the likelihood function as the product of the marginal distribution of one outcome and the conditional distribution of the second outcome given the previous one. Factorization model captures the additional information contained in the correlation between the outcomes, it is more efficient than models that ignore potential dependencies between the outcomes. In our context, factorization model accounts for variability in PK data by considering the influence of immunogenicity. Based on our simulation studies, the factorization model provides more accurate and efficient estimates of the treatment effect in the PK data by taking into account the impact of immunogenicity. These findings are supported by two PK similarity clinical studies with a highly immunogenic biologic.
Burden, clinical presentation and risk factors of advanced HIV disease in pregnant Mozambican women
Authors: Nhampossa Tacilta , González Raquel , Nhacolo Arsenio , Garcia-Otero Laura , Quintó Llorenç , Mazuze Maura , Mendes Anete , Casellas Aina , Bambo Gizela , Couto Aleny , Sevene Esperança , Munguambe Khátia , Menendez Clara 
Published: October 2022

Abstract
Background
Information on the frequency and clinical features of advanced HIV disease (AHD) in pregnancy and its effects on maternal and perinatal outcomes is limited. The objective of this study was to describe the prevalence and clinical presentation of AHD in pregnancy, and to assess the impact of AHD in maternal and perinatal outcomes in Mozambican pregnant women.

Methods
This is a prospective and retrospective cohort study including HIV-infected pregnant women who attended the antenatal care (ANC) clinic at the Manhiça District Hospital between 2015 and 2020. Women were followed up for 36 months. Levels of CD4 + cell count were determined to assess AHD immune-suppressive changes. Risk factors for AHD were analyzed and the immune-suppressive changes over time and the effect of AHD on pregnancy outcomes were assessed.

Results
A total of 2458 HIV-infected pregnant women were enrolled. The prevalence of AHD at first ANC visit was 14.2% (349/2458). Among women with AHD at enrolment, 76.2% (260/341) were on antiretroviral therapy (ART). The proportion of women with AHD increased with age reaching 20.5% in those older than 35 years of age (p < 0.001). Tuberculosis was the only opportunistic infection diagnosed in women with AHD [4.9% (17/349)]. There was a trend for increased CD4 + cell count in women without AHD during the follow up period; however, in women with AHD the CD4 + cell count remained below 200 cells/mm3 (p < 0.001). Forty-two out of 2458 (1.7%) of the women were severely immunosuppressed (CD4 + cell count < 50 cells/mm3). No significant differences were detected between women with and without AHD in the frequency of maternal mortality, preterm birth, low birth weight and neonatal HIV infection.

Conclusions
After more than two decades of roll out of ART in Mozambique, over 14% and nearly 2% of HIV-infected pregnant women present at first ANC clinic visit with AHD and severe immunosuppression, respectively. Prompt HIV diagnosis in women of childbearing age, effective linkage to HIV care with an optimal ART regimen and close monitoring after ART initiation may contribute to reduce this burden and improve maternal and child survival.
Psychometric properties of the Last-7-Day Sedentary Time Questionnaire (SIT-Q-7d): Testing the validity and reliability among general population
Authors: Bakhtari Aghdam Fatemeh , Aziz-Zadeh Sepideh , Musavi Saeed , Abbasalizad-Farhangi Mahdieh 
Published: October 2022

Abstract
Backgrounds
Sedentary behavior (SB) is an independent risk factor causing chronic diseases. Previous studies compared sitting time mostly with physical activity. The present study aimed to evaluate the validity and reliability of the Last-7-Day Sedentary Time Questionnaire (SIT-Q-7d) in Iran. Moreover, SB was assessed among the study participants.

Methods
The current validity study was conducted among 290 subjects (51.7% males vs. 48.3% females) with a mean age of 34.81 ± 9.63 years in Poldasht, Iran. Sampling was done using simple random sampling and the data were collected using the SIT-Q-7d. To confirm the validity of the questionnaire, forward–backward translation method, content validity, and construct validity were used. Furthermore, temporal stability was calculated by the test–retest method and internal consistency coefficient (ICC).

Results
Our results confirmed the content validity of the questionnaire (content validity score: 0.90 and content validity index: 0.80). Using exploratory factor analysis (EFA), seven factors of SB were identified as follows: eating while sitting down, doing domestic affairs, screen time, leisure time, studying books, watching TV, and attending family gatherings. The reliability of the questionnaire was confirmed using Cronbach’s alpha (α = 0.7). In addition, temporal stability was confirmed by test–retest method and ICC was 0.9 (95% CI: 83–97).

Conclusion
Our results confirmed that the Persian version of SIT-Q-7d is a reliable and valid tool for assessing SB.
Surgical outcomes between posterior decompression alone and posterior decompression with fusion surgery among patients with Meyerding grade 2 degenerative spondylolisthesis: a multicenter cohort study
Authors: Tozawa Keiichiro , Matsubayashi Yoshitaka , Kato So , Doi Toru , Taniguchi Yuki , Kumanomido Yudai , Higashikawa Akiro , Yosihida Yuichi , Kawamura Naohiro , Sasaki Katsuyuki , Azuma Seiichi , Yu Jim , Hara Nobuhiro , Iizuka Masaaki , Ono Takashi , Fukushima Masayoshi , Takeshita Yujiro , Tanaka Sakae , Oshima Yasushi 
Published: October 2022

Abstract
Background
Whether lumbar decompression with fusion surgery is effective against Meyerding grade 2 degenerative spondylolisthesis (DS) is unknown. Therefore, the current study aimed to compare the surgical outcomes between posterior decompression alone and posterior decompression with fusion surgery among patients with grade 2 DS with central canal stenosis.

Methods
This retrospective cohort study included prospectively registered patients (n = 3863) who underwent surgery for degenerative lumbar spinal canal stenosis at nine high-volume spine centers from April 2017 to July 2019. Patients with grade 2 DS and central canal stenosis were included in the analysis. Patients with radiculopathy, including foraminal stenosis, degenerative scoliosis, and concomitant anterior spinal fusion, and those with a previous history of lumbar surgery were excluded. The participants were divided into the decompression alone group (group D) and decompression with fusion surgery group (group F). Data about patient-reported outcomes, including Numeric Rating Scale (low back pain, leg pain, leg numbness, and foot numbness), Oswestry Disability Index, EuroQol Five-Dimensional questionnaire, and 12-Item Short-Form Health Survey scores, were obtained preoperatively and 2 years postoperatively.

Results
In total, 2354 (61%) patients, including 42 (1.8%) with grade 2 DS (n = 18 in group D and n = 24 in group F), completed the 2-year follow-up. Group D had a higher proportion of female patients than group F. However, the two groups did not significantly differ in terms of other baseline demographic characteristics. Group D had a significantly shorter surgical time and lower volume of intraoperative blood loss than group F. Postoperative patient-reported outcomes did not significantly differ between the two groups, although the preoperative degree of low back pain was higher in group F than in group D. The slip degree of group D did not worsen during the follow-up period.

Conclusion
The surgical outcomes were similar regardless of the addition of fusion surgery among patients with grade 2 DS. Decompression alone was superior to decompression with fusion surgery as it was associated with a lower volume of intraoperative blood loss and shorter surgical time.
Novel scoring system combined with a virtual reality technique for the preoperative evaluation of the stone-free status after flexible ureteroscopy: the H.L.P.E.S. score
Authors: Gu Jianglin , Luo Shengjun , Jiang Li , Hu Daixing , Zhao Guozhi , Tang Wei 
Published: October 2022

Abstract
Objective
The original S.O.L.V.E. scoring system was modified using virtual reality technology, and a new H.L.P.E.S scoring system was constructed to improve the accuracy of predicting the stone-free rate after flexible ureteroscopy.

Methods
We retrospectively analyzed clinical and virtual reality data of 150 patients with renal calculi who underwent flexible ureteroscopy at the First Affiliated Hospital of Chongqing Medical University, Chongqing, China, from September 2019 to January 2022. Factors affecting the stone-free rate were evaluated in univariate and multiple logical regression analyses. Factors were divided by cut-off value under the receiver-operating characteristic curve and scored accordingly to a well-known international scoring system. Area under the curve predicted the stone-free rate. The accuracy and superiority of the stone-free rate after flexible ureterorenoscopy was compared between this scoring system and the S.O.L.V.E, R.I.R.S, T.O.HO, and RUSS scores.

Results
Multiple logistic regression showed that the stone surface area, renal pelvis volume, and length of the calyces funnel were correlated with stone-free rate (P < 0.01, P = 0.021, P = 0.019, respectively). The H.L.P.E.S. score included stone surface area (1–2 points), renal pelvis volume (1–2 points), length of calyces funnel (1–2 points), pelvic calyceal height (1–2 points), and essence of stone (1–2 points). The area under the receiver-operating characteristic curve of H.L.P.E.S. score was 0.927, which was higher than the S.O.L.V.E., R.I.R.S., T.O.HO, and RUSS scores.

Conclusion
H.L.P.E.S. scoring can effectively predict the stone-free rate after flexible ureteroscopy for renal calculi and is superior to other scoring systems.
Up-regulation of miR-133a-3p promotes ovary insulin resistance on granulosa cells of obese PCOS patients via inhibiting PI3K/AKT signaling
Authors: Yang Xiaoman , Wang Kehua , Lang Jiajia , Guo Danyang , Gao Haixia , Qiu Yue , Jin Xiaohan , Zhang Mingyue , Shi Jiaxiu , Ma QianQian , Ma Qian , Wen Zixi 
Published: October 2022

Abstract
Background
MicroRNAs are a type of non-coding single-stranded RNA, which is involved in the regulation of ovary insulin resistance (IR). This study aims to explore the underlying mechanisms of miR-133a-3p regulating ovary IR in obese polycystic ovary syndrome (PCOS).

Methods
Granulosa cells (GCs) were extracted from follicular fluids of PCOS patients (obese PCOS group and non-obese PCOS group) and healthy women (control group). The expression of miR-133a-3p in GCs was detected by qRT-PCR. The targets and pathways of miR-133a-3p were predicted by bioinformatics analyses. The protein levels of PI3K, p-AKT, GLUT4, p-GSK-3β, and p-FOXO1 were measured by Western blotting.

Results
MiR-133a-3p was highly expressed in GCs from PCOS patients, especially in obese PCOS patients. The protein levels of PI3K and p-AKT was downregulated in GCs from PCOS patients. There were 11 target genes of miR-133a-3p enriching in PI3K/AKT signaling pathway. miR-133a-3p mimic downregulated the expression of PI3K, p-AKT, and GLUT4, and upregulated the protein levels of p-GSK-3β and p-FOXO1. miR-133a-3p inhibitor presented the opposite effect of miR-133a-3p mimic.

Conclusion
MiR-133a-3p promotes ovary IR on GCs of obese PCOS patients via inhibiting PI3K/AKT signaling pathway. This study lays a foundation for further research on the mechanism of ovary IR in obese PCOS patients.
Investigating the role of health information technology in the control and management of Systemic Lupus Erythematosus (SLE): a systematic review
Authors: Moulaei Khadijeh , Rajaei Elham , Ahmadian Leila , Khajouei Reza 
Published: October 2022

AbstractBackgroundDespite the use of health information technology (HIT) for controlling and managing lupus, its effectiveness has not been well studied. The objective of this study was to investigate the role of HIT in controlling and managing lupus.MethodsWe searched Scopus, PubMed, Web of Science, and Embase, using "self-management", "self-care" and "Systemic Lupus Erythematosus" keywords. Two researchers selected relevant papers and extracted data using a data collection form. Disagreements were resolved in consultation with the third and fourth researchers. After extraction, the data were analyzed.ResultsTotally, 23 papers met the inclusion criteria. About 75% of the studies used web and telephone-based technologies. Most services provided with health technologies were ‘Training’ and ‘consulting’. The ‘lifestyle" and ‘Consultation and education’ axes were the most widely used HIT services to control and manage lupus. While, ‘Better management and control of the disease’, ‘Increasing knowledge and awareness of people about lupus’ and ‘Improving behaviors and attitudes toward self-management and self-care’ were also the most important outcomes. ‘Collectiing patient data and information’, 'Providing education and consultation services to patients', 'Measuring patient-reported outcomes', and 'Increasing patients' knowledge and awareness of their disease' were the most important advantages of various technologies. 'Slow internet speed' and 'Challenges and problems related to appearance and usability' and 'Patient concerns about privacy and misuse of their data' were three disadvantages of technologies.ConclusionThe findings showed that HIT can improve the management and control of lupus and facilitate self-efficacy, self-care, and self-management in patients. The axes and data elements identified in this study can be the basis for developing and implementing efficient HIT-based systems to improve, control, and manage lupus.
Workload and quality of nursing care: the mediating role of implicit rationing of nursing care, job satisfaction and emotional exhaustion by using structural equations modeling approach
Authors: Maghsoud Fatemeh , Rezaei Mahboubeh , Asgarian Fatemeh Sadat , Rassouli Maryam 
Published: October 2022

Abstract
Background
Nursing workload and its effects on the quality of nursing care is a major concern for nurse managers. Factors which mediate the relationship between workload and the quality of nursing care have not been extensively studied. This study aimed to investigate the mediating role of implicit rationing of nursing care, job satisfaction and emotional exhaustion in the relationship between workload and quality of nursing care.

Methods
In this cross-sectional study, 311 nurses from four different hospitals in center of Iran were selected by convenience sampling method. Six self-reported questionnaires were completed by the nurses. The data were analyzed by SPSS version 16. Structural equation modeling was used to determine the relationships between the components using Stata 14 software.

Results
Except direct and mutual relationship between workload and quality of nursing care (P ≥ 0.05), the relationship between other variables was statistically significant (P < 0.05). The hypothesized model fitted the empirical data and confirmed the mediating role of implicit rationing of nursing care, job satisfaction and emotional exhaustion in the relationship between workload and the quality of nursing care (TLI, CFI > 0.9 and RMSEA < 0.08 and χ2/df < 3).

Conclusion
Workload affects the quality of the provided nursing care by affecting implicit rationing of nursing care, job satisfaction and emotional exhaustion. Nurse managers need to acknowledge the importance of quality of nursing care and its related factors. Regular supervision of these factors and provision of best related strategies, will ultimately lead to improve the quality of nursing care.