bluuebunny/crossref_metadata_2025_split huggingface dataset:
Changes in Bone Turnover, Inflammatory, Oxidative Stress, and Metabolic Markers in Women Consuming Iron plus Vitamin D Supplements: A Randomized Clinical Trial
Authors: Abiri Behnaz , Azizi-Soleiman Fatemeh , Vafa Mohammadreza , Safavi Morteza , Kazemi Seyyed Morteza , Salehi Masood , Zaeri Farid , Sadeghi Homa 
Published: December 2019

Abstract
Background We aimed to investigate whether combination of vitamin D and iron supplementation, comparing vitamin D alone, could modify bone turnover, inflammatory, oxidative stress, and metabolic markers. Methods Women with hemoglobin (Hb)≤12.7 g/dL and 25OHD≤29 ng/mL vitamin D deficiency/insufficiency aged 18-45 years (n=100) were recruited into a trial to receive either 1000 IU/d vitamin D3 plus 27 mg/d iron (D-Fe) or vitamin D3 plus placebo supplements (D-P) for 12 weeks. Results In D-Fe group, significant decreases in red blood cells (RBC) (P=0.001), hematocrit (Hct) (P=0.004) and increases in mean corpuscular hemoglobin concentration (MCHC)(P=0.001), 25OHD (P<0.001), osteocalcin (P<0.001), high-density cholesterol (HDL) (P=0.041), and fasting blood sugar (FBS) (P<0.001) were observed. D-P group showed significant decreases of RBC (P<0.001), Hb (P<0.001), Hct (P<0.001), mean corpuscular volume (MCV) (P=0.004), mean corpuscular hemoglobin (MCH) (P<0.001), MCHC (P=0.005), serum ferritin (P<0.001), and low-density cholesterol (LDL) (P=0.016) and increases of 25OHD (P<0.001), osteocalcin (P<0.001), C-terminal telopeptide (CTX) (P=0.025), triglyceride (TG) (P=0.004), FBS (P<0.001), and interleukin-6 (IL-6) (P=0.001) at week 12. After the intervention, the D-P group had between-group increases in mean change in the osteocalcin (P=0.007) and IL-6 (P=0.033), and decreases in the RBC (P<0.001), Hb (P<0.001), Hct (P<0.001), MCV (P=0.001), compared to the D-Fe group. There were significant between-group changes in MCH (P<0.001), MCHC (P<0.001), ferritin (P<0.001), and serum iron (P=0.018). Conclusions Iron-vitamin D co-supplementation does not yield added benefits for improvement of bone turnover, inflammatory, oxidative stress, and metabolic markers; whereas, vitamin D alone may have some detrimental effects on inflammatory and metabolic markers.
Hidden analyses: A review of current reporting practice and recommendations for more transparent reporting of initial data analyses
Authors: Huebner Marianne , Vach Werner , Cessie Saskia le , Schmidt Carsten Oliver , Lusa Lara 
Published: December 2019

Abstract
Background: In the data pipeline from the data collection process to the planned statistical analyses, initial data analysis (IDA) typically takes place between the end of the data collection and do not touch the research questions. A systematic process for IDA and clear reporting of the findings would help to understand the potential shortcomings of a dataset, such as missing values, or subgroups with small sample sizes, or shortcomings in the collection process, and to evaluate the impact of these shortcomings on the research results. A clear reporting of findings is also relevant when making datasets available to other researchers. Initial data analyses can provide valuable insights into the suitability of a data set for a future research study. Our aim was to describe the current practice of reporting of initial data analyses in observational studies in five highly ranked medical journals with focus on data cleaning, screening, and reporting of findings which led to a potential change in the analysis plan.Methods: This review was carried out using systematic search strategies with eligibility criteria for articles to be reviewed. A total of 25 papers about observational studies were selected from five medical journals. Each paper was reviewed by two reviewers and IDA statements were further discussed by all authors. The consensus was reported.Results: IDA statements were reported in the methods, results, discussion, and supplement of papers. Ten out of 25 papers (40%) included a statement about data cleaning. Data screening statements were included in all articles, and 18 (72%) indicated the methods used to describe them. Item missingness was reported in 11 papers (44%), unit missingness in 15 papers (60%). Eleven papers (44%) mentioned some changes in the analysis plan. Reported changes referred to missing data treatment, unexpected values, population heterogeneity and aspects related to variable distributions or data properties. Conclusion: Reporting of initial data analyses were sparse, and statements on IDA were located throughout the research articles. There is a lack of systematic reporting of IDA. We conclude the article with recommendations on how to overcome shortcomings in the current practice of IDA reporting in observational studies.
Distribution of blaOXA, blaSHV, and blaTEM type extended-spectrum β-lactamase genes in multi-drug resistant Gram-negative isolates from burn patients of Lahore, Pakistan
Authors: Haider Muhammad Hayat , Ain Noor Ul , Abrar Samyyia , Riaz Saba 
Published: December 2019

Abstract
Background Multidrug resistant Gram-negative bacterial pathogens are becoming a lethal source of infections and associated complications of sepsis and multiple organ failure following burn injuries. Genotypic variants of bla OXA , bla SHV and bla TEM type extended-spectrum-β-lactamases (ESBLs) have been detected in Pseudomonas aeruginosa , Enterobacteriaceae and other type of bacteria. These hydrolytic enzymes are responsible for the degradation of broad-spectrum antimicrobials including third generation cephalosporins. We aimed to determine the distribution of ESBLs gene variants among MDR pathogens from post burn infections.Methods A total of 358 specimens were collected during the period from 15 th August 2017 to 15 th August 2018 from burnt patients at Jinnah Burn and Reconstructive Surgery Centre (JB&RSC).Results 53.57% cephalosporins resistant isolates were found to be associated with a slightly higher frequency of 50.7% community-acquired and 49.30% nosocomial infections. 72% of these infections was found to be associated with males (p-value = 0.919, OR = 1.038). The age of burn victims ranged from 4 to 85 years (Mean=28.95, SD=±15.65). Pseudomonas spp., were the predominant as 49.33% followed by 22.67% Klebsiella spp., 20% Acinetobacter spp., and 8% Proteus spp., strains. There were 83.33% multidrug resistant isolates and meropenem, imipenem, and amikacin were found to be effective against 28.70%, 25.30%, and 26.00% of cephalosporins resistant strains respectively. Lowest sensitivity of phenotypic tests was observed as 16% ESBLs were detected by double disk synergism test (DDST) and 14% were confirmed by combination disk test (CDT). Molecular detection proved to be effective for the detection of 79.71% bla TEM , 37.68% bla OXA , and 18.84% bla SHV isolates. bla TEM genes were confirmed in 18.18% CDT positive isolates with 62.67% diagnostic accuracy (95% CI = 54.70, 70.00) and 88.42% specificity (95% CI = 80.45, 93.41). All of the bla TEM positive isolates were resistant to cefuroxime and 98.18% were resistant to cephradine, and piperacillin.Conclusion The antimicrobial resistance associated with the ESBLs producing Pseudomonas spp., and Enterobacteriaceae is becoming a challenge for the treatment and survival of burn patients. The higher frequency of MDR isolates and detection of bla TEM , bla OXA , and bla SHV genes confirms that management of burn patients should be improved to prevent the infections.
Machine Learning Algorithms to Predict the Mortality of Carbapenem Resistant Klebsiella Pneumoniae bacteremia
Authors: Liang Qiqiang , Qian Fang , Chen Yibing , Xu Zhijun , Xu Zhijiang , Huang Man 
Published: December 2019

Abstract
Purpose To establish mortality prediction models in 14 days of Carbapenem-Resistant Klebsiella Pneumoniae bacteremia using Machine learning.Materials and Methods It is a single-center retrospective study. We collect the relevant clinical information of all patients with Carbapenem-Resistant Klebsiella Pneumoniae (CRKP) bacteremia in the past 5 years using the local database. Data analysis and verification are carried out by multiple logical regression, decision tree, random forest, support vector machine (SVM), and XGBoost.Result This study includes 187 patients with 40 related variables. In multiple logical regression, acute renal injury (P=0.003), Apache II score (P=0.036), immunodeficiency (P=0.025), severe thrombocytopenia (P=0.025) and septic shock (P=0.044) are the high-risk factors for 14 days mortality of CRKP bloodstream infections. According to the importance of those parameters, risk scoring is established to predict the survival rate of CRKP bacteremia. The analysis of the five models, with 70% training set and 30% test set, show the comprehensive performance of random forest (AUROC=0.953, precision=91.85%) is slightly better than that of XGBoost (AUROC=0.912, precision=86.41%) and SVM (AUROC=0.936, precision=79.89%) in predicting 14-day mortality of CRKP bacteremia. The multiple logical regression model (AUROC=0.825, precision=81.52%) is the second, and the decision tree model (AUROC=0.712, precision=79.89%) is not very ideal.Conclusion Machine learning has good performances in predicting 14-day mortality of CRKP bacteremia than multiple logical regression. Acute renal injury, severe thrombocytopenia, and septic shock are the high-risk factors of CRKP bacteremia mortality.
New insights on the function of plant acyl carrier proteins from comparative and evolutionary analysis
Authors: Yang Xuezhen , Liu Xiaoxue , Zhou Yanchen , Zhang Fan , Huang Lan , Wang Jun , Song Jian , Qiu Lijuan 
Published: December 2019

Abstract
BackgroundAcyl carrier proteins (ACPs) play a central role in both plastidial and mitochondrial Type II fatty acid synthesis in plant cells. However, a large proportion of plant ACPs remain functionally uncharacterized, and their evolutionary history remains elusive. ResultsIn present study, 97 putative ACPs were identified from ten angiosperm species examined. Based on phylogenetic analysis, ACP genes were grouped into plastidial (cpACP: ACP1/2/3/4/5) and mitochondrial (mtACP: mtACP1/mtACP2/mtACP3) ACPs. Protein sequence (motifs and length), tertiary structure, and gene structure (exon number, average intron length, and intron phase) were highly conserved in different ACP subclades. The differentiation of ACPs into distinct types occurred 85–98 and 45–57 million years ago. A limited proportion of ACP genes experience tandem or segmental duplication, corresponding to two rounds of whole genome duplication. Ka/Ks ratios revealed that duplicated ACP genes underwent a purifying selection. Regarding expression patterns, most ACPs were expressed constitutively and tissue-specifically. Notably, the average expression levels of ACP1, mtACP3, and mtACP1 were positively correlated with those of ACP3, ACP4, and mtACP2, respectively. Analysis of cis-elements showed that seven motifs (CACTFTPPCA1, DOFCOREZM, GT1CONSENSUS, CAATBOX1, ARR1AT, POLLEN1LELAT52, and GATABOX) related to tissue-specific, ABA, and light-mediated gene regulation were ubiquitous in all ACPs investigated, which shed new light on the regulation patterns of these central enzymatic partners of the FAS system. ConclusionsThis study presents a thorough overview of angiosperm ACP gene families and provides informative clues for the functional characterization of plant ACPs in the future.
Efficacy of the erector spinae plane block in lumbar spinal surgery patients: a systematic review
Authors: Qiu Yong , Zhang Teng-jiao , Meng Ling-bing , Hua Zhen 
Published: December 2019

Abstract
Background: Erector spinae palne block (ESPB) as a new trunk fascia block technique was proposed in 2016. Because of its clear analgesic effect and simple operation, it has aroused the interest of many nerve block experts. However, there are few clinical studies on ESPB for lumbar surgery, and its benefits are controversial. The goal of this review paper is to summarize the use of ESPB for lumbar spine surgery in order to better understand and promote this technique.Methods: Pubmed, EMBASE, Cochrane library, ClinicalTrial.gov databases were searched up to July 30, 2019. According to the inclusion and exclusion criteria established in advance, “lumbar spine surgery” and “ESPB” related MesH terms, free-text words were used. Data on pain scores, analgesic consumptions and adverse effects were reported. All processes follow PRISMA statement guidelines.Results: A total of 171 participants from 11 publications were identified, including two randomized controlled trials, one retrospective cohort study, four case report, four cases series. Block operation plane from T8 to L4. The main anesthetics used in block are bupivacaine, ropivacaine and lidocaine. There was evidence for reducing postoperative pain scores and analgesic consumptions.Conclusion: ESPB in lumbar spine surgery have the potential to relieve lumbar postoperative pain and reduce the use of analgesic drugs. Randomized controlled trials of high quality and large samples are needed to further clarify the benefits of ESPB in lumbar surgery patients.
Fluid Overload After Coronary Artery Bypass Graft in Patients on Maintenance Hemodialysis is Associated with Prolonged Time on Mechanical Ventilation
Authors: silva sirlei , Consolim-Colombo Fernanda Marciano , Rodrigues Renata Gomes , Gaiotto Fábio Antonio , Hajjar Ludhmila Abrahão , Moysés Rosa Maria Affonso , Elias Rosilene Motta 
Published: December 2019

Abstract
Background: Fluid overload is a risk factor for morbidity, mortality, and prolonged ventilation time after surgery. Patients on maintenance hemodialysis might be at higher risk. We hypothesized that fluid accumulation would be directly associated with extended ventilation time in patients on hemodialysis, as compared to patients with chronic kidney disease not on dialysis (CKD3-4) and patients with normal renal function (reference group).Methods: this is a prospective observational study that included patients submitted to isolated and elective coronary artery bypass surgery, divided in 3 groups: reference (N=167, normal renal function), CKD3-4 (N=84, estimated glomerular filtration rate 30-60ml/min/1.73m2), and hemodialysis (N=31, maintenance hemodialysis). The same observer followed patients daily from the surgery to the hospital discharge. Results: Fluid accumulation correlated with time on mechanical ventilation in patients on hemodialysis (r=0.627, p=0.003), but not in the CKD3-4 group (r=-0.068, p=0.652) and in the reference group (r=-0.085, p=0.363). Multivariate analysis revealed that the fluid accumulation, scores of sequential organ failure assessment (SOFA) in the day following surgery, and the study group were independently associated with time in mechanical ventilation. Among patients on hemodialysis, the time from the surgery to the first hemodialysis session also accounted for the time on mechanical ventilation. Conclusions: Fluid accumulation is an important risk factor for lengthening mechanical ventilation, particularly in patients on hemodialysis. Future studies are warranted to address the ideal timing for initiating dialysis in this scenario in an attempt to reduce fluid accumulation and avoid prolonged ventilation time and hospital stay.
Full-length transcriptome sequencing and comparative transcriptomic analysis to uncover genes involved in early gametogenesis in the gonads of Amur sturgeon (Acipenser schrenckii)
Authors: Zhang Xiujuan , Zhou Jiabin , Li Linmiao , Huang Wenzhong , Ahmad Hafiz Ishfaq , Li Huiming , Jiang Haiying , Chen Jinping 
Published: December 2019

Abstract
Background Sturgeons (Acipenseriformes) are polyploid chondrostean fish that constitute an important model species for studying development and evolution in vertebrates. To better understand the mechanisms of reproduction regulation in sturgeon, this study combined PacBio isoform sequencing (Iso-Seq) with Illumina short-read RNA-seq methods to discover full-length genes involved in early gametogenesis of the Amur sturgeon, Acipenser schrenckii .Results A total of 50.04 G subread bases were generated from two SMRT cells, and herein 164,618 nonredundant full-length transcripts (unigenes) were produced with an average length of 2,782 bp from gonad tissues (three testes and four ovaries) from seven 3-year-old A. schrenckii individuals. The number of ovary-specific expressed unigenes was greater than those of testis (19,716 vs. 3,028), and functional assignment indicated that 6 of 14 annotated KEGG pathways were directly ovary-related and had abundant transcripts and differential expression genes. Importantly, 60 early gametogenesis-related genes (involving 755 unigenes) were successfully identified, and exactly 50 percent (30/60) of those showed differential expression in testes and ovaries. The Amh and Gsdf with testis-biased expression, and Foxl2 and Cyp19a with ovary-biased expression strongly suggested the important regulatory roles in spermatogenesis and oogenesis of A. schrenckii , respectively. We also found the four novel Sox9 transcript variants, which increase the numbers of regulatory genes and imply function complexity of early gametogenesis. Finally, a total of 236,672 AS events (involving 36,522 unigenes) were detected, and 10,556 putative long noncoding RNAs (lncRNAs) and 4,339 predicted transcript factors (TFs) were also respectively identified, which all significantly associated with the early gametogenesis of A. schrenckii .Conclusions Overall, our results provide new genetic resources of full-length transcription data and information as a genomic-level reference for sturgeon. Crucially, we explored the comprehensive genetic characteristics that differ between the testes and ovaries of A. schrenckii in the early gametogenesis stage. These provide candidate genes and theoretical basis for further the mechanisms of reproduction regulation of sturgeon.
Efficient Biosynthesis of R-(-)-linalool through Adjusting Expression Strategy and Increasing GPP Supply in Escherichia coli
Authors: Wang Xun , Wu Jing , Chen Jiaming , Xiao Longjie , Li Xun 
Published: December 2019

Abstract
Background: R-(-)-linalool is a versatile acyclic monoterpene alcohol with applications in the flavor and fragrance, pharmaceutical, and agrochemical industries. However, plant extraction furnishes only limited and unstable R-(-)-linalool yields that do not satisfy market demand. Therefore, a sustainable yet efficient and productive method of R-(-)-linalool synthesis is urgently needed. Results: To induce the R-(-)-linalool biosynthesis pathway in E. coli , we expressed heterologous (3R)-linalool synthase (LIS) from Lavandula angustifolia (laLIS). We then enhanced R-(-)-linalool production in the cells using a suitable LIS from Streptomyces clavuligerus (bLIS). The bLIS expression was markedly elevated by using optimized ribosomal binding sites (RBSs) and protein fusion tags. R-(-)-linalool output rose from 4.8 mg L -1 to 33.4 mg L -1 . To increase the geranyl diphosphate (GPP) content in E. coli , we tested various alterations in geranyl diphosphate synthases (GPPSs) and their mutants. The final E. coli strain harboring GPPS from Abies grandis ( Ag GPPS) accumulated ≤ 100.1 mg L -1 R-(-)-linalool after 72 h shake-flask fermentation. This yield gain constitutes a 60.7-fold improvement in R-(-)-linalool biosynthesis over the parent strain. Fed-batch cultivation of the engineered strain in a 1.3-L fermenter yielded 1,027.3 mg L -1 R-(-)-linalool. Conclusions: In this study, an efficient R-(-)-linalool production pathway was induced in E. coli via the heterologous MVA pathway, AgGPPS, and (3R)-linalool synthase (bLIS). By overexpressing the key enzyme in the engineered E. coli strain, R-(-)-linalool production reached 100.1 mg L -1 and 1,027.3 mg L -1 under shake flask- and fed-batch fermentation conditions, respectively. The latter is the highest reported R-(-)-linalool yield to date using an engineered E. coli strain. The strategies of key enzyme overexpression and mutation could lay theoretical and empirical foundations for engineering terpenoid pathways and optimizing other metabolic pathways.
Camelina sativa meal hydrolysate as sustainable biomass for the production of carotenoids by Rhodosporidium toruloides
Authors: Bertacchi Stefano , Bettiga Maurizio , Porro Danilo , Branduardi Paola 
Published: December 2019

Abstract
Background: The sustainability of biorefineries is strongly related to the origin, the availability and the market of the biomass used as feedstock. Moreover, one of the pillars of circular economy aims at reducing waste, ideally to zero. These considerations well justify the increasing industrial interest in exploiting many and diverse residual biomasses. This work focuses on the valorization of the leftover from Camelina sativa oil extraction, named Camelina meal. Despite Camelina meal is used as animal feed, there is an increasing interest in further valorizing its macromolecular content or its nutritional value. Results: Here we valorized Camelina meal hydrolysates by using them as nutrient and energy source for shake-flask fermentations where Rhodosporidium toruloides , a yeast natural producer of carotenoids, accumulated these pigments as desired product. Initially, by total acid hydrolysis we determined that in Camelina meal carbohydrates account for a maximum of 30.8 ± 1.0 %. However, since the acid hydrolysis is not optimal for subsequent microbial fermentation, an enzymatic hydrolysis protocol was assessed, obtaining a maximum sugar recovery of 53.3%. Having stated that, by Separate Hydrolysis and Fermentation, with or without water insoluble solids (SHF, SHF+WIS), or Simultaneous Saccharification and Fermentation (SSF) we obtained 5.51 ± 0.67, 12.64 ± 2.57, and 15.97 ± 0.67 mg/L of carotenoids, respectively, from Camelina meal hydrolysate. Significantly, the presence of WIS, possibly containing microbial inhibitors, correlates with a higher titer of carotenoids, which can be seen as scavengers. Conclusions: The proposed study paves the way for the development of bioprocesses based on the exploitation of Camelina meal, scarcely investigated in the field before, as feedstock. The processes depicted provide an example of how different final products of industrial interests can be obtained from this leftover, such as pure carotenoids and carotenoid-enriched Camelina meal for the feed industry, without diminishing but possibly increasing its initial value. These data provide valuable basis for the economic evaluations necessary to assess the feasibility of a bioprocess based on Camelina meal to obtain high-value added products.
Study On The Biomechanical Properties Of Rabbit Venous Arterialization
Authors: Zhang Yuhao , Niu Pei , Zhang Zhimin , Niu Xiaolong , Shen Wenzeng , Hao Liangchao , Zhou Yujuan , Liu Fulin 
Published: December 2019

Abstract

Objective : To investigate the mechanisms underlying restenosis following coronary artery bypass grafting using bridging veins.Method : We established a rabbit model of venous arterialisation, by transplanting veins into the arterial system as bridging vessels and investigated vessel tensile mechanical and histomorphological properties. Result : Control vein elasticity (k = 16.20) was less than that of the control artery (k = 58.04; P < 0.05), and vein walls were thinner. Following venous arterialisation, proliferating cell nuclear antigen and alpha-actin were upregulated and vein walls thickened (P < 0.05), with elasticity after venous arterialisation (k = 86.26) significantly higher than that of control veins (P < 0.05). Conclusion : This indicates that venous intima is damaged by high pressure following arterialisation, resulting in gradual restenosis, with thickening of the venous intima and an increase in vessel elasticity. Clinically, there is potential to repeat these experiments to determine the elastic extremum of the great saphenous vein and control the pressure in the lumen of this vessel, to ensure minimal damage to the intima before anastomosis, thereby facilitating improvement of long-term patency rates following vein bridge surgery. Whether the increase in venous bridge elasticity after venous arterialisation can be controlled, with the aim of preventing early-stage restenosis, warrants investigation.