bluuebunny/crossref_metadata_2025_split huggingface dataset:
Simulated solar light-driven photocatalytic degradation of trichloroethylene in water using BiOBr promoted by sulfite addition
Authors: Jung Bahngmi , Deng Wei , Li Ying , Batchelor Bill , Abdel-Wahab Ahmed 
Published: January 2020

Abstract
Background
Photodegradation of trichloroethylene (TCE) in aqueous solution under simulated solar light irradiation was studied under different experimental conditions to determine the reaction mechanism and kinetics that control TCE degradation using bismuth oxybromide (BiOBr) in the presence of sulfite. Photocatalysts were synthesized to be more responsive to visible light under simulated solar light and particular attention was focused on the reactive specie formed by reaction of the sulfite on the surface of BiOBr under simulated sunlight.

Result
Degradation rate of TCE was greatly enhanced by the presence of sulfite, and the enhancement increased with sulfite dose to a maximum that was retained at higher sulfite doses. Degradation rate of TCE was also affected by other factors, such as initial TCE concentration, BiOBr dose, and solution pH. In addition, the cycling performance of BiOBr was examined, and the amount of TCE degraded was almost constant over increasing cycle numbers when initial sulfite concentration was high enough to maintain a suitable sulfite concentration throughout the experiment. When TCE was degraded by BiOBr in the presence of sulfite under simulated sunlight irradiation, the major by-product measured was the non-hazardous chloride ion, and dechlorination efficiency was about 58%.

Conclusion
This study extended the use of a potential effective photocatalyst (BiOBr) to a semi-volatile organic contaminant (TCE), not limited to mainly focus on organic dyes, and evaluated the use of sulfite as a hole scavenger in order to enhance the degradation of TCE without needing to manipulate the structure of BiOBr. The active species being responsible for TCE degradation in BiOBr/TCE/sulfite system under simulated solar light was the sulfite radical (SO3·−), and the photocatalytic activity of BiOBr did not decrease over a number of treatment cycles when SIV dose was sufficient.
Genome-wide analyses of cassava Pathogenesis-related (PR) gene families reveal core transcriptome responses to whitefly infestation, salicylic acid and jasmonic acid
Authors: Irigoyen Maria L. , Garceau Danielle C. , Bohorquez-Chaux Adriana , Lopez-Lavalle Luis Augusto Becerra , Perez-Fons Laura , Fraser Paul D. , Walling Linda L. 
Published: January 2020

Abstract
Background
Whiteflies are a threat to cassava (Manihot esculenta), an important staple food in many tropical/subtropical regions. Understanding the molecular mechanisms regulating cassava’s responses against this pest is crucial for developing control strategies. Pathogenesis-related (PR) protein families are an integral part of plant immunity. With the availability of whole genome sequences, the annotation and expression programs of the full complement of PR genes in an organism can now be achieved. An understanding of the responses of the entire complement of PR genes during biotic stress and to the defense hormones, salicylic acid (SA) and jasmonic acid (JA), is lacking. Here, we analyze the responses of cassava PR genes to whiteflies, SA, JA, and other biotic aggressors.

Results
The cassava genome possesses 14 of the 17 plant PR families, with a total of 447 PR genes. A cassava PR gene nomenclature is proposed. Phylogenetic relatedness of cassava PR proteins to each other and to homologs in poplar, rice and Arabidopsis identified cassava-specific PR gene family expansions. The temporal programs of PR gene expression in response to the whitefly (Aleurotrachelus socialis) in four whitefly-susceptible cassava genotypes showed that 167 of the 447 PR genes were regulated after whitefly infestation. While the timing of PR gene expression varied, over 37% of whitefly-regulated PR genes were downregulated in all four genotypes. Notably, whitefly-responsive PR genes were largely coordinately regulated by SA and JA. The analysis of cassava PR gene expression in response to five other biotic stresses revealed a strong positive correlation between whitefly and Xanthomonas axonopodis and Cassava Brown Streak Virus responses and negative correlations between whitefly and Cassava Mosaic Virus responses. Finally, certain associations between PR genes in cassava expansions and response to biotic stresses were observed among PR families.

Conclusions
This study represents the first genome-wide characterization of PR genes in cassava. PR gene responses to six biotic stresses and to SA and JA are demonstrably different to other angiosperms. We propose that our approach could be applied in other species to fully understand PR gene regulation by pathogens, pests and the canonical defense hormones SA and JA.
Fluorescent amplification for next generation sequencing (FA-NGS) library preparation
Authors: Chiniquy Jennifer , Garber Megan E. , Mukhopadhyay Aindrila , Hillson Nathan J. 
Published: January 2020

Abstract
Background
Next generation sequencing (NGS) has become a universal practice in modern molecular biology. As the throughput of sequencing experiments increases, the preparation of conventional multiplexed libraries becomes more labor intensive. Conventional library preparation typically requires quality control (QC) testing for individual libraries such as amplification success evaluation and quantification, none of which occur until the end of the library preparation process.

Results
In this study, we address the need for a more streamlined high-throughput NGS workflow by tethering real-time quantitative PCR (qPCR) to conventional workflows to save time and implement single tube and single reagent QC. We modified two distinct library preparation workflows by replacing PCR and quantification with qPCR using SYBR Green I. qPCR enabled individual library quantification for pooling in a single tube without the need for additional reagents. Additionally, a melting curve analysis was implemented as an intermediate QC test to confirm successful amplification. Sequencing analysis showed comparable percent reads for each indexed library, demonstrating that pooling calculations based on qPCR allow for an even representation of sequencing reads. To aid the modified workflow, a software toolkit was developed and used to generate pooling instructions and analyze qPCR and melting curve data.

Conclusions
We successfully applied fluorescent amplification for next generation sequencing (FA-NGS) library preparation to both plasmids and bacterial genomes. As a result of using qPCR for quantification and proceeding directly to library pooling, the modified library preparation workflow has fewer overall steps. Therefore, we speculate that the FA-NGS workflow has less risk of user error. The melting curve analysis provides the necessary QC test to identify and troubleshoot library failures prior to sequencing. While this study demonstrates the value of FA-NGS for plasmid or gDNA libraries, we speculate that its versatility could lead to successful application across other library types.
Identifying critical state of complex diseases by single-sample Kullback–Leibler divergence
Authors: Zhong Jiayuan , Liu Rui , Chen Pei 
Published: January 2020

Abstract
Background
Developing effective strategies for signaling the pre-disease state of complex diseases, a state with high susceptibility before the disease onset or deterioration, is urgently needed because such state usually followed by a catastrophic transition into a worse stage of disease. However, it is a challenging task to identify such pre-disease state or tipping point in clinics, where only one single sample is available and thus results in the failure of most statistic approaches.

Methods
In this study, we presented a single-sample-based computational method to detect the early-warning signal of critical transition during the progression of complex diseases. Specifically, given a set of reference samples which were regarded as background, a novel index called single-sample Kullback–Leibler divergence (sKLD), was proposed to explore and quantify the disturbance on the background caused by a case sample. The pre-disease state is then signaled by the significant change of sKLD.

Results
The novel algorithm was developed and applied to both numerical simulation and real datasets, including lung squamous cell carcinoma, lung adenocarcinoma, stomach adenocarcinoma, thyroid carcinoma, colon adenocarcinoma, and acute lung injury. The successful identification of pre-disease states and the corresponding dynamical network biomarkers for all six datasets validated the effectiveness and accuracy of our method.

Conclusions
The proposed method effectively explores and quantifies the disturbance on the background caused by a case sample, and thus characterizes the criticality of a biological system. Our method not only identifies the critical state or tipping point at a single sample level, but also provides the sKLD-signaling markers for further practical application. It is therefore of great potential in personalized pre-disease diagnosis.
Characterising avenin-like proteins (ALPs) from albumin/globulin fraction of wheat grains by RP-HPLC, SDS-PAGE, and MS/MS peptides sequencing
Authors: Zhang Yujuan , Hu Xin , Juhasz Angela , Islam Shahidul , Yu Zitong , Zhao Yun , Li Gang , Ding Wenli , Ma Wujun 
Published: January 2020

Abstract
Background
Wheat grain avenin-like proteins (ALPs) belong to a recently discovered class of wheat grain storage protein. ALPs in wheat grains not only have beneficial effects on dough quality but also display antifungal activities, which is a novel observation for wheat storage proteins. Previous studies have shown that ALPs are likely present in the albumin/globulin fractions of total protein extract from wheat flour. However, the accumulation characteristics of these ALPs in the mature wheat grain remains unknown.

Results
In the present study, a total of 13 ALPs homologs were isolated and characterized in the albumin/globulin fractions of the wheat protein extract. A combination of multiple techniques including RP-HPLC, SDS-PAGE, MALDI-TOF and peptide sequencing were used for accurate separation and identification of individual ALP homolog. The C-terminal TaALP-by-4AL/7DS, TaALP-by-4AL/7AS/7DS, TaALP-bx/4AL/7AS/7DS, TaALP-ay-7DS, TaALP-ay-4AL, TaALP-ax-4AL, TaALP-ax-7AS, and TaALP-ax-7DS, were separated as individual protein bands from wheat flour for the first time. These unique ALPs peptides were mapped to the latest wheat genome assembly in the IWGSC database. The characteristic defence related proteins present in albumin and globulin fractions, such as protein disulfide-isomerase (PDI), grain softness protein (GSP), alpha-amylase inhibitors (AAIs) and endogenous alpha-amylase/subtilisin inhibitor were also found to co-segregate with these identified ALPs, avenin-3 and α-gliadins. The molecular weight range and the electrophoresis segregation properties of ALPs were characterised in comparison with the proteins containing the tryp_alpha_amyl domain (PF00234) and the gliadin domain (PF13016), which play a role in plant immunity and grain quality. We examined the phylogenetic relationships of the AAIs, GSP, avenin-3, α-gliadins and ALPs, based on the alignment of their functional domains. MALDI-TOF profiling indicated the occurrence of certain post-translations modifications (PTMs) in some ALP subunits.

Conclusions
We reported for the first time the complete profiling of ALPs present in the albumin/globulin fractions of wheat grain protein extracts. We concluded that majority of the ALPs homologs are expressed in wheat grains. We found clear evidence of PTMs in several ALPs peptides. The identification of both gliadin domain (PF13016) and Tryp_alpha_amyl domain (PF00234) in the mature forms of ALPs highlighted the multiple functional properties of ALPs in grain quality and disease resistance.
Effect of postoperative Trendelenburg position on shoulder pain after gynecological laparoscopic procedures: a randomized clinical trial
Authors: Zeeni Carine , Chamsy Dina , Khalil Ali , Abu Musa Antoine , Al Hassanieh Majed , Shebbo Fadia , Nassif Joseph 
Published: January 2020

Abstract
Background
Laparoscopic surgery has become a standard of care for many gynecological surgeries due to its lower morbidity, pain and cost compared to open techniques. Unfortunately, the use of carbon dioxide (CO2) to insufflate the abdomen is the main contributor to post-operative shoulder pain.

Methods
We aim to assess the effect of postoperative Trendelenburg position on shoulder pain after gynecological laparoscopic procedures. We hypothesize that maintaining the patient in Trendelenburg for 24 h postoperatively will significantly decrease postoperative shoulder pain and analgesic consumption. After obtaining written informed consent, 108 patients were prospectively randomized into two groups. In the control group, patients underwent standard gynecologic laparoscopic procedures; then after passive deflation of the pneumoperitoneum at the end of the surgery, the patients were placed in supine head up position in the post anesthesia care unit (PACU) and received our institution’s common postoperative care. Patients in the intervention group were subjected to the same maneuver but were positioned in a Trendelenburg position (20 °) once fully awake and cooperative in the PACU and retained this position for the first 24 h. Numerical rating scale (NRS) was used to assess shoulder pain and nausea upon patient arrival to the PACU, at 4, 6, 12 (primary outcome) and 24 h postoperatively. Time to first rescue pain medication, total rescue pain medications and overall satisfaction with pain control were recorded. 101 patients were included in the final data analysis.

Results
Both groups were comparable in terms of baseline characteristics. NRS pain scores were significantly lower in the intervention group at 12 h compared to the control group (0 [0–1] versus 5 [1–4], p < 0.001), furthermore improvement in postoperative shoulder pain between time of arrival to PACU (time zero) and 12 h postoperatively was significantly higher in patients allocated to the experimental group compared to the control group. Pain scores were significantly lower in patients allocated to the experimental group versus the control group (0 [0–1] versus 5 [1–4], p < 0.001).

Conclusion
In conclusion, Trendelenburg position is an easy non-pharmacologic intervention that is beneficial in reducing postoperative shoulder pain following gynecologic laparoscopic surgery.

Trial registration
Retrospectively registered at Clinicaltrials.gov, registration number NCT04129385, date of registration: June 28, 2019
The utility of the brain trauma evidence to inform paramedic rapid sequence intubation in out-of-hospital stroke
Authors: Fouche Pieter Francsois , Jennings Paul Andrew , Boyle Malcolm , Bernard Stephen , Smith Karen 
Published: January 2020

Abstract
Background
Rapid sequence intubation (RSI) is used to secure the airway of stroke patients. Randomized controlled trial evidence exists to support the use of paramedic RSI for traumatic brain injury (TBI), but cannot necessarily be applied to stroke RSI because of differences between the stroke and TBI patient. To understand if the TBI evidence can be used for stroke RSI, we analysed a retrospective cohort of TBI and strokes to compare how survival is impacted differently by RSI when comparing strokes and TBI.

Methods
This study was a retrospective analysis of 10 years of in-hospital and out-of-hospital data for all stroke and TBI patients attended by Ambulance Victoria, Australia. Logistic regression predicted the survival for ischemic and haemorrhagic strokes as well as TBI. The constituents of RSI, such a medications, intubation success and time intervals were analysed against survival using interactions to asses if RSI impacts survival differently for strokes compared to TBI.

Results
This analysis found significant interactions in the RSI-only group for age, number of intubation attempts, atropine, fentanyl, pulse rate and perhaps scene time and time- to-RSI. Such interactions imply that RSI impact survival differently for TBI versus strokes. Additionally, no significant difference in survival for TBI was found, with a − 0.7% lesser survival for RSI compared to no-RSI; OR 0.86 (95% CI 0.67 to 1.11; p = 0.25). Survival for haemorrhagic stroke was − 14.1% less for RSI versus no-RSI; OR 0.44 (95% CI 0.33 to 0.58; p = 0.01) and was − 4.3%; OR 0.67 (95% CI 0.49 to 0.91; p = 0.01) lesser for ischemic strokes.

Conclusions
Rapid sequence intubation and related factors interact with stroke and TBI, which suggests that RSI effects stroke survival in a different way from TBI. If RSI impact survival differently for strokes compared to TBI, then perhaps the TBI evidence cannot be used for stroke RSI.
Sample size issues in time series regressions of counts on environmental exposures
Authors: Armstrong Ben G. , Gasparrini Antonio , Tobias Aurelio , Sera Francesco 
Published: January 2020

Abstract
Background
Regression analyses of time series of disease counts on environmental determinants are a prominent component of environmental epidemiology. For planning such studies, it can be useful to predict the precision of estimated coefficients and power to detect associations of given magnitude. Existing generic approaches for this have been found somewhat complex to apply and do not easily extend to multiple series studies analysed in two stages. We have sought a simpler approximate approach which can easily extend to multiple series and give insight into factors determining precision.

Methods
We derive approximate expressions for precision and hence power in single and multiple time series studies of counts from basic statistical theory, compare the precision predicted by these with that estimated by analysis in real data from 51 cities of varying size, and illustrate the use of these estimators in a realistic planning scenario.

Results
In single series studies with Poisson outcome distribution, precision and power depend only on the usable variation of exposure (i.e. that conditional on covariates) and the total number of disease events, regardless of how many days those are spread over. In multiple time series (eg multi-city) studies focusing on the meta-analytic mean coefficient, the usable exposure variation and the total number of events (in all series) are again the sole determinants if there is no between-series heterogeneity or within-series overdispersion. With heterogeneity, its extent and the number of series becomes important. For all but the crudest approximation the estimates of standard errors were on average within + 20% of those estimated in full analysis of actual data.

Conclusions
Predicting precision in coefficients from a planned time series study is possible simply and given limited information. The total number of disease events and usable exposure variation are the dominant factors when overdispersion and between-series heterogeneity are low.
Evaluation of ultrasound-guided Freka-Trelumina enteral nutrition tube placement in the treatment of acute pancreatitis
Authors: Liu Zhijun , Guo Jintao , Ren Weidong , Tang Shaoshan , Huang Ying , Huang Liping , Sun Siyu , Lin Lianjie 
Published: January 2020

AbstractBackgroundEnteral nutrition should be implemented as early as possible in patients with moderate or severe acute pancreatitis. This study was designed to evaluate the feasibility and Deffectiveness of ultrasound-guided Freka-Trelumina tube placement for enteral nutrition in acute pancreatitis.MethodsPatients with severe acute pancreatitis admitted to Shengjing Hospital of China Medical University who needed Freka-Trelumina tube placement for enteral nutrition and gastrointestinal decompression were included in the current study. The relevant evaluation indicators of tube placement included the success rate of tube placement, tube placement time, tube shift rate, and blocking rate. In addition, the evaluation indicators of ultrasound-guided tube placement (from 1 January 2018 to 31 July 2019) were compared with those of previous endoscope-guided placement (from 1 January 2015 to 31 December 2017) by analysing the data from the electronic medical record system.ResultsThe success rate of ultrasound-guided tube placement was 90.7% (49/54). All 49 patients tolerated the Freka-Trelumina feeding tube. The average ultrasound-guided tube placement time for the 49 patients was 18.4 ± 12.8 min (range, 5–36 min). The Freka-Trelumina feeding tube had a shift rate of 10.2% (5/49). The blocking rate of the Freka-Trelumina feeding tube was 12.2% (6/49). The success rate of tube placement, tube shift rate and blocking rate for endoscope-guided tube placement were 100% (62/62), 11.3% (7/62), and 12.9% (8/62), respectively. The average endoscope-guided tube placement time for the 62 patients was 16.5 ± 5.7 min (range, 12–31 min). The comparison between the ultrasound-guided group and the endoscope-guided group showed that the success rate of tube placement, tube placement time, tube shift rate and blocking rate were similar.ConclusionThe ultrasound-guided method can be done non-invasively at the bedside, which is safe and convenient, and the Freka-Trelumina feeding tube can be placed in time to achieve the goal of early enteral nutrition and gastrointestinal decompression.
Association of cognitive impairment and elderly mortality: differences between two cohorts ascertained 6-years apart in China
Authors: Duan Jun , Lv Yue-Bin , Gao Xiang , Zhou Jin-Hui , Kraus Virginia Byers , Zeng Yi , Su Hong , Shi Xiao-Ming 
Published: January 2020

Abstract
Background
Cognitive impairment is a major contributor to mortality among the elderly. However, the relationship between cognitive impairment evaluated by educational levels and mortality and the trend between cognitive impairment and mortality with time are unclear. We aim to evaluate the differences in associations of cognitive impairment, taking the stratification by educational levels into account, with all-cause mortality and further explore the relationship of cognitive impairment with mortality in different age and sex groups in two cohorts ascertained 6 years apart in China.

Methods
A total of 13,906 and 13,873 Chinese elderly aged 65 years and older were included in the 2002–2008 and 2008–2014 cohorts from the Chinese Longitudinal Healthy Longevity Survey (CLHLS). Mortality data was ascertained from interviews with family members or relatives of participants. Cognitive function, evaluated by the Mini-Mental State Examination (MMSE), were defined by different cut-offs taking educational background into account. Cox models were used to explore the relationship of cognitive impairment with mortality.

Results
For the 2002–2008 and 2008–2014 cohorts, 55,277 and 53,267 person-years were followed up, and the mean (SD) age were 86.5 (11.6) and 87.2 (11.3) years, respectively. Compared to normal cognition, cognitive impairment was independently associated with higher mortality risk after controlling for potential confounders, with hazard ratios (HRs) of 1.32 (95% confidence interval [CI], 1.25–1.39) in 2002–2008 cohort and 1.26 (95% CI, 1.19–1.32) in 2008–2014 cohort, stratified by educational levels. The trend of cognitive impairment with all-cause mortality risk decreased from 2002 to 2008 to 2008–2014 cohort, while no significant interaction of cognitive impairment with cohort for all-cause mortality was observed. The associations of cognitive impairment and mortality were decreased with age in the two cohorts.

Conclusions
Cognitive impairment evaluated by different cut-offs were associated with increased risk of mortality, especially among those aged 65–79 years in the two cohorts; this advocates that periodic screening for cognitive impairment among the elderly is warranted.