bluuebunny/crossref_metadata_2025_split huggingface dataset:
Molecular Engineering Improves Antigen Quality and Enables Integrated Manufacturing of A Trivalent Subunit Vaccine Candidate for Rotavirus
Authors: Dalvie Neil , Brady Joseph , Crowell Laura , Tracey Mary Kate , Biedermann Andrew , Kaur Kawalijt , Hickey John M. , Kristensen Duane Lee , Bonnyman Alexandra , Rodriguez-Aponte Sergio , Whittaker Charles , Bok Marina , Vega Celina , Mukhopadhyay Tarit , Joshi Sangeeta , Volkin David , Parreno Viviana , Love Kerry R. , Love J. Christopher 
Published: December 2020

Abstract
BackgroundVaccines comprising recombinant subunit proteins are well-suited to low-cost and high-volume production for global use. The design of manufacturing processes to produce subunit vaccines depends, however, on the inherent biophysical traits presented by an individual antigen of interest. New candidate antigens typically require developing custom processes for each one and may require unique steps to ensure sufficient yields without product-related variants. ResultsWe describe a holistic approach for the molecular design of recombinant protein antigens—considering both their manufacturability and antigenicity—informed by bioinformatic analyses such as RNA-seq, ribosome profiling, and sequence-based prediction tools. We demonstrate this approach by engineering the product sequences of a trivalent non-replicating rotavirus vaccine (NRRV) candidate to improve titers and mitigate product variants caused by N-terminal truncation, hypermannosylation, and aggregation. The three engineered NRRV antigens retained their original antigenicity and immunogenicity, while their improved manufacturability enabled concomitant production and purification of all three serotypes in a single, end-to-end perfusion-based process using the biotechnical yeast Komagataella phaffii. ConclusionsThis study demonstrates that molecular engineering of subunit antigens using advanced genomic methods can facilitate their manufacturing in continuous production. Such capabilities have potential to lower the cost and volumetric requirements in manufacturing vaccines based on recombinant protein subunits.
Efficient Bioconversion of Raspberry Ketone in Escherichia Coli Using Fatty Acids Feedstocks
Authors: Chang Chen , Liu Bo , Bao Yihong , Tao Yong , Liu Weifeng 
Published: December 2020

Abstract
BackgroundPhenylpropanoid including raspberry ketone, is a kind of important natural plant product and widely used in pharmaceuticals, chemicals, cosmetics, and healthcare products. Bioproduction of phenylpropanoid in Escherichia coli and other microbial cell factories is an attractable approach considering the low phenylpropanoid contents in plants. However, it is usually difficult to produce high titer phenylpropanoid production when fermentation using glucose as carbon source. Developing novel bioprocess using alternative sources might provide a solution to this problem. In this study, typical phenylpropanoid raspberry ketone was used as the target product to develop a biosynthesis pathway for phenylpropanoid production from fatty acids, a promising alternative low-cost feedstock. ResultsA raspberry ketone biosynthesis module was developed and optimized by introducing 4-coumarate-CoA ligase (4CL), benzalacetone synthase (BAS), and raspberry ketone reductase (RZS) in Escherichia coli strains CR1-CR4. Then strain CR5 was developed by introducing raspberry ketone biosynthesis module into a fatty acids-utilization chassis FA09 to achieve production of raspberry ketone from fatty acids feedstock. However, the production of raspberry ketone was still limited by the low biomass and unable to substantiate whole-cell bioconversion process. Thus, a process by coordinately using fatty-acids and glycerol was developed. In addition, we systematically screened and optimized fatty acids-response promoters. The optimized promoter Pfrd3 was then successfully used for the efficient expression of key enzymes of raspberry ketone biosynthesis module during bioconversion from fatty acids. The final engineered strain CR8 could efficiently produce raspberry ketone repeatedly using bioconversion from fatty acids feedstock strategy, and about 291.3 mg/L raspberry ketone was produced.ConclusionMetabolically engineered Escherichia coli strains were successfully developed for raspberry ketone production from fatty acids using several strategies, including optimization of bioconversion process and fine-tuning key enzyme expression. This study provides an essential reference to establish the low-cost biological manufacture of phenylpropanoids compounds.
Within-Household Clustering of Genetically Related Plasmodium Falciparum Infections In A Moderate Transmission Area of Uganda
Authors: Briggs Jessica , Kuchta Alison , Murphy Max , Tessema Sofonias , Arinaitwe Emmanuel , Rek John , Chen Anna , Nankabirwa Joaniter I , Drakeley Chris , Smith David , Bousema Teun , Kamya Moses , Rodriguez-Barraquer Isabel , Staedke Sarah , Dorsey Grant , Rosenthal Philip J , Greenhouse Bryan 
Published: December 2020

Abstract
Background: Evaluation of genetic relatedness of malaria parasites is a useful tool for understanding transmission patterns, but patterns are not easily detectable in areas with moderate to high malaria transmission. To evaluate the feasibility of detecting genetic relatedness in a moderate malaria transmission setting, we measured relatedness of Plasmodium falciparum infections in cohort participants from randomly selected households in the Kihihi sub-county of Uganda (annual entomological inoculation rate of 27 infectious bites per person). Methods: All infections detected via microscopy or Plasmodium-specific loop mediated isothermal amplification from passive and active case detection during August 2011-March 2012 were genotyped at 26 microsatellite loci, providing data for 349 samples from 230 participants living in 80 households. Pairwise genetic relatedness was calculated using identity by state (IBS).Results: As expected, genetic diversity was high (mean heterozygosity [He]=0.73), and the majority (76.5%) of samples were polyclonal. Despite the high genetic diversity, fine-scale population structure was detectable, with significant spatiotemporal clustering of highly related infections. Although the difference in malaria incidence between households at higher (mean 1127 meters) vs. lower elevation (mean 1015 meters) was modest (1.4 malaria cases per person-year versus 1.9 per person-year, respectively), we found a significant difference in multiplicity of infection (2.2 versus 2.6, p = 0.008) and, more strikingly, a higher proportion of highly related infections within households (6.3% vs 0.9%, p = 0.0005) at higher elevation compared to lower elevation. Conclusions: Genetic data from a relatively small number of diverse, multiallelic loci reflected fine scale patterns of malaria transmission. Given the increasing interest in applying genetic data to augment malaria surveillance, our study provides evidence that genetic data can be used to inform transmission patterns at local spatial scales even in moderate transmission areas.
Laboratory and Field Studies on the Use of Artificial Mussels as a Monitoring Tool of Platinum Exposure in the Freshwater Environment.
Authors: Labuschagne Marelize , Zimmermann Sonja , Smit Nico J. , Erasmus Johannes H. , Nachev Milen , Sures Bernd , Wepener Victor 
Published: December 2020

Abstract
BackgroundThe artificial mussel (AM) is a passive sampling device that was originally developed for monitoring metal concentrations in the marine environment but is also increasingly used in freshwater environments. The AM consists of a non-permeable Perspex tube, which contains Chelex-100 resin, water diffuses through the semi-permeable membranes where the metals bind to the Chelex-100. The AM allows for the determination of the dissolved, bioaccessible metal fraction in water bodies without killing organisms, as well as environments with unfavorable conditions for living bioindicators. In the present study, the use of the AM was adapted for the monitoring of platinum (Pt) in a freshwater ecosystem. ResultsTherefore, the elution of Pt from the Chelex-100 beads was optimized. Two modifications to the original method for the use of AMs are recommended, i.e. washing and separation of the beads through centrifugation and elution with a mixture of 4.5 mL HNO3 and 0.5 mL HCl for approximately 2-3 hours to ensure the release of all Pt bound to the beads. Additionally, the uptake kinetics of the AM were determined under laboratory conditions over a wide exposure concentration range (0.1-1000 µg/L) showing highly correlated Pt accumulation in the AMs with the aqueous exposure concentration. For the tested Pt exposure concentrations of 0.1, 1, 10, and 100 µg/L, the Pt concentrations in the AMs increased during the exposure period of 6 weeks. At the highest exposure concentration of 1000 µg/L, the increase stagnated after 3 weeks. To validate the AM in the field, the Pt accumulation of the AM was assessed together with that of freshwater clams (Corbicula fluminalis africana), muscle and liver tissue of three fish species sharptooth catfish (Clarias gariepinus), common carp (Cyprinus carpio) and Mozambique tilapia (Oreochromis mossambicus), as well as water hyacinths (Eichhornia crassipes) at two sampling sites in the Pt mining area of South Africa. ConclusionResults from the present study showed that the AM is a promising tool to monitor Pt concentrations in the freshwater environment at contaminated sites.
Reliable Wolf-Dog Hybrid Detection in Europe Using a Reduced SNP Panel Developed for Non-Invasively Collected Samples
Authors: Harmoinen Jenni , von Thaden Alina , Aspi Jouni , Kvist Laura , Cocchiararo Berardino , Jarausch Anne , Gazzola Andrea , Sin Teodora , Lohi Hannes , Hytönen Marjo K. , Kojola Ilpo , Stronen Astrid Vik , Caniglia Romolo , Mattucci Federica , Galaverni Marco , Godinho Raquel , Ruiz-González Aritz , Randi Ettore , Muñoz-Fuentes Violeta , Nowak Carsten 
Published: December 2020

Abstract
BackgroundUnderstanding the processes that lead to hybridization of wolves and dogs is of scientific and management importance, particularly over large geographical scales, as wolves can disperse great distances. However, a method to efficiently detect hybrids in routine wolf monitoring is lacking. Microsatellites offer only limited resolution due to the low number of markers showing distinctive allele frequencies between wolves and dogs. Moreover, calibration across laboratories is time-consuming and costly. In this study, we selected a panel of 96 ancestry informative markers for wolves and dogs, derived from the Illumina CanineHD Whole-Genome BeadChip (174K). We designed very short amplicons for genotyping on a microfluidic array, thus making the method suitable also for non-invasively collected samples. ResultsGenotypes based on 93 SNPs from wolves sampled throughout Europe, purebred and non-pedigree dogs, and suspected hybrids showed that the new panel accurately identifies parental individuals, first-generation hybrids and first-generation backcrosses to wolves, while second- and third-generation backcrosses to wolves were identified as advanced hybrids in almost all cases. Our results support the hybrid identity of suspect individuals and the status of individuals regarded as wolves to be wolves. We also show the adequacy of these markers to assess hybridization at a European-wide scale and the importance of including samples from reference populations, as migrants are increasingly more common.ConclusionsCompared to microsatellites, this method is faster to implement, economically more feasible and results are directly comparable across laboratories. The new panel is thus suitable as a new tool for wolf-dog hybrid assessments and monitoring on a continental scale.
Circadian Variations in the Occurrence of Intracerebral Hemorrhage from Different Sources of Income: A Hospital-Based Cross-Sectional Study
Authors: Wang Yan-Yue , Yan Ning , Wang En-Yuan , Pu Yun-Tao 
Published: December 2020

Abstract
Background: The onset time of intracerebral hemorrhage (ICH) may be closely related to the working style and living habits of people, which are determined by different income sources in China. Therefore, our purpose was to investigate the Circadian Variations in the occurrence of ICH from different sources of income. Methods: This retrospective study enrolled 4,327 patients with ICH. Based on the time of a day at which the patients developed symptoms, the classifiable onset time was assigned to one of eight three-hour intervals. And based on different income sources, they were categorized into three groups: Farmers, Wage-earners and Freelancers. Characteristics and risk factors of patients were then summarized, and the circadian variation of three groups of patients’ known time of onset and those stratified by gender and age were analyzed.Results: The frequency of ICH onset exhibited significant circadian variation among the three income groups, demonstrating a bimodal distribution in the daytime, with a nadir during the night (all P < 0.001). Three groups showed a significant initial peak between 06:01 and 09:00, with a smaller second peak that between 15:01 and 18:00 for Farmers and Wage-earners and 18:01 and 21:00 for Freelancers. After stratification by gender and age, all demonstrated a bimodal distribution except women in Wage-earners and under 65 years of age in Wage-earners. Conclusions: Different circadian variations of ICH onset time were found in patients with different income sources in southwest China's Chongqing Municipality cohort. Moreover, the frequency and distribution pattern of peak hours were closely related to the working style and living habits of people with different income sources.
Discontinuation of Prophylactic Antiepileptic Drugs in Patients with Intracerebral Hemorrhage
Authors: Wong Yi-Sin , Wu Chi-Shun , Ong Cheung-Ter 
Published: December 2020

Abstract
Background: The risk factors for seizures in patients with intracerebral hemorrhage (ICH) stroke and the effect of prophylactic anticonvulsant are not well understood. Limited studies investigated the risk of seizure after discontinuing prophylactic antiepileptic drugs in patients with ICH. This study aimed to investigate the role of valproic acid (VA) for seizure prevention and to access the risk of seizure after anticonvulsant withdrawal in patients with spontaneous ICH.Methods: Between 2013 and 2015, 177 patients with ICH were enrolled in this 3-year retrospective study. Seizure was classified as early seizure (first seizure within 1 week of ICH), delayed seizure (first seizure after 1 week), and late seizure (any seizure after 1 week). Binary logistic regression was used to evaluate the relationship between baseline clinical factors and late seizure between study VA was prescribed or discontinued based on the decision of the physician in charge.Results: Seizures occurred in 24 patients, including early seizure in 6.78% (12/177) of the patients, delayed seizure in 7.27% (12/165) of the patients without early seizure, and late seizure in 9.60% (17/177) of the patients. Most seizures occurred within the first year. Binary logistic regression analysis showed ICH with cortex involvement as the independent risk factor for seizures. VA did not decrease the risk of seizure. Patients with ICH with cortical involvement using prophylactic anticonvulsant for longer than 3 months did not decrease risk of seizure (Odds ratio 1.86, 95% CI: 0.43-8.05).Conclusion: Spontaneous ICH with cortex involvement is the risk factor for seizure. Most seizures occurred within 1 year after stroke onset over a 3-year follow up. Discontinuation Prophylactic antiepileptic drug within 3 months in patients do not increase risk of seizure. VA cannot prevent seizure in patients with ICH.
Drought Tolerant Wheat Varieties Enrich Seed Microbiomes For Beneficial Microbes Under Drought Conditions
Authors: Hone Holly , Mann Ross , Yang Guodong , Kaur Jatinder , Tannenbaum Ian , Li Tongda , Spangenberg German , Sawbridge Timothy 
Published: December 2020

Abstract
Climate change is predicted to increase the incidence and severity of drought conditions, posing a significant challenge for agriculture globally. Plant microbiomes have been demonstrated to aid crop species mitigate drought stress. In this study the wheat seed microbiomes from lines with contrasting drought tolerances were interrogated for microbes that alleviate drought stress. Metagenomic and culture-based methods were used to profile and characterise the seed microbiome composition of four drought tolerant and three drought susceptible wheat lines under rainfed and drought conditions. Curtobacterium flaccumfaciens (Cf D3-25) and Arthrobacter sp. (Ar sp. D4-14) were isolates enriched in drought tolerant lines under drought conditions and demonstrated the ability to promote wheat growth under drought conditions. Members of Triticeae inoculated with Cf D3-25 and Ar sp. D4-14 showed a biostimulation affect. This study indicates seed microbiomes from genetically distinct wheat lines enrich for beneficial bacteria in ways that are both line-specific and responsive to environmental stress. As such, seed from stress-phenotyped lines represents an invaluable resource for the identification of beneficial microbes with plant growth promoting activity that could improve commercial crop production, particularly under drought stress.
Effectiveness of Interventions for Prevention of Common Infections in People Who Use Opioids: A Protocol for a Systematic Review of Systematic Reviews
Authors: Kudrina Irina , Puzhko Svetlana , Filion Kristian B. , Gore Genevieve , Paraskevopoulos Elena , Windle Sarah , Martel Marc O , Eisenberg Mark J. 
Published: December 2020

Abstract
Background. The North American opioid crisis is driven by opioid-related mortality and morbidity, including opioid use-associated infections (OUAIs), resulting in a substantial burden for society. Users of legal and illegal opioids are at an increased risk of OUAIs compared to individuals not using opioids. As reported for hepatitis C virus (HCV), human immunodeficiency virus (HIV), bacterial, fungal, and other infections, OUAIs transmission and acquisition risks may be modifiable. Several systematic reviews (SRs) synthetized data regarding interventions to prevent infections in persons using drugs (e.g., opioid substitution therapy, needle and syringes exchange programs, psycho-social interventions); however, their conclusions varied. Therefore, SR of published SRs is needed to synthesize the highest level of evidence on the scope and effectiveness of interventions to prevent OUAIs in people using opioids legally or illegally. Methods. We will comprehensively search for SRs in the PubMed, Embase, PsycINFO, Cochrane Database of Systematic Reviews, Epistemonikos and Google Scholar databases from inception to November 2020. Data selection and extraction for each SR will be performed independently by two researchers, with disagreements resolved by consensus. All SRs regarding interventions with evaluated effectiveness to prevent OUAI in legal and/or illegal opioid users will be eligible. Risk of bias assessment will be performed using the AMSTAR2 tool. The results will be qualitatively synthesized, and a typology of interventions’ effectiveness with a statement on the strength of evidence for each category will be created. Discussion. Our pilot search of PubMed resulted in 379 SRs analyzing the effectiveness of interventions to prevent HCV and HIV in persons who inject different types of drugs, including opioids. Of these 379 SRs, eight evaluated primary studies where participants used opioids and would therefore be eligible for inclusion. The search results thus justify the application of SR of SRs approach. Comprehensive data on the scope and effectiveness of existing interventions to prevent OUAIs will help policy makers to plan and implement preventive interventions and will assist clinicians in the guidance for their patients using opioids. SR registration: Registered in PROSPERO on July 30, 2020 (#195929).
Application of Mediastinal Drainage Tube in Intrathoracic Esophageal Anastomotic Leakage for Early Diagnosis and Effective Treatment: A Retrospective Study
Authors: Ma Hainong , Song Xu , Li Jie , Zhao Guofang 
Published: December 2020

Abstract
Background: Intrathoracic esophageal anastomotic leakage (AL) is one of the most fatal complications after esophagectomy. In this study, we tried to place an additional drainage tube in esophagus bed and evaluate its effect in early diagnosis and treatment of AL.Methods: From January 2010 to August 2020, a total of 312 patients, who suffered from esophageal or cardia carcinoma, underwent esophageal resection with intrathoracic esophagogastric anastomosis. Among them, we identified 138 patients with only one pleural drainage tube as “Control Group” and 174 patients with a pleural drainage tube and an additional mediastinal drainage tube (MDT) as “Tube Group”. The incidence of postoperative AL, time to diagnosis, time to recovery, and patient outcome were analyzed.Results: There were no significant differences in the AL rate (P = 0.837) and postoperative pain between two groups. However, in the Tube Group, almost all the patients were definitely diagnosed prior to the appearance of hyperpyrexia, which was regarded as the earliest and most common symptom after AL. Moreover, in the Tube Group, there was significant decrease in the incidence of uncurable fistula, which required re-operation or variable treatments under gastroscopy, when compared to the Control Group (P = 0.032). Finally, patients in the Tube Group were associated with reduced post AL hospital day (P = 0.015) and lower mortality, although there was no significant difference (P = 0.188), than in the Control Group.Conclusions: Placement of a MDT can not prevent the AL, but it is an effective method to diagnose AL earlier and facilitate the fistula healing and patient recovery.
Early Single-Stage Surgical Revascularization of Pulmonary Artery in Unilateral Absence of a Pulmonary Artery
Authors: Li Wenlei , Ma Li , Xia Shuliang , Zou Minghui , Chen Weidan , Chen Xinxin 
Published: December 2020

Abstract
BackgroundThis research aims to summarize the findings of the early single-stage revascularization of remnant pulmonary artery in unilateral absent intrapericardial pulmonary artery. MethodsWe retrospectively analyzed the medical records of 10 patients with unilateral absent pulmonary artery, in which 7 were right and 3 were left, the median age and median weight at surgery was 4 months and 5.2 kg, respectively. The patients received operation from January 2009 to June 2020. ResultsTen patients, 1 case associated with atrial septal defect, 2 cases with tetralogy of Fallot, and 1 case with aortopulmonary window. The median diameter of the affected hilar pulmonary artery remnants was 3.1mm (1.6-5mm), and the Z value was -3.66±1.86 (range, -6.7 to -1.75). All the patients received single-stage revascularization: tube graft interposition in 3 patients, autologous pericardial roll in 4, direct anastomosis in one, and main pulmonary artery flap angioplasty in the rest 3. No hospital deaths occurred. The follow-up period was 1 month to 5.6 years. One case underwent percutaneous balloon dilatation due to new pulmonary artery stenosis. Nonetheless, the results were encouraging, symptoms have improved in all patients. The Z value of the latest ipsilateral pulmonary artery diameter was -2.34±1.18 (range, -4.52 to -1.35), a significantly improvement when compared to the preoperative value.ConclusionsSingle-stage pulmonary artery revascularization is effective at restoring normal antegrade flow to the affected lung, resulting in improved diameter of the PA, and patient’s symptoms. However, transcatheter intervention may diminish the new pulmonary artery stenosis temporarily, reoperation is still needed in the long-term follow-up.