bluuebunny/crossref_metadata_2025_split huggingface dataset:
Efficient lactic acid production from dilute acid-pretreated lignocellulosic biomass by a synthetic consortium of engineered Pseudomonas putida and Bacillus coagulans
Authors: Zou Lihua , Ouyang Shuiping , Hu Yueli , Zheng Zhaojuan , Ouyang Jia 
Published: November 2021

Abstract
Background
Lignocellulosic biomass is an attractive and sustainable alternative to petroleum-based feedstock for the production of a range of biochemicals, and pretreatment is generally regarded as indispensable for its biorefinery. However, various inhibitors that severely hinder the growth and fermentation of microorganisms are inevitably produced during the pretreatment of lignocellulose. Presently, there are few reports on a single microorganism that can detoxify or tolerate toxic mixtures of pretreated lignocellulose hydrolysate while effectively transforming sugar components into valuable compounds. Alternatively, microbial coculture provides a simpler and more efficacious way to realize this goal by distributing metabolic functions among different specialized strains.

Results
In this study, a novel synthetic microbial consortium, which is composed of a responsible for detoxification bacterium engineered Pseudomonas putida KT2440 and a lactic acid production specialist Bacillus coagulans NL01, was developed to directly produce lactic acid from highly toxic lignocellulosic hydrolysate. The engineered P. putida with deletion of the sugar metabolism pathway was unable to consume the major fermentable sugars of lignocellulosic hydrolysate but exhibited great tolerance to 10 g/L sodium acetate, 5 g/L levulinic acid, 10 mM furfural and HMF as well as 2 g/L monophenol compound. In addition, the engineered strain rapidly removed diverse inhibitors of real hydrolysate. The degradation rate of organic acids (acetate, levulinic acid) and the conversion rate of furan aldehyde were both 100%, and the removal rate of most monoaromatic compounds remained at approximately 90%. With detoxification using engineered P. putida for 24 h, the 30% (v/v) hydrolysate was fermented to 35.8 g/L lactic acid by B. coagulans with a lactic acid yield of 0.8 g/g total sugars. Compared with that of the single culture of B. coagulans without lactic acid production, the fermentation performance of microbial coculture was significantly improved.

Conclusions
The microbial coculture system constructed in this study demonstrated the strong potential of the process for the biosynthesis of valuable products from lignocellulosic hydrolysates containing high concentrations of complex inhibitors by specifically recruiting consortia of robust microorganisms with desirable characteristics and also provided a feasible and attractive method for the bioconversion of lignocellulosic biomass to other value-added biochemicals.
Bacterial composition of midgut and entire body of laboratory colonies of Aedes aegypti and Aedes albopictus from Southern China
Authors: Lin Datao , Zheng Xiaoying , Sanogo Benjamin , Ding Tao , Sun Xi , Wu Zhongdao 
Published: November 2021

Abstract
Background
Aedes aegypti and Aedes albopictus are invasive mosquito species and significantly impact human health in southern China. Microbiota are confirmed to affect the development and immunity of mosquitoes. However, scientists have focused more on midgut microbiota of female mosquitoes and bacterial differences between female and male Aedes mosquitoes. The relationship between the midgut and entire body microbiota of Aedes is unclear. In this study, we collected mosquito samples reared under the same laboratory conditions and compared the microbial composition of midgut and entire bodies of Aedes aegypti and Aedes albopictus using 16S rRNA gene sequencing.

Methods
In this study, we collected mosquito samples reared under the same laboratory conditions and compared the microbial composition of midgut and entire bodies of Aedes aegypti and Aedes albopictus using 16S rRNA gene sequencing.

Results
A total of 341 OTUs were identified, showing that Proteobacteria was the dominant phylum and Methylobacterium the dominant genus in both Aedes aegypti and Aedes albopictus. The bacterial diversity and community structures of the entire bodies were similar between males and females in both Aedes aegypti and Aedes albopictus. Conversely, the bacterial compositions of male and female Aedes aegypti and Aedes albopictus were significantly different. NMDS analysis, UPGMA analysis, diversity indices and OTU distribution demonstrated that compositions and structures in midgut microbiota were similar but significantly different in the entire bodies of Aedes aegypti and Aedes albopictus. Functional prediction analysis showed that metabolism and environmental information processing were the dominant KEGG pathways at level 1. Our study showed that there were significantly different level 2 and 3 KEGG pathways in the midgut microbiota (16 level 2 and 24 level 3) and the entire bodies (33 level 2 and 248 level 3) between female Aedes albopictus and Aedes Aegypti.

Conclusions
Our findings that Aedes aegypti and Aedes albopictus reared in the same laboratory harbor a similar gut bacterial microbiome but different entire body microbiota imply that the gut microbiota of adult mosquitoes is environmentally determined regardless of the host genotype, but the entire body microbiota is more genetically determined. Our findings improved the understanding of the microbiota in the entire and partial tissues of Aedes mosquitoes.

Graphical abstract
Molecular and MALDI-TOF MS identification of swallow bugs Cimex hirundinis (Heteroptera: Cimicidae) and endosymbionts in France
Authors: Hamlili Fatima Zohra , Bérenger Jean-Michel , Diarra Adama Zan , Parola Philippe 
Published: November 2021

AbstractBackgroundThe Cimicidae are obligatory blood-feeding ectoparasites of medical and veterinary importance. We aim in the current study to assess the ability of MALDI-TOF MS to identifyCimex hirundinisswallow bugs collected in house martin nests.MethodsSwallow bugs were picked out from abandoned nests of house martin swallows and identified morphologically to the species level. The bugs were randomly selected, dissected and then subjected to MALDI-TOF MS and molecular analyses.ResultsA total of 65 adults and 50 nymphs were used in the attempt to determine whether this tool could identify the bug species and discriminate their developmental stages. Five adults and four nymphs ofC. hirundinisspecimens were molecularly identified to update our MS homemade arthropod database. BLAST analysis ofCOIgene sequences from theseC. hirundinisrevealed 98.66–99.12% identity with the corresponding sequences ofC. hirundinisof the GenBank. The blind test against the database supplemented with MS reference spectra showed 100% (57/57)C. hirundinisadults and 100% (46/46)C. hirundinisnymphs were reliably identified and in agreement with morphological identification with logarithmic score values between 1.922 and 2.665. Ninety-nine percent ofC. hirundinisspecimens tested were positive forWolbachiaspp. The sequencing results revealed that they were identical toWolbachia massiliensis, belonging to the new T-supergroup strain and previously isolated fromC. hemipterus.ConclusionsWe report for the first time to our knowledge a case of human infestation by swallow bugs (C. hirundinis) in France. We also show the usefulness of MALDI-TOF MS in the rapid identification ofC. hirundinisspecimens and nymphs with minimal sample requirements. We phylogenetically characterized the novelWolbachiastrain (W. massiliensis) infectingC. hirundinisand compared it to other recognizedWolbachiaclades.Graphical Abstract
Comment on: Emergence of the invasive malaria vector Anopheles stephensi in Khartoum State, Central Sudan
Authors: Kolaczinski Jan , Al-Eryani Samira , Chanda Emmanuel , Fernandez-Montoya Lucia 
Published: November 2021

AbstractThis letter comments on the article “Emergence of the invasive malaria vector Anopheles stephensi in Khartoum State, Central Sudan” published in Parasites and Vectors 2021, 14:511. Here we aim of provide a response to this paper in the broader context of the invasion and spread of An. stephensi in the Horn of Africa, and the required response to it. We agree with the authors that the arrival of this invasive vector in Khartoum State is of high public health concern. Equally concerning, however, we found that the detection of the vector by the authors in 2018 seemingly took 3 years to communicate to the Ministry of Health and World Health Organization (WHO), and was reliant on an academic journal. We consider that this short report sets a poor example of how public health threats should be reported. Suitable communication alternatives to alert public health authorities to such threats have been put in place by the WHO and its Member States, and are well known to at least some of the authors of the short report. We would like to encourage all readers not to follow the example of Ahmed et al. but instead act as responsible public health professionals by drawing on the established reporting mechanisms and escalate potential threats as soon as they are identified.
Graphical Abstract
Spatial distribution and risk factors for human cysticercosis in Colombia
Authors: Galipó Erika , Dixon Matthew A. , Fronterrè Claudio , Cucunubá Zulma M. , Basáñez Maria-Gloria , Stevens Kim , Flórez Sánchez Astrid Carolina , Walker Martin 
Published: November 2021

Abstract
Background
Cysticercosis is a zoonotic neglected tropical disease (NTD) that affects humans and pigs following the ingestion of Taenia solium eggs. Human cysticercosis poses a substantial public health burden in endemic countries. The World Health Organization (WHO) aims to target high-endemicity settings with enhanced interventions in 17 countries by 2030. Between 2008 and 2010, Colombia undertook a national baseline serosurvey of unprecedented scale, which led to an estimated seroprevalence of T. solium cysticercus antibodies among the general population of 8.6%. Here, we use contemporary geostatistical approaches to analyse this unique dataset with the aim of understanding the spatial distribution and risk factors associated with human cysticercosis in Colombia to inform how best to target intervention strategies.

Methods
We used a geostatistical model to estimate individual and household risk factors associated with seropositivity to T. solium cysticercus antibodies from 29,253 people from 133 municipalities in Colombia. We used both independent and spatially structured random effects at neighbourhood/village and municipality levels to account for potential clustering of exposure to T. solium. We present estimates of the distribution and residual correlation of seropositivity at the municipality level.

Results
High seroprevalence was identified in municipalities located in the north and south of Colombia, with spatial correlation in seropositivity estimated up to approximately 140 km. Statistically significant risk factors associated with seropositivity to T. solium cysticercus were related to age, sex, educational level, socioeconomic status, use of rainwater, consumption of partially cooked/raw pork meat and possession of dogs.

Conclusions
In Colombia, the distribution of human cysticercosis is influenced by socioeconomic considerations, education and environmental factors related to the spread of T. solium eggs. This information can be used to tailor national intervention strategies, such as targeting spatial hotspots and more highly exposed groups, including displaced people and women. Large-scale seroprevalence surveys accompanied by geospatial mapping are an essential step towards reaching the WHO’s 2021‒2030 NTD roadmap targets.

Graphical Abstract
The Aliment to Bodily Condition knowledgebase (ABCkb): a database connecting plants and human health
Authors: Trautman Aaron , Linchangco Richard , Walstead Rachel , Jay Jeremy J. , Brouwer Cory 
Published: November 2021

Abstract
Objective
Overconsumption of processed foods has led to an increase in chronic diet-related diseases such obesity and type 2 diabetes. Although diets high in fresh fruits and vegetables are linked with healthier outcomes, the specific mechanisms for these relationships are poorly understood. Experiments examining plant phytochemical production and breeding programs, or separately on the health effects of nutritional supplements have yielded results that are sparse, siloed, and difficult to integrate between the domains of human health and agriculture. To connect plant products to health outcomes through their molecular mechanism an integrated computational resource is necessary.

Results
We created the Aliment to Bodily Condition Knowledgebase (ABCkb) to connect plants to human health by creating a stepwise path from plant $$\rightarrow$$
→
plant product $$\rightarrow$$
→
human gene $$\rightarrow$$
→
pathways $$\rightarrow$$
→
indication. ABCkb integrates 11 curated sources as well as relationships mined from Medline abstracts by loading into a graph database which is deployed via a Docker container. This new resource, provided in a queryable container with a user-friendly interface connects plant products with human health outcomes for generating nutritive hypotheses. All scripts used are available on github (https://github.com/atrautm1/ABCkb) along with basic directions for building the knowledgebase and a browsable interface is available (https://abckb.charlotte.edu).
Comparison of hydroxyethylstarch (HES 130/0.4) and 5% human albumin for volume substitution in pediatric neurosurgery: A retrospective, single center study
Authors: Schick Martin A. , Pippir Jonas , Struck Manuel F. , Brugger Jürgen , Neuhaus Winfried , Wunder Christian 
Published: November 2021

Abstract
Objective
Colloid solutions are commonly used to maintain perioperative fluid homeostasis. In regard to perioperative infant-centered care, data about the impact of colloids are rare. New data suggest a possible positive effect of hydroxyethyl starch (HES) concerning blood brain barrier. Therefore we conduct a retrospective single center study of children scheduled for neurosurgery, age < five with a blood loss > 10% of body blood volume, receiving either 6% HES 130/0.4 or 5% human albumin (HA).

Results
Out of 913 patients, 86 were included (HES = 30; HA = 56). Compared to HES [16.4 ± 9.2 ml/kg body weight (mean ± SD)] HA group received more colloid volume (25.7 ± 11.3), which had more blood loss [HA 54.8 ± 45.0; HES 30.5 ± 30.0 (%) estimated blood volume] and higher fluid balances. Fibrinogen was decreased and activated partial thromboplastin time was elevated in HA group. Urinary output, creatinine and urea levels did not differ between the two groups. Serum calcium, total protein levels were lower in HES group. HA treated infants tended to have shorter ICU and hospital stays. We conclude that none of the investigated colloid solutions were without leverage to infants. Consequently randomized controlled trials about perioperative goal-directed fluid replacement of children undergoing (neuro)-surgery with major blood loss are needed.
Database on the coverage of the “Bolsa-Família” conditioning cash-transfer program: Brazil, 2005 to 2021
Authors: Baroni Lais , Alves Ronaldo Fernandes Santos , Boccolini Cristiano Siqueira , Salles Rebecca , Gritz Raquel , Paixão Balthazar , Boccolini Patricia de Moraes Mello 
Published: November 2021

Abstract
Objectives
The “Bolsa-Família” Program (PBF) is a Brazilian conditional cash-transfer program in which families should comply with health, education, and social assistance conditionalities. The program aims to fight poverty and hunger, promoting nutrition and health services for low-income populations. This paper presents a database on the coverage of monitoring and compliance with the PBF health conditionalities in Brazil from January 2005 to July 2021.

Data description
Database on the PBF conditioning cash-transfer program coverage in Brazil from 2005 to 2021. It comprises information on the number of families benefited, health conditionalities, and the follow-up on vaccination and nutrition of children under seven years old. The cities and semesters are the minimal aggregation units.
Power calculator for detecting allelic imbalance using hierarchical Bayesian model
Authors: Sherbina Katrina , León-Novelo Luis G. , Nuzhdin Sergey V. , McIntyre Lauren M. , Marroni Fabio 
Published: November 2021

Abstract
Objective
Allelic imbalance (AI) is the differential expression of the two alleles in a diploid. AI can vary between tissues, treatments, and environments. Methods for testing AI exist, but methods are needed to estimate type I error and power for detecting AI and difference of AI between conditions. As the costs of the technology plummet, what is more important: reads or replicates?

Results
We find that a minimum of 2400, 480, and 240 allele specific reads divided equally among 12, 5, and 3 replicates is needed to detect a 10, 20, and 30%, respectively, deviation from allelic balance in a condition with power > 80%. A minimum of 960 and 240 allele specific reads divided equally among 8 replicates is needed to detect a 20 or 30% difference in AI between conditions with comparable power. Higher numbers of replicates increase power more than adding coverage without affecting type I error. We provide a Python package that enables simulation of AI scenarios and enables individuals to estimate type I error and power in detecting AI and differences in AI between conditions.
Correlation of serum electrolytes with serial miRNA in advanced stage non-small cell lung cancer (NSCLC) in Indonesia
Authors: Hanafi Arif Riswahyudi , Jayusman Achmad Mulawarman , Imelda Priscillia , Alfasunu Serafim , Sadewa Ahmad Hamim , Pramono Dibyo , Heriyanto Didik Setyo , Haryana Sofia Mubarika , Kresno Siti Boedina 
Published: November 2021

Abstract
Objective
This study aims to evaluate the correlation between electrolytes and serial miRNAs from our previous study. We want to prove that there is the molecular basis that underlying electrolytes disturbances as the predictive indicator to the outcome in NSCLC patients.

Results
There were positive correlation between potassium level with miR-34 (p  = 0.008, r  = 0.366), miR-148 (p  = 0.004, r  = 0.394) and miR-155 (p  = 0.031, r  = 0.300).
Npr2 mutant mice show vasodilation and undeveloped adipocytes in mesentery
Authors: Sogawa-Fujiwara Chizuru , Fujiwara Yasuhiro , Hanagata Atsuki , Yang Qunhui , Mihara Taiki , Kaji Noriyuki , Kunieda Tetsuo , Hori Masatoshi 
Published: November 2021

Abstract
Objective
The biological importance for the signaling of C-type natriuretic peptide (CNP) and natriuretic peptide receptor B (NPR-B) has been recognized. However, the details remain unclear and are debatable. The Npr2 is a gene of NPR-B, and we previously reported a unique phenotype of a spontaneous mutant mouse lacking Npr2 (Npr2slw/slw), such as severe ileus-like disorder with bloodless blood vessels. In this study, we analyzed the bloodless mesenteric vascular morphology of Npr2slw/slw by histological observation to clarify the effects of the CNP/NPR-B signal deficiency.

Results
Blood vessels in the mesentery were clearly dilated in the preweaning Npr2slw/slw mice. Additionally, in the Npr2slw/slw mice, the lacteals were partially dilation or randomly direction mucosal epithelial cells in villi, and mesenteric adipocytes were undeveloped. These findings provide important information for understanding the role of CNP/NPR-B signals on intestine with mesentery.
Volatile organic breath components and exercise induced bronchoconstriction in asthmatic children
Authors: van der Kamp M. R. , Driessen J. M. M. , van der Schee M. P. , Thio B. J. , de Jongh F. H. C. 
Published: November 2021

Abstract
Introduction
Asthma is one of the most common chronic diseases in childhood and is generally characterized by exercise induced bronchoconstriction (EIB). Assessing EIB is time consuming and expensive as it requires a fully equipped pulmonary function laboratory. Analysis of volatile organic compounds (VOCs) in breath is a novel technique for examining biomarkers which may associate with asthma features. The aim of this pilot study was to identify potential markers in the relationship between EIB and VOCs.

Methods
Children between four and 14 years old were asked to provide a breath sample prior to undergoing an exercise challenge test to assess for EIB.

Results
Breath samples were collected and analyzed in 46 asthmatic children, 21 with EIB and 25 without EIB (NO-EIB). Molecular features (MFs) were not significantly different between EIB and NO-EIB controls. 29 of the 46 children were corticosteroid naïve, 10 with EIB and 13 without. In the corticosteroid naïve group EIB was associated with increased MF23 and MF14 in the lower breath sample (p-value < 0.05).

Conclusion
This pilot study shows that EIB was related to an increased MF14 and MF23 in corticosteroid naïve children. The tentative identities of these compounds are octanal and dodecane/tetradecane respectively. These candidate biomarkers have a potential to enable non-invasive diagnosis of EIB in steroid-naïve children.
Trial registration This study is registered in the Netherlands trial register (trial no. NL6087) at 14 February 2017.
Chemical toxicity prediction based on semi-supervised learning and graph convolutional neural network
Authors: Chen Jiarui , Si Yain-Whar , Un Chon-Wai , Siu Shirley W. I. 
Published: November 2021

AbstractAs safety is one of the most important properties of drugs, chemical toxicology prediction has received increasing attentions in the drug discovery research. Traditionally, researchers rely on in vitro and in vivo experiments to test the toxicity of chemical compounds. However, not only are these experiments time consuming and costly, but experiments that involve animal testing are increasingly subject to ethical concerns. While traditional machine learning (ML) methods have been used in the field with some success, the limited availability of annotated toxicity data is the major hurdle for further improving model performance. Inspired by the success of semi-supervised learning (SSL) algorithms, we propose a Graph Convolution Neural Network (GCN) to predict chemical toxicity and trained the network by the Mean Teacher (MT) SSL algorithm. Using the Tox21 data, our optimal SSL-GCN models for predicting the twelve toxicological endpoints achieve an average ROC-AUC score of 0.757 in the test set, which is a 6% improvement over GCN models trained by supervised learning and conventional ML methods. Our SSL-GCN models also exhibit superior performance when compared to models constructed using the built-in DeepChem ML methods. This study demonstrates that SSL can increase the prediction power of models by learning from unannotated data. The optimal unannotated to annotated data ratio ranges between 1:1 and 4:1. This study demonstrates the success of SSL in chemical toxicity prediction; the same technique is expected to be beneficial to other chemical property prediction tasks by utilizing existing large chemical databases. Our optimal model SSL-GCN is hosted on an online server accessible through: https://app.cbbio.online/ssl-gcn/home.