bluuebunny/crossref_metadata_2025_split huggingface dataset:
Multi-locus sequence analyses reveal a clonal L. borgpetersenii genotype in a heterogeneous invasive Rattus spp. community across the City of Johannesburg, South Africa
Authors: Moseley Mark Hamish , Naidoo Kovashnee , Bastos Armanda , Retief Liezl , Frean John , Telfer Sandra , Rossouw Jennifer 
Published: October 2020

Abstract
BackgroundRattus spp. are frequently implicated as key reservoir hosts for leptospirosis, one of the most common, but neglected, bacterial zoonoses in the world. Although leptospirosis is predicted to be a significant public health threat in Africa, studies from the continent are limited. Methods Rattus spp. (n=171) were sampled (January-May 2016) across the City of Johannesburg, South Africa’s largest inland metropole. Rattus spp. genetic diversity was evaluated by full length (1140 bp) cyt b sequencing of 42 samples. For comparison, a further 12 R. norvegicus samples collected in Cape Town, South Africa’s largest coastal metropole, were also genotyped. Leptospira infections were identified and genotyped using real-time PCR and multi-locus (lfb1, secY, lipL41) DNA sequencing. Results Five R. norvegicus haplotypes were identified across Johannesburg, four of which have not previously been detected in South Africa, and one in Cape Town. Across Johannesburg we identified a Leptospira spp. infection prevalence of 44% (75/171) and noted significant differences in the prevalence between administrative regions within the metropole. Multi-locus sequence analyses identified a clonal genotype consistent with L. borgpetersenii serogroup Javanica (serovar Ceylonica).DiscussionThe prevalence of infection identified in this study is amongst the highest detected in Rattus spp. in similar contexts across Africa. Despite the complex invasion history suggested by the heterogeneity in R. norvegicus haplotypes identified in Johannesburg, a single L. borgpetersenii genotype was identified in all infected rodents. The lack of L. interrogans in a rodent community dominated by R. norvegicus is notable, given the widely recognised host-pathogen association between these species and evidence for L. interrogans infection in R. norvegicus in Cape Town. It is likely that environmental conditions (cold, dry winters) in Johannesburg may limit the transmission of L. interrogans. Spatial heterogeneity in prevalence suggest that local factors, such as land use, influence disease risk in the metropole. ConclusionIn South Africa, as in other African countries, leptospirosis is likely underdiagnosed. The high prevalence of infection in urban rodents in Johannesburg suggest that further work is urgently needed to understand the potential public health risk posed by this neglected zoonotic pathogen.
Investigation of the piroplasm diversity circulating in wildlife and cattle of the greater Kafue ecosystem, Zambia
Authors: Squarre David , Nakamura Yukiko , Hayashida Kyoko , Kawai Naoko , Chambaro Herman , Namangala Boniface , Sugimoto Chihiro , Yamagish Junya 
Published: October 2020

Abstract
Background

Piroplasms are vector-borne intracellular hemoprotozoan parasites that infect wildlife and livestock. Wildlife species are reservoir hosts to a diversity of piroplasms and play an important role in the circulation, maintenance and evolution of these parasites. The potential for likely spillover of both pathogenic and non-pathogenic piroplasm parasites from wildlife to livestock is underlined when common ecological niche is shared in the presence of a competent vector.

Method

To investigate piroplasm diversity in parasite community in wildlife and cattle population of the greater Kafue ecosystem , we utilized PCR to amplify the 18S rRNA V4 hyper-variable region and meta-barcoding strategy using illumina MiSeq sequencing platform and amplicon sequence variant (ASV) based bioinformatics pipeline to generate high resolution data which discriminate sequences down to a single nucleotide difference.

Results

A parasite community of 45 ASVs corresponding to 23 species consisting of 4 genera of Babesia , Theileria , Hepatozoon and Colpodella, were identified in wildlife and cattle population from the study area. Theileria species were observed in buffalo, impala, hartebeest, sable antelope, sitatunga, wild dog and cattle. In contrast, Babesia species were only observed in cattle and wild dog. Our results demonstrate possible spillover of these hemoprotozoan parasites from wildlife, especially buffalo, to cattle population in the wildlife-livestock interface.

Conclusion

We demonstrated that the deep amplicon sequencing of the 18S rRNA V4 hyper-variable region for wildlife was informative. Our results illustrated the diversity of piroplasma and the specificity of their hosts. They led us to speculate possible ecological cycle including transmission from wildlife to domestic animals in the greater Kafue ecosystem. Thus, this approach may contribute to the establishment of appropriate disease control strategies in wildlife-livestock interface areas.
Methylotrophy, alkane-degradation, and pigment production as defining features of the globally distributed yet-uncultured phylum Binatota
Authors: Murphy Chelsea , Dunfield Peter , Sheremet Andriy , Spear John , Stepanauskas Ramunas , Woyke Tanja , Elshahed Mostafa , Youssef Noha 
Published: October 2020

Abstract
The recent leveraging of genome-resolved metagenomics has opened a treasure trove of genomes from novel uncultured microbial lineages, yet left many clades undescribed. We here present a global analysis of genomes belonging to the Binatota (UBP10), a globally distributed, yet-uncharacterized bacterial phylum. All orders in the Binatota encoded the capacity for aerobic methylotrophy using methanol, methylamine, sulfomethanes, chloromethanes, and potentially methane as substrates. Methylotrophy in the Binatota was characterized by order-specific substrate degradation preferences, as well as extensive metabolic versatility, i.e. the utilization of diverse sets of genes, pathways and combinations to achieve a specific metabolic goal. The genomes also encoded an arsenal of alkane hydroxylases and monooxygenases, potentially enabling growth on a wide range of alkanes and fatty acids. Pigmentation is inferred from a complete pathway for carotenoids (lycopene, β and γ carotenes, xanthins, chlorobactenes, and spheroidenes) production. Further, the majority of genes involved in bacteriochlorophyll a, c, and d biosynthesis were identified; although absence of key genes and failure to identify a photosynthetic reaction center precludes proposing phototrophic capacities. Analysis of 16S rRNA databases showed Binatota’s preferences to terrestrial and freshwater ecosystems, hydrocarbon-rich habitats, and sponges supporting their suggested potential role in mitigating methanol and methane emissions, alkanes degradation, and nutritional symbiosis with sponges. Our results expand the lists of methylotrophic, aerobic alkane degrading, and pigment-producing lineages. We also highlight the consistent encountering of incomplete biosynthetic pathways and gene shrapnel in microbial genomes, a phenomenon necessitating careful assessment when assigning putative functions based on a set-threshold of pathway completion.
Data-Driven Reaction Coordinate Discovery in Overdamped and non-Conservative Systems: Application to Optical Matter Structural Isomerization
Authors: Chen Shiqi , Peterson Curtis , Parker John , Rice Stuart A. , Ferguson Andrew , Scherer Norbert 
Published: October 2020

Abstract
Powerful technique as it is to study the collective fluctuations and structural transitions in under-damped conservative systems, normal mode analysis cannot be applied to the optical matter (OM) system, an overdamped system subject to non-conservative forces, which consists of (nano-)particle constituents in solution that can self-organize into ordered arrays bound by electrodynamic interactions. We propose a data-driven approach based on principal component analysis (PCA) of deviations from a reference structure to determine the soft collective modes of non-conservative overdamped systems, such as OM structures, and harmonic linear discriminant analysis (HLDA) of time trajectories to estimate the reaction coordinate for structural transitions, which is demonstrated for structural isomerization of a six-particle OM system. The reaction coordinate we discover is in accord with committor analysis and the identified mechanism is in agreement with experiment. The PCA-HLDA approach to data-driven discovery of reaction coordinates aids in the understanding of non-conservative and overdamped systems.
Direct 1,3-butadiene biosynthesis in Escherichia coli via a tailored ferulic acid decarboxylase mutant
Authors: Mori Yutaro , Noda Shuhei , Shirai Tomokazu , Kondo Akihiko 
Published: October 2020

Abstract
The C4 unsaturated compound 1,3-butadiene is an important monomer in synthetic rubber and engineering plastic production. However, microorganisms cannot directly produce 1,3-butadiene using glucose as a renewable carbon source via biological processes. This study constructed a novel artificial metabolic pathway for 1,3-butadiene production from glucose in Escherichia coli by combining the cis,cis-muconic acid (ccMA)-producing pathway and tailored ferulic acid decarboxylase mutants. The rational enzyme design of the substrate-binding site by computational simulation improved 1,3-butadiene-producing ccMA decarboxylation with a small mutant library. We found that changing dissolved oxygen and controlling pH were important factors for 1,3-butadiene production. Using dissolved oxygen–stat fed-batch fermentation in a 1-L jar fermenter, we could produce 2.1 g L− 1 of 1,3-butadiene. These results indicated that using a rational enzyme design, we can produce unnatural/nonbiological compounds (those that are made from petroleum and cannot be produced by microorganisms) using glucose as a renewable carbon source.
Visible Colorimetric Dosimetry of UV and Ionizing Radiations by a Dual-Module Photochromic Nanocluster
Authors: Lu Huangjie , Xie Jian , Wang Xin-Xu , Wang Yaxing , Li Zi-Jian , Diefenbach Kariem , Pan Qing-Jiang , Wang Jian-Qiang , Wang Shuao , Lin Jian 
Published: October 2020

Abstract
Radiation dosimeters displaying conspicuous response of irradiance are highly desirable over the recent decade owing to the growing demand of monitoring high-energy radiation and environmental exposure. Herein, we present the first case of dosimetry based on a discrete nanocluster by judicious incorporating heavy Th6 polynuclear centers as radiation attenuator and organic linkers as photo-responsive sensor to enhance chromic response. Rather unusual dual-module photochromic transitions upon multiple external stimuli including UV, β-ray, and γ-ray are integrated into this single material. The striking color change, and more significantly, the visible chromic transition of luminescence in response to accumulating radiation dose allow an on-site quantitative platform for naked-eye detection of ionization radiations over a broad range (1–80 kGy). SC-XRD and DFT calculations revealed that the dual-module photochromism can be attributed to a unique π(TPC)→π*(TPC) intermolecular charge transfer (IeMCT) driven by enhanced π-π stacking interaction between the adjacent TPC moieties upon irradiations.
Effect of Autologous Fibrin Glue on Seroma Reduction after Modified Radical Mastectomy for Breast Cancer: A Randomized Controlled Trial
Authors: Faisal Mohammed , Salem Sara , Kamel Noha , Zaher Haidi Abd El , Bakr Ahmed Abo , Fathy Hamada 
Published: October 2020

Abstract
Introduction Breast cancer stands out as the second most common cancer in the world with incidence 35.1% of all malignancies among females in Egypt. Fluid build-up after breast surgery is still the most annoying complication which leads to worse outcome. We aimed to evaluate whether autologous fibrin glue might lessen the formation of seroma following modified radical mastectomy. Methods This was a randomized controlled trial designed to configure the effect of autologous fibrin glue given in the study group using the drain in comparison to a control group who received the drain only; seroma volume was calculated every 24 hrs. For all of the cases. The drains were removed when the daily drainage was less than 30 ml for 3 consecutive days. Results We recruited 30 patients to each of the two groups. Age, pathology, breast cancer stage, number of lymph nodes and tumour size did not differ significantly between groups. A comparison of the median days to drain removal showed 8 days reduction in median days to drain removal compared in the intervention group (7 days) than the control (15 days). The patients in the fibrin glue group had a significantly lower cumulative drain output volume (mean ± SD of 505.6 ± 209.3 ml) than those in the control group (1674.1± 1373.8 ml). Additionally, the patients treated with fibrin glue had a significantly shorter postoperative length of stay (8.5 (7–10) days) than the controls (15 (10–23) days. Conclusions Autologous fibrin glue significantly decrease seroma formation post-modified radical mastectomy. Research Registry Unique Identifying Number: researchregistry5372.
Designing next generation recombinant protein expression platforms by modulating the cellular stress response in Escherichia coli
Authors: Guleria Richa , Jain Priyanka , Verma Madhulika , Mukherjee Krishna Jyoti 
Published: October 2020

Abstract
Background

A cellular stress response (CSR) is triggered upon recombinant protein synthesis which acts as a global feedback regulator of protein expression. To remove this key regulatory bottleneck, we had previously proposed that genes that are up-regulated post induction could be part of the signaling pathways which activate the CSR. Knocking out some of these genes which were non-essential and belonged to the bottom of the E. coli regulatory network had provided higher expression of GFP and L-asparaginase .

Results

We chose the best performing double knockout E. coli BW25113 ΔelaAΔcysW and demonstrated its ability to enhance the expression of the toxic Rubella E1 glycoprotein by 2.5-fold by tagging it with sf GFP at the C-terminal end to better quantify expression levels. Transcriptomic analysis of this hyper-expressing mutant showed that a significantly lower proportion of genes got down-regulated post induction, which included genes for transcription, translation, protein folding and sorting, ribosome biogenesis, carbon metabolism, amino acid and ATP synthesis. This down-regulation which is a typical feature of the CSR was clearly blocked in the double knockout strain leading to its enhanced expression capability. Finally, we supplemented the expression of substrate uptake genes glpK and glpD whose down-regulation was not prevented in the double knockout, thus ameliorating almost all the negative effects of the CSR and obtained a further doubling in recombinant protein yields.

Conclusion

The study validated the hypothesis that these up-regulated genes act as signaling messengers which activate the CSR and thus, despite having no casual connection with recombinant protein synthesis, can improve cellular health and protein expression capabilities. Combining gene knockouts with supplementing the expression of key down-regulated genes can counter the harmful effects of CSR and help in the design of a truly superior host platform for recombinant protein expression.
Cytokine biomarker phenotype for early prediction and triage of sepsis in blunt trauma patients
Authors: Wang Jun , Wen Dalin , Sun Jianhui , Zeng Shi , Du Juan , Cui Li , Zhang Huacai , Zeng Ling , Du Dingyuan , Zhang Lianyang , Deng Jin , Jiang Jianxin , Zhang Anqiang 
Published: October 2020

Abstract
BackgroundSepsis is a life-threatening condition associated with an exacerbated production of cytokines that can promote a hyperactive response to infection or induce immunoparalysis. The trauma victim’s inherent state of hyperinflammation frequently camouflages septic events, delaying the initiation of targeted therapy. Thus, this study aimed to establish the profiles of cytokines in trauma patients to characterize the nature of the immune responses to sepsis, which might enable early prediction and individualized treatments to be developed and targeted.MethodsA 15-plex human cytokine magnetic bead assay system was used to measure analytes in citrated plasma samples. Analysis of these cytokine kinetics was performed on 40 patients with severe blunt trauma admitted to our trauma center between March 2016 and February 2017 with Injury Severity Score (ISS) more than 20 with regard to sepsis (Sepsis-3) over a 14-day time course.ResultsIn total, six cytokines changed in trauma patients between the different timepoints at day 1, 3, 5, 7, and 14. Additionally, IL-6, IL-10, IL-15, MDC, GRO, sCD40L, G-CSF, and FGF-2 significantly distinguished between sepsis and nonsepsis at day 3 and afterward with an area under the curve of up to 0.90 when the eight biomarkers (P < 0.001) were combined. Event-related analysis demonstrated 1.5- to 4-fold serum level changes for these cytokines within 72 hours before clinically apparent sepsis. ConclusionCytokine profiles demonstrate high discriminatory ability to timely identify evolving traumatic sepsis. These abrupt changes allow sepsis detection up to 72 hours before clinically overt deterioration. Measurement of these cytokines might enable future studies to better predict, diagnose, and characterize traumatic sepsis, as well as confer the potential for physicians to timely initiate treatment with reduced mortality and costs.
Extended lymphadenectomy benefits patients with borderline resectable pancreatic head cancer —— a single-center retrospective study
Authors: Zhu Jiqiao , Lyu Shao-Cheng , Wang Jing , Li Xian-Liang , Lang Ren , He Qiang 
Published: October 2020

Abstract
Background: Whether standard lymphadenectomy or extended lymphadenectomy should be performed is still under debate during pancreaticoduodenectomy (PD). We aimed to compare their morbidity and mortality rates among patients with pancreatic head cancer (PHC). Material and methods: In this retrospective study, a total of 322 patients were enrolled. According to the scope of intraoperative lymph node dissection, patients were divided into extended lymphadenectomy group (n=120) and standard lymphadenectomy group (n=202). Based on the resectability of the tumor, there were 198 cases of resectable PHC and 124 cases of boardline resectable PHC, respectively, in which further stratified analysis was carried out according to the extent of lymph node dissection.Results: All patients completed the operation successfully, with a perioperative morbidity rate of 27.9% and mortality rate of 0.9%. As for the overall patients, patients in the extended lymphadenectomy group had higher NLR, longer operation time, more intraoperative blood loss, lymph node dissection and patients with BRPHC. (P<0.05) The 1-, 2- and 3-year overall survival rates of patients with extended lymphadenectomy and standard lymphadenectomy were 71.9%, 50.6%, 30.0% and 70.0%, 32.9%, 21.5%, respectively. (P=0.068) With regards to patients with BRPHC, the number of lymph node dissection in the extended lymphadenectomy group was more, (P<0.05) and the 1-, 2- and 3-year overall survival rates of patients with extended lymphadenectomy and standard lymphadenectomy were 60.7%, 43.3%, 27.4% and 43.2%, 17.7%, 17.7%, respectively. (P=0.007)Conclusions: Patients with BRPHC tended to have vast lymph node metastasis. Extended lymphadenectomy can improve their long-term survival.
Tumor ferroptosis status demonstrated vulnerability to chemotherapy and reflected immune-activation in colorectal cancer
Authors: Lv Yang , Feng QingYang , Zhang ZhiYuan , Zheng Peng , Zhu DeXiang , Mao YiHao , Xu YuQiu , Ji MeiLing , Xu JianMin , He GuoDong 
Published: October 2020

Abstract
Background: Existing studies for ferroptosis and prognosis in colorectal cancer (CRC) were limited. In this study, we aim to investigate the prognostic role of ferroptosis markers in patients with CRC and exploration of its micro-environmental distributions. Methods: A total of 911 patients from 2008 to 2013 with CRC were enrolled. Immunohistochemical staining was performed for CRC patients’ tissue microarray. Selection and prognostic validation of markers were based on mRNA data from the cancer genome atlas (TCGA) database. Gene Set Enrichment Analysis (GSEA) was performed to indicate relative immune landmarks and hallmarks. Ferroptosis and immune contexture were examined by CIBERSORT. Survival outcomes were analyzed by Kaplan-meier analysis and cox analysis.Results: A panel of 42 genes was selected. Through mRNA expression difference and prognosis analysis, GPX4, NOX1 and ACSL4 were selected as candidate markers. By IHC, increased GPX4, decreased NOX1 and decreased FACL4 indicate poor prognosis and worse clinical characteristics. Ferroptosis score based on GPX4, NOX1 and ACSL4 was constructed and validated with high C-index. Low ferroptosis score can also demonstrate the better progression free survival and better adjuvant chemotherapy (ACT) responsiveness. Moreover, tumor with low ferroptosis score tend to be infiltrated with more CD4+ T cells, CD8+ T cells and less M1 macrophage. Finally, we found that IFN-γ was potentially the central molecule at the crossroad between ferroptosis and onco-immune response. Conclusion: Ferroptosis plays important role on CRC tumor progression, ACT response and prognosis. Ferroptosis contributes to immune-supportive responses and IFN-γ was the central molecule for this process.
Financial Inclusion and Saving Culture of Individuals in Uganda: A Case of Central Division, Kabale Municipality
Authors: Musinguzi Isaac , Richard Ayebare , Muwanguzi Elizabeth 
Published: October 2020

Abstract
The study was about Financial Inclusion and savings in Uganda. A case of central division, Kabale Municipality. Financial Inclusion seeks to overcome the friction that hinders markets from expanding access to, and use of formal financial products and services to a broad number of people. The Objectives of the study were; to examine how access to financial services affects deposits made to formal financial institutions, to find out the effect of usage of financial services on deposits made to formal financial institutions and; to investigate the relationship between quality of financial services available and deposits made to formal financial institutions. The study adopted a cross-sectional survey research design. A sample size of 390 respondents from a population of 15,092 people was used. Findings of the study established a direct positive relationship between Financial Inclusion and savings. The regression results showed that savings as measured by percentage of the respondent’s monthly income earnings that is saved, was influenced by Access to formal financial products and services (p=0.031), usage of formal financial products and services (p=0.015) and Quality of formal financial products and services (p=0.021). The independent variables in the regression model with positive coefficient showed a direct relationship with the dependent variable. Therefore, the study concluded that savings increases proportionately with more access to formal financial products, usage and increase in quality of formal financial products. The study also recommended that financial institutions should create financial products which are tailored to fit various individual needs. Again, these financial institutions should create many outlets through Agent Banking and this would prevent the people from saving in their homes and rather save with the financial institutions since savings do not benefit only the individuals but the economy as a whole.