bluuebunny/crossref_metadata_2025_split huggingface dataset:
Bacteria-derived ferrichrome inhibits tumor progression in sporadic colorectal neoplasms and colitis-associated cancer
Authors: IWAMA TAKUYA , Fujiya Mikihiro , Konishi Hiroaki , Tanaka Hiroki , Murakami Yuki , Kunogi Takehito , Sasaki Takahiro , Takahashi Keitaro , Ando Katsuyoshi , Ueno Nobuhiro , Kashima Shin , Moriichi Kentaro , Tanabe Hiroki , Okumura Toshikatsu 
Published: December 2020

Abstract
BACKGROUND: Colorectal cancers develop through several pathways, including the adenoma–carcinoma sequence and colitis-associated carcinogenesis. An altered intestinal microflora has been reported to be associated with the development and progression of colorectal cancer via these pathways. We identified Lactobacillus casei-derived ferrichrome as a mediator of the bacterial anti-tumor effect of colorectal cancer cells through the upregulation of DDIT3. In this study, we investigated the anti-tumor effects of ferrichrome on precancerous conditions and cancer cells associated with sporadic as well as colitis-associated colorectal cancer.METHODS: SRB and MTT assays were performed to assess growth inhibition in vitro. Eighteen organoids were prepared from biopsy specimens obtained by colonoscopy. An AOM-DSS carcinogenesis model and xenograft model of colorectal cancer cells were generated for the assessment of the tumor suppressive effect of ferrichrome in vivo. RESULTS: Ferrichrome inhibited the cell growth of colorectal cancer cells in vitro and in in vivo xenograft models. Ferrichrome exerted a strong tumor-suppressive effect that was superior to that of currently available anti-tumor agents, including 5-FU and cisplatin, both in vitro and in vivo. The tumor-suppressive effect of the combination of ferrichrome and 5-FU was superior to that of single treatment with either drug. The tumor suppressive effects of ferrichrome were confirmed through the upregulation of DDIT3 in patient-derived organoids of adenoma and carcinoma. Ferrichrome inhibited the tumor progression in the AOM-DSS model while exhibiting no anti-inflammatory effect in the DSS-colitis model, suggesting that ferrichrome inhibited cancer cells, but not a precancerous condition, via the colitis-associated pathway.CONCLUSIONS: Ferrichrome exerts a tumor suppressive effect on precancerous conditions and cancer cells associated with sporadic as well as colitis-associated colorectal cancer. The anti-tumor effect of ferrichrome was mediated by the upregulation of DDIT3, and was superior to that of 5-FU or cisplatin. These results suggest that Lactobacillus brevis-derived ferrichrome may be a candidate anti-tumor drug for the treatment of colorectal neoplasms.
Developing an inter-professional transition course to improve team-based HIV care for Sub-Saharan Africa
Authors: Kiguli-Malwadde Elsie , Budak Jehan Z , Chilemba Evelyn , Semitala Fred , Von Zinkernagel Deborah , Mosepele Mosepele , Conradie Hoffie , Khanyola J , Haruruvizhe Clara , Martin Shayanne , Kazembe Abigail , De Villiers M , Reid Michael J A 
Published: December 2020

Abstract
Background With funding from the United States Health Resources Service Administration (HRSA), a consortium of health professional training institutions from Africa developed HIV-specific, interprofessional, team-based educational resources to better support trainees during the transition period between pre-service training and professional practice.Methods Ten faculty members representing nine medical and nursing schools in sub-Saharan Africa (SSA) developed a training package of modules focused on core clinical, public health, interprofessional education (IPE), and quality improvement (QI) domains related to HIV service delivery. Curriculum development was informed by a rapid needs assessment of existing tools and future needs for HIV education across 27 SSA health professions training institutions. A total of 17 modules were developed, targeted at newly qualified health care professionals to be taught in a series of two-day workshops meant to complement existing institution specific HIV-curricula. Results Between April and July 2019, a comprehensive case-based HIV training package was developed to support trainees in transition from pre-service training to independent professional practice. Each module, addressing different elements of interprofessional practice, was intended to be delivered in an interprofessional format. Thus far, 70 health professions training institutions in 14 countries have implemented the program; 547 educators facilitated STRIPE workshops, with a total of 5,027 learners trained between September 2019 and September 2020.Conclusions To our knowledge this is the first IPE HIV-specific curriculum explicitly focused on enhancing the quality of training provided to graduating health care professionals working in SSA. The collaborative, cross-institutional, interprofessional approach to curriculum development provides a benchmark for how best-practice approaches to education can be disseminated in SSA.
The yearly financing need of providing paid maternity leave in the informal sector in Indonesia
Authors: Siregar Adiatma , Pitriyan Pipit , Hardiawan Donny , Zambrano Paul , Vilar-Compte Mireya , Belismelis Graciela Ma Teruel , Moncada Meztli , Tamayo David , Carroll Grace , Perez-Escamilla Rafael , Mathisen Roger 
Published: December 2020

Abstract
Background The economic cost of not breastfeeding in Indonesia is estimated at US$1.5–9.4 billion annually, the highest in South East Asia. Half of the 33.6 million working women of reproductive age (WRA) in Indonesia (15-49 years) are informal employees, meaning they are working as casual workers or they are self-employed (small scale business) and assisted by unpaid/family worker(s). No specific maternity protection entitlements are currently available for WRA working informally in Indonesia. This study aims to estimate the financing need of providing maternity leave cash transfer (MCT) for WRA working in the informal sector in Indonesia.Method The costing methodology used is the adapted version of the World Bank methodology by Vilar-Compte et al, following pre-set steps to estimate costs using national secondary data. We used the 2018 Indonesian National Socio-Economic Survey to estimate the number of women working informally who gave birth within the last year. The population covered, potential cash transfer’s unitary cost, the incremental coverage of the policy in terms of time and coverage, and the administrative costs were used to estimate the cost of MCT for the informal sector. Result At 100% coverage for 13 weeks of leave, the yearly financing need of MCT ranged from US$175million (US$152/woman) to US$669million (US$583/woman). The share of the yearly financing need did not exceed 0.5% of Indonesian Gross Domestic Product (GDP).Conclusion The yearly financing need of providing MCT for eligible WRA working in the informal sector is economically attractive as it amounts to less than 0.5% of GDP nominal of Indonesia. While such a program would be perceived as a marked increase from current public health spending at the onset, such an investment could substantially contribute to the success of breastfeeding and substantial corresponding public health savings given that more than half of working Indonesian WRA are employed in the informal sector. Such policies should be further explored while taking into consideration realistic budget constraints and implementation capacity.
Identification and co-expression analysis of long noncoding RNAs and mRNAs involved in the deposition of intramuscular fat in Aohan fine-wool sheep
Authors: Han Fuhui , Li Jing , Liu Nan , Zhao Ranran , Liu Lirong , Li Lanlan , Li Qian , He Jianning 
Published: December 2020

Abstract
Background: Intramuscular fat (IMF) content has become one of the most important indicators for measuring meat quality, and levels of IMF are affected by various genes. Long non-coding RNAs (lncRNAs) are widely expressed non-coding RNAs that play an important regulatory role in a variety of biological processes; however, research on the lncRNAs involved in sheep IMF deposition is still in its infancy. Aohan fine-wool sheep (AFWS), one of China's most important meat-hair, dual-purpose sheep breed, provides a great model for studying the role of lncRNAs in the regulation of IMF deposition. We identified lncRNAs by RNA sequencing in Longissimus thoracis et lumborum (LTL) samples of sheep at two ages: 2 months (Mth-2) and 12 months (Mth-12). Results: We identified a total of 26,247 genes and 6,935 novel lncRNAs in LTL samples of sheep. Among these, 199 mRNAs and 61 lncRNAs were differentially expressed. We then compared the structural characteristics of lncRNAs and mRNAs. We obtained target genes of differentially expressed lncRNAs (DELs) and performed enrichment analyses using Gene Ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG). We found that target mRNAs were enriched in metabolic processes and developmental pathways. One pathway was significantly enriched, namely tight junction. Based on the analysis of critical target genes, we obtained seven candidate lncRNAs that potentially regulated lipid deposition and constructed a lncRNA-mRNA co-expression network that included MSTRG.4051.3-FZD4, MSTRG.16157.3-ULK1, MSTRG.21053.3-PAQR3, MSTRG.19941.2-TPI1, MSTRG.12864.1-FHL1, MSTRG.2469.2-EXOC6 and MSTRG.21381.1-NCOA1. We speculated that these candidate lncRNAs might play a role by regulating the expression of target genes. We randomly selected five mRNAs and five lncRNAs to verify the accuracy of the sequencing data by qRT-PCR.Conclusions: Our study identified the differentially expressed mRNAs and lncRNAs during intramuscular lipid deposition in Aohan fine-wool sheep. The work may widen the knowledge about the annotation of the sheep genome and provide a working basis for investigating intramuscular fat deposition in sheep.
Application of 3D printing and distributed manufacturing during the first-wave of COVID-19 pandemic. Our experience at a third-level university hospital.
Authors: Perez-Mañanes Ruben , José Sonia García de San , Desco-Menéndez Manuel , Sánchez-Arcilla Ignacio , González-Fernández Esmeralda , Vaquero-Martín Javier , González-Garzón Javier Pascau , Mediavilla-Santos Lydia , Trapero-Moreno Diego , Calvo-Haro José Antonio 
Published: December 2020

Abstract
Background 3D printing and distributed manufacturing represent a paradigm shift in the health system that is becoming critical during the COVID-19 pandemic. University hospitals are also taking on the role of manufacturers of custom-made solutions thanks to 3D printing technology. Case Presentation We present a monocentric observational case study regarding the distributed manufacturing of three groups of products during the period of the COVID-19 pandemic from 14 March to 10 May 2020: personal protective equipment, ventilatory support, and diagnostic and consumable products. Networking during this period has enabled the delivery of a total of 17,276 units of products manufactured using 3D printing technology. The most manufactured product was the face shields and ear savers, while the one that achieved the greatest clinical impact was the mechanical ventilation adapters and swabs. The products were manufactured by individuals in 57.3% of the cases, and our hospital acted as the main delivery node in a hub with 10 other hospitals. The main advantage of this production model is the fast response to stock needs, being able to adapt almost in real time.Conclusions The role of 3D printing in the hospital environment allows the reconciliation of in-house and distributed manufacturing with traditional production, providing custom-made adaptation of the specifications, as well as maximum efficiency in the working and availability of resources, which is of special importance at critical times for health systems such as the current COVID-19 pandemic.
Predicting Insect Invasiveness with Whole-Genome Sequencing Data
Authors: Huang Cong , Yang Nianwan , Wang Shuping , Fan Xiaodan , Pian Cong , Luo Jiapeng , Li Xi , Lang Kun , Xing Longsheng , Jiang Mingxing , Liu Wanxue , Qian Wanqiang , Simberloff Daniel , Wan Fanghao , Li Fei 
Published: December 2020

Abstract
Background: Invasive alien insects threaten agriculture, biodiversity, and human livelihoods globally. Unfortunately, insect invasiveness still cannot be reliably predicted. Empirical policies of insect pest quarantine and inspection are mainly designed against species that are already problematic.Results: We conducted a comparative genomic analysis of 37 invasive insect species and six non-invasive insect species, showing that the gene families associated with defense, protein and nucleic acid metabolism, chemosensory function, and transcriptional regulation were significantly expanded in invasive insects, suggesting that enhanced abilities in self-protection, nutrition exploitation, and locating food or mates are intrinsic features conferring invasiveness in insects. By using these intrinsic genome features, we proposed an invasiveness index and estimated the invasiveness of 99 other insect species with genome data, classifying them as highly, moderately, or minimally invasive. Insects possessing all these aforementioned enhanced abilities are predicted to be highly invasive, and vice versa. Next, a logistic-regression classifier was trained to predict insect invasiveness, achieving 93.2% accuracy. Conclusions: We present evidence that several traits may confer invasiveness in insects and these features can be used to predict insect invasiveness accurately, and we quantify insect invasiveness with an invasiveness index.
RASMA: A Reverse Search Algorithm for Mining Maximal Frequent Subgraphs
Authors: Salem Saeed , Alokshiya Mohammed , Hasan Mohammad Al 
Published: December 2020

Abstract
Background: Given a collection of coexpression networks over a set of genes, identifying subnetworks that appear frequently is an important research problem known as mining frequent subgraphs. Maximal frequent subgraphs is a representative set of frequent subgraphs; A frequent subgraph is maximal if it does have a super-graph that is frequent. In the bioinformatics discipline, methodologies for mining frequent and/or maximal frequent subgraphs can be used to discover interesting network motifs that elucidate complex interactions among genes, reflected through the edges of the frequent subnetworks. Further study of frequent coexpression subnetworks enhances the discovery of biological modules and biological signatures for gene expression and disease classification. Results: We propose a reverse search algorithm, called RASMA, for mining frequent and maximal frequent subgraphs in a given collection of graphs. A key innovation in RASMA is a connected subgraph enumerator that uses a reverse-search strategy to enumerate connected subgraphs of an undirected graph. Using this enumeration strategy, RASMA obtains all maximal frequent subgraphs very efficiently. To overcome the computationally prohibitive task of enumerating all frequent subgraphs while mining for the maximal frequent subgraphs, RASMA employs several pruning strategies that substantially improve its overall runtime performance. Experimental results show that on large gene coexpression networks, the proposed algorithm efficiently mines biologically relevant maximal frequent subgraphs. Conclusion: Extracting recurrent gene coexpression subnetworks from multiple gene expression experiments enables the discovery of functional modules and subnetwork biomarkers. We have proposed a reverse search algorithm for mining maximal frequent subnetworks. Enrichment analysis of the extracted maximal frequent subnetworks reveals that subnetworks that are frequent are highly enriched with known biological ontologies.
Engineering prokaryotic regulator IrrE to enhance stress tolerance in budding yeast
Authors: Wang Li , Wang Xin , He Zhi-Qiang , Zhou Si-Jie , Xu Li , Tan Xiao-Yu , Xu Tao , Li Bing-Zhi , Yuan Ying-Jin 
Published: December 2020

Abstract
Background: Stress tolerance is one of the important desired microbial traits for industrial bioprocess and global regulatory protein engineering is an efficient approach to improve strain tolerance. In our study, IrrE, a global regulatory protein from prokaryotic organism Deinococcus radiodurans, was engineered to confer yeast the improved tolerance to the inhibitors in lignocellulose hydrolysates or high temperature.Results: Three IrrE mutants were developed through directed evolution and the expression of these mutants could improve the yeast fermentation rate by 3- to 4-fold in the presence of multiple inhibitors. Subsequently, the tolerance to multiple inhibitors of single-site mutants based on the mutations from the variants was then evaluated, and eleven mutants including L65P, I103T, E119V, L160F, P162S, M169V, V204A, R244G, Base 824 Deletion, V299A and A300V were identified to be critical for the improved FAP tolerance. Further studies indicated that IrrE caused genome-wide transcriptional perturbation in yeast, and the mutant I24 led to the rapid growth of Saccharomyces cerevisiae mainly by regulating the transcription level of transcription activators/factors, protecting the intracellular environment and enhancing the antioxidant capacity under inhibitor environment, which reflected the plasticity of IrrE. Meanwhile, we observed that the expression of the wild-type or mutant IrrE could also protect Saccharomyces cerevisiae from the damage caused by thermal stress. The recombinant yeast strains were able to grow with glucose at 42 ºC.Conclusions: IrrE from Deinococcus radiodurans can be engineered as a tolerance-enhancer for Saccharomyces cerevisiae. Systematic research on the regulatory model and mechanism of a prokaryotic global regulatory factor IrrE to increase yeast tolerance provided valuable insights for the improvement of microbial tolerance to complex industrial stress conditions.
Mesenchymal Stem Cells and Acelluar Products Attenuate Murine Induced Colitis
Authors: Li Yan , Altemus Jessica , Lightner Amy L. 
Published: December 2020

Abstract
Background: Mesenchymal stem cells (MSCs) are a well-established immunosuppressive agent which can also promote tissue repair and regeneration. Recent studies have demonstrated MSCs as a novel therapeutic for inflammatory bowel disease (IBD), a chronic idiopathic inflammatory disorder of the gastrointestinal tract. However, the precise role of MSCs in regulating immune-responses is controversial, and its significance in the pathogenesis of IBD uncertain. In addition, MSCs’ acellular product, extracellular vesicles (EVs), may also play an important role in the armamentarium of therapeutics, but how EVs compare to MSCs remains undefined due to the lack of side-by-side comparative investigation. We herein compared MSCs and their associated EVs side-by-side using a DSS-induced colitis model. Methods: A DSS-induced colitis model was used. At Day 4, mice received adipose derived MSCs, MSC derived EVs, or placebo. Weight loss, stool consistency and hematochezia was charted. At day 8, murine colons were harvested, histologic analysis performed, and serum/tissue cytokine analysis conducted. Results: MSCs and EVs demonstrated equivalent immunosuppressive functions with DSS-treated mice through decreased colonic lymphocyte infiltration and attenuated disease severity after both MSC and EV treatment. Furthermore, both MSCs and EVs have an equivalent ability to inhibit inflammation in the DSS colitis model. Conclusions: These results suggest that (i) both MSCs and EVs are effective therapeutic candidates for a DSS-induced mouse colitis model, (ii) MSCs and EVs have similar immunosuppressive and anti-inflammatory functions, and (iii) EVs may present a novel future therapeutic for the treatment of IBD.
Genome analysis of Spiroplasma citri strains from different host plants and its leafhopper vectors
Authors: Rattner Rachel , Thapa Shree Prasad , Dang Tyler , Osman Fatima , Selvaraj Vijayanandraj , Maheshwari Yogita , Pagliaccia Deborah , Espindola Andres S. , Hajeri Subhas , Chen Jianchi , Coaker Gitta , Vidalakis Georgios , Yokomi Raymond 
Published: December 2020

Abstract
Background Spiroplasma citri comprises a complex of bacteria that cause diseases in citrus, horseradish, carrot, sesame, and also infect a wide array of ornamental and weed species. S. citri is transmitted in a persistent propagative manner by the beet leafhopper, Neoaliturus tenellus in North America and Circulifer haematoceps in the Mediterranean region. Leafhopper transmission and the pathogen’s wide host range serve as drivers of genetic diversity. This diversity was examined by comparing the genome sequences of seven S. citri strains from the United States (BR12, CC2, C5, C189, LB319, BLH-13, and BLH-MB) collected from different hosts and times with other publicly available spiroplasmas.Results Phylogenetic analysis using 16S rRNA sequences from 39 spiroplasmas obtained from NCBI database showed that S. citri strains, along with S. kunkelii and S. phoeniceum, two other plant pathogenic spiroplasmas, formed a monophyletic group. To refine genetic relationships among S. citri strains, phylogenetic analyses with 863 core orthologous sequences were performed. Strains that clustered together were: CC-12 and C5; C189 and R8-A2; BR12, BLH-MB, BLH13 and LB 319. Strain GII3-3 remained in a separate branch. Sequence rearrangements were observed among S. citri strains, predominantly in the center of the chromosome. One to nine plasmids were identified in the seven S. citri strains analyzed in this study. Plasmids were most abundant in strains isolated from the beet leafhopper, followed by strains from carrot, Chinese cabbage, horseradish and citrus, respectively. All these S. citri strains contained one plasmid with high similarity to plasmid pSci6 from S. citri strain GII3-3X which is known to confer insect transmissibility. Additionally, 17 to 25 prophage-like elements were identified in these genomes, which may promote rearrangements and contribute to repetitive regions. Conclusions The genome of seven S. citri strains were found to contain a single circularized chromosome, ranging from 1.58 Mbp to 1.74 Mbp and 1,597-2,232 protein-coding genes. These strains possessed a plasmid similar to pSci6 from the GII3-3X strain associated with leafhopper transmission. Prophage sequences found in the S. citri genomes may contribute to the extension of its host range. These findings increase our understanding of S. citri genetic diversity.