bluuebunny/crossref_metadata_2025_split huggingface dataset:
Bacteriological Profile, Antibiotic Susceptibility Pattern and Predictors of bacteremia among Children with Bloodstream Infection
Authors: Chaki Samina Nazir , Msuya Levina , Mchaile Deborah , Mahande Michael Johnson , Mbwasi Ronald Mwitalemi , Philemon Rune Nathaniel 
Published: April 2021

Abstract
Background: Bloodstream infections are major causes of morbidity and mortality among children in Sub-Saharan countries. This study aimed to determine the prevalence of bacteremia, etiological agents’ antibiotic susceptibility pattern and predictors of bacteremia among children with bloodstream Infection.Methodology: This hospital-based cross-section study involved children aged two months to thirteen years. All children meeting the inclusion criteria during the study period were enrolled. All consenting parents were interviewed via a questionnaire to collect data, followed by a thorough physical assessment and venipuncture was done to collect blood samples. Data were analysed using SPSS version 23.Results: Among 242 study participants, 154(63.6%) were male and blood cultures were positive in 37(15.3%). Gram-positive and gram-negative bacteria constituted 32(80%) and 8(20%), respectively. The frequent pathogen found was Staphylococcus aureus 25(62.5%), followed by Enterococcus spp. 4(10%), Escherichia coli 4(10%), Pseudomonas aeruginosa 3(7.5%), Streptococcus pyogenes 3(7.5%) and 1(2.5%) Klebsiella pneumonia. The majority of bacterial isolates showed high resistance to commonly used antibiotics in the study area. Predictors of bacteremia were severe malnutrition, hydrocephalus, hyperglycemia, lethargy and BSI with no foci of infection. Conclusion: Prevalence of bacteremia was 15.3%. Gram-positive bacteria were more prevalent than gram-negative bacteria. Staphylococcus aureus and Escherichia coli were the prevalent isolates causing BSI. Effective antibiotics for both gram-negative & gram-positive organisms are imipenem, meropenem and piperacillin-tazobactam followed by amikacin; vancomycin & clindamycin for gram-positive organisms. To curb the growing antimicrobial resistance that we see in this and other studies, continuous antimicrobial stewardship is necessary, else we risk failing to treat BSI.
Identification of Tumor Microenvironment-related Prognostic Genes in Colorectal Cancer based on Bioinformatic Methods
Authors: Liu Yi , Cheng Long , Li Chao , Zhang Chen , Lei Wang , Zhang Jiantao 
Published: April 2021

Abstract
Colorectal cancer (CRC) ranks fourth among the deadliest cancers globally, and the progression is highly affected by the tumor microenvironment (TME). This study explores the relationship between TME and colorectal cancer prognosis and identifies prognostic genes related to the CRC microenvironment. We collected the gene expression data from The Cancer Genome Atlas (TCGA) and calculated the scores of stromal/immune cells and their relations to clinical outcomes in colorectal cancer by the ESTIMATE algorithm. Lower immune scores were significantly related to malignant progression of CRC (stage, p=0.014; metastasis, p=0.001). We screened 292 differentially expressed genes (DEGs) by dividing CRC cases into high and low stromal/immune score groups. Functional enrichment analyses and protein-protein interaction (PPI) networks illustrated that these DEGs were closely involved in immune response, cytokine-cytokine receptor interaction, and chemokine signaling pathway. Six DEGs (FABP4, MEOX2, MMP12, ERMN, TNFAIP6, and CHST11) with prognostic value were identified by survival analysis and validated in an independent cohort (GSE17386). The six DEGs were significantly related to immune cell infiltration levels based on the Tumor Immune Estimation Resource (TIMER). The results might contribute to discovering new diagnostic and prognostic biomarkers and new treatment targets for colorectal cancer.
Topological dislocation modes in three-dimensional acoustic topological insulators
Authors: Qiu Chunyin , Ye Liping , Xiao Meng , Li Tianzi , Du Juan , Ke Manzhu , Liu Zhengyou 
Published: April 2021

Abstract
Dislocations are ubiquitous in three-dimensional solid-state materials. The interplay of such real space topology with the emergent band topology defined in reciprocal space gives rise to gapless helical modes bound to the line defects. This is known as bulk-dislocation correspondence, in contrast to the conventional bulk-boundary correspondence featuring topological states at boundaries. However, to date rare compelling experimental evidences have been presented for this intriguing topological observable in solid-state systems, owing to the huge challenges in creating controllable dislocations and conclusively identifying topological signals. Here, using a three-dimensional acoustic topological insulator with precisely controllable dislocations, we report an unambiguous experimental evidence for the long-desired bulk-dislocation correspondence, through directly measuring the gapless dispersion of the one-dimensional topological dislocation modes. Remarkably, as revealed in our further experiments, the pseudospin-locked dislocation modes can be unidirectionally guided in an arbitrarily-shaped dislocation path. The peculiar topological dislocation transport, expected in a variety of classical wave systems, can provide unprecedented control over wave propagations.
B cell depletion treatment decreases Th17 cells in patients with rheumatoid arthritis
Authors: Bounia Constantina A. , Liossis Stamatis-Nick C 
Published: April 2021

Abstract
Introduction: We aimed to evaluate for any possible effects of treatment with rituximab (RTX) on the peripheral Th17 and Treg subpopulations in patients with rheumatoid arthritis (RA).Patients and methods: We analyzed 16 patients with RA initiating RTX treatment, 11 patients with RA initiating abatacept treatment, 11 patients with RA treated with other medications, 8 patients with other autoimmune rheumatic diseases initiating RTX, and 14 healthy volunteers. Th17 cells (CD4+IL23R+IL17A+) and Treg cells (CD4+CD25hiFoxP3+) were evaluated flow-cytometrically.Results: Th17 cells from patients treated with RTX decreased significantly at weeks 8 and 16 (mean ± SEΜ: 3.01% ± 0.54℅ CD4+ cells at week 0 vs. 1.53% ± 0.24℅ at week 8 vs 1.10% ± 0.20℅ at week 16, p = 0.0004). Reductions of Th17 cells were evident in:clinical responders (DAS28 score ≤ 3.2), ACPA (+) and RF (-) patients; circulating Tregs remained stable. Th17 and Tregs were not affected by ABA treatment or by changes in disease activity. Tregs, but not Th17 cells, decreased following treatment with RTX in patients with other autoimmune diseases (0.75% ± 0.16% at week 0 vs. 0.43% ± 0.16% at week 8, p = 0.033).Conclusion: RTX-induced B cell depletion results in a significant reduction of circulating Th17 cell percentages, whereas it has no effect on Tregs of patients with RA. This reduction of Th17 cells was evident particularly in responders to RTX treatment, ACPA+ and RF (-) patients with RA.
Scutellarin alleviates type 2 diabetes (HFD/low dose STZ)- induced cardiac injury through modulation of oxidative stress, inflammation, apoptosis and fibrosis in mice
Authors: Huo Yan , Mijiti Abudureheman , Cai Ruonan , Gao Zhaohua , Aini Maierpu , Mijiti Abudukadier , Wang Zhaoling , Qie Rui 
Published: April 2021

Abstract
Background: Diabetes is a serious global health concern which severely affected public health as well as socio-economic growth worldwide. Scutellarin (SCU), a bioactive flavonol is known for its efficacious action against a range of ailments including cardiovascular problems. The present study conducted to find out possible protective effect and its associated mechanisms of SCU on experimental type 2 diabetes-induced cardiac injury.Methods: Type 2 diabetes was induced by treating animals with high fat diet for 4 weeks and a single intraperitoneal dose (35 mg/kg body weight) of streptozotocin and diabetic animals received SCU (10 or 20 mg/kg/day) for 6 weeks.Results: SCU attenuated type 2 diabetes-induced hyperglycemia, body weight loss, hyperlipidemia, cardiac functional damage with histo-pathological alterations and fibrosis. SCU treatment to type 2 diabetic mice exacerbated oxidative stress, inflammatory status and apoptosis in heart. Furthermore, the underlying mechanisms for such mitigation of oxidative stress, inflammation and apoptosis in heart involved modulation of Nrf2/Keap1 pathway, TLR4/MyD88/NF-κB mediated inflammatory pathway and intrinsic (mitochondrial) apoptosis pathway, respectively.Conclusions: The current findings suggest that SCU is effective in protecting type 2 diabetes-induced cardiac injury by attenuating oxidative stress and inflammatory responses and apoptosis and it is also worth considering the efficacious potential of SCU to treat diabetic cardiomyopathy patients.
Identification of a Novel SARS-CoV-2 Strain with Truncated Protein in ORF8 Gene by Next Generation Sequencing
Authors: DeRonde Stephanie , Deuling Hannah , Parker Jayme , Chen Jack 
Published: April 2021

Abstract
Using next generation sequencing technology, we identified a truncated protein mutation located in the ORF8 gene which is near the end of the genome from nucleotides 27,878 to 27,958. The mutation in this novel strain created a stop codon and translates to the novel truncated ORF8 protein, creating a much smaller protein than most other strains of SARS-CoV-2. The novel truncated mutation is most closely related to nine SARS-CoV-2 strains found in Washington state. Our results show a novel strain of SARS-CoV-2 with a truncated ORF8 gene. This shortens the translated ORF8 protein. The effects of ORF8 protein and its functions are still uncertain but a truncated ORF8 could affect antibody response, severity of infection and inflammatory response.
Anti-inflammatory Effect of Lactobacillus Plantarum IDCC 3501 and Its Safety Evaluation
Authors: Yang Soo-Yeon , Chae Seung A , Bang Won Yeong , Ban O-Hyun , Kim Soo-Jung , Jung Young Hoon , Yang Jungwoo 
Published: April 2021

Abstract
This study investigated the anti-inflammatory activity of L. plantarum IDCC 3501 isolated from kimchi (Korean fermented food) and its safety. When lipopolysaccharide (LPS)-induced RAW 264.7 macrophages were treated with cell-free supernatant from L. plantarum IDCC 3501, the mRNA expression level of inflammatory markers (i.e., TNF-α, IL-1β, and IL-6) was significantly reduced. The decreased cell viability by LPS was recovered and NO production in LPS-induced cell was also decreased. The genes responsible for antibiotic resistance and virulence were not detected from the genome analysis of this strain. Consistent with this, minimal inhibitory concentrations against various antibiotics, biogenic amines and D-lactate production, as well as enzymatic and hemolysis activities indicated that L. plantarum IDCC 3501 did not produce any harmful compounds during fermentation. Also, no acute toxicity and mortality were observed in a murine mouse model when feeding with L. plantarum IDCC 3501. Based on our findings, L. plantarum IDCC 3501 is safe and beneficial for human consumption.
Improved Prognostic Stratification of Patients With pN3b Oral Cavity Cancer Based on Maximum Standardized Uptake Value of Metastatic Nodes, Lymph Node Ratio, and Level of Cervical Nodal Metastases
Authors: Cheng Nai-Ming , Kang Chung-Jan , Tsai Chi-Ying , Yang Lan-Yan , Lee Li-Yu , Lin Chien-Yu , Hsueh Chuen , Fan Kang-Hsing , Wang Hung-Ming , Hsieh Chia-Hsun , Ng Shu-Hang , Yeh Chih-Hua , Lin Chih-Hung , Tsao Chung-Kan , Fang Tuan-Jen , Huang Shiang-Fu , Lee Li-Ang , Fang Ku-Hao , Wang Yu-Chien , Lin Wan-Ni , Hsin Li-Jen , Yen Tzu-Chen , Liao Chun-Ta 
Published: April 2021

Abstract
Objective
We sought to improve the prognostic stratification of patients with pN3b oral cavity squamous cell carcinoma (OCSCC) through a combined analysis of FDG-PET parameters and clinicopathological risk factors (RFs).
Methods
Complete data on maximum standardized uptake values derived from FDG-PET of neck metastatic nodes (SUV-nodal-max) and clinicopathological RFs were available for 257 patients with pN3b disease. Participants with pN0/pN1/pN2 (n = 1318/199/213) disease were included for comparison purposes.
Results
Using the 5-year disease-free survival (DFS) rate as the outcome of interest, the optimal cutoff points for SUV-nodal-max and lymph node ratio (LNR) were 15.9 and 0.17, respectively. After stratification with SUV-nodal-max and clinicopathological RFs, the 5-year DFS rates for patients with pN3 disease were as follows: SUV-nodal-max < 15.9 (n = 226) versus SUV-nodal-max ≥ 15.9 (n = 31), 49%/21%, p = 0.000003; LNR < 0.17 (n = 230) versus LNR ≥ 0.17 (n = 27), 49%/17%, p = 0.000117; absence (n = 230) versus presence (n = 27) of neck level IV/V metastases, 49%/15%, p = 0.000004. Multivariable analyses revealed that SUV-nodal-max ≥ 15.9, LNR ≥ 0.17, and the presence of level IV/V metastases were independent prognosticators for 5-year distant metastases (DM), DFS, disease-specific survival (DSS) and overall survival (OS) rates. Based on these variables, we devised a scoring system that identified three distinct prognostic subgroups of low (score 0, n = 190), intermediate (score 1, n = 51), and high (scores 2 − 3, n = 16) risk. The 5-year rates of pN0/pN1/pN2/pN3b of our cohort and the low/intermediate/high risk subgroups of pN3b were as follows: DM, 3%/12%/20%/38% and 31%/52%/89%; DFS, 83%/72%/65%/46% and 54%/26%/0%; DSS, 92%/79%/71%/52% and 59%/36%/8%; OS, 81%/62%/54%/38% and 42%/31%/6%, respectively; all p < 0.001.
Conclusion
A scoring system based on maximum SUV-nodal, LNR, and level IV/V metastases helps improve the prognostic stratification of OCSCC patients with pN3 disease.
Effects of probiotics supplementation on placental microbiome in healthy women undergoing spontaneous delivery
Authors: Yang Ping , Li Zhe , DENG TYE KIAN , Lu Tong , Chen Yuyi , He Zonglin , Zhou Juan , Xiao Xiaomin 
Published: April 2021

Abstract
PurposeTo investigate the effect of orally supplemented probiotic on term placental microbiota and provide possible evidences for clinical management of pregnant women.MethodsA population-based cohort of specimens were collected from 37 healthy nulliparous pregnant women who underwent systemic examination. The pregnant women were divided randomly into probiotics group and control group. We collected placental specimens during spontaneous delivery at term. The placental samples were taken for analyzing microbiome with the 16S rRNA amplicon sequencing of V4 region.ResultsThere were no significant differences between two groups in clinical characteristics. The placental microbiota from normal vaginal delivery were composed of Bacteroides, Lactobacillus and Ralstonia. The relative abundant of Prevotella_9, Faecalibacterium, and Escherichia_Shigella etc. in probiotic group was significantly higher than that control group(p<0.05). Probiotics supplementation could affect the network structure of placental microbiota.ConclusionsThe characteristics of the placental microbiome changed after probiotics supplementation and the network structure of interaction tended to be loose. The probiotic supplementation may be useful in regulating the interaction network of placental microbiota.
Medical Treatments for Idiopathic Pulmonary Fibrosis: a Protocol for a Systematic Review and Network Meta-analysis
Authors: Pitre Tyler , Mah Jasmine , Cui Sonya , Zhang Melanie C. , Husnudinov Renata , Khalid Faran , Helmeczi Wryan , Su Johnny , Banfield Laura , Jones Aaron 
Published: April 2021

Abstract
Background: Idiopathic pulmonary fibrosis (IPF) is a respiratory disorder of unknown etiology with a poor prognosis. There are novel therapies that have been studied in randomized controlled trials since the last network meta-analysis that may be of interest to academics and clinicians.Methods: We will perform a network meta-analysis on eligible randomized controlled trials of patients with IPF. We intend to search MEDLINE, EMBASE, Cochrane and clinicaltrials.org in order to complete a comprehensive search for adult IPF patients being treated with at least one of 21 of the selected medical therapies. A team will screen and extract eligible trials. We will perform Bayesian random-effects network meta-analysis. We will use GRADE and RoB 2.0 to assess the certainty and quality of the evidence. Discussion: There is a need for an updated meta-analysis on IPF medical therapies, including novel medical therapies. We intend on studying up to 21 medical therapies in the network meta-analysis to provide the most accurate and updated summary of the evidence for IPF treatments. Systematic review registrations: https://osf.io/afbhd/
Fungi in the Antarctic cryosphere: using DNA metabarcoding to reveal fungal diversity in glacial ice from the Antarctic Peninsula region
Authors: de Menezes Graciéle , Câmara Paulo , Pinto Otávio , Convey Peter , Carvalho-Silva Micheline , Simões Jefferson , Rosa Carlos , Rosa Luiz 
Published: April 2021

Abstract
We assessed fungal diversity present in glacial of the Antarctic Peninsula using DNA metabarcoding through high throughput sequencing (HTS). We detected a total of 353,879 fungal DNA reads, representing 94 genera and 184 taxa, in glacial ice fragments obtained from seven sites in the north-west Antarctic Peninsula and South Shetland Islands. The phylum Ascomycota dominated the sequence diversity, followed by Basidiomycota and Mortierellomycota. Penicillium sp., Cladosporium sp., Penicillium atrovenetum, Epicoccum nigrum, Pseudogymnoascus sp. 1, Pseudogymnoascus sp. 2, Phaeosphaeriaceae sp. and Xylaria grammica were the most dominant taxa, respectively. However, the majority of the fungal diversity comprised taxa of rare and intermediate relative abundance, predominately known mesophilic fungi. High indices of diversity and richness were calculated, along with moderate index of dominance, which varied among the different sampling sites. Only 26 (14%) of the total fungal taxa detected were present at all sampling sites. The identified diversity was dominated by saprophytic taxa, followed by known plant and animal pathogens and a low number of symbiotic fungi. Our data suggest that Antarctic glacial ice may represent a hotspot of previously unreported fungal diversity; however, further studies are required to integrate HTS and culture approaches to confirm viability of the taxa detected.
Factors Associated With Malaria Vaccine Uptake in Sunyani Municipality, Ghana
Authors: Tabiri Dennis , Ouédraogo Jean Claude Romaric Pingdwindé , Nortey Priscilla 
Published: April 2021

Abstract
Introduction: Malaria has and continues to be a major disease of public health concern affecting several million people worldwide. WHO started a pilot study on a malaria vaccine (RTS,S) in Ghana and two other countries in 2019. This study aimed at assessing the factors associated with uptake of the vaccine in the Sunyani Municipality of Ghana.Methods: The study was a cross-sectional study employing a quantitative approach. Stratified sampling technique was used to select respondents. A structured questionnaire was administered to parents/caregivers with children eligible to have taken the first three doses of the malaria vaccine by December 2019. The Child Welfare Clinic (CWC) cards of the eligible children were also inspected. Ordinal logistic regression analysis was done to determine the association between the independent variables and full vaccine uptake.Results: Uptake of RTS,S 1 was 94.1%. However, this figure reduced to 90.6% for RTS,S 2, and 78.1% for RTS,S 3. Children with a parent who had been educated up to the tertiary level had 4.72 [AOR: 4.72, 95%CI: 1.27 – 17.55] increased odds of full uptake as compared to those who completed secondary education. Parents whose children had experienced fever as an adverse reaction were more likely to send their kids for the malaria vaccine as compared to those who children had ever suffered abscess as an adverse reaction [AOR: 2.27, 95%CI: 1.13 – 5.10]. Children with parents who thought vaccines were becoming too many for children had 71% [AOR: 0.29, 95%CI: 0.14 – 0.61] reduced odds of full uptake as compared to those who thought otherwise.Conclusion: Uptake of RTS,S 1 and RTS,S 2 in Sunyani Municipality meets WHO’s target coverage for vaccines, however, RTS,S 3 uptake does not. Furthermore, there is a growing perception amongst parents/caregivers that vaccines are becoming too many for children which negatively affects uptake.
Rapid Morphologic and Molecular Activation of Microglial Cells by Stimulation of the P2X7 Receptor Correlates with Neuron Loss
Authors: Campagno Keith E , Lu Wennan , Jassim Assraa Hassan , Albalawi Farraj , Cenaj Aurora , Tso Huen-Yee , Clark Sophia P , Puttipong Sripinun , Gómez Néstor Más , Mitchell Claire H 
Published: April 2021

Abstract
Background: The endogenous signals leading to microglial activation represent central components of neuroinflammatory cascades. Given ATP release accompanies mechanical strain to neural tissue, and the P2X7R for ATP is expressed on microglial cells, we examined the morphological and molecular consequences of P2X7R stimulation in vivo and in vitro in detail to enhance understanding of the response. Methods: IL-1β release was determined with ELISA. Expression of mRNA used qPCR. ATP release was determined with the luciferin/luciferase assay while fura-2 indicated cytoplasmic calcium. Microglial migration used Boyden chambers. Morphological changes were quantified from Iba1-immunostained cells. Results: Sholl analysis of Iba1-stained cells showed retraction of microglial ramifications one day after injection of P2X7R agonist BzATP into mouse retinae. Mean branch length also decreased, while cell body size and expression of Nos2, Tnfa, Arg1, Chil3 increased. BzATP induced similar morphological changes in ex vivo tissue isolated from Cx3CR1-GFP mice, suggesting cell recruitment was unnecessary. Primary microglial cultures were developed to investigate the autonomous nature of the response. Isolated microglial cells expressed P2X7R, while increased intracellular Ca 2+ triggered by BzATP and blocked by antagonist A839977 confirmed functional expression. BzATP induced process retraction and cell body enlargement within minutes in isolated microglial cells, and increased expression of Nos2 and Arg1 . BzATP both increased expression of IL-1β, and triggered a substantial release, suggesting P2X7R both primes and activates the NLRP3 inflammasome. ATP increased microglial migration, but this required P2Y12R, not P2X7R involvement. As ATP release often accompanies mechanical strain, responses to intraocular pressure elevation were determined. Transient elevation increased ATP release and led to microglial process retraction, cell body enlargement and gene upregulation resembling the responses to BzATP injection. These pressure-dependent changes to microglia were reduced in P2X7R -/- mice. Critically, the loss of retinal ganglion cell neurons accompanying increased pressure was correlated with microglial activation in C57Bl/6J, but not P2X7R -/- mice.Conclusions: P2X7R stimulation induced morphological and molecular markers of activation in retinal microglial cells in vivo and in vitro , affecting IL-1β release and rapid process retraction but not cell migration. Parallel responses accompanied transient pressure elevation, suggesting ATP release and P2X7R stimulation contribute to the microglial response to rising pressure.