bluuebunny/crossref_metadata_2025_split huggingface dataset:
Bradymonabacteria, a novel bacterial predator group with versatile survival strategies in saline environments
Authors: Mu Da-Shuai , Wang Shuo , Liang Qi-Yun , Du Zhao-Zhong , Tian Renmao , Ouyang Yang , Wang Xin-Peng , Zhou Aifen , Gong Ya , Chen Guan-Jun , Nostrand Joy Van , Yang Yunfeng , Zhou Jizhong , Du Zongjun 
Published: March 2020

Abstract
Background: Bacterial predation is an important selective force in microbial community structure and dynamics. However, only a limited number of predatory bacteria have been reported, and their predatory strategies and evolutionary adaptations remain elusive. We recently isolated a novel group of bacterial predators, Bradymonabacteria, representative of the novel order Bradymonadales in δ- Proteobacteria . Compared with those of other bacterial predators (e.g., Myxococcales and Bdellovibrionales ), the predatory and living strategies of Bradymonadales are still largely unknown.
Results: Based on individual coculture of Bradymonabacteria with 281 prey bacteria, Bradymonabacteria preyed on diverse bacteria but had a high preference for Bacteroidetes . Genomic analysis of 13 recently sequenced Bradymonabacteria indicated that these bacteria had conspicuous metabolic deficiencies, but they could synthesize many polymers, such as polyphosphate and polyhydroxyalkanoates. Dual-transcriptome analysis of cocultures of Bradymonabacteria and prey suggested a potential contact-dependent predation mechanism. Comparative genomic analysis with 24 other bacterial predators indicated that Bradymonabacteria had different predatory and living strategies. Furthermore, we identified Bradymonadales from 1552 publicly available 16S rRNA amplicon sequencing samples, indicating that Bradymonadales was widely distributed and highly abundant in saline environments. Phylogenetic analysis showed that there may be six subgroups in this order; each subgroup occupied a different habitat.
Conclusions: Bradymonabacteria have unique living strategies that differ from those of so-called “obligate” or “facultative” predators. Thus, we propose a framework to categorize the current bacterial predators into 3 groups: (i) highly prey-dependent predators, (ii) facultatively prey-dependent predators, and (iii) prey-independent predators. Our findings provide an ecological and evolutionary framework for Bradymonadales and highlight their potential ecological roles in saline environments.
In vitro and Numerical Simulation of Blood Removal from Cerebrospinal Fluid: Comparison of Lumbar Drain to Neurapheresis Therapy
Authors: Khani Mohammadreza , Sass Lucas , Sharp M. Keith , McCabe Aaron , Verbick Laura Zitella , Lad Shivanand , martin bryn 
Published: March 2020

Abstract
Background: Blood removal from cerebrospinal fluid (CSF) in post-subarachnoid hemorrhage patients may reduce the risk of related secondary brain injury. We formulated a computational fluid dynamics (CFD) model to investigate the impact of a dual-lumen catheter-based CSF filtration system, called NeurapheresisTM therapy, on blood removal from CSF compared to lumbar drain. Methods: A subject-specific multiphase CFD model of CSF system-wide solute transport was constructed based on MRI measurements. The Neurapheresis catheter geometry was added to the model within the spinal subarachnoid space (SAS). Neurapheresis flow aspiration and return rate was 2.0 and 1.8 mL/min, versus 0.2 mL/min drainage for lumbar drain. Blood was modeled as a bulk fluid phase within CSF with a 10% initial tracer concentration and identical viscosity and density as CSF. Subject-specific oscillatory CSF flow was applied at the model inlet. The dura and spinal cord geometry were considered to be stationary. Spatial-temporal tracer concentration was quantified based on time-average steady-streaming velocities throughout the domain under Neurapheresis therapy and lumbar drain. To help verify CFD results, an optically clear in vitro CSF model was constructed with fluorescein used as a blood surrogate. Quantitative comparison of numerical and in vitro results was performed by linear regression of spatial-temporal tracer concentration over 24-hours.Results: After 24-hours, tracer concentration was reduced to 4.9% under Neurapheresis therapy compared to 6.5% under lumbar drain. Tracer clearance was most rapid between the catheter aspiration and return ports. Neurapheresis therapy was found to have a greater impact on steady-streaming compared to lumbar drain. Steady-streaming in the cranial SAS was ~50X smaller than in the spinal SAS for both cases. CFD results were strongly correlated with the in vitro spatial-temporal tracer concentration under Neurapheresis therapy (R2=0.89 with +2.13% and -1.93% tracer concentration confidence interval). Conclusion: A subject-specific CFD model of CSF system-wide solute transport was used to investigate the impact of Neurapheresis therapy on tracer removal from CSF compared to lumbar drain over a 24-hour period. Neurapheresis therapy was found to substantially increase tracer clearance compared to lumbar drain. The multiphase CFD results were verified by in vitro fluorescein tracer experiments.
The spatiotemporal distribution of human brucellosis in mainland China from 2007-2016
Authors: Liang Peifeng , Zhao Yuan , Zhao Jianhua , Pan Dongfeng , Guo Zhongqin 
Published: March 2020

Abstract
Background: Despite the considerable efforts made to address the issue of brucellosis worldwide, its prevalence in dairy products continues to be difficult to estimate and represents a key public health issue around the world. The aim of the study was to understand the epidemiology of this disease in mainland China. We set out to investigate the yearly spatial distribution and possible hotspots of the disease. Methods: Human brucellosis data from mainland China between 2007 and 2016 were collected from the China Information System for Disease Control and Prevention. A geographic information system ArcGIS10.3 (ESRI, Redlands) was used to identify potential changes in the spatial and temporal distribution of human brucellosis in mainland China during the study period. These distributions were evaluated using three-dimensional trend analysis and spatial autocorrelation analyse. A gravity-center was used to analyse the migration track of human brucellosis. Results: A total of 399,578 cases of human brucellosis were reported during the 10-year study period. The monthly incidence of brucellosis in China demonstrates clear seasonality. Spring and summer are the peak seasons, while May is the peak month for brucellosis. Three-dimensional trend analysis suggests that brucellosis is on the rise from south to north, and that the epidemic situation in northern China is more severe. Between 2007 and 2016, the overall migration distance of the brucellosis incidence gravity-center was 906.43 km, and the direction was southwest. However, the overall gravity center of brucellosis was still in the northern part of China. In the global autocorrelation analysis, brucellosis in China demonstrated a non-random distribution between 2013 and 2014, with spatial autocorrelation ( Z > 1.96, P < 0.05) and a clustering trend, while no clustering trend was found from 2007 to 2012 or from 2015 to 2016. In the local autocorrelation analysis, a Low-Low cluster phenomenon was found in the south of China in 2013 and 2014. Conclusion: Human brucellosis remains a widespread challenge, particularly in northern China. The hotspots highlight potential high-risk areas which may require special plans and resources for monitoring and controlling the disease.
Cytokine profile and nitric oxide levels in peritoneal macrophages of BALB/c mice exposed to Fucose-Mannose Ligand of Leishmania infantum combined with Glycyrrhizin
Authors: Hasan Namdar Ahmadabad , shafiei reza , Reza Hatam Gholam , Reza Zolfaghari Emameh , Ashok Aspatwar 
Published: March 2020

Abstract
Background

The Fucose-Mannose Ligand (FML) of Leishmania infantum is a complex glycoprotein which does not elicit adequate immunogenicity in human. In recent years, adjuvant compounds derived from plants have been used for improving the immunogenicity of the vaccines. Glycyrrhizin (GL) is a natural triterpenoid saponin that has known immunomodulatory activities. In the present study, we investigated the effects of a co-treatment with FML and GL on the production of cytokines and nitric oxide ( NO) by macrophages, in vitro .

Methods

Lipopolysaccharide (LPS) stimulated murine peritoneal macrophages were treated with FML (5 μg/ml) of Leishmania infantum and various concentrations of GL (1 μg/ml, or 10 μg/ml or 20 μg/ml). After 48h of treatment, cell culture supernatants were recovered and the levels of TNF-α, IL-10, IL-12p70, and IP-10 were measured by sandwich ELISA and NO concentration by Griess reaction.

Results

Our results indicated that the treatment of activated macrophages with FML plus GL leads to enhanced production of NO, TNF-α, IL-12p70, and reduction of IL-10 levels in comparison with FML treatment alone.

Conclusions

We, therefore, concluded that GL can improve the immunostimulatory effect of FML on macrophages and leads to polarization of them toward an M1-like phenotype.
microRNA profiling in the Weddell Seal suggests novel regulatory mechanisms contributing to diving adaptation
Authors: Dolfin Luca Penso , Haerty Wilfried , Hindle Allyson , Palma Federica Di 
Published: March 2020

Abstract
Background. The Weddell Seal (Leptonychotes weddelli) represents a remarkable example of adaptation to diving among marine mammals. This species is capable of diving >900 m deep and remaining underwater for more than 60 minutes. A number of key physiological specializations have been identified, including the low levels of aerobic, lipid-based metabolism under hypoxia, significant increase in oxygen storage in blood and muscle; high blood volume and extreme cardiovascular control. These adaptations have been linked to increased abundance of key proteins, suggesting an important, yet still understudied role for gene reprogramming. In this study, we investigate the possibility that post-transcriptional gene regulation by microRNAs (miRNAs) has contributed to the adaptive evolution of diving capacities in the Weddell Seal.Results. Using small RNA data across 4 tissues (cortex, heart, muscle and plasma), in 3 biological replicates, we generate the first miRNA annotation in this species, consisting of 559 high confidence, manually curated miRNA loci. Evolutionary analyses of miRNA gain and loss highlight a high number of Weddell seal specific miRNAs. 416 miRNAs were differentially expressed (DE) among tissues, whereas 83 miRNAs were differentially expressed (DE) across all tissues between pups and adults and 188 miRNAs demonstrated developmental changes in specific tissues only. mRNA targets of these altered miRNAs identify possible protective mechanisms in individual tissues, particularly relevant to hypoxia tolerance, anti-apoptotic pathways, and nitric oxide signal transduction. Novel, lineage-specific miRNAs associated with developmental changes target genes with roles in angiogenesis and vasoregulatory signaling.Conclusions. Altogether, we provide an overview of miRNA composition and evolution in the Weddell seal, and the first insights into their possible role in the specialization to diving.
Clinical, biochemical and genetic analysis of a Chinese Han pedigree with holocarboxylase synthetase deficiency: a case report
Authors: Zheng Zhenzhu , Yuan Gaopin , Zheng Minyan , Lin Yiming , Zheng Faming , Jiang Mengyi , Zhu Lin , Fu Qingliu 
Published: March 2020

Abstract
Background: Holocarboxylase synthetase (HLCS) deficiency is a rare inborn disorder of biotin metabolism, which results in the defect of several biotin-dependent carboxylases and presents with metabolic ketoacidosis and skin lesions. Case presentation : In this study, we have reported a Chinese Han pedigree with HLCS deficiency diagnosed using next-generation sequencing and validated with Sanger sequencing of HLCS and BTD gene. The Chinese proband carries a common missense mutation c.1522C>T (p.Arg508Trp) in exon 9 of HLCS gene, which generates an increased K m for biotin. A novel frameshift mutation c.1006_1007delGA (p.Glu336Thrfs*15) in exon 6 of H L CS gene produces a low Vmax and is predicted to be deleterious through PROVEAN and MutationTaster. A novel heterozygous mutation c.638_642delAACAC (p.His213Profs*4) in BTD gene is also identified. Otherwise, the proband presents abnormal BAEP suggesting hearing damage in the acute episode. Conclusions: A Chinese proband carries a reported Arg508Trp variant, a novel 2-bp frameshift mutation c.1006_1007delGA (p.Glu336Thr) expanding mutational spectrum of HLCS gene, and a novel heterozygous mutation c.638_642delAACAC (p.His213Profs*4) expanding mutational spectrum of BTD gene. Furthermore, the reversible hearing damage is rarely reported in the patients with HLCS deficiency, which deserves for further discussion.
Virtual reality-based action observation facilitates acquisition of body-powered prosthetic control skills
Authors: Yoshimura Manabu , Kurumadani Hiroshi , Hirata Junya , Osaka Hiroshi , Senoo Katsutoshi , Date Shota , Ueda Akio , Ishii Yosuke , Kinoshita Seiji , Hanayama Kozo , Sunagawa Toru 
Published: March 2020

Abstract
Background Regular body-powered prosthesis (bp-prosthesis) training often facilitates acquisition of skills through repeated practice but requires adequate time and motivation. Therefore, if there are auxiliary tools, such as indirect training, skill acquisition may be easy. In this study, we examined the effects of action observation (AO) using virtual reality (VR) as an auxiliary tool. We examined two different modalities during AO, VR and tablet device (Tab), and two perspectives, first- and third-person perspectives. This study aimed to examine whether AO training using VR is effective in acquiring bp-prosthetic control skills in the short term. Methods Forty healthy right-handed participants simulated bp-prosthesis with the non-dominant hand. They were divided into five groups with different interventions and displays for AO: first-person perspective on VR (VR1st), third-person perspective on VR (VR3rd), first-person perspective on Tab (Tab1st), third-person perspective on Tab (Tab3rd), and control group (Con) without AO. Participants of VR1st, VR3rd, Tab1st, and Tab3rd observed the video image of experts operating prosthesis twice, 10 min each time. We evaluated the immersion during the video observation using the Visual Analog Scale. Prosthetic control skills were evaluated using the box and block test (BBT) and bowknot task (BKT). Results In BBT, no significant enhancements of prosthetic control skills between groups were found. In contrast, the BKT change rates of prosthetic control skills in VR1st and VR3rd were significantly higher than those in Con (p < 0.001). Additionally, immersion scores of VR1st and VR3rd were higher than those of Tab3rd (p < 0.05), and there was a significant negative correlation between immersion and BKT change rate (Spearman’s rs = -0.47, p < 0.01). Conclusions In BKT (bilateral manual dexterity), VR video viewing led to significantly better short-term prosthetic control acqusition than Con. Additionally, it was suggested that the higher the immersion, the shorter the BKT task execution time. Our findings suggest that VR-based AO training is effective in acquiring bp-prosthetic control in the short term. Especially, it is effective for bilateral prosthetic control, which is necessary in the daily life of upper limb amputees.
SMAFIRA-c: A benchmark text corpus for evaluation of approaches to relevance ranking and knowledge discovery in the biomedical domain
Authors: Butzke Daniel , Dulisch Nadine , Dunst Sebastian , Steinfath Matthias , Neves Mariana , Mathiak Brigitte , Grune Barbara 
Published: March 2020

Abstract
Background The engineering of elaborate and innovative tools to navigate the ever growing biomedical knowledge base, instanced in PubMed/Medline, must be guided by genuine case studies addressing `real world´ user needs. Furthermore, algorithm-based predictions regarding `similarity´, `relatedness´ or `relevance´ of pieces of information (e.g. relevance ranking) should be transparent and comprehensible to users. Results We here present a corpus of abstracts (n = 300) annotated on document level representing three case studies in the experimental biomedical domain. The SMAFIRA corpus mirrors `real-world´ information retrieval needs, i.e. the identification of potential alternatives to given animal experiments that support `equivalent´ scientific purposes while using basically different experimental methodology. Since in most cases not even the authors of `relevant´ research papers are aware of such a possible implication of their experimental approaches, our case studies actually illustrate knowledge discovery. Annotation of abstracts (regarding `equivalence´) was conducted by one researcher with broad domain knowledge (in one case study supported by a second opinion from a domain expert) and was informed by a newly created model describing distinguishable stages in experimental biomedicine. Furthermore, such stages were linked to generic scientific purposes. This perspective thus may share some commonalities with topic modelling approaches. Annotation of `relevance´ (i.e. `equivalence´ of scientific purpose plus alternative methodology) relied on expert knowledge in the domain of animal use alternatives. The case studies were used for an evaluation of rankings which were provided by the `similar articles´ algorithm employed in PubMed. Conclusions Building on approved techniques utilized in the domain of intellectual property, we have adapted the concept of `equivalence´ to support a transparent, reproducible and stringent comparison of biomedical textual documents with regards to the implied scientific objectives. This concept may allow for text mining with improved resolution and may aid the retrieval of appropriate animal use alternatives. Computer science researchers in the field of biomedical knowledge discovery may also use our corpus, which is designed to grow essentially in the near future, as a reliable and informative benchmark for the evaluation of algorithms supporting such a goal. Annotations are available from GitHub.
Markers of remodeling in subcutaneous adipose tissue are strongly associated with overweight and insulin sensitivity in healthy non-obese men
Authors: Åkra Sissel , Aksnes Tonje A. , Flaa Arnljot , Eggesbø Heidi B. , Opstad Trine Baur , Njerve Ida U. , Seljeflot Ingebjørg 
Published: March 2020

Abstract
Background Alteration in extracellular matrix (ECM) in adipose tissues (AT) has been associated with insulin resistance, diabetes and obesity. Aim To investigate whether selected biomarkers of ECM remodeling in AT associate with the amount and distribution of abdominal AT and with insulin sensitivity and other glucometabolic variables. Materials and Methods Subcutaneous AT and fasting blood samples were collected in 103 middle-aged healthy non-obese men. Gene expression in AT was determined by RT-PCR and distribution of AT by computed tomography, separated into subcutaneous, deep subcutaneous and visceral AT. Circulating levels were determined by ELISA, and insulin sensitivity was measured by glucose clamp technique, assessing glucose disposal rate (GDR). Results Metalloproteinase (MMP)-9, tissue inhibitor of MMP (TIMP)-1 and plasminogen activator inhibitor (PAI)-1 expression in AT correlated significantly to the amount of AT in all compartments (r s =0.41-0.53, all p ≤0.01), and to insulin sensitivity, insulin, C-peptide, waist circumference and body mass index (BMI) (r s =0.25–0.57, all p ≤0.05). When dichotomizing the glucometabolic variables at median levels the expression of MMP-9 was 5.3 fold higher in subjects with insulin sensitivity below median (GDR<6.3mg/kg/min) ( p =0.002) and 3.1 fold higher in subjects with BMI above median level (>23.5kg/m 2 ) ( p =0.013). Galectin-3 did not associate with the amount of AT, but inversely with insulin and c.peptide ((p<0.01m both). Conclusion In our healthy non-obese middle-aged population AT-expressed genes, central in remodeling of ECM, associated strongly with the amount of abdominal AT, overweight and insulin sensitivity, indicating AT-remodeling to be important also in non-obese individuals. The remodeling process seems furthermore to play a central role for glucometabolic disturbances.
Isolated meniscal ramp lesion without obvious ACL rupture
Authors: Jiang Jun , Ni Lei , Chen Jian 
Published: March 2020

Abstract
Background To study isolated meniscal ramp lesion without obvious ACL rupture, analysis its clinical characteristics and evaluate clinical effect of all-inside horizontal mattress suture. Methods From 2015-2017, there are 20 isolated meniscal ramp lesion patients without obvious ACL rupture in our hospital. These isolated ramp lesions were arthroscopically repaired through all-inside horizontal mattress suturing method with 12 0 Mitek Omnispan meniscal repairing system. MRI was performed preoperatively and postoperatively 3 months later during follow-up. The Tegner-lysholm score and VAS score were recorded preoperatively and postoperatively at 2 years follow-up. T-test was performed to detect statistical significance. Results MRI postoperatively 3 months later shows healing of the isolated ramp lesion. Postoperatively at 2 years follow-up, VAS score was significantly decreased and Tegner-lysholm score was significantly raised comparing preoperatively. All patients recover their knee function without pain, including walking, stairs climbing and descending, squatting et al. Conclusion Isolated meniscal ramp lesion without obvious ACL rupture may exist because of ACL longitudinal splits. Through all-inside horizontal mattress suturing method with 12 0 Mitek Omnispan meniscal repairing system, isolated ramp lesion can be repaired through routine anterolateral and anteromedial portal.
Risk of opportunistic infections in patients with rheumatoid arthritis initiating abatacept: cumulative clinical trial data
Authors: Simon Teresa A , Dong Lixian , Winthrop Kevin L. 
Published: March 2020

Abstract
Background : To evaluate incidence of opportunistic infections (OIs) in patients with rheumatoid arthritis (RA) treated with abatacept in clinical trials. Methods : This pooled analysis of 16 randomized, double-blind/open-label trials, with ≥1 abatacept (intravenous or subcutaneous) arm, and with/without placebo control covered cumulative (controlled short-term and open-label long-term) abatacept exposure periods. OIs were analyzed separately in controlled (abatacept and placebo individually) and cumulative periods. OIs were identified using a prespecified list; events were independently adjudicated. Unadjusted incidence rates (IRs; per 100 patient-years) with 95% confidence intervals (CIs) were calculated. Results : In cumulative periods, 7,044 patients received abatacept, with mean (standard deviation) duration of exposure of 36.9 (26.2) months (21,335 patient-years of exposure). IRs (95% CI) of OIs for abatacept were low in both controlled (0.17 [0.05–0.43]), placebo (0.56 [0.22–1.15]), and cumulative (0.21 [0.15–0.28]) periods. There was 1 case of tuberculosis in both the abatacept (IR [95% CI]: 0.04 [0.00-0.24]) and placebo (IR [95% CI]: 0.08 [0.00-0.44]) groups during the controlled periods; 16 verified tuberculosis cases (IR [95% CI]: 0.08 [0.05-0.12]) were reported in the cumulative period. Herpes zoster was reported numerically more often with abatacept (IR 1.9 [1.4–2.5]), versus placebo (1.7 [1.1–2.6]) in the controlled periods; within the cumulative period, herpes zoster IR (95% CI) was 1.53 (1.36–1.71) for abatacept-treated patients. Conclusion : In controlled periods of the clinical trials, abatacept-treated patients had similarly low rates of OIs compared with placebo-treated patients. Overall, OI rates were similar among abatacept-treated patients in the controlled and cumulative periods.