bluuebunny/crossref_metadata_2025_split huggingface dataset:
Haemosporidioses in wild Eurasian blackbirds (Turdus merula) and song thrushes (T. philomelos): an in situ hybridization study with emphasis on exo-erythrocytic parasite burden
Authors: Himmel Tanja , Harl Josef , Pfanner Simone , Nedorost Nora , Nowotny Norbert , Weissenböck Herbert 
Published: January 2020

Abstract
Background Passerine birds are frequently infected with diverse haemosporidian parasites. While infections are traditionally considered benign in wild birds, recent studies demonstrated mortalities of passerine species due to exo-erythrocytic development of the parasites, which can damage organs in affected hosts. However, exo-erythrocytic development remains insufficiently investigated for most haemosporidian species and thus little is known about the virulence of tissue stages in wild passerine birds. The aim of the present study was to investigate natural haemosporidian infections in deceased Eurasian blackbirds (Turdus merula) and song thrushes (Turdus philomelos) and to determine parasite burden and associated histological effects. Methods For molecular analysis, blood and tissue samples from 306 thrushes were screened for Plasmodium, Haemoproteus and Leucocytozoon parasites by nested PCR. For the detection of parasite stages in organ samples, tissue sections were subjected to chromogenic in situ hybridization (CISH) using genus- and species-specific probes targeting the rRNAs of parasites. Exo-erythrocytic parasite load was semi-quantitatively assessed and histological lesions were evaluated in haematoxylin-eosin-stained sections. Results By PCR, 179 of 277 Eurasian blackbirds and 15 of 29 song thrushes were positive for haemosporidians. Parasites of all three genera were detected, with Plasmodium matutinum LINN1 and Plasmodium vaughani SYAT05 showing the highest prevalence. CISH revealed significant differences in exo-erythrocytic parasite burden between lineages in Eurasian blackbirds, with P. matutinum LINN1 frequently causing high exo-erythrocytic parasite burdens in various organs that were associated with histological alterations. Song thrushes infected with P. matutinum LINN1 and birds infected with other haemosporidian lineages showed mostly low exo-erythrocytic parasite burdens. Two Eurasian blackbirds infected with Leucocytozoon sp. TUMER01 showed megalomeronts in various organs that were associated with inflammatory reactions and necroses. Conclusion This study suggests that P. matutinum LINN1, a common lineage among native thrushes, regularly causes high exo-erythrocytic parasite burdens in Eurasian blackbirds, which may result in disease and mortalities, indicating its high pathogenic potential. The findings further illustrate that the same parasite lineage may show different levels of virulence in related bird species which should be considered when assessing the pathogenicity of haemosporidian parasite species. Finally, the study provides evidence of virulent Leucocytozoon sp. TUMER01 infections in two Eurasian blackbirds caused by megalomeront formation.
Existence and possible roles of independent non-CpG methylation in mammalian brain
Authors: Lee Jong-Hun , Saito Yutaka , Park Sung-Joon , Nakai Kenta 
Published: January 2020

Abstract
Background DNA methylations at non-CpG sites (mCpHs) yield weak enrichment signals and co-localize with methylated CpGs (mCpGs). Accordingly, they are thought to represent byproducts of hyperactive methyltransferases. However, recent studies revealed that mCpHs are highly cell type-specific and associated with cellular functions in mammal, although their distributional and functional dependency to mCpGs remains to be elucidated.Results Through computational analysis of a large publicly available DNA methylation dataset from human and mouse cells, we revealed that mCpHs tend to co-localize with mCpGs in pluripotent stem cells but not in brain cells. A systematic investigation using an empirical hidden Markov model confirmed that there are genomic regions where CpGs and CpHs are differentially methylated in the brain cells (~25%). Remarkably, the regions were frequently located in putative enhancers, and mCpHs within the enhancers were greatly increased as brain aged. We detected 1669 hyper-mCpH enhancers functionally enriched to immune system development, aberration of which can lead to neuro-inflammation and neuro-degeneration. Conclusions In mammalian brain cells, there are genomic regions where CpH alone is methylated (or de-methylated). The mCpHs are accumulated in enhancers as brain aged, potentially associated to neuro-inflammation and degeneration. Altogether, this study provides insight into the roles of non-CpG methylation as an epigenetic code in the genomes of mammalian brain cells.
The high resistance of bacteria to clindamycin and cefepime: a call to revisit antibiotics reserved for use at tertiary hospitals in Tanzania
Authors: Mikomangwa Wigilya P. , Bwire George M. , Kilonzi Manase , Mlyuka Hamu , Mutagonda Ritah , Kibanga Wema , Marealle Alphonce Ignace , Minzi Omary , Mwambete Kennedy D. 
Published: January 2020

Abstract
Background Antibiotic resistance poses burden to the community and health care services. Efforts are being made at local, national and global level to combat the rise of antibiotic resistance including antibiotic stewardship. Surveillance to antibiotic resistance is of importance to aid in planning and implementing infection prevention and control measures. The study was conducted to assess the resistance pattern to cefepime, clindamycin and meropenem, which are reserved antibiotics for use at tertiary hospitals in Tanzania Methods A Hospital-based antibiotic resistance surveillance was conducted between July and November 2019 using 201 consecutively selected clinical isolates at Muhimbili National Hospital and Bugando Medical Center, Tanzania. All organisms isolated were identified based on colony morphology, Gram staining and relevant biochemical tests. Antibiotic susceptibility testing was performed on Muller-Hinton agar using Kirby-Bauer disc diffusion method. Antibiotic susceptibility on the selected antibiotic discs (cefepime, clindamycin and meropenem) was performed according to the protocol by National Committee for Clinical Laboratory Standards. Results A total of 201 clinical samples were tested in this study. Urine (39.8%, n=80) and blood (35.3%, n=71) accounted for most of the collected samples followed by pus (16.9%, n=34). The overall bacterial resistance to clindamycin, cefipime and meropenem was 70.1%, 72.4% and 8.5% respectively. Most (88.9%) of Enterococcus spp were resistant to clindamycin. About 68.4% Staphylococcus aureus isolates were resistant to clindamycin whereby 56.3%, 75.6%, 93.8% and 100% of the tested Escherichia coli , Klebsiella spp , Pseudomonas aeruginosa and Enterobacter cloacae respectively, were cefepime resistant. About 8.5% of isolated Klebsiella spp were resistant and 6.4% had intermediate susceptibility to meropenem. Also, Pseudomonas aeruginosa was resistant by 31.2% and 25% had intermediate susceptibility to meropenem. All Acinetobacter baumannii and Proteus spp (both 100.0%, n=4) were susceptible to meropenem. Conclusion The overall bacterial resistance to clindamycin and cefepime is high and low in meropenem. Henceforth, culture and susceptibility results should be used to guide the use of these antibiotics. Antibiotics with low resistance rate should be introduced to the reserve category and continuous antibiotic surveillance is warranted.
Risk of multi-drug resistant Campylobacter spp. and residual antimicrobials at poultry farms and live bird markets in Bangladesh
Authors: Neogi Sucharit Basu , Islam Md. Mehedul , Islam SK Shaheenur , Akhter A.H.M. Taslima , Sikder Md. Mahmudul Hasan , Yamasaki Shinji , Kabir S. M. Lutful 
Published: January 2020

Abstract
Background: Understanding potential risks of multi-drug resistant (MDR) pathogens from the booming poultry sector is a crucial public health concern. Campylobacter spp. are among the most important zoonotic pathogens associated with MDR infections in poultry and human. This study systematically examined potential risks and associated socio-environmental factors of MDR Campylobacter spp. in poultry farms and live bird markets (LBMs) of Bangladesh. Methods: Microbial culture and PCR-based methods were applied to examine the occurrence and MDR patterns of Campylobacter spp. at hatcheries (n = 33), broiler farms (n = 122) and LBMs (n = 69). Antimicrobial residues in broiler meat and liver samples (n = 50) were detected by advanced chromatographic techniques. A questionnaire based cross-sectional survey was conducted on socio-environmental factors. Results: In poultry farms, Campylobacter spp. was primarily found in broiler cloacal swab (21/49, 43%), followed by drinking water (8/24, 33%), and meat (8/28, 29%) samples of broilers. Remarkably, in live bird markets, Campylobacter spp. was detected in higher prevalence in broiler meat (14/26, 54%), which could have an association with bacterial contamination in drinking water (11/21, 52%) and floor (9/21, 43%). Representative isolates (n = 71) were differentiated into two species: Campylobacter jejuni (66%) and Campylobacter coli (34%). Majority of C. jejuni (33/47, 70%) and C. coli (14/24, 58%) strains were observed to be MDR, showing resistance to amoxycilin, tetracycline and erythromycin, and additionally ciprofloxacin, norfloxacin, streptomycin, and azithromycin. Residual antimicrobials, including oxytetracycline, ciprofloxacin and enrofloxacin, were detected in majority of broiler liver (79%) and meat (62%) samples. Alarmingly, 33% and 19% of the liver and meat samples, respectively, contained residual antimicrobial concentration above acceptable limit. Inadequate personal and environmental hygiene, unscrupulously use of antimicrobials, improper waste disposal, and lack of health surveillance and quarantine facilities of diseased birds were distinguishable risk factors, with local diversity and compound influences on MDR pathogens. Conclusion: Potential contamination sources and anthropogenic risk factors associated with the alarming occurrence of MDR Campylobacter, noted in this study, would aid in developing interventions to minimize the increasing risks of poultry-associated MDR pathogens under ‘One Health’ banner that includes poultry, human and environment perspectives.
Preparation of uniformly labelled 13C- and 15N-plants using customised growth chambers
Authors: Ceranic Asja , Doppler Maria , Büschl Christoph , Parich Alexandra , Xu Kangkang , Koutnik Andrea , Bürstmayr Hermann , Lemmens Marc , Schuhmacher Rainer 
Published: January 2020

Abstract
Background Stable isotopically labelled organisms found wide application in life science research including plant physiology, plant stress and defense as well as metabolism related sciences. Therefore, the reproducible production of plant material enriched with stable isotopes such as 13 C and 15 N is of considerable interest. A high degree of enrichment (>96 atom%) with a uniformly distributed isotope (global labelling) is accomplished by a continuous substrate supply during plant growth/cultivation. In the case of plants, 13 C-labelling can be achieved by growth in 13 CO 2(g) atmosphere while global 15 N labelling needs 15 N- containing salts in the watering/nutrient solution. Here, we present a method for the preparation of 13 C and 15 N labelled plants by the use of closed growth chambers and hydroponic nutrient supply. The method is exemplified with durum wheat.Results In total, 330 g of globally 13 C- and 295 g of 15 N labelled T. durum wheat was produced during 87 cultivation days. For this, a total of 3.88 mol of 13 CO 2(g) and 58 mmol of 15 N were consumed. The degree of enrichment was determined by LC-HRMS and ranged between 96-98 atom% for 13 C and 95-99 atom% for 15 N, respectively. Additionally, the isotopically labelled plant extracts were successfully used for metabolome-wide internal standardisation of native T.durum plants. Application of an isotope-assisted LC-HRMS workflow enabled the detection of 652 truly wheat-derived metabolites out of which 143 contain N.Conclusion A reproducible cultivation which makes use of climate chambers and hydroponics was successfully adapted to produce highly enriched, uniformly 13 C- and 15 N-labelled wheat. The obtained plant material is suitable to be used in all kinds of isotope-assisted research. The described technical equipment and protocol can easily be applied to other plants to produce 13 C-enriched biological samples when the necessary specific adaptations e.g. temperature and light regime, as well as nutrient supply are considered. Additionally, the 15 N-labelling method can also be carried out under regular glasshouse conditions without the need for customised atmosphere.
Annexin A1 peptide Ac2-26 mitigates ventilator-induced lung injury in acute respiratory distress syndrome rats by enhancing endothelial nitric oxide synthase activity
Authors: Ju Yingnan , Zhao Xiaoqing , Zhang Lili , Sun Haibin , Tai Qihang , Xu Guangxiao , Gao Wei 
Published: January 2020

Abstract
Background Mechanical ventilation is an important therapeutic strategy for supporting patients with acute respiratory distress syndrome (ARDS). However, ventilation can exacerbate lung injury and lead to ventilator-induced lung injury (VILI). This study aimed to evalaute the effect and mechanism of Annexin A1 (AnexA1) peptide Ac2-26 on VILI in ARDS rats. Methods To evalaute the effect and mechanism of Annexin A1 (AnexA1) peptide Ac2-26 on VILI in ARDS rats, Male SD rats were anesthetized, and intubated, followed by injected with vehicle as the control S group or with lipopolysaccharides (LPS) to induce ARDS. The ARD rats were ventilated, randomized and injected intravenously with vehicle, Ac2-26 or Ac2-26 and L-NIO (an inhibitor of nitric oxide synthase) as the V, VA and VA/L groups, respectively. Their arterial blood gases were analyzed longitudinally for PaO 2 /FiO 2 ratio, and the wet-to-dry lung weights and total protein concentrations in bronchoalveolar lavage fluid (BALF) were measured. The lung injury and inflammatory factors were quantified. The oxidative stress response was measured. The impact of Ac2-26 on the LPS-related cytotoxicity against A549 cells was analyzed. Results Compared with the S group, ARDS and ventilation impaired the lung function and caused lung injury in rats. Compared with V group, Ac2-26 treatment significantly ameliorated the lung function, reduced the VILI-related alveolocapillary permeability, lung injury and endothelial/epithelial cell apoptosis, oxidative stress and inflammation in VILI rats, but promoted AKT1 expression and eNOS phosphorylation, which were partially inhibited by co-treatment with L-NIO. Moreover, Ac2-26 protected against LPS-induced apoptosis of human A549 cells in vitro . Conclusions Ac2-26 effectively mitigated the severity of VILI partially by enhancing endothelial nitric oxide synthase expression in the lung of rats.
Generative Adversarial Networks for Pre-training of Medical Image Segmentation Networks
Authors: Chen Kun , Wang Manning , Song Zhijian 
Published: January 2020

Abstract
Background: Deep neural networks have been widely used in medical image segmentation and have achieved state-of-the-art performance in many tasks. However, different from the segmentation of natural images or video frames, the manual segmentation of anatomical structures in medical images needs high expertise so the scale of labeled training data is very small, which is a major obstacle for the improvement of deep neural networks performance in medical image segmentation. Methods: In this paper, we proposed a new end-to-end generation-segmentation framework by integrating Generative Adversarial Networks (GAN) and a segmentation network and train them simultaneously. The novelty is that during the training of the GAN, the intermediate synthetic images generated by the generator of the GAN are used to pre-train the segmentation network. As the advances of the training of the GAN, the synthetic images evolve gradually from being very coarse to containing more realistic textures, and these images help train the segmentation network gradually. After the training of GAN, the segmentation network is then fine-tuned by training with the real labeled images. Results: We evaluated the proposed framework on four different datasets, including 2D cardiac dataset and lung dataset, 3D prostate dataset and liver dataset. Compared with original U-net and CE-Net, our framework can achieve better segmentation performance. Our framework also can get better segmentation results than U-net on small datasets. In addition, our framework is more effective than the usual data augmentation methods. Conclusions: The proposed framework can be used as a pre-train method of segmentation network, which helps to get a better segmentation result. Our method can solve the shortcomings of current data augmentation methods to some extent.
ECG Biometrics using RNN and CNN
Authors: Belo David , Bento Nuno , Silva Hugo , Fred Ana , Gamboa Hugo 
Published: January 2020

Abstract
Background: Biometric Systems (BS) are based on a pattern recognition problem where the individual traits of a person are coded and compared. The Electrocardiogram (ECG) as a biometric emerged, as it fulfills the requirements of a BS. Methods: Inspired by the high performance shown by Deep Neural Networks(DNN), this work proposes two architectures to improve current results in both identification and authentication: Temporal Convolutional Neural Network (TCNN) and Recurrent Neural Network (RNN). The last two results weresubmitted to a simple classifier, which exploits the error of prediction of theformer and the scores given by the last. Results: The robustness and applicability of these architectures were tested onFantasia, MIT-BIH and CYBHi databases. The TCNN outperforms the RNNachieving 100%, 96% and 90% of accuracy, respectively, for identification and 0.0%, 0.1% and 2.2% equal error rate for authentication. Conclusions: When comparing to previous work, both architectures reachedresults beyond the state-of-the-art. Even though this experience was a success,the inclusion of these techniques may provide a system that could reduce thevalidation acquisition time.
Mutation Screening of DUOX2 Gene in Children with Congenital Hypothyroidism
Authors: Chen Xiao-Yu , Liu Yong , Liu Jian-Hua , Qin Xiaosong 
Published: January 2020

Abstract
Background: Congenital hypothyroidism(CH) is generally known as the most common neonatal endocrine disorder. However, the mutational spectrum of DUOX2 gene and the relationship between genotype and phenotype have not been fully established among Chinese CH patients. Therefore, The aim of this study was to screen DUOX2 mutations in Chinese patients with CH and to research the relationship between DUOX2 genotype and clinical phenotype.Methods: Eighty-six patients with CH were recruited from northeastern region of China. Peripheral venous blood samples were collected, genomic DNA was extracted , PCR and next-generation sequencing (NGS) were used to analyze all exons of DUOX2. Detailed medical data were collected, and the relationship between DUOX2 genotype and the clinical phenotype was preliminarily investigated.Results: NGS analysis of DUOX2 gene identified a total of 20 different gene variants in 26 patients(30.2%), which was consistent with the gene variants in Asian populations, among these variants 16 were known to be pathogenic or likely to be pathogenic, and four were suspected to be of uncertain significance. Three mutations (p.K530X, p.L1343F and p.R1110Q) were highly recurrent in our patient cohort. By using protein homology modeling method, the analysis of its three-dimensional structure suggested that the mutations p.336_337del and p.T1107fs caused the change of the protein.Conclusions: In our study, p.336_337del and p.T1107fs were found to be novel variants and p.K530X with the highest prevalence. Children with DUOX2 single allele heterozygous mutation or compound heterozygous mutation exhibited different morphological developments of the thyroid.
A Cost-of-Illness analysis of β-Thalassaemia major in children in Sri Lanka
Authors: Reed-Embleton Hamish , Arambepola Savinda , Dixon Simon , Maldonado Behrouz Nezafat , Premawardhena Anuja , Arambepola Mahinda , Khan Jahangir A. M. , Allen Stephen 
Published: January 2020

Abstract
Background Sri Lanka has a high prevalence of β-thalassaemia major. Clinical management is complex and long-term and includes regular blood transfusion and iron chelation therapy. The economic burden of β-thalassaemia for the Sri Lankan healthcare system and households is currently unknown. Methods A prevalence-based, cost-of-illness study was conducted on the Thalassaemia Unit, Department of Paediatrics, Kandy Teaching Hospital, Sri Lanka. Data were collected from clinical records, consultations with the head of the blood bank and a consultant paediatrician directly involved with the care of patients, alongside structured interviews with families to gather data on the personal costs incurred such as those for travel. Results Thirty-four children aged 2-17 years with transfusion dependent thalassaemia major and their parent/guardian were included in the study. The total average cost per patient year to the hospital was $US 2601 of which $US 2092 were direct costs and $US 509 were overhead costs. Mean household expenditure was $US 206 per year with food and transport per transfusion ($US 7.57 and $US 4.26 respectively) being the highest cost items. Nine (26.5%) families experienced catastrophic levels of healthcare expenditure (>10% of income) in the care of their affected child. The poorest households were the most likely to experience such levels of expenditure.
Veber’s Rules in Terahertz Light
Authors: Plinski Edward F , Plinska Stanislawa 
Published: January 2020

Abstract
Background: The Attenuated Total Reflection (ATR) technique of spectroscopy in combination using the terahertz technique is being investigated to find rotatable bonds, which are considered as one of the rules of thumb given by Veber et al.. Results: Histidine, as one of the most studied pharmacological preparations, is used in an experiment to test our research. Three rotatable bonds have been found and thus the results published in pharmaceutical data guides have been confirmed. Conclusion: The results are obtained in a terahertz spectrometer equipped with a Dove prism, where an ATR technique is applied. The samples in two forms, polycrystalline and as a solution in alcohol, are used to check the methodology. Histidine molecules, dissolved in alcohol and thus freed from intermolecular bonds, exposed the rotations around the three bonds. Thus, the validity of the ATR-THz research methodology used in the search for rotating bonds in drug candidates molecules is confirmed. The goal of the method presented in the paper is to support pharmacological research, and pharmaceutical industry, as well.