bluuebunny/crossref_metadata_2025 huggingface dataset:
SMART PARKING SYSTEM DENGAN SISTEM RESERVASI
Authors: Ramsari Nopi
Published: January 2020

Area Parkir sudah menjadi kebutuhan bagi masyarakat perkotaan, terutama dibutuhkan ditempat-tempat umum seperti mall, tempat wisata/rekreasi, bandara, perkantoran, hotel, kampus dan lain-lain. Karena terbatasnya area parkir sehingga menyebabkan pencarian area parkir sulit karana ketidaktahuan dimana tempat parkir yang tersedia karena kurangnya informasi slot parkir mana yang penuh atau kosong sehingga dapat menyebabkan kemacetan, polusi, pemborosan bahan bakar dan tentunya kadangkala banyak memakan waktu dan tenaga.

Seiring dengan kemajuan Teknologi maka terdapat sejumlah sistem yang dapat mengautomasikan pengelolaan parkir, namun hal ini masih belum diimbangi dengan manajemen dalam pencarian spot parkir karena belum adanya verifikasi pengemudi akan parkir atau tidak. Dengan menerapkan sensor RFID pada sistem parkir, sehingga sistem memberikan peringatan kepada pengemudi apabila tidak berhak untuk parkir, pengemudi dapat melakukan reservasi/pemesanan tempat parkir melalui sistem, selain itu juga sistem dapat memberikan notifikasi kepada petugas parkir.

Dengan aplikasi smartparking ini diharapkan pengguna jasa parkir dapat mengetahui lokasi slot parkir yang kosong dan dapat digunakan untuk parkir dengan cepat sehingga dapat meningkatkan efisiensi tenaga dan waktu.
ANALISA TERHADAP LAYANAN PASIEN PADA DATA WAREHOUSE RSUD DR.R. GOETENG TAROENADIBRATA PURBALINGGA MENGGUNAKAN LAPORAN OLAP DENGAN NINE-STEP METHODOLOGY
Authors: Destarini Pradika , Priyanto Agus , Febriani Atik
Published: January 2020

RSUD dr.R.Goeteng Taroenadibrata Purbalingga merupakan salah satu rumah sakit pemerintahan daerah yang sebagai pusat layanan kesehatan di Purbalingga. Setiap hari hampir ratusan pasien yang harus dilayani oleh rumah sakit tersebut, sehingga semakin bertambahnya data kunjungan pasien khususnya rawat inap dan rawat jalan yang harus dikelolapun semakin banyak. Data warehouse sendiri merupakan salah satu cara yang digunakan dalam proses analisa serta pembuatan laporan yang di butuhkan suatu perusahaan atau instansi pemerintahan pada data dengan jumlah yang banyak. Data yang digunakan dalam penelitian ini adalah data kunjungan pasien rawat jalan dan rawat inap periode tahun 2013 sampai dengan 2017. Adanya sistem laporan Online Analytical Processing (OLAP) berfungsi untuk mempermudah dan mempercepat proses pengumpulan data untuk penyajian informasi sesuai dengan kebutuhan pihak rumah sakit. Nine-Step Methodology digunakan dalam penelitian ini sebagai pengembangan data warehouse yang meliputi Pemilihan Proses, Pemilihan Grain,Identifikasi dan Penyesuaian, Pemilihan Fakta, Penyimpanan Pre-calculation di tabel fakta, Memastikan tabel dimensi, Pemilihan durasi database, Melacak perubahan dimensi secara perlahan, serta Penentuan prioritas dan model query. Hasil yang di dapat dalam penelitian ini dapat mempercepat dalam penyajian informasi sesuai kebutuhan sehingga mampu memaksimalkan dalam menganalisis informasi tersebut.
LOGIKA FUZZY SUGENO UNTUK PENGAMBILAN KEPUTUSAN DALAM PENJADWALAN DAN PENGINGAT SERVICE SEPEDA MOTOR
Authors: Saputri Ariesta Dwi , Ramadhani Rima Dias , Adhitama Rifki
Published: January 2020

Data pengguna sepeda motor tahun 2016 berdasarkan Badan Pusat Statistik terdapat 105.150.082 pengguna di Indonesia . Angka ini adalah angka yang terbanyak dari semua total kendaraan. Menurut katadata.co.id, terdapat 98.000 kali kecelakan yang terjadi pada tahun 2017. Hal ini didominasi oleh kendaraan khususnya sepeda motor. Kecelakan yang ditimbulkan disebabkan oleh kelalaian pengguna sepeda motor dalam merawat motornya tersebut. Upaya dalam mengantisipasi terjadinya kecelakaan salah satunya adalah melakukan pengecekan kendaraan bermotor secara rutin. Menurut buku panduan sepeda motor, bahwa setiap kali motor yang digunakan wajib untuk melakukan pengecekan minimal 3 bulan sekali agar motor tetap pada performa utamanya. Metode yang digunakan untuk pengambilan keputusan dalam penjadwalan dan pengingat menggunakan metode fuzzy sugeno. Fuzzy merupakan suatu cara untuk memetakan suatu ruang input ke dalam suatu ruang output . Solusi yang ditawarkan pada penelitian ini akan aplikasi mobile yang dikhususkan untuk pengguna sepeda motor dalam melakukan perawatan rutin sebagai penjadwalan dan pengingat. Hasil yang didapatkan Berdasarkan pengujian manual dan pengujian melalui system yakni 16 siap service dan 14 tidak siap service. Presentase keakuratan system dengan perhitungan manual 100% sama dengan perhitngan system. Prensentasi pengaruh terhadap perawatan motor adalah 88.27% setuju terhadap pembuatan aplikasi ini untuk perawatan motor terhadap kecelakaan motor.
Root dentine thickness of danger zone in mesial roots of mandibular first molars
Authors: Zhou Guangchao , Leng Diya , Li Mingming , Zhou Yang , Zhang Cuifeng , Sun Chao , Wu Daming
Published: January 2020

Background: Better understanding of the danger zone anatomy in mesial roots (MRs) of mandibular first molars (MFMs) may serve to decrease the risk of mishaps. This study aimed to measure the minimal distal dentine thicknesses of danger zone in MRs of MFMs in a native Chinese population using cone-beam computed tomography (CBCT).
Methods: CBCT images of 1792 MFMs from 898 Chinese patients were analyzed. The minimal distal dentine thicknesses of the mesiobuccal (MB) and mesiolingual (ML) canals below the furcation 1, 2, 3, 4, 5 mm were measured. The association between the minimal distal dentine thicknesses and the root lengths, patient’s age and gender, side were assessed.
Results: The minimal distal dentine thicknesses of MB and ML canals are located 3∼4 mm below the furcation for both men and women. There are no differences between MB and ML canals, while the minimal distal dentine thicknesses of MB and ML canals were higher in men than women ( P <0.05), except at 1 and 3 mm of ML canals ( P >0.05). The minimal distal dentine thicknesses of MB and ML canals increased with age in both men and women at each location ( P <0.05). The minimum distal dentine thickness at every location were significantly different between long teeth and short teeth both in men and women ( P < 0.05), with short teeth having the smallest mean values. There are no significant differences between two sides ( P >0.05).
Conclusions: The minimal distal dentine thicknesses of MRs in MSMs have close correlation with root length, patient’s age and gender.
Phytochemical and comparative transcriptome analyses reveal different regulatory mechanisms in the terpenoid biosynthesis pathways between Matricaria recutita L. and Chamaemelum nobile L.
Authors: tai yuling , Hou Xiaojuan , Liu Chun , Sun Jiameng , Guo Chunxiao , Su Ling , Jiang Wei , Ling Chengcheng , Wang Chengxiang , Wang Huanhuan , Pan Guifang , Si Xiongyuan , Yuan Yi
Published: January 2020

Background Matricaria recutita (German chamomile) and Chamaemelum nobile (Roman chamomile) belong to the botanical family Asteraceae. These two herbs are not only morphologically distinguishable, but their secondary metabolites – especially the essential oils present in flowers are also different, especially the terpenoids. The aim of this project was to preliminarily identify regulatory mechanisms in the terpenoid biosynthetic pathways that differ between German and Roman chamomile by performing comparative transcriptomic and metabolomic analyses. Results We determined the content of essential oils in disk florets and ray florets in these two chamomile species, and found that the terpenoid content in flowers of German chamomile is greater than that of Roman chamomile. In addition, a comparative RNA-seq analysis of German and Roman chamomile showed that 54% of genes shared >75% sequence identity between the two species. In particular, more highly expressed DEGs (differentially expressed genes) and TF (transcription factor) genes, different regulation of CYPs (cytochrome P450 enzymes), and rapid evolution of downstream genes in the terpenoid biosynthetic pathway of German chamomile could be the main reasons to explain the differences in the types and levels of terpenoid compounds in these two species. In addition, a phylogenetic tree constructed from single copy genes showed that German chamomile and Roman chamomile are closely related to Chrysanthemum nankingense. Conclusion This work provides the first insights into terpenoid biosynthesis in two species of chamomile. The candidate unigenes related to terpenoid biosynthesis will be important in molecular breeding approaches to modulate the essential oil composition of Matricaria recutita and Chamaemelum nobile.
Are Malaysian Type 2 Diabetes patients willing to be trained to speak to their offspring about risk of diabetes and preventive measures?
Authors: Badlishah-Sham Siti Fatimah , Ramli Anis Safura , Isa Mohamad Rodi , Mohd-Zaki Nurzakiah , Whitford David Leonard
Published: January 2020

Background : Offspring of diabetes patients have an absolute risk of 20-40% of developing the condition. Diabetes patients should be encouraged to speak to their offspring regarding diabetes risk and prevention strategies. The Health Belief Model conceptualises that the higher the perceived risk, the more likely an individual will modify their behaviour. The objectives of this study were to i) determine the distribution of type 2 diabetes patients regarding their willingness to accept training to speak to their offspring, ii) determine the distribution of type 2 diabetes patients regarding their willingness to accept training based on the HBM and iii) to determine the factors associated with their willingness to accept training.
Methods : This was a cross-sectional study amongst type 2 diabetes patients attending two primary care clinics in Malaysia. Sociodemographic data and knowledge of diabetes risk factors were collected. The adapted, translated and validated Diabetes Mellitus in the Offspring Questionnaire-Malay version (DMOQ-Malay) was self-administered. Statistical analysis included descriptive statistics, univariate and multiple logistic regression.
Results : A total of 425 participants were recruited. Of these, 61.6% were willing to accept training. In MLogR, six variables were found to be significantly associated with willingness to accept training. These were i) positive family history [Adj. OR 2.06 (95% CI: 1.27, 3.35)], ii) having correct knowledge that being overweight is a risk factor [Adj. OR 1.49 (95%CI: 1.01, 2.29)], iii) correctly identifying age 40 years old as a risk factor [Adj. OR 1.88 (95%CI: 1.22, 2.90)], iv) agreeing that speaking to their offspring would help them to prevent type 2 diabetes [Adj. OR 4.34 (95%: 1.07, 17.73)], v) being neutral with the statement ‘I do not have much contact with my offspring’ [Adj. OR: 0.31 (95% CI: 0.12, 0.810] and vi) being neutral with the statement ‘my offspring are not open to advice from me’ [Adj. OR: 0.63 (95% CI: 0.31, 0.84].
Conclusion : The majority of type 2 diabetes patients were willing to accept training to speak to their offspring to prevent diabetes. A training module should be designed to enhance their knowledge, attitude and skills to become family health educators.
Predicting patient outcomes in psychiatric hospitals with routine data: a machine learning approach
Authors: Wolff Jan , Gary Alexander , Jung Daniela , Normann Claus , Kaier Klaus , Binder Harald , Domschke Katharina , Klimke Ansgar , Franz Michael
Published: January 2020

Background: A common problem in machine learning applications is availability of data at the point of decision making. The aim of the present study was to use routine data readily available at admission to predict aspects relevant to the organization of psychiatric hospital care. A further aim was to compare the results of a machine learning approach with those obtained through a traditional method and those obtained through a naive baseline classifier.
Methods: The study included consecutively discharged patients between 1 st of January 2017 and 31 st of December 2018 from nine psychiatric hospitals in Hesse, Germany. We compared the predictive performance achieved by stochastic gradient boosting (GBM) with multiple logistic regression and a naive baseline classifier. We tested the performance of our final models on unseen patients from another calendar year and from different hospitals.
Results: The study included 45,388 inpatient episodes. The models’ performance, as measured by the area under the Receiver Operating Characteristic curve, varied strongly between the predicted outcomes, with relatively high performance in the prediction of coercive treatment (area under the curve: 0.83) and 1:1 observations (0.80) and relatively poor performance in the prediction of short length of stay (0.69) and non-response to treatment (0.65). The GBM performed slightly better than logistic regression. Both approaches were substantially better than a naive prediction based solely on basic diagnostic grouping.
Conclusion: The present study has shown that administrative routine data can be used to predict aspects relevant to the organisation of psychiatric hospital care. Future research should investigate the predictive performance that is necessary to provide effective assistance in clinical practice for the benefit of both staff and patients.
A maternal GOT1 novel variant associated with early-onset severe preeclampsia identified by whole-exome sequencing
Authors: Zhang Lin , Cao Zheng , Feng Fan , Xu Ya-Nan , LI LIN , Gao Hong
Published: January 2020

Background This study wants to know the genetic cause of preeclampsia (PE) which is a leading cause of maternal and perinatal death, but the underlying molecular mechanisms that cause PE remain poorly understood. Many single nucleotide polymorphisms have been identified by genome-wide association studies and were found to be associated with PE; however, few studies have used whole-exome sequencing (WES) to identify PE mutations. Methods Five patients with severe early-onset preeclampsia (EOPE) were recruited, and WES was performed on each patient. Sanger sequencing was used to confirm the potential causative genetic mutation. Results After a stringent bioinformatics analysis, a rare mutation in the GOT1 gene, c.44C>G:p.P15R, was found in one patient. Bioinformatics analysis showed that the mutation site is highly conserved across several species and was predicted to be a pathogenic mutation according to several online mutational function prediction software packages. Further structural biology homology modeling suggested that P15R would change the electric environment of enzymatic center, and might affect the binding affinity of substrate or product. Conclusion We demonstrated for the first time that the mutation in GOT1 may be associated with EOPE, the results of this study provide researchers and clinicians with a better understanding of the molecular mechanisms that underlie maternal severe EOPE.
Integrative analysis of outer membrane vesicles proteomics and whole-cell transcriptome analysis of eravacycline induced Acinetobacter baumannii strains
Authors: Kesavan DineshKumar , Vasudevan Aparna , Wu Liang , Chen Jianguo , Su Zhaoliang , Wang Shengjun , Xu Huaxi
Published: January 2020

Background Acinetobacter baumannii is a multidrug-resistant (MDR) hazardous bacterium with very high antimicrobial resistance profiles. Outer membrane vesicles (OMVs ) help directly and/or indirectly towards antibiotic resistance in these organisms. The present study aims to look on the proteomic profile of OMV as well as on the bacterial transcriptome upon exposure and induction with eravacycline, a new synthetic fluorocycline. RNA sequencing analysis of whole-cell and LC-MS/MS proteomic profiling of OMV proteome abundance were done to identify the differential expression among the eravacycline-induced A. baumannii ATCC 19606 and A. baumannii clinical strain JU0126. Results The differentially expressed genes from the RNA sequencing were analysed using R package and bioinformatics software and tools. Genes encoding drug efflux and membrane transport were upregulated among the DEGs from both ATCC 19606 and JU0126 strains. As evident with the induction of eravacycline resistance, ribosomal proteins were upregulated in both the strains in the transcriptome profiles and also resistance pumps, such as MFS, RND, MATE and ABC transporters. High expression of stress and survival proteins were predominant in the OMVs proteome with ribosomal proteins, chaperons, OMPs OmpA, Omp38 upregulated in ATCC 19606 strain and ribosomal proteins, toluene tolerance protein, siderophore receptor and peptidases in the JU0126 strain. The induction of resistance to eravacycline was supported by the presence of upregulation of ribosomal proteins, resistance-conferring factors and stress proteins in both the strains of A. baumannii ATCC 19606 and JU0126, with the whole-cell gene transcriptome towards both resistance and stress genes while the OMVs proteome enriched more with survival proteins. Conclusion The induction of resistance to eravacycline in the strains were evident with the increased expression of ribosomal and transcription related genes/proteins. Apart from this resistance-conferring efflux pumps, outer membrane proteins and stress-related proteins were also an essential part of the upregulated DEGs. However, the expression profiles of OMVs proteome in the study was independent with respect to the whole-cell RNA expression profiles with low to no correlation. This indicates the possible role of OMVs to be more of back-up additional protection to the existing bacterial cell defence during the antibacterial stress.
Community and health staff perceptions on non-communicable disease management in El Salvador Health System: a qualitative study
Authors: Vidal Nicole , León-García Montserrat , Jiménez Marta , Bermúdez Keven , De Vos Pol
Published: January 2020

Non-communicable Diseases (NCDs) are the leading cause of global mortality and disability, with a rising burden in low- and middle-income countries. Their multifactorial aetiology, and their requirement of long-term care, imply the need for comprehensive approaches. From 2009, the Ministry of Health (MoH) in El Salvador has developed a national public health system based on comprehensive primary health care. This study aims to describe the different stakeholders’ perceptions about the management of NCDs along the pathways of care in this health system. During three fieldwork periods in 2018, three complementary qualitative data collection methods were deployed and conducted in high prevalence of NCDs settings within El Salvador. First, we used illness narrative methodology to document the life histories of people living with a chronic disease and being treated in second and third level health facilities. Second, through social mapping, we analysed support-resources that NCD patients used throughout the process of their illness within the same settings. Third, semi-structured interviews were conducted in the same locations, with both chronic patients and health personnel working at different levels of the primary health care setting. Participants were recruited through purposive and snowball sampling, and a deductive approach was implemented for coding during the analysis phase. After grouping codes into potential themes, a thematic framework was elaborated through a reflexive approach and triangulation of the data. This innovative approach of combining three well-defined qualitative analysis frameworks identified key implications for the implementation of a comprehensive approach to NCDs management in resource-poor settings. The following dimensions are identified: 1) social risk factors and barriers to care; 2) patient pathways to NCDs care; 3) resources available identified through social connections mapping; 4) trust in social connections; 5) community health promotion and prevention of NCDs management. The Salvadoran public health system has been able to strengthen its comprehensive approach to NCDs, combining a clinical approach – including long term follow-up – with a preventive community-based strategy. The structural collaboration between the health system and the (self)organized community has been key to identify failings, discuss tensions and work out adapted solutions.
Informal caregivers’ views on the quality of healthcare services provided to older patients aged 80 or more in the hospital and 30 days after discharge
Authors: Lilleheie Ingvild , Debesay Jonas , Bye Asta , Bergland Astrid
Published: January 2020

Background:In the European Union (EU), informal caregivers provide 60% of all care. Informal caregiving ranges from assistance with daily activities and provision of direct care to helping care recipients to navigate within complex healthcare and social services systems. While recent caregiver surveys document the impact of informal caregivers, systematic reviews show that they have unmet needs. Because of the political desire to reduce the length of hospital stays, older patients are discharged from the hospital ‘quicker and sicker’ than before. The transition between different levels of the healthcare system and the period after hospital discharge is critical for elderly patients.Caregivers’ perspectives on the quality of older patients’ care journeys between levels of the healthcare system may provide valuable information for healthcare providers and policymakers. This study aims to explore older patient’s informal caregivers’ views on healthcare quality in the hospital and in the first 30 days after hospitalisation.Method:We conducted semi-structured individual interviews with 12 participants to explore and describe informal caregivers’ subjective experiences of providing care to older relatives. The interviews were then transcribed and analysed thematically.Results:The analysis yielded the overarching theme ‘Informal caregivers – a health service alliance – quality contributor’, which was divided into four main themes: ‘Fast in, fast out’, ‘Scant information’, ‘Disclaimer of responsibility’ and ‘A struggle to secure professional care’. The healthcare system seemed to pay little attention to ensuring mutual understandings between those involved in discharge, treatment and coordination. The participants experienced that the healthcare providers’ main focus was on the patients’ diseases, although the health services are supposed to view patients holistically.Conclusion:Based on the information given by informal caregivers, health services must take into account each person’s needs and preferences. To deliver quality healthcare, better coordination between inter-professional care teams and the persons they serve is necessary. Health professionals must strengthen the involvement of caregivers in transitions between care and healthcare. Future work should evaluate targeted strategies for formal caregivers to cooperate, support and empower family members as informal caregivers.
Patients perspective of m-health adoption factors in the developing world. Development of a Proposed framework
Authors: Addotey-Delove Michael Nii-Addotey , Scott Richard E. , Mars Maurice
Published: January 2020

Patient perceptions and experiences of mobile health (m-health) systems have been recognised as an important element to consider in the adoption of m-health based technologies. Though much research supports this, published studies that focus on m-health use by patients appear to highlight these issues in an isolated rather than holistic manner. Consequently, there is no encompassing framework that serves as a guide for effective implementation and maximum adoption of m-health from the perspective of patients in the developing world. This review documents patient adoption issues, and uses these to develop a framework of patient adoption issues for m-health in the developing world.
A structured literature search was conducted using PubMed and Scopus. For PubMed a consolidated search string combined ‘MESH’ terms and ‘All Fields’ terms for selected keywords. For Scopus an equally consolidated search string was used. The searches were restricted to articles in English during the period January 2000 - December2019 and relevant to the developing world. Duplicate articles were removed. Titles and abstracts were screened by all authors for inclusion, and those studies that met the inclusion criteria were selected for full-text review. Review and data abstraction was performed by two authors.
Fifty-four (54) articles reported factors that impact patient adoption. Review and data abstraction identified specific factors, initially classified under 22 categories, that promote or impede m-health adoption in the developing world. Continued iterative review and discussion reduced these to 7 primary categories, with 21 sub-categories.
The review showed: great inconsistency in the approach and tools used in published studies; multiple factors impact patient adoption of m-health in the developing world; the specific factors vary from setting to setting and by recency of findings. Successful adoption of m-health by patients in the developing world critically depends on addressing the factors identified in the proposed framework, and assessing them prior to implementation of m-health initiatives in any specific setting. The framework will serve to: increase the consistency of patient adoption studies, form the basis for informed policy decisions by stakeholders, and provide the foundation for greater success of future m-health implementations for patients in the developing world.
Identifying predictive patients’ characteristics in case of High Flow Nasal Cannula failure when used for post-extubation failure
Authors: Terstappen Afra L.E. , Haas Lenneke E.M. , Seumeren Esther S.E. van , Balzereit Anja , Endeman Henrik
Published: January 2020

Background: High Flow Nasal Cannula (HFNC) is a relatively new but broadly used type of oxygen therapy. Hence, not much is known about HFNC in the setting of post-extubation failure. Aim of this study is to identify patients’ characteristics that predict failure of HFNC when used for post-extubation failure.
Methods: This retrospective, observational study was conducted in a Dutch ICU. Between 2008 and 2014 all subjects aged 18 and older who started with HFNC due to respiratory failure within 2 to 72 hours after extubation were included. Primary outcome was patient characteristics predicting failure of HFNC. Failure was defined as reintubation or death following HFNC. Success was defined as the opportunity to stop HFNC after a non-specified time. Secondary outcome was the difference in length of stay (LOS) and mortality between the success and failure group.
Results: A total of 246 subjects were included; in 135 (55%) cases HFNC failed. The success and failure group were comparable in terms of age, primary diagnosis and duration of mechanical ventilation prior to extubation. HFNC was started median 14 (min-max: 2-71) after extubation. Significant differences were found for breathing frequency (success: 21 (9-45)/min vs failure: 24(7-45)/min, p=0.009) and the presence of acute kidney injury (51% vs. 79%, p=0.003). There was a non-significant difference in pH pH (7.42(7.27-7.56) vs. 7.41 (7.13-7.58), p=0.08) After logistic breathing frequency (p=0.02) and pH (p=0.01) remained independent predictors of HFNC failure. LOS at the ICU after starting HFNC differed (success: median 131, min-max: 12-1432 hours vs. failure: 250 (23-4726) hours p<0.001. ICU and hospital mortality were not significantly different between groups.
Conclusion: In more than half of the patients HFNC failed when used for post-extubation failure. Breathing frequency and pH were predictors of HFNC failure.
Hidden analyses: A review of current reporting practice and recommendations for more transparent reporting of initial data analyses
Authors: Huebner Marianne , Vach Werner , Cessie Saskia le , Schmidt Carsten Oliver , Lusa Lara
Published: January 2020

Background In the data pipeline from the data collection process to the planned statistical analyses, initial data analysis (IDA) typically takes place between the end of the data collection and do not touch the research questions. A systematic process for IDA and clear reporting of the findings would help to understand the potential shortcomings of a dataset, such as missing values, or subgroups with small sample sizes, or shortcomings in the collection process, and to evaluate the impact of these shortcomings on the research results. A clear reporting of findings is also relevant when making datasets available to other researchers. Initial data analyses can provide valuable insights into the suitability of a data set for a future research study. Our aim was to describe the current practice of reporting of initial data analyses in observational studies in five highly ranked medical journals with focus on data cleaning, screening, and reporting of findings which led to a potential change in the analysis plan. Methods This review was carried out using systematic search strategies with eligibility criteria for articles to be reviewed. A total of 25 papers about observational studies were selected from five medical journals. Each paper was reviewed by two reviewers and IDA statements were further discussed by all authors. The consensus was reported. Results IDA statements were reported in the methods, results, discussion, and supplement of papers. Ten out of 25 papers (40%) included a statement about data cleaning. Data screening statements were included in all articles, and 18 (72%) indicated the methods used to describe them. Item missingness was reported in 11 papers (44%), unit missingness in 15 papers (60%). Eleven papers (44%) mentioned some changes in the analysis plan. Reported changes referred to missing data treatment, unexpected values, population heterogeneity and aspects related to variable distributions or data properties. Conclusion Reporting of initial data analyses were sparse, and statements on IDA were located throughout the research articles. There is a lack of systematic reporting of IDA. We conclude the article with recommendations on how to overcome shortcomings in the current practice of IDA reporting in observational studies.
The Bifunctional Enzyme, GenB4, Catalyzes the Last Step of Gentamicin 3’,4’-Di-Deoxygenation via Reduction and Transamination Activities
Authors: Chen Xiao tang , Zhang Hui , Zhou Shaotong , Bi Mingjun , Qi Shizhou , Gao Huiyuan , Ni Xianpu , Xia Huanzhang
Published: January 2020

Background: New semi-synthetic aminoglycoside antibiotics generally use chemical modifications to avoid inactivity from pathogens. One of the most used modifications is 3’,4’-di-deoxygenation, which imitates the structure of gentamicin. However, the mechanism of di-deoxygenation has not been clearly elucidated.
Results: Here, we report that the bifunctional enzyme, GenB4, catalyzes the last step of gentamicin 3’,4’-di-deoxygenation via reduction and transamination activities. Following disruption of gen B4 in wild-type M. echinospora , its products accumulated in 6’-deamino-6’-oxoverdamicin ( 1 ), verdamicin C2a ( 2 ), and its epimer, verdamicin C2 ( 3 ). Following disruption of gen B4 in M. echinospora △ gen K, its products accumulated in sisomicin ( 4 ) and 6’-N-methylsisomicin ( 5 , G-52). Following in vitro catalytic reactions, GenB4 transformed sisomicin ( 4 ) to gentamicin C1a ( 9 ) and transformed verdamicin C2a ( 2 ) and its epimer, verdamicin C2 ( 3 ), to gentamicin C2a ( 11 ) and gentamicin C2 ( 12 ), respectively.
Conclusion: This finding indicated that in addition to its transamination activity, GenB4 exhibits specific 4’,5’ double-bond reducing activity and is responsible for the last step of gentamicin 3’,4’-di-deoxygenation. Taken together, we propose three new intermediates that may refine and supplement the specific biosynthetic pathway of gentamicin C components and lay the foundation for the complete elucidation of di-deoxygenation mechanisms.
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

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

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

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

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

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

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.