bluuebunny/crossref_metadata_2025_split huggingface dataset:
Machine learning-based identification and rule-based normalization of adverse drug reactions in drug labels
Authors: Tiftikci Mert , Özgür Arzucan , He Yongqun , Hur Junguk 
Published: December 2019

AbstractBackgroundUse of medication can cause adverse drug reactions (ADRs), unwanted or unexpected events, which are a major safety concern. Drug labels, or prescribing information or package inserts, describe ADRs. Therefore, systematically identifying ADR information from drug labels is critical in multiple aspects; however, this task is challenging due to the nature of the natural language of drug labels.ResultsIn this paper, we present a machine learning- and rule-based system for the identification of ADR entity mentions in the text of drug labels and their normalization through the Medical Dictionary for Regulatory Activities (MedDRA) dictionary. The machine learning approach is based on a recently proposed deep learning architecture, which integrates bi-directional Long Short-Term Memory (Bi-LSTM), Convolutional Neural Network (CNN), and Conditional Random Fields (CRF) for entity recognition. The rule-based approach, used for normalizing the identified ADR mentions to MedDRA terms, is based on an extension of our in-house text-mining system, SciMiner. We evaluated our system on the Text Analysis Conference (TAC) Adverse Drug Reaction 2017 challenge test data set, consisting of 200 manually curated US FDA drug labels. Our ML-based system achieved 77.0% F1 score on the task of ADR mention recognition and 82.6% micro-averaged F1 score on the task of ADR normalization, while rule-based system achieved 67.4 and 77.6% F1 scores, respectively.ConclusionOur study demonstrates that a system composed of a deep learning architecture for entity recognition and a rule-based model for entity normalization is a promising approach for ADR extraction from drug labels.
Genomewide analysis of circular RNA in pituitaries of normal and heat-stressed sows
Authors: Zhang Haojie , Hu Baoyu , Xiong Jiali , Chen Ting , Xi Qianyun , Luo Junyi , Jiang Qingyan , Sun Jiajie , Zhang Yongliang 
Published: December 2019

Abstract
Background
As a newly characterized type of noncoding RNA, circular RNA (circRNA) has been shown to have functions in diverse biological processes of animals. It has been reported that several noncoding RNAs may regulate animals’ response to heat stress which can be easily induced by hyperthermia in summer. However, the expression and functions of circRNAs in the pituitary of sows and whether they participate in heat stress adaption are still unclear.

Results
In this study, we found that high temperature over the thermoneutral zone of sows during the summer increased the serum heat shock protein 70 (HSP70) level, decreased the superoxide dismutase (SOD) vitality and prolactin (PRL) concentration, and induced heat stress in sows. Then, we explored circRNA in the pituitary of heat-stressed and normal sows using RNA sequencing and bioinformatics analysis. In total, 12,035 circRNAs were detected, with 59 circRNAs differentially expressed, including 42 up-regulated and 17 down-regulated circRNAs in pituitaries of the heat-stressed sows. Six randomly selected circRNAs were identified through reverse transcription PCR followed by DNA sequencing and other 7 randomly selected differentially expressed circRNAs were verified by quantitative real-time PCR analysis. The predicted target genes regulated by circRNAs through sponging microRNAs (miRNAs) were enriched in metabolic pathway. Furthermore, the predicted circRNA–miRNA–mRNA interactions showed that some circRNAs might sponge miRNAs to regulate pituitary-specific genes and heat shock protein family members, indicating circRNA’s roles in pituitary hormone secretion and heat stress response.

Conclusions
Our results provided a meaningful reference to understand the functions of circRNA in the porcine pituitary and the mechanisms by which circRNA may participate in animals’ response to heat stress.
An improved catalogue of putative synaptic genes defined exclusively by temporal transcription profiles through an ensemble machine learning approach
Authors: Pazos Obregón Flavio , Palazzo Martín , Soto Pablo , Guerberoff Gustavo , Yankilevich Patricio , Cantera Rafael 
Published: December 2019

AbstractBackgroundAssembly and function of neuronal synapses require the coordinated expression of a yet undetermined set of genes. Previously, we had trained an ensemble machine learning model to assign a probability of having synaptic function to every protein-coding gene inDrosophila melanogaster. This approach resulted in the publication of a catalogue of 893 genes which we postulated to be very enriched in genes with a still undocumented synaptic function. Since then, the scientific community has experimentally identified 79 new synaptic genes. Here we use these new empirical data to evaluate our original prediction. We also implement a series of changes to the training scheme of our model and using the new data we demonstrate that this improves its predictive power. Finally, we added the new synaptic genes to the training set and trained a new model, obtaining a new, enhanced catalogue of putative synaptic genes.ResultsThe retrospective analysis demonstrate that our original catalogue was significantly enriched in new synaptic genes. When the changes to the training scheme were implemented using the original training set we obtained even higher enrichment. Finally, applying the new training scheme with a training set including the 79 new synaptic genes, resulted in an enhanced catalogue of putative synaptic genes. Here we present this new catalogue and announce that a regularly updated version will be available online at:http://synapticgenes.bnd.edu.uyConclusionsWe show that training an ensemble of machine learning classifiers solely with the whole-body temporal transcription profiles of known synaptic genes resulted in a catalogue with a significant enrichment in undiscovered synaptic genes. Using new empirical data provided by the scientific community, we validated our original approach, improved our model an obtained an arguably more precise prediction. This approach reduces the number of genes to be tested through hypothesis-driven experimentation and will facilitate our understanding of neuronal function.Availabilityhttp://synapticgenes.bnd.edu.uy
Genomic dissection of the most prevalent Listeria monocytogenes clone, sequence type ST87, in China
Authors: Wang Yan , Luo Lijuan , Li Qun , Wang Hong , Wang Yiqian , Sun Hui , Xu Jianguo , Lan Ruiting , Ye Changyun 
Published: December 2019

Abstract
Background
Listeria monocytogenes consists of four lineages that occupy a wide variety of ecological niches. Sequence type (ST) 87 (serotype 1/2b), belonging to lineage I, is one of the most common STs isolated from food products, food associated environments and sporadic listeriosis in China. Here, we performed a comparative genomic analysis of the L. monocytogenes ST87 clone by sequencing 71 strains representing a diverse range of sources, different geographical locations and isolation years.

Results
The core genome and pan genome of ST87 contained 2667 genes and 3687 genes respectively. Phylogenetic analysis based on core genome SNPs divided the 71 strains into 10 clades. The clinical strains were distributed among multiple clades. Four clades contained strains from multiple geographic regions and showed high genetic diversity. The major gene content variation of ST87 genomes was due to putative prophages, with eleven hotspots of the genome that harbor prophages. All strains carry an intact CRISRP/Cas system. Two major CRISPR spacer profiles were found which were not clustered phylogenetically. A large plasmid of about 90 Kb, which carried heavy metal resistance genes, was found in 32.4% (23/71) of the strains. All ST87 strains harbored the Listeria pathogenicity island (LIPI)-4 and a unique 10-open read frame (ORF) genomic island containing a novel restriction-modification system.

Conclusion
Whole genome sequence analysis of L. monocytogenes ST87 enabled a clearer understanding of the population structure and the evolutionary history of ST87 L. monocytogenes in China. The novel genetic elements identified may contribute to its virulence and adaptation to different environmental niches. Our findings will be useful for the development of effective strategies for the prevention and treatment of listeriosis caused by this prevalent clone.
Targeting the DPP-4-GLP-1 pathway improves exercise tolerance in heart failure patients: a systematic review and meta-analysis
Authors: Chen Chengcong , Huang Ying , Zeng Yongmei , Lu Xiyan , Dong Guoqing 
Published: December 2019

Abstract
Background
The most significant manifestation of heart failure is exercise intolerance. This systematic review and meta-analysis was performed to investigate whether dipeptidyl peptidase-4 (DPP-4) inhibitors or glucagon-like peptide 1 receptor agonists (GLP-1 RAs), widely used anti-diabetic drugs, could improve exercise tolerance in heart failure patients with or without type 2 diabetes mellitus.

Methods
An electronic search of PubMed, EMBASE and the Cochrane Library was carried out through March 8th, 2019, for eligible trials. Only randomized controlled studies were included. The primary outcome was exercise tolerance [6-min walk test (6MWT) and peak O2 consumption], and the secondary outcomes included quality of life (QoL), adverse events (AEs) and all-cause death.

Result
After the literature was screened by two reviewers independently, four trials (659 patients) conducted with heart failure patients with or without type 2 diabetes met the eligibility criteria. The results suggested that targeting the DPP-4-GLP-1 pathway can improve exercise tolerance in heart failure patients [MD 24.88 (95% CI 5.45, 44.31), P = 0.01] without decreasing QoL [SMD -0.51 (95% CI -1.13, 0.10), P = 0.10]; additionally, targeting the DPP-4-GLP-1 pathway did not show signs of increasing the incidence of serious AEs or mortality.

Conclusion
Our results suggest that DPP-4 inhibitors or GLP-1 RAs improve exercise tolerance in heart failure patients. Although the use of these drugs for heart failure has not been approved by any organization, they may be a better choice for type 2 diabetes mellitus patients with heart failure. Furthermore, as this pathway contributes to the improvement of exercise tolerance, it may be worth further investigation in exercise-intolerant patients with other diseases.
Old subjects with sepsis in the emergency department: trend analysis of case fatality rate
Authors: Fabbri Andrea , Marchesini Giulio , Benazzi Barbara , Morelli Alice , Montesi Danilo , Bini Cesare , Rizzo Stefano Giovanni 
Published: December 2019

Abstract
Background
The burden of sepsis represents a global health care problem. We aimed to assess the case fatality rate (CFR) and its predictors in subjects with sepsis admitted to a general Italian hospital from 2009 to 2016, stratified by risk score.

Methods
We performed a retrospective analysis of all sepsis-related hospitalizations after Emergency Department (ED) visit in a public Italian hospital in an 8-year period. A risk score to predict CFR was computed by logistic regression analysis of selected variables in a training set (2009–2012), and then confirmed in the whole study population. A trend analysis of CFR during the study period was performed dividing patient as high-risk (upper tertile of risk score) or low-risk.

Results
Two thousand four hundred ninety-two subjects were included. Over time the incidental admission rate (no. of sepsis-related admissions per 100 total admissions) increased from 4.1% (2009–2010) to 5.4% (2015–2016); P < 0.001, accompanied by a reduced CFR (from 38.0 to 18.4%; P < 0.001). A group of 10 variables (admission to intensive care unit, cardio-vascular dysfunction, HIV infection, diabetes, age ≥ 80 years, respiratory diseases, number of organ dysfunction, digestive diseases, dementia and cancer) were selected by the logistic model to predict CFR with good accuracy: AUC 0.873 [0.009]. Along the years CFR decreased from 31.8% (2009–2010) to 25.0% (2015–2016); P = 0.007. The relative proportion of subjects ≥80 years (overall, 52.9% of cases) and classified as high-risk did not change along the years. CFR decreased only in low-risk subjects (from 13.3 to 5.2%; P < 0.001), and particularly in those aged ≥80 (from 18.2 to 6.6%; P = 0.003), but not in high-risk individuals (from 69.9 to 64.2%; P = 0.713).

Conclusion
Between 2009 and 2016 the incidence of sepsis-related hospitalization increased in a general Italian hospital, with a downward trend in CFR, only limited to low-risk patients and particularly to subjects ≥80 years.
Meaning in life and health care use: findings from a nationally representative study of older adults in Germany
Authors: Hajek André , König Hans-Helmut 
Published: December 2019

Abstract
Background
There is a lack of studies examining the link between meaning in life and health care use. Meaning in life refers to a sense of comprehension and significance in life. Consequently, the purpose of this study was to investigate the association between meaning in life and health care use.

Methods
Cross-sectional data from the German Ageing Survey, a nationally representative sample of older adults, was used for this study (in the analytical sample: n = 3850; year 2002). The frequency of GP and specialist visits in the past 12 months were used as outcome measures. Meaning in life was assessed using a single item measure. Based on Andersen’s model, covariates were selected. Sex, age, family status, occupational status, income, self-rated health, physical functioning, depressive symptoms, and the number of physical illnesses were adjusted for in a multiple regression analysis.

Results
After adjusting for various potential confounders, there was a positive association between meaning in life and GP (IRR: 1.04, 95%-CI: 1.01–1.08) as well as specialist visits (IRR: 1.07, 95%-CI: 1.02–1.12) in a multiple regression analysis. With the exception of employment status (retired vs. employed), income and need factors, no covariates were consistently associated with both outcome measures.

Conclusions
This study highlighted the association between meaning in life and health care use. Our results indicate that there are other factors that are associated with health care use, beyond need-variables. This might help to identify individuals at risk for under- or overuse of health care services.
Validating a screening agar for linezolid-resistant enterococci
Authors: Werner Guido , Fleige Carola , Klare Ingo , Weber Robert E. , Bender Jennifer K. 
Published: December 2019

AbstractBackgroundLinezolid is an alternative treatment option for infections with multidrug-resistant Gram-positive bacteria including vancomycin-resistant enterococci. Some countries report an increasing number of isolates with resistance to linezolid. The recent publication of the Commission for Hospital Hygiene in Germany on enterococci/VRE recommends screening for linezolid-resistant enterococci (LRE). However, a suitable selective medium or a genetic test is not available. Our aim was to establish a selective screening agar for LRE detection and validate its application with a comprehensive collection of clinical LRE and linezolid-susceptible enterococci.MethodsWe decided to combine the selective power of an enterococcal screening agar with a supplementation of linezolid. Several rounds of analyses with reference, control and test strains and under varying linezolid concentrations of a wider and a smaller range were investigated and assessed. The collection of linezolid-resistant enterococcal control strains included isolates with different resistance mechanisms (23S rDNA mutations,cfr(B),optrA,poxtA). Finally, we validated our LRE screening agar with 400 samples sent to our National Reference Centre in 2019.ResultsSeveral rounds of pre-tests and confirmatory analyses favored Enterococcosel® Agar supplemented with a concentration of 2 mg/L linezolid. A 48 h incubation period was essential for accurate identification of LRE strains. Performance of the LRE screening agar revealed a sensitivity of 96.6% and a specificity of 94.4%.ConclusionsHere we describe preparation of a suitable screening agar and a procedure to identify LRE isolates with high accuracy.
Typing of hereditary renal amyloidosis presenting with isolated glomerular amyloid deposition
Authors: Li Danyang , Liu Dan , Xu Hui , Yu Xiao-juan , Zhou Fu-de , Zhao Ming-hui , Wang Su-xia 
Published: December 2019

AbstractBackgroundThe commonly used methods for amyloid typing include immunofluorescence or immunohistochemistry (IHC), which sometimes may come with diagnostic pitfalls. Mass spectrometry (MS)-based proteomics has been recognized as a reliable technique in amyloid typing.Case presentationWe reported two middle-aged patients who presented with proteinuria, hypertension and normal renal function, and both had a family history of renal diseases. The renal biopsies of both patients revealed renal amyloidosis with the similar pattern by massive exclusively glomerular amyloid deposition. The IHC was performed by using a panel of antibodies against the common types of systemic amyloidosis, and demonstrated co-deposition of fibrinogen Aα chain and apolipoprotein A-I in the glomerular amyloid deposits of each patient. Then the MS on amyloid deposits captured by laser microdissection (LMD/MS) and genetic study of gene mutations were investigated. The large spectra corresponding to ApoA-I in case 1, and fibrinogen Aα chain in case 2 were identified by LMD/MS respectively. Further analysis of genomic DNA mutations demonstrated a heterozygous mutation of p. Trp74Arg in ApoA-I in case 1, and a heterozygous mutation of p. Arg547GlyfsTer21 in fibrinogen Aα chain in case 2.ConclusionsThe current study revealed that IHC was not reliable for accurate amyloid typing, and that MS-based proteomics and genetic analysis were essential for typing of hereditary amyloidosis.
Reducing intrapartum fetal deaths through low-dose high frequency clinical mentorship in a rural hospital in Western Kenya: a quasi-experimental study
Authors: Shikuku Duncan N. , Mukosa Rita , Peru Taphroze , Yaite Alice , Ambuchi Janerose , Sisimwo Kenneth 
Published: December 2019

AbstractBackgroundIntrapartum fetal mortality can be prevented by quality emergency obstetrics and newborn care (EmONC) during pregnancy and childbirth. This study evaluated the effectiveness of a low-dose high-frequency onsite clinical mentorship in EmONC on the overall reduction in intrapartum fetal deaths in a busy hospital providing midwife-led maternity services in rural Kenya.MethodsA quasi-experimental (nonequivalent control group pretest – posttest) design in a midwife-led maternity care hospitals. Clinical mentorship and structured supportive supervision on EmONC signal functions was conducted during intervention. Maternity data at two similar time points: Oct 2015 to July 2016 (pre) and August 2016 to May 2017 (post) reviewed. Indicators of interest at Kirkpatrick’s levels 3 and 4 focusing on change in practice and health outcomes between the two time periods were evaluated and compared through a two-sample test of proportions. Proportions andp-values were reported to test the strength of the evidence after the intervention.ResultsSpontaneous vaginal delivery was the commonest route of delivery between the two periods in both hospitals. At the intervention hospital, assisted vaginal deliveries (vacuum extractions) increased 13 times (0.2 to 2.5%,P < 0.0001), proportion of babies born with low APGAR scores requiring newborn resuscitation doubled (1.7 to 3.7%,P = 0.0021), proportion of fresh stillbirths decreased 5 times (0.5 to 0.1%,P = 0.0491) and referred cases for comprehensive emergency obstetric care doubled (3.0 to 6.5%,P < 0.0001) with no changes observed in the control hospital. The proportion of live births reduced (98 to 97%,P = 0.0547) at the control hospital. Proportion of macerated stillbirths tripled at the control hospital (0.4 to 1.4%,P = 0.0039) with no change at the intervention hospital.ConclusionTargeted mentorship improves the competencies of nurse/midwives to identify, manage and/or refer pregnancy and childbirth cases and/or complications contributing to a reduction in intrapartum fetal deaths. Scale up of this training approach will improve maternal and newborn health outcomes.
Is there respectful maternity care in Poland? Women’s views about care during labor and birth
Authors: Baranowska Barbara , Doroszewska Antonina , Kubicka-Kraszyńska Urszula , Pietrusiewicz Joanna , Adamska-Sala Iwona , Kajdy Anna , Sys Dorota , Tataj-Puzyna Urszula , Bączek Grażyna , Crowther Susan 
Published: December 2019

Abstract
Background
Abuse against women in labor starts with subtle forms of discrimination that can turn into overt violence. Therefore it is crucial to work towards prevention and elimination of disrespect and ill-treatment in medical facility perinatal care in which staff allows such abuse.
The aim of the study was to analyze the experiences of women related to perinatal care. Special emphasis was put on experiences that had traits indicating disrespectful and offensive care during childbirth in medical facilities providing perinatal care.

Methods
This was a cross-sectional survey. A questionnaire was prepared for respondents who gave birth in medical facilities. Information about the study was posted on the website of a non-governmental foundation dealing with projects aimed at improving perinatal care. The respondents gave online consent for processing the submitted data. 8378 questionnaires were submitted. The study was carried out between February 06 and March 20, 2018. The results were analyzed using the Chi-square independence test. The analysis was carried out at the significance level of 0.05 in Excel, R and SPSS.

Results
During their hospital stay, 81% of women in the study experienced violence or abuse from medical staff on at least one occasion. The most common abuse was having medical procedures without prior consent. Inappropriate comments made by staff related to their own or a woman’s situation were reported in 25% of situations, whilst 20% of women experienced nonchalant treatment. In the study 19.3% of women reported that the staff did not properly care for their intimacy and 1.7% of the respondents said that the worst treatment was related to feeling anonymous in the hospital.

Conclusions
The study shows that during Polish perinatal care women experience disrespectful and abusive care. Most abuse and disrespect involved violation of the right to privacy, the right to information, the right to equal treatment, and the right to freedom from violence. The low awareness of abuses and complaints reported in the study may result from women’s ignorance about relevant laws related to human rights.