bluuebunny/crossref_metadata_2025_split huggingface dataset:
An attention-based deep learning model for clinical named entity recognition of Chinese electronic medical records
Authors: Li Luqi , Zhao Jie , Hou Li , Zhai Yunkai , Shi Jinming , Cui Fangfang 
Published: December 2019

AbstractBackgroundClinical named entity recognition (CNER) is important for medical information mining and establishment of high-quality knowledge map. Due to the different text features from natural language and a large number of professional and uncommon clinical terms in Chinese electronic medical records (EMRs), there are still many difficulties in clinical named entity recognition of Chinese EMRs. It is of great importance to eliminate semantic interference and improve the ability of autonomous learning of internal features of the model under the small training corpus.MethodsFrom the perspective of deep learning, we integrated the attention mechanism into neural network, and proposed an improved clinical named entity recognition method for Chinese electronic medical records called BiLSTM-Att-CRF, which could capture more useful information of the context and avoid the problem of missing information caused by long-distance factors. In addition, medical dictionaries and part-of-speech (POS) features were also introduced to improve the performance of the model.ResultsBased on China Conference on Knowledge Graph and Semantic Computing (CCKS) 2017 and 2018 Chinese EMRs corpus, our BiLSTM-Att-CRF model finally achieved better performance than other widely-used models without additional features(F1-measure of 85.4% in CCKS 2018, F1-measure of 90.29% in CCKS 2017), and achieved the best performance with POS and dictionary features (F1-measure of 86.11% in CCKS 2018, F1-measure of 90.48% in CCKS 2017). In particular, the BiLSTM-Att-CRF model had significant effect on the improvement of Recall.ConclusionsOur work preliminarily confirmed the validity of attention mechanism in discovering key information and mining text features, which might provide useful ideas for future research in clinical named entity recognition of Chinese electronic medical records. In the future, we will explore the deeper application of attention mechanism in neural network.
Healthcare utilisation in general practice and hospitals in the year preceding a diagnosis of cancer recurrence or second primary cancer: a population-based register study
Authors: Rasmussen Linda Aagaard , Jensen Henry , Virgilsen Line Flytkjær , Falborg Alina Zalounina , Møller Henrik , Vedsted Peter 
Published: December 2019

Abstract
Background
The organisation of cancer follow-up is under scrutiny in many countries, and general practice is suggested to become more involved. A central focus is timely detection of recurring previous cancer and new second primary cancer. More knowledge on the patient pathway before cancer recurrence and second primary cancer is warranted to ensure the best possible organisation of follow-up. We aimed to describe the healthcare utilisation in the year preceding a diagnosis of cancer recurrence or second primary cancer.

Methods
This nationwide register study comprises patients diagnosed with bladder, breast, colorectal, endometrial, lung, malignant melanoma and ovarian cancer in Denmark in 2008–2016. The frequency of healthcare contacts during the 12 months preceding a cancer recurrence or second primary cancer was estimated and compared to the frequency of cancer survivors in cancer remission. The main analyses were stratified on sex and healthcare setting. Furthermore, two sub-analyses were stratified on 1) sex, healthcare setting and age group and on 2) sex, healthcare setting and comorbidity status.

Results
The study population consisted of 7832 patients with recurrence and 2703 patients with second primary cancer. On average, the patients were in contact with general practice one time per month in the 12th month preceding a new cancer diagnosis (recurrence or second primary cancer). Increasing contact rates were seen from 7 months before diagnosis in general practice and from 12 months before diagnosis in hospitals. This pattern was more pronounced in patients with cancer recurrence, younger patients and patients with no comorbidity. For instance, the contact rate ratios for hospital contacts in non-comorbid women with recurrence demonstrated 30% more contacts in the 12th month before recurrence and 127% more contacts in the 2nd month before recurrence.

Conclusions
The results show that cancer survivors are already seen in general practice on a regular basis. The increasing contact rates before a diagnosis of cancer recurrence or second primary cancer indicate that a window of opportunity exists for more timely diagnosis; this is seen in both general practice and in hospitals. Thus, cancer survivors may benefit from improvements in the organisation of cancer follow-up.
Improvement of shared decision making in integrated stroke care: a before and after evaluation using a questionnaire survey
Authors: Voogdt-Pruis H. R. , Ras T. , van der Dussen L. , Benjaminsen S. , Goossens P. H. , Raats I. , Boss G. , van Hoef E. F. M. , Lindhout M. , Tjon-A-Tsien M. R. S. , Vrijhoef H. J. M. 
Published: December 2019

Abstract
Background
Shared decision making (SDM) is at the core of policy measures for making healthcare person-centred. However, the context-sensitive nature of the challenges in integrated stroke care calls for research to facilitate its implementation. This before and after evaluation study identifies factors for implementation and concludes with key recommendations for adoption.

Methods
Data were collected at the start and end of an implementation programme in five stroke services (December 2017 to July 2018). The SDM implementation programme consisted of training for healthcare professionals (HCPs), tailored support, development of decision aids and a social map of local stroke care. Participating HCPs were included in the evaluation study: A questionnaire was sent to 25 HCPs at baseline, followed by 11 in-depth interviews. Data analysis was based on theoretical models for implementation and 51 statements were formulated as a result. Finally, all HCPs were asked to validate and to quantify these statements and to formulate recommendations for further adoption.

Results
The majority of respondents said that training of all HCPs is essential. Feedback on consultation and peer observation are considered to help improve performance. In addition, HCPs stated that SDM should also be embedded in multidisciplinary meetings, whereas implementation in the organisation could be facilitated by appointed ambassadors. Time was not seen as an inhibiting factor. According to HCPs, negotiating patients’ treatment decisions improves adherence to therapy. Despite possible cognitive or communications issues, all are convinced patients with stroke can be involved in a SDM-process. Relatives play an important role too in the further adoption of SDM. HCPs provided eight recommendations for adoption of SDM in integrated stroke care.

Conclusions
HCPs in our study indicated it is feasible to implement SDM in integrated stroke care and several well-known implementation activities could improve SDM in stroke care. Special attention should be given to the following activities: (1) the appointment of knowledge brokers, (2) agreements between HCPs on roles and responsibilities for specific decision points in the integrated stroke care chain and (3) the timely investigation of patient’s preferences in the care process – preferably before starting treatment through discussions in a multidisciplinary meeting.
Preliminary validation of the PRImary care facility Management Evaluation tool (PRIME-Tool), a national facility management survey implemented in Ghana
Authors: Uy Jhanna , Macarayan Erlyn K. , Ratcliffe Hannah L. , Miller Kate , Otupiri Easmon , Awoonor-Williams John Koku , Hirschhorn Lisa R. , Lipsitz Stuart R. , Schwarz Dan , Bitton Asaf 
Published: December 2019

AbstractBackgroundThe management quality of healthcare facilities has consistently been linked to facility performance, but available tools to measure management are costly to implement, often hospital-specific, not designed for low- and middle-income countries (LMICs), nor widely deployed. We addressed this gap by developing the PRImary care facility Management Evaluation Tool (PRIME-Tool), a primary health care facility management survey for integration into routine national surveys in LMICs. We present an analysis of the tool’s psychometric properties and suggest directions for future improvements.MethodsThe PRIME-Tool assesses performance in five core management domains: Target setting, Operations, Human resources, Monitoring, and Community engagement. We evaluated two versions of the PRIME-Tool. We surveyed 142 primary health care (PHC) facilities in Ghana in 2016 using the first version (27 items) and 148 facilities in 2017 using the second version (34 items). We calculated floor and ceiling effects for each item and conducted exploratory factor analyses to examine the factor structure for each year and version of the tool. We developed a revised management framework and PRIME-tool as informed by these exploratory results, further review of management theory literature, and co-author consensus.ResultsThe majority (17 items in 2016, 23 items in 2017) of PRIME-Tool items exhibited ceiling effects, but only three (2 items in 2016, 3 items in 2017) showed floor effects. Solutions suggested by factor analyses did not fully fit our initial hypothesized management domains. We found five groupings of items that consistently loaded together across each analysis and named these revised domains as Supportive supervision and target setting, Active monitoring and review, Community engagement, Client feedback for improvement, and Operations and financing.ConclusionThe revised version of the PRIME-Tool captures a range of important and actionable information on the management of PHC facilities in LMIC contexts. We recommend its use by other investigators and practitioners to further validate its utility in PHC settings. We will continue to refine the PRIME-Tool to arrive at a parsimonious tool for tracking PHC facility management quality. Better understanding the functional components of PHC facility management can help policymakers and frontline managers drive evidence-based improvements in performance.
The X chromosome of the German cockroach, Blattella germanica, is homologous to a fly X chromosome despite 400 million years divergence
Authors: Meisel Richard P. , Delclos Pablo J. , Wexler Judith R. 
Published: December 2019

AbstractBackgroundSex chromosome evolution is a dynamic process that can proceed at varying rates across lineages. For example, different chromosomes can be sex-linked between closely related species, whereas other sex chromosomes have been conserved for > 100 million years. Cases of long-term sex chromosome conservation could be informative of factors that constrain sex chromosome evolution. Cytological similarities between the X chromosomes of the German cockroach (Blattella germanica) and most flies suggest that they may be homologous—possibly representing an extreme case of long-term conservation.ResultsTo test the hypothesis that the cockroach and fly X chromosomes are homologous, we analyzed whole-genome sequence data from cockroaches. We found evidence in both sequencing coverage and heterozygosity that a significant excess of the same genes are on both the cockroach and fly X chromosomes. We also present evidence that the candidate X-linked cockroach genes may be dosage compensated in hemizygous males. Consistent with this hypothesis, three regulators of transcription and chromatin on the fly X chromosome are conserved in the cockroach genome.ConclusionsOur results support our hypothesis that the German cockroach shares the same X chromosome as most flies. This may represent the convergent evolution of the X chromosome in the lineages leading to cockroaches and flies. Alternatively, the common ancestor of most insects may have had an X chromosome that resembled the extant cockroach and fly X. Cockroaches and flies diverged ∼ 400 million years ago, which would be the longest documented conservation of a sex chromosome. Cockroaches and flies have different mechanisms of sex determination, raising the possibility that the X chromosome was conserved despite the evolution of the sex determination pathway.
The British E. coli O157 in cattle study (BECS): factors associated with the occurrence of E. coli O157 from contemporaneous cross-sectional surveys
Authors: Henry Madeleine K. , McCann Catherine M. , Humphry Roger W. , Morgan Mair , Willett Alice , Evans Judith , Gunn George J. , Tongue Sue C. 
Published: December 2019

Abstract
Background
Escherichia coli O157 is a bacterial pathogen associated with severe disease in humans for which cattle are an important reservoir of infection. The identification of possible risk factors for infection in cattle could facilitate the development of control strategies and interventions to mitigate the risk to human health. The purpose of this study was to utilize data collected in 2014–2015 during the two contemporaneous cross-sectional surveys of the British E. coli O157 in Cattle Study (BECS) to investigate potential risk factors for E. coli O157 status in cattle destined for the food chain.

Results
In the England & Wales survey only one variable, herd size, was associated with the outcome farm-level E. coli O157 positive status. The odds increased for each additional animal in the herd. In the Scotland survey, as well as a measure of herd size (the number of cattle aged 12–30 months), having brought breeding females on to the farm in the last year also increased the odds, whereas farms sampled in spring were less likely to be positive compared to those sampled in autumn.
On the positive farms, in both surveys, an increase in the proportion of pats positive for E. coli O157 was associated with animals being housed at the time of sampling. However, the effect of housing on pat-level prevalence within positive groups was lower on farms from England & Wales than from Scotland (OR 0.45 (95% C.I. 0.24–0.86)).

Conclusion
For the first time, factors associated with farm-level E. coli O157 status have been investigated in two contemporaneous surveys with comparable study design. Although factors associated with farm-level E. coli O157 status differed between the two surveys, one consistent factor was an association with a measure of herd size. Factors associated with the proportion of E. coli O157 positive pats within a positive farm were similar in both surveys but differed from those associated with farm-level status. These findings raise the hypothesis that measures to protect public health by reducing the risk from cattle may need to be tailored, rather than by assuming that a GB-wide protocol is the best approach.
Meibomian gland dysfunction (MGD), as diagnosed by non-contact infrared Meibography, in dogs with ocular surface disorders (OSD): a retrospective study
Authors: Viñas Marta , Maggio Federica , D’Anna Nunzio , Rabozzi Roberto , Peruccio Claudio 
Published: December 2019

Abstract
Background
Meibomian gland dysfunction (MGD) is one of the possible conditions underlying ocular surface disorders (OSD). Prevalence of MGD in dogs affected by OSD has not yet been reported. We aimed to evaluate the prevalence of MGD among OSD canine patients, which had been assessed by non-contact infrared meibography and interferometry, and to identify MGD associated factors that might guide its diagnosis. Medical records of canine patients examined for OSD between 2016 and 2019 were reviewed. The frequency of MGD was evaluated within different categories (skull conformation, gender, eye and STT-1). The putative MGD risk factors and frequency of MGD within grades of interferometry were evaluated in a regression analysis model and reported as odd ratios (ORs).

Results
One hundred fifty eyes from 81 dogs with OSD were included with median age 75 months (range 3–192) and female representation with 52%. MGD was present in 70% of the examined eyes. MGD risk was higher in males ORadj = 3.015 (95% CI: 1.395–6.514) (P = 0.005) and older patients ORadj = 1.207 (95% CI: 1.081–1.348) (P = 0.001). No significant differences were found between left and right eyes (P = 0.66) or between the two types of skull conformation (P = 0.477) and MGD presence. MGD was associated to the lowest lipid layer (LL) thickness, as assessed by interferometry (grade 0) OR = 16.00 (95% CI: 2.104–121.68) (P < 0.001). STT values were not significantly associated with the presence of MGD (P > 0.05).

Conclusions
MGD is a common underlying pathology in OSD. Being male and higher age are risk factors for MGD. An interferometry grade 0 may guide OSD diagnosis towards MGD.
Development and clinical applications of cancer immunotherapy against PD-1 signaling pathway
Authors: Wakabayashi Grace , Lee Yu-Ching , Luh Frank , Kuo Chun-Nan , Chang Wei-Chiao , Yen Yun 
Published: December 2019

AbstractDramatic advances in immune therapy have emerged as a promising strategy in cancer therapeutics. In addition to chemotherapy and radiotherapy, inhibitors targeting immune-checkpoint molecules such as cytotoxic T-lymphocyte antigen-4 (CTLA-4), programmed cell death receptor-1 (PD-1) and its ligand (PD-L1) demonstrate impressive clinical benefits in clinical trials. In this review, we present background information about therapies involving PD-1/PD-L1 blockade and provide an overview of current clinical trials. Furthermore, we present recent advances involving predictive biomarkers associated with positive therapeutic outcomes in cancer immunotherapy.
Effects of indoor residual spraying and outdoor larval control on Anopheles coluzzii from São Tomé and Príncipe, two islands with pre-eliminated malaria
Authors: Chen Ying-An , Lien Jih-Ching , Tseng Lien-Fen , Cheng Chien-Fu , Lin Wan-Yu , Wang Hurng-Yi , Tsai Kun-Hsien 
Published: December 2019

AbstractBackgroundVector control is a key component of malaria prevention. Two major vector control strategies have been implemented in São Tomé and Príncipe (STP), indoor residual spraying (IRS) and outdoor larval control usingBacillus thuringiensis israelensis(Bti). This study evaluated post-intervention effects of control strategies on vector population density, composition, and knockdown resistance mutation, and their implications for malaria epidemiology in STP.MethodsMosquitoes were collected by indoor and outdoor human landing catches and mosquito light traps in seven districts. Mosquito density was calculated by numbers of captured adult mosquitoes/house/working hour. Mitochondrial cytochromecoxidase subunit I (COI) was PCR amplified and sequenced to understand the spatial–temporal population composition of malaria vector in STP. Knockdown resistance L1014F mutation was detected using allele-specific PCR. To estimate the malaria transmission risks in STP, a negative binomial regression model was constructed. The response variable was monthly incidence, and the explanatory variables were area, rainfall, entomological inoculation rate (EIR), andkdrmutation frequency.ResultsMalaria vector in STP is exophilicAnopheles coluzziiwith significant population differentiation between Príncipe and São Tomé (mean FST = 0.16, p < 0.001). Both vector genetic diversity and knockdown resistance mutation were relatively low in Príncipe (mean ofkdrfrequency = 15.82%) compared to São Tomé (mean ofkdrfrequency = 44.77%). Annual malaria incidence rate in STP had been rapidly controlled from 37 to 2.1% by three rounds of country-wide IRS from 2004 to 2007. Long-term application ofBtisince 2007 kept the mosquito density under 10 mosquitoes/house/hr/month, and malaria incidence rate under 5% after 2008, except for a rising that occurred in 2012 (incidence rate = 6.9%). Risk factors of area (São Tomé compared to Príncipe), rainfall, outdoor EIR, andkdrmutation frequency could significantly increase malaria incidence by 9.33–11.50, 1.25, 1.07, and 1.06 fold, respectively.ConclusionsIndoor residual spraying could rapidly decreaseAnophelesdensity and malaria incidence in STP. Outdoor larval control usingBtiis a sustainable approach for controlling local vector with exophilic feature and insecticide resistance problem. Vector control interventions should be intensified especially at the north-eastern part of São Tomé to minimize impacts of outbreaks.
Changing plasma cytokine, chemokine and growth factor profiles upon differing malaria transmission intensities
Authors: Aguilar Ruth , Campo Joseph J. , Chicuecue Silvia , Cisteró Pau , Català Alba , Luis Leopoldina , Ubillos Itziar , Galatas Beatriz , Aide Pedro , Guinovart Caterina , Moncunill Gemma , Dobaño Carlota 
Published: December 2019

AbstractBackgroundMalaria epidemiological and immunological data suggest that parasite tolerance wanes in the absence of continuous exposure to the parasite, potentially enhancing pathogenesis. The expansion of control interventions and elimination campaigns raises the necessity to better understand the host factors leading to susceptibility or tolerance that are affected by rapid changes in malaria transmission intensity (MTI). Mediators of cellular immune responses are responsible for the symptoms and pathological alterations during disease and are expected to change rapidly upon malaria exposure or cessation.MethodsThe plasma concentrations of 30 cytokine, chemokine and growth factors in individuals of all ages from a malaria endemic area of southern Mozambique were compared between 2 years of different MTI: 2010 (lower, n = 234) and 2013 (higher, n = 143). The effect of the year on the correlations between cytokines, chemokines and growth factors and IgGs toPlasmodium falciparum(markers of exposure) was explored. The effects of age, sex, neighbourhood and parasitaemia on analyte levels and their interactions with year were also assessed.ResultsAn inverse correlation of several cellular immune mediators with malarial antibodies in 2013, and a lack of correlation or even a positive correlation in 2010 were observed. Most cytokines, chemokines and growth factors, regardless of their immune function, had higher concentrations in 2010 compared with 2013 inP. falciparum-infected and uninfected subjects. Age and neighbourhood showed an effect on analyte concentrations.ConclusionsThe results show a different regulation of the cellular immune response in 2010 vs 2013 which could be related to a loss of immune-tolerance after a decline in MTI in 2010 and previous years, and a rapid re-establishment of tolerance as a consequence of more continuous exposure as MTI began increasing in 2012. Cellular immune mediators warrant further investigation as possible surrogates of MTI-associated host susceptibility or tolerance.