bluuebunny/crossref_metadata_2025_split huggingface dataset:
Automatic extraction of cancer registry reportable information from free-text pathology reports using multitask convolutional neural networks
Authors: Alawad Mohammed , Gao Shang , Qiu John X , Yoon Hong Jun , Blair Christian J , Penberthy Lynne , Mumphrey Brent , Wu Xiao-Cheng , Coyle Linda , Tourassi Georgia 
Published: August 2019

Abstract

Objective
We implement 2 different multitask learning (MTL) techniques, hard parameter sharing and cross-stitch, to train a word-level convolutional neural network (CNN) specifically designed for automatic extraction of cancer data from unstructured text in pathology reports. We show the importance of learning related information extraction (IE) tasks leveraging shared representations across the tasks to achieve state-of-the-art performance in classification accuracy and computational efficiency.

Materials and Methods
Multitask CNN (MTCNN) attempts to tackle document information extraction by learning to extract multiple key cancer characteristics simultaneously. We trained our MTCNN to perform 5 information extraction tasks: (1) primary cancer site (65 classes), (2) laterality (4 classes), (3) behavior (3 classes), (4) histological type (63 classes), and (5) histological grade (5 classes). We evaluated the performance on a corpus of 95 231 pathology documents (71 223 unique tumors) obtained from the Louisiana Tumor Registry. We compared the performance of the MTCNN models against single-task CNN models and 2 traditional machine learning approaches, namely support vector machine (SVM) and random forest classifier (RFC).

Results
MTCNNs offered superior performance across all 5 tasks in terms of classification accuracy as compared with the other machine learning models. Based on retrospective evaluation, the hard parameter sharing and cross-stitch MTCNN models correctly classified 59.04% and 57.93% of the pathology reports respectively across all 5 tasks. The baseline models achieved 53.68% (CNN), 46.37% (RFC), and 36.75% (SVM). Based on prospective evaluation, the percentages of correctly classified cases across the 5 tasks were 60.11% (hard parameter sharing), 58.13% (cross-stitch), 51.30% (single-task CNN), 42.07% (RFC), and 35.16% (SVM). Moreover, hard parameter sharing MTCNNs outperformed the other models in computational efficiency by using about the same number of trainable parameters as a single-task CNN.

Conclusions
The hard parameter sharing MTCNN offers superior classification accuracy for automated coding support of pathology documents across a wide range of cancers and multiple information extraction tasks while maintaining similar training and inference time as those of a single task–specific model.
Usage of query-based health information exchange after event notifications
Authors: Vest Joshua R , Hilts Katy Ellis , Ancker Jessica S , Unruh Mark Aaron , Jung Hye-Young 
Published: August 2019

AbstractObjectivesThis study sought to quantify the association between event notifications and subsequent query-based health information exchange (HIE) use among end users of three different community health information organizations.Materials and MethodsUsing system-log data merged with user characteristics, regression-adjusted estimates were used to describe the association between event notifications and subsequent query-based HIE usage.ResultsApproximately 5% of event notifications were associated with query-based HIE usage within 30 days. In adjusted models, odds of query-based HIE usage following an event notification were higher for older patients and for alerts triggered by a discharge event. Query-based HIE usage was more common among specialty clinics and Federally Qualified Health Centers than primary care organizations.Discussion and ConclusionIn this novel combination of data, 1 in 20 event notifications resulted in subsequent query-based HIE usage. Results from this study suggest that event notifications and query-based HIE can be applied together to address clinical and population health use cases.
Environmental Drivers of Questing Activity of Juvenile Black-Legged Ticks (Acari: Ixodidae): Temperature, Desiccation Risk, and Diel Cycles
Authors: Thomas Christina E , Burton Emily S , Brunner Jesse L 
Published: August 2019

AbstractVector feeding behavior can have a profound influence on the transmission of vector-borne diseases. In the case of black-legged ticks, Ixodes scapularis Say, which vectors the agents of Lyme disease, babesiosis, and other pathogens, the timing and propensity of questing can determine which hosts are fed upon as well as the risk of contact with humans. Yet we know little about the controls and constraints on tick host-finding behavior under natural conditions. Ticks must balance the need to quest for blood meal hosts with the risk of desiccation, all on a fixed energy budget. Prior research, primarily in the laboratory, has shown that questing activity varies with conditions (e.g., temperature, relative humidity), light-dark cycles, and energy reserves, but the findings have been idiosyncratic and the dominant factor(s) in nature remains unknown. We measured questing activity of nymphs and larvae throughout the day and night and over several weeks in enclosures across a range of suitable tick habitats within a site in the Northeast. Activity of nymphs increased slightly during dawn and dusk, opposite of larvae, and declined slightly with air temperature and rain, but these patterns were weak and inconsistent among replicate sites. Rather it appears a fraction of ticks were questing most of the time, regardless of conditions. Our study suggests neither climatic conditions or light-dark cycles have appreciable influence on tick questing behavior.
Integrative analysis of hexaploid wheat roots identifies signature components during iron starvation
Authors: Kaur Gazaldeep , Shukla Vishnu , Kumar Anil , Kaur Mandeep , Goel Parul , Singh Palvinder , Shukla Anuj , Meena Varsha , Kaur Jaspreet , Singh Jagtar , Mantri Shrikant , Rouached Hatem , Pandey Ajay Kumar 
Published: August 2019

AbstractIron (Fe) is an essential micronutrient for all organisms. In crop plants, Fe deficiency can decrease crop yield significantly; however, our current understanding of how major crops respond to Fe deficiency remains limited. Herein, the effect of Fe deprivation at both the transcriptomic and metabolic level in hexaploid wheat was investigated. Genome-wide gene expression reprogramming was observed in wheat roots subjected to Fe starvation, with a total of 5854 genes differentially expressed. Homoeologue and subgenome-specific analysis unveiled the induction-biased contribution from the A and B genomes. In general, the predominance of genes coding for nicotianamine synthase, yellow stripe-like transporters, metal transporters, ABC transporters, and zinc-induced facilitator-like protein was noted. Expression of genes related to the Strategy II mode of Fe uptake was also predominant. Our transcriptomic data were in agreement with the GC-MS analysis that showed the enhanced accumulation of various metabolites such as fumarate, malonate, succinate, and xylofuranose, which could be contributing to Fe mobilization. Interestingly, Fe starvation leads to a significant temporal increase of glutathione S-transferase at both the transcriptional level and enzymatic activity level, which indicates the involvement of glutathione in response to Fe stress in wheat roots. Taken together, our result provides new insight into the wheat response to Fe starvation at the molecular level and lays the foundation to design new strategies for the improvement of Fe nutrition in crops.
Evidence for Residual Immunity to Smallpox After Vaccination and Implications for Re-emergence
Authors: Kunasekaran Mohana Priya , Chen Xin , Costantino Valentina , Chughtai Abrar Ahmad , MacIntyre Chandini Raina 
Published: August 2019

AbstractIntroductionSmallpox has been eradicated but advances in synthetic biology have increased the risk of its re-emergence. Residual immunity in individuals who were previously vaccinated may mitigate the impact of an outbreak, but there is a high degree of uncertainty about the duration and degree of residual immunity. Both cell-mediated and humoral immunity are thought to be important but the exact mechanisms of protection are unclear. Guidelines usually suggest vaccine-induced immunity wanes to zero after 3–10 years post vaccination, whereas other estimates show long term immunity over decades.Materials and MethodsA systematic review of the literature was conducted to quantify the duration and extent of residual immunity to smallpox after vaccination.ResultsTwenty-nine papers related to quantifying residual immunity to smallpox after vaccination were identified: neutralizing antibody levels were used as immune correlates of protection in 11/16 retrospective cross-sectional studies, 2/3 epidemiological studies, 6/7 prospective vaccine trials and 0/3 modeling studies. Duration of protection of &gt;20 years was consistently shown in the 16 retrospective cross-sectional studies, while the lowest estimated duration of protection was 11.7 years among the modeling studies. Childhood vaccination conferred longer duration of protection than vaccination in adulthood, and multiple vaccinations did not appear to improve immunity.ConclusionsMost studies suggest a longer duration of residual immunity (at least 20 years) than assumed in smallpox guidelines. Estimates from modeling studies were less but still greater than the 3–10 years suggested by the WHO Committee on International Quarantine or US CDC guidelines. These recommendations were probably based on observations and studies conducted while smallpox was endemic. The cut-off values for pre-existing antibody levels of &gt;1:20 and &gt;1:32 reported during the period of endemic smallpox circulation may not be relevant to the contemporary population, but have been used as a threshold for identifying people with residual immunity in post-eradication era studies. Of the total antibodies produced in response to smallpox vaccination, neutralizing antibodies have shown to contribute significantly to immunological memory. Although the mechanism of immunological memory and boosting is unclear, revaccination is likely to result in a more robust response. There is a need to improve the evidence base for estimates on residual immunity to better inform planning and preparedness for re-emergent smallpox.
Constraining cold accretion on to supermassive black holes: molecular gas in the cores of eight brightest cluster galaxies revealed by joint CO and CN absorption
Authors: Rose Tom , Edge A C , Combes F , Gaspari M , Hamer S , Nesvadba N , Peck A B , Sarazin C , Tremblay G R , Baum S A , Bremer M N , McNamara B R , O’Dea C , Oonk J B R , Russell H , Salomé P , Donahue M , Fabian A C , Ferland G , Mittal R , Vantyghem A 
Published: August 2019

Abstract
To advance our understanding of the fuelling and feedback processes which power the Universe’s most massive black holes, we require a significant increase in our knowledge of the molecular gas which exists in their immediate surroundings. However, the behaviour of this gas is poorly understood due to the difficulties associated with observing it directly. We report on a survey of 18 brightest cluster galaxies lying in cool cores, from which we detect molecular gas in the core regions of eight via carbon monoxide (CO), cyanide (CN) and silicon monoxide (SiO) absorption lines. These absorption lines are produced by cold molecular gas clouds which lie along the line of sight to the bright continuum sources at the galaxy centres. As such, they can be used to determine many properties of the molecular gas which may go on to fuel supermassive black hole accretion and AGN feedback mechanisms. The absorption regions detected have velocities ranging from −45 to 283 km s−1 relative to the systemic velocity of the galaxy, and have a bias for motion towards the host supermassive black hole. We find that the CN N = 0 − 1 absorption lines are typically 10 times stronger than those of CO J = 0 − 1. This is due to the higher electric dipole moment of the CN molecule, which enhances its absorption strength. In terms of molecular number density CO remains the more prevalent molecule with a ratio of CO/CN ∼10, similar to that of nearby galaxies. Comparison of CO, CN, and H i observations for these systems shows many different combinations of these absorption lines being detected.
A new possible accretion scenario for ultra-luminous X-ray sources
Authors: Kobayashi Shogo B , Nakazawa K , Makishima K 
Published: August 2019

ABSTRACT
Using archival data from Suzaku, XMM–Newton, and NuSTAR, nine representative ultra-luminous X-ray sources (ULXs) in nearby galaxies were studied. Their X-ray spectra were all reproduced with a multicolour disc emission model plus its Comptonization. However, the spectral shapes of individual sources changed systematically depending on the luminosity, and defined three typical spectral states. These states differ either in the ratio between the Comptonizing electron temperature and the innermost disc temperature, or in the product of Compton y-parameter and fraction of the Comptonized disc photons. The luminosity range at which a particular state emerges was found to scatter by a factor of up to 16 among the eight ULXs. By further assuming that the spectral state is uniquely determined by the Eddington ratio, the sample ULXs are inferred to exhibit a similar scatter in their masses. This gives a model-independent support to the interpretation of ULXs in terms of relatively massive black holes. None of the spectra showed noticeable local structures. Especially, no Fe K-shell absorption/emission lines were detected, with upper limits of 30–40 eV in equivalent width from the brightest three among the sample: NGC 1313 X-1, Holmberg IX X-1, and IC 342 X-1. These properties disfavour ordinary mass accretion from a massive companion star, and suggest direct Bondi–Hoyle accretion from dense parts of the interstellar medium.
Polymerization retardation isothermal amplification (PRIA): a strategy enables sensitively quantify genome-wide 5-methylcytosine oxides rapidly on handy instruments with nanoscale sample input
Authors: Chen Danping , Wang Yang , Mo Mingming , Zhang Junjie , Zhang Yanfei , Xu Yuzhi , Liu Si-Yang , Chen Jun , Ma Yingjun , Zhang Li , Dai Zong , Cai Chun , Zou Xiaoyong 
Published: August 2019

Abstract
The current methods for quantifying genome-wide 5-methylcytosine (5mC) oxides are still scarce, mostly restricted with two limitations: assay sensitivity is seriously compromised with cost, assay time and sample input; epigenetic information is irreproducible during polymerase chain reaction (PCR) amplification without bisulfite pretreatment. Here, we propose a novel Polymerization Retardation Isothermal Amplification (PRIA) strategy to directly amplify the minute differences between epigenetic bases and others by arranging DNA polymerase to repetitively pass large electron-withdrawing groups tagged 5mC-oxides. We demonstrate that low abundant 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC) and 5-carboxycytosine (5caC) in genomic DNA can be accurately quantified within 10 h with 100 ng sample input on a laboratory real-time quantitative PCR instrument, and even multiple samples can be analyzed simultaneously in microplates. The global levels of 5hmC and 5fC in mouse and human brain tissues, rat hippocampal neuronal tissue, mouse kidney tissue and mouse embryonic stem cells were quantified and the observations not only confirm the widespread presence of 5hmC and 5fC but also indicate their significant variation in different tissues and cells. The strategy is easily performed in almost all research and medical laboratories, and would provide the potential capability to other candidate modifications in nucleotides.
Log-periodic quantum magneto-oscillations and discrete-scale invariance in topological material HfTe5
Authors: Wang Huichao , Liu Yanzhao , Liu Yongjie , Xi Chuanying , Wang Junfeng , Liu Jun , Wang Yong , Li Liang , Lau Shu Ping , Tian Mingliang , Yan Jiaqiang , Mandrus David , Dai Ji-Yan , Liu Haiwen , Xie Xincheng , Wang Jian 
Published: August 2019

Abstract
Discrete-scale invariance (DSI) is a phenomenon featuring intriguing log-periodicity that can be rarely observed in quantum systems. Here, we report the log-periodic quantum oscillations in the longitudinal magnetoresistivity (ρxx) and the Hall traces (ρyx) of HfTe5 crystals, which reveal the DSI in the transport-coefficients matrix. The oscillations in ρxx and ρyx show the consistent logB-periodicity with a phase shift. The finding of the logB oscillations in the Hall resistance supports the physical mechanism as a general quantum effect originating from the resonant scattering. Combined with theoretical simulations, we further clarify the origin of the log-periodic oscillations and the DSI in the topological materials. This work evidences the universality of the DSI in the Dirac materials and provides indispensable information for a full understanding of this novel phenomenon.
Models of Mental Health Triage for Individuals Coming to the Attention of the Police Who May Be Experiencing Mental Health Crisis: A Scoping Review
Authors: Park Alice , Booth Alison , Parker Adwoa J , Scantlebury Arabella , Wright Kath , Webber Martin 
Published: August 2019

AbstractPolice routinely encounter individuals experiencing mental distress, despite being ill-equipped to do so. Mental health triage aims to address these concerns. A range of approaches to triage has been introduced; however, no overview exists. We conducted a systematic scoping review of mental health triage co-responding schemes. Eleven databases were searched to identify the literature; each scheme was charted and described. Thirty-three studies describing 47 schemes were included. Intervention details were generally poorly reported, however, differences in personnel, training and information sharing were identified. There are multiple schemes in practice based on the co-responding model. Robust research into the cost and effectiveness of mental health triage is needed.
Patients With Greater Stroke Severity and Premorbid Disability Are Less Likely to Receive Therapist Consultations and Intervention During Acute Care Hospitalization
Authors: Capo-Lugo Carmen E , Askew Robert L , Naidech Andrew , Prabhakaran Shyam 
Published: August 2019

Abstract

Background
A substantial number of patients with stroke never receive acute care therapy services, despite the fact that therapy after stroke reduces the odds of death and disability and improves patients’ functioning.

Objective
The aim of this study was to estimate the proportion of and factors associated with receipt of therapist consultations and interventions during acute care hospitalization following ischemic and hemorrhagic stroke.

Design
This was a single-center longitudinal observational study.

Methods
Adults with a diagnosis of ischemic or hemorrhagic stroke (N = 1366) were enrolled during their hospitalization in an acute stroke center in a large metropolitan area. The main outcomes were receipt of therapist consultations, interventions, or both.

Results
Participants with acute hemorrhagic stroke (intracerebral: odds ratio [OR] = 0.34 [95% CI = 0.19–0.60]; subarachnoid: OR = 0.52 [95% CI = 0.28–0.99]) and with greater stroke severity by National Institutes of Health Stroke Scale (NIHSS) score (NIHSS score of &gt; 15: OR = 0.34 [95% CI = 0.23–0.51]) were less likely to receive therapist consultations. Participants with moderate stroke severity (NIHSS score of 6–15: OR = 1.43 [95% CI = 1.01–2.33]) were more likely to receive therapy interventions. Those who were able to ambulate before admission were more than 5 times as likely to receive therapy interventions (OR = 5.08 [95% CI = 1.91–13.52]). Also, participants with longer lengths of stay (ie, more intensive care unit and non–intensive care unit days) were more likely to receive therapist consultations and interventions. Tests or procedures were the most common reasons for unsuccessful attempts to complete therapist consultations.

Limitations
Lack of operational and qualitative data prohibited detailed explorations of barriers to delivery of therapist consultations and interventions.

Conclusions
Approximately 1 in 4 participants with acute stroke received neither a consultation nor an intervention. Efforts to improve the delivery of acute care therapy services are needed to optimize care for these people.
How economics frames political debates: macroeconomic forecasting in the French planning commissions
Authors: Angeletti Thomas 
Published: August 2019

AbstractThis article analyzes how economics can frame political debates using economic policy devices. It examines the FIFI macroeconomic model’s introduction into the French planning processes of the mid-1960s and argues that economists perform two operations, selection and qualification, which play a key role in structuring political debates on the French economy’s future. Building on archives and in-depth interviews, I show how the FIFI model was a central component of the Sixth Plan (1971–1975): it was designed to produce simulations of state intervention in the French economy and organize planning commissions debates. Studying the struggles and controversies surrounding this model and the economic policies promoted by it, the article ultimately shows how certain political options are made publicly available while others are discarded.
NLN Core Competencies for Nurse Educators: Are They Present in the Course Descriptions of Academic Nurse Educator Programs?
Authors: Fitzgerald Ann , McNelis Angela M. , Billings Diane M. 
Published: August 2019

Abstract

AIM
As an initial approach to determining representation of the NLN Core Competencies for Nurse Educators in Master’s of Science in Nursing Education and Post-Master’s Certificate programs, the study identified the presence of the competencies in course descriptions.

BACKGROUND
The competencies are the gold standard to ensure academic nurse educators have the knowledge and skill to teach, assist learners, develop curricula, and implement effective evaluation methods.

METHOD
A descriptive design that applied web scraping techniques was used to collect data from school web pages, including course descriptions, credit hours, practica information, distance accessibility, and Certified Nurse Educator exam preparation.

RESULTS
Four competencies were well represented (≥85 percent), and four competencies were poorly represented (<50 percent) in a sample of 529 schools.

CONCLUSION
Programs should review courses and course descriptions for inclusion of all competency areas that prepare nurse educators and make revisions to address poorly represented competencies.
The multiple roles of mite allergens in allergic diseases
Authors: Vitiello Gianfranco , Biagioni Benedetta , Parronchi Paola 
Published: August 2019

Purpose of review
Mites are the most worldwide spread allergens and relevant causative of respiratory allergies. Life cycle, component allergens, biological activity and immunogenicity are discussed in depth.

Recent findings
It is now known that mite allergens are able to stimulate the innate immune system through different receptors, for example, TLRs and PARs. The activation of the cells in the airway mucosa is followed by type 2 polarizing cytokine production in predisposed individuals. This complex network plays a pivotal role into the promotion of Th2 differentiation.

Summary
This is a comprehensive review regarding all the mite allergens known so far, including their location within dust mites, composition, biological activities and binding receptors relevant to the fate of the immunological response.