Scaling-up NLP Pipelines to Process Large Corpora of Clinical Notes

Introduction: This article is part of the Focus Theme of Methods of Information in Medicine on “Big Data and Analytics in Healthcare”.

Objectives: This paper describes the scale-up efforts at the VA Salt Lake City Health Care System to address processing large corpora of clinical notes through a natural language processing (NLP) pipeline. The use case described is a current project focused on detecting the presence of an indwelling uri-nary catheter in hospitalized patients and subsequent catheter-associated urinary tract infections.

Methods: An NLP algorithm using v3NLP was developed to detect the presence of an indwelling urinary catheter in hospitalized patients. The algorithm was tested on a small corpus of notes on patients for whom the presence or absence of a catheter was already known (reference standard). In planning for a scale-up, we estimated that the original algorithm would have taken 2.4 days to run on a larger corpus of notes for this project (550,000 notes), and 27 days for a corpus of 6 million records representative of a national sample of notes. We approached scaling-up NLP pipelines through three techniques: pipeline replication via multi-threading, intra-annotator threading for tasks that can be further decomposed, and remote annotator services which enable annotator scale-out.

Results: The scale-up resulted in reducing the average time to process a record from 206 milliseconds to 17 milliseconds or a 12-fold increase in performance when applied to a corpus of 550,000 notes.

Conclusions: Purposely simplistic in nature, these scale-up efforts are the straight forward evolution from small scale NLP processing to larger scale extraction without incurring associated complexities that are inherited by the use of the underlying UIMA framework. These efforts represent generalizable and widely applicable techniques that will aid other computationally complex NLP pipelines that are of need to be scaled out for processing and analyzing big data.

The effect of purse-string approximation versus linear approximation of ileostomy reversal wounds on morbidity rates and patient satisfaction: the 'STOMA' trial

BACKGROUND

Ileostomy reversal is associated with surgical site infection (SSI) rates as high as 37%. Recent literature suggests that employing a purse-string approximation (PSA) of the reversal wound reduces this rate of SSI. Thus we wished to perform a randomised controlled trial to compare SSI rates in purse-string versus linear closure (PLC) wounds following ileostomy reversal.

METHODS

A randomised, controlled trial was conducted at University Hospital Limerick. Sixty-one patients undergoing ileostomy reversal were included. Thirty-four patients were randomised to PSA and 27 patients to linear closure. The primary endpoint was incidence of SSI and secondary endpoints measured were quality of life and satisfaction with cosmesis. Statistical analysis was performed on a per protocol basis using SPSS version 22.0.

RESULTS

Three patients in the PSA group developed an SSI compared to 8 in the PLC group at 30 days (8 vs 30%, p = 0.03). The mean time to SSI diagnosis was faster in the PSA group (3 vs 12.3 days, p = 0.08). Patients who developed SSI experienced a longer mean length of stay (6.8 vs 11.4 days, p = 0.012). On multivariate analysis, PLC was the only predictive factor of SSI formation (p < 0.001). There was no difference in patient satisfaction between the two study groups (p = 0.14).

CONCLUSIONS

PSA of wounds following ileostomy reversal significantly reduces SSI formation compared to linear approximation without any effect on patient satisfaction.

Transient Behavior of the Metal Interface in Lithium Metal-Garnet Batteries

The interface between solid electrolytes and Li metal is a primary issue for solid-state batteries. Introducing a metal interlayer to conformally coat solid electrolytes can improve the interface wettability of Li metal and reduce the interfacial resistance, but the mechanism of the metal interlayer is unknown. In this work, we used magnesium (Mg) as a model to investigate the effect of a metal coating on the interfacial resistance of a solid electrolyte and Li metal anode. The Li-Mg alloy has low overpotential, leading to a lower interfacial resistance. Our motivation is to understand how the metal interlayer behaves at the interface to promote increased Li-metal wettability of the solid electrolyte surface and reduce interfacial resistance. Surprisingly, we found that the metal coating dissolved in the molten piece of Li and diffused into the bulk Li metal, leading to a small and stable interfacial resistance between the garnet solid electrolyte and the Li metal. We also found that the interfacial resistance did not change with increase in the thickness of the metal coating (5, 10, and 100 nm), due to the transient behavior of the metal interface layer.

The Picture Talk Project: Starting a Conversation with Community Leaders on Research with Remote Aboriginal Communities of Australia

BACKGROUND

Researchers are required to seek consent from Indigenous communities prior to conducting research but there is inadequate information about how Indigenous people understand and become fully engaged with this consent process. Few studies evaluate the preference or understanding of the consent process for research with Indigenous populations. Lack of informed consent can impact on research findings.

METHODS

The Picture Talk Project was initiated with senior Aboriginal leaders of the Fitzroy Valley community situated in the far north of Western Australia. Aboriginal people were interviewed about their understanding and experiences of research and consent processes. Transcripts were analysed using NVivo10 software with an integrated method of inductive and deductive coding and based in grounded theory. Local Aboriginal interpreters validated coding. Major themes were defined and supporting quotes sourced.

RESULTS

Interviews with Aboriginal leaders (n = 20) were facilitated by a local Aboriginal Community Navigator who could interpret if necessary and provide cultural guidance. Participants were from all four major local language groups of the Fitzroy Valley; aged 31 years and above; and half were male. Themes emerging from these discussions included Research-finding knowledge; Being respectful of Aboriginal people, Working on country, and Being flexible with time; Working together with good communication; Reciprocity-two-way learning; and Reaching consent.

CONCLUSION

The project revealed how much more there is to be learned about how research with remote Aboriginal communities should be conducted such that it is both culturally respectful and, importantly, meaningful for participants. We identify important elements in community consultation about research and seeking consent.

Characterizing the inpatient care of young adults experiencing early psychosis

Introduction/objectives

The available literature suggests that treatments and health services for psychosis are considered to be poorly organized and highly variable. Little is known, however, about how inpatient care is provided to individuals experiencing early psychosis. To facilitate quality improvement activities, we characterized the care this patient group receives in an inner city hospital.

Methods

We performed chart reviews of individuals admitted to psychiatric inpatient units at St. Paul's Hospital, Vancouver, British Columbia between 01/04/2014 and 31/03/2016. Those who were 17–25 years of age and hospitalized for psychotic symptoms at the time of admission were included. Demographic and health service use were summarized using descriptive characteristics.

Results

We identified 73 inpatients (mean age = 22; males = 78%; Caucasian = 41%) that met study inclusion criteria, having a combined total of 102 care episodes and an average length of stay of 30.7 days (median = 18; min = 3; max = 268). Half of the care episodes were repeat admissions, with up to 30% of the patients readmitted within 28 days of discharge. Physical and mental status examinations (MSE) were performed in virtually all care episodes, although frequency is low (31.4% had daily physical examinations and 18.6% had MSE every nursing shift). In 49% and 50% of care episodes, patients were given oral antipsychotics and discharged on depot medications. Even when indicated, not all care episodes had follow-up appointments (60%) or referrals to income assistance (35%), community mental health teams (61%), and housing support (38%).

Conclusions

Specific programs are needed to address current gaps in inpatient care for patients with early psychosis.

Disclosure of interest

The authors have not supplied their declaration of competing interest.

A PROFESSIONAL PORTFOLIO OF LEARNING FOR UNDERGRADUATE NURSING STUDENTS

Traditionally, the assessment of clinical competence has been completed using 'paper based' systems which is still the predominant approach in Undergraduate Nursing Programs.

A PROFESSIONAL PORTFOLIO OF LEARNING FOR UNDERGRADUATE NURSING STUDENTS

Traditionally, the assessment of clinical competence has been completed using 'paper based' systems which is still the predominant approach in Undergraduate Nursing Programs.

From security to trust

The use of information technology for information management in healthcare is fundamentally about facilitating the holding of much more comprehensive data on people throughout the health system. More comprehensive health information obviously creates the potential for greatly improved health-care. At the same time, however, it raises concerns about the amount of information about individuals flowing through the system. This information has the potential not only to benefit the community but also to be used in ways which are discriminatory or otherwise harmful. This paper argues that if the potential of information technology to benefit information management in health-care is to be realized, there must be a shift in the culture of the health sector, to one which has a far greater emphasis on consumer privacy than is presently evident.

Synergistic Ultrathin Functional Polymer-Coated Carbon Nanotube Interlayer for High Performance Lithium-Sulfur Batteries

Lithium-sulfur (Li-S) batteries have been intensively investigated as a next-generation rechargeable battery due to their high energy density of 2600 W·h kg(-1) and low cost. However, the systemic issues of Li-S batteries, such as the polysulfide shuttling effect and low Coulombic efficiency, hinder the practical use in commercial rechargeable batteries. The introduction of a conductive interlayer between the sulfur cathode and separator is a promising approach that has shown the dramatic improvements in Li-S batteries. The previous interlayer work mainly focused on the physical confinement of polysulfides within the cathode part, without considering the further entrapment of the dissolved polysulfides. Here, we designed an ultrathin poly(acrylic acid) coated single-walled carbon nanotube (PAA-SWNT) film as a synergic functional interlayer to address the issues mentioned above. The designed interlayer not only lowers the charge transfer resistance by the support of the upper current collector but also localizes the dissolved polysulfides within the cathode part by the aid of a physical blocking and chemical bonding. With the synergic combination of PAA and SWNT, the sulfur cathode with a PAA-SWNT interlayer maintained higher capacity retention over 200 cycles and achieved better rate retention than the sulfur cathode with a SWNT interlayer. The proposed approach of combining a functional polymer and conductive support material can provide an optimiztic strategy to overcome the fundamental challenges underlying in Li-S batteries.

Improving the High-Voltage Li2FeMn3O8 Cathode by Chlorine Doping

High-capacity and high-voltage cathode materials are desirable for high-energy-density lithium ion batteries. Among various cathode materials, Li2FeMn3O8 is attractive due to its high working voltage, low toxicity, and low cost. However, its superior electrochemical properties are significantly limited by the intrinsic defects in the Li2FeMn3O8 cathode, which makes the theoretical working voltage (4.9 V) and capacity (148 mAh/g) hard to reach. In this paper, we demonstrated that Cl doping can effectively increase the capacity and working voltage of the Li2FeMn3O8 cathode. X-ray photoelectron spectroscopy reveals that Cl doping reduced the valence state and increased the electron binding energy in cations and thus increased the voltage and enhanced the capacity of the Li2FeMn3O8 cathode. Our results also indicate that Cl doping can be a promising low-cost method to improve the electrochemical performance of various oxide cathode materials, including LiCoO2 and LiMn2O4.

Prevalence of pancreatic, hepatic and renal microscopic lesions in post-mortem samples from Cavalier King Charles spaniels

OBJECTIVES

The objective of this study was to describe the prevalence of microscopic pancreatic, hepatic and renal lesions in post-mortem samples from Cavalier King Charles spaniels.

METHODS

The prevalence of microscopic lesions was determined by routine histopathology and compared to ante-mortem clinical signs.

RESULTS

There was evidence of chronic pancreatitis in 51·9% of the cases, and age correlated with severity. Renal lesions were diagnosed in 52·2% of cases, most of which were inflammatory. Ante-mortem diagnosis of pancreatic and renal disease was 25 and 16·7%, respectively. Primary hepatic lesions were diagnosed in 11·1% of cases; secondary hepatic lesions were diagnosed in 64·8%.

CLINICAL SIGNIFICANCE

Pancreatic and renal lesions are common in Cavalier King Charles spaniels, but they have similar rates of hepatic disease as the general population. The increasing prevalence of pancreatic lesions with age suggests that it might be a progressive condition.