Towards generalizable entity-centric clinical coreference resolution

OBJECTIVE

This work investigates the problem of clinical coreference resolution in a model that explicitly tracks entities, and aims to measure the performance of that model in both traditional in-domain train/test splits and cross-domain experiments that measure the generalizability of learned models.

METHODS

The two methods we compare are a baseline mention-pair coreference system that operates over pairs of mentions with best-first conflict resolution and a mention-synchronous system that incrementally builds coreference chains. We develop new features that incorporate distributional semantics, discourse features, and entity attributes. We use two new coreference datasets with similar annotation guidelines - the THYME colon cancer dataset and the DeepPhe breast cancer dataset.

RESULTS

The mention-synchronous system performs similarly on in-domain data but performs much better on new data. Part of speech tag features prove superior in feature generalizability experiments over other word representations. Our methods show generalization improvement but there is still a performance gap when testing in new domains.

DISCUSSION

Generalizability of clinical NLP systems is important and under-studied, so future work should attempt to perform cross-domain and cross-institution evaluations and explicitly develop features and training regimens that favor generalizability. A performance-optimized version of the mention-synchronous system will be included in the open source Apache cTAKES software.

Geographical differences in survival of dogs with non-Hodgkin lymphoma treated with a CHOP based chemotherapy protocol

BACKGROUND

In humans geographical differences in the incidence and presentation of various cancers have been reported. However, much of this information has not been collected in veterinary oncology.

AIM

The purpose of this study was to determine if a geographic difference in progression free survival exists for dogs with lymphoma treated within the US.

MATERIALS AND METHODS

Medical records of 775 cases of canine lymphoma from 3 US regions (west, south and north), treated with CHOP chemotherapy, were retrospectively evaluated. Cases were collected from referral institutions and were required to have received at least one doxorubicin treatment and have follow up information regarding time to progression.

RESULTS

Significant differences in sex (p = 0.05), weight (p = 0.049), stage (p < 0.001), immunophenotype (p = <0.001), and number of doxorubicin doses (p = 0.001) were seen between regions. Upon univariate analysis, progression free survival (PFS) differed by region (p = 0.006), stage (p = 0.009), sub-stage (p = 0.0005), and immunophenotype (p = 0.001). A multivariable Cox regression model showed that dogs in the western region had a significantly shorter PFS when compared to the south and east.

CONCLUSION

PFS was significantly affected by stage, sub-stage and phenotype.

Krüppel-Like Factor 15 Mediates Glucocorticoid-Induced Restoration of Podocyte Differentiation Markers

Podocyte injury is the inciting event in primary glomerulopathies, such as minimal change disease and primary FSGS, and glucocorticoids remain the initial and often, the primary treatment of choice for these glomerulopathies. Because inflammation is not readily apparent in these diseases, understanding the direct effects of glucocorticoids on the podocyte, independent of the immunomodulatory effects, may lead to the identification of targets downstream of glucocorticoids that minimize toxicity without compromising efficacy. Several studies showed that treatment with glucocorticoids restores podocyte differentiation markers and normal ultrastructure and improves cell survival in murine podocytes. We previously determined that Krüppel-like factor 15 (KLF15), a kidney-enriched zinc finger transcription factor, is required for restoring podocyte differentiation markers in mice and human podocytes under cell stress. Here, we show that in vitro treatment with dexamethasone induced a rapid increase of KLF15 expression in human and murine podocytes and enhanced the affinity of glucocorticoid receptor binding to the promoter region of KLF15 In three independent proteinuric murine models, podocyte-specific loss of Klf15 abrogated dexamethasone-induced podocyte recovery. Furthermore, knockdown of KLF15 reduced cell survival and destabilized the actin cytoskeleton in differentiated human podocytes. Conversely, overexpression of KLF15 stabilized the actin cytoskeleton under cell stress in human podocytes. Finally, the level of KLF15 expression in the podocytes and glomeruli from human biopsy specimens correlated with glucocorticoid responsiveness in 35 patients with minimal change disease or primary FSGS. Thus, these studies identify the critical role of KLF15 in mediating the salutary effects of glucocorticoids in the podocyte.

Small Intracranial Aneurysm Treatment Using Target (®) Ultrasoft (™) Coils

PURPOSE

The introduction of small, soft, complex-shaped microcoils has helped facilitate the endovascular treatment of small intracranial aneurysms (IAs) over the last several years. Here, we evaluate the initial safety and efficacy of treating small IAs using only Target(®) Ultrasoft(™) coils.

MATERIALS AND METHODS

A retrospective review of a prospectively maintained clinical database at a single, high volume, teaching hospital was performed from September 2011 to May 2015. IAs smaller than or equal to 5.0 mm in maximal dimension treated with only Target(®) Ultrasoft(™) coils were included.

RESULTS

A total of 50 patients with 50 intracranial aneurysms were included. Subarachnoid hemorrhage from index aneurysm rupture was the indication for treatment in 23 of 50 (46%) cases, and prior subarachnoid hemorrhage (SAH) from another aneurysm was the indication for treatment in eight of 50 (16%) cases. The complete aneurysm occlusion rate was 70% (35/50), the minimal residual aneurysm rate was 14% (7/50), and residual aneurysm rate was 16% (8/50). One intraoperative aneurysm rupture occurred. Three patients died during hospitalization from clinical sequelae of subarachnoid hemorrhage. Follow-up at a mean of 13.6 months demonstrated complete aneurysm occlusion in 75% (30/40) of cases, near complete occlusion in 15% (6/40) of cases, and residual aneurysm in 10% (4/40) of cases, all four of which were retreated.

CONCLUSION

Our initial results using only Target(®) Ultrasoft(™) coils for the endovascular treatment of small intracranial aneurysms demonstrate initial excellent safety and efficacy profiles.

Use of Pipeline Flex is associated with reduced fluoroscopy time, procedure time, and technical failure compared with the first-generation Pipeline embolization device

Background

Flow diversion with the Pipeline embolization device is a well-established method of intracranial aneurysm treatment. However, deployment of the first-generation device (Pipeline Classic) can be technically challenging. The Pipeline Flex contains the same flow-diverting stent with a modified delivery system.

Objective

To compare procedural outcomes between the first-generation device (Pipeline Classic) and the Pipeline Flex.

Methods

Thirty-eight of the first 40 consecutive patients who underwent intracranial aneurysm treatment with the Pipeline Flex and 58 of the most recent 60 consecutive patients who underwent treatment with the Pipeline Classic at our institution were evaluated. Patient demographics, aneurysm characteristics, technical procedural details, and early outcomes were analyzed.

Results

The two groups were comparable for age, gender, and location of target aneurysms. Use of Pipeline Flex decreased procedure time by 44.2 min (p≤0.001) and fluoroscopy time by 22.0 min (p=0.001) compared with the Pipeline Classic. Similarly, radiation exposure was less in the Flex group with a mean difference of 3473.5 Gy cm2 (p=0.002), while contrast usage was decreased with a mean difference of 22.3 mL (p=0.007). These differences remained significant in multivariate regression analysis. Finally, the rate of device deployment failure was lower in the Flex group (7.1%) than in the Classic group (23.9%) (p=0.034).

Conclusions

Use of Pipeline Flex significantly reduces the total procedure and fluoroscopy time, contrast usage, patient radiation exposure, and proportion of recaptured devices in comparison with the Pipeline Classic, probably owing to an enhanced delivery system that allows for more reliable and controlled deployment.

Incidence and lifetime costs of injuries in the United States

BACKGROUND

Standardized methodologies for assessing economic burden of injury at the national or international level do not exist.

OBJECTIVE

To measure national incidence, medical costs, and productivity losses of medically treated injuries using the most recent data available in the United States, as a case study for similarly developed countries undertaking economic burden analyses.

METHOD

The authors combined several data sets to estimate the incidence of fatal and non-fatal injuries in 2000. They computed unit medical and productivity costs and multiplied these costs by corresponding incidence estimates to yield total lifetime costs of injuries occurring in 2000.

MAIN OUTCOME MEASURES

Incidence, medical costs, productivity losses, and total costs for injuries stratified by age group, sex, and mechanism.

RESULTS

More than 50 million Americans experienced a medically treated injury in 2000, resulting in lifetime costs of $406 billion; $80 billion for medical treatment and $326 billion for lost productivity. Males had a 20% higher rate of injury than females. Injuries resulting from falls or being struck by/against an object accounted for more than 44% of injuries. The rate of medically treated injuries declined by 15% from 1985 to 2000 in the US. For those aged 0-44, the incidence rate of injuries declined by more than 20%; while persons aged 75 and older experienced a 20% increase.

CONCLUSIONS

These national burden estimates provide unequivocal evidence of the large health and financial burden of injuries. This study can serve as a template for other countries or be used in intercountry comparisons.

Enhanced Recovery After Surgery (ERAS) for gastrointestinal surgery, part 2: consensus statement for anaesthesia practice

Background

The present interdisciplinary consensus review proposes clinical considerations and recommendations for anaesthetic practice in patients undergoing gastrointestinal surgery with an Enhanced Recovery after Surgery (ERAS) programme.

Methods

Studies were selected with particular attention being paid to meta‐analyses, randomized controlled trials and large prospective cohort studies. For each item of the perioperative treatment pathway, available English‐language literature was examined and reviewed. The group reached a consensus recommendation after critical appraisal of the literature.

Results

This consensus statement demonstrates that anaesthesiologists control several preoperative, intraoperative and postoperative ERAS elements. Further research is needed to verify the strength of these recommendations.

Conclusions

Based on the evidence available for each element of perioperative care pathways, the Enhanced Recovery After Surgery (ERAS ^®) Society presents a comprehensive consensus review, clinical considerations and recommendations for anaesthesia care in patients undergoing gastrointestinal surgery within an ERAS programme. This unified protocol facilitates involvement of anaesthesiologists in the implementation of the ERAS programmes and allows for comparison between centres and it eventually might facilitate the design of multi‐institutional prospective and adequately powered randomized trials.

Isolation of sophorose during sophorolipid production and studies of its stability in aqueous alkali: epimerisation of sophorose to 2-O-β-D-glucopyranosyl-D-mannose

NMR and anion exchange chromatography analysis of the waste streams generated during the commercial production of sophorolipids by the yeast Candida bombicola identified the presence of small but significant quantities (1% w/v) of free sophorose. Sophorose, a valuable disaccharide, was isolated from the aqueous wastes using a simple extraction procedure and was purified by chromatography on a carbon celite column providing easy access to large quantities of the disaccharide. Experiments were undertaken to identify the origin of sophorose and it is likely that acetylated sophorose derivatives were produced by an enzyme catalysed hydrolysis of the glucosyl-lipid bond of sophorolipids; the acetylated sophorose derivatives then undergo hydrolysis to release the parent disaccharide. Treatment of sophorose with aqueous alkali at elevated temperatures (0.1M NaOH at 50 °C) resulted in C2-epimerisation of the terminal reducing sugar and its conversion to the corresponding 2-O-β-D-glucopyranosyl-D-mannose which was isolated and characterised. In aqueous alkaline solution β-(1,2)-linked glycosidic bonds do not undergo either hydrolysis or peeling reactions.

Donation After Circulatory Determination of Death Lung Transplantation for Pulmonary Arterial Hypertension: Passing the Toughest Test

Lung transplantation (LTx) is a therapeutic option for severe pulmonary arterial hypertension (PAH) patients failing optimal medical therapy. The use of donation after circulatory determination of death (DCDD) donor lungs for PAH LTx has rarely been reported, primarily reflecting concerns that DCDD lungs represent extended criteria donors, at risk of morbidity and mortality. A retrospective study of all Alfred Hospital DCDD and DNDD (donation after neurologic determination of death) PAH LTx was undertaken. Protocolized fluid/inotrope/ventilator and extracorporeal membrane oxygenation (ECMO) strategies were utilized. Since our first DCDD LTx in 2006, 512 LTx have been performed. Of 31 PAH recipients, 11 received DCDD lungs (11% of DCDD LTx) and 20 received DNDD lungs (5% of DNDD LTx) (p = 0.04). Only one PAH patient died on the LTx waiting list. Peri-LTx ECMO was utilized in 3/11 (27%) DCDD and 6/20 (30%) DNDD PAH LTx (p = 0.68). Primary graft dysfunction, intensive care, and overall stay were the same in both groups. Survival at 1 and 8 years was 100% and 80% for DCDD versus 100% and 70% for DNDD LTx (p = 0.88), respectively. In conclusion, excellent results can be achieved for PAH LTx. DCDD donor lungs are not extended lungs per se having passed the toughest test.

Semi-supervised Learning for Phenotyping Tasks

Supervised learning is the dominant approach to automatic electronic health records-based phenotyping, but it is expensive due to the cost of manual chart review. Semi-supervised learning takes advantage of both scarce labeled and plentiful unlabeled data. In this work, we study a family of semi-supervised learning algorithms based on Expectation Maximization (EM) in the context of several phenotyping tasks. We first experiment with the basic EM algorithm. When the modeling assumptions are violated, basic EM leads to inaccurate parameter estimation. Augmented EM attenuates this shortcoming by introducing a weighting factor that downweights the unlabeled data. Cross-validation does not always lead to the best setting of the weighting factor and other heuristic methods may be preferred. We show that accurate phenotyping models can be trained with only a few hundred labeled (and a large number of unlabeled) examples, potentially providing substantial savings in the amount of the required manual chart review.

Photoemission Circular Dichroism and Spin Polarization of the Topological Surface States in Ultrathin Bi2Te3 Films

Circular dichroism (CD) observed by photoemission, being sensitive to the orbital and spin angular momenta of the electronic states, is a powerful probe of the nontrivial surface states of topological insulators, but the experimental results thus far have eluded a comprehensive description. We report a study of Bi2Te3 films with thicknesses ranging from one quintuple layer (two-dimensional limit) to 12 layers (bulk limit) over a wide range of incident photon energy. The data show complex variations in magnitude and sign reversals, which are nevertheless well described by a theoretical calculation including all three photoemission mechanisms: dipole transition, surface photoemission, and spin-orbit coupling. The results establish the nontrivial connection between the spin-orbit texture and CD.

Lidocaine patch for acute pain management: a meta-analysis of prospective controlled trials

BACKGROUND

Local anesthetic is one of the cornerstones of multimodal analgesia. We investigated the efficacy of the lidocaine patch for acute pain management.

METHODS

We searched MEDLINE, CINAHL, Scopus, and the Cochrane Controlled Trials Register for published prospective controlled clinical trials that evaluated the analgesic effect of the lidocaine patch for acute or postoperative pain management (1966--2014). The outcomes were postoperative opioid consumption, pain intensity and length of hospital stay.

RESULTS

Five trials comparing the lidocaine patch with control (no treatment/placebo) for acute or postoperative pain treatment/management were included in this meta-analysis. Data was analyzed on 251 patients. Between the lidocaine patch group and the control group, no significant difference was found for all three outcomes (all p > 0.05). For postoperative opioid consumption, mean difference (MD) was -8.2 mg morphine equivalent (95% CI -28.68, 12.24). For postoperative pain intensity, MD was -9.1 mm visual analog scale or equivalent (95% CI -23.31, 5.20). For length of hospital stay, MD was -0.2 days (95% CI -0.80, 0.43).

CONCLUSION

Application of a lidocaine patch may not be an effective adjunct for acute and postoperative pain management, in terms of pain intensity, opioid consumption and length of hospital stay.

LIMITATIONS

The limitations were a small number of included studies, potential biases from some unblinded studies, clinical heterogeneity between studies, and incomplete reported data for adjunct analgesics.

Negation's not solved: generalizability versus optimizability in clinical natural language processing

A review of published work in clinical natural language processing (NLP) may suggest that the negation detection task has been “solved.” This work proposes that an optimizable solution does not equal a generalizable solution. We introduce a new machine learning-based Polarity Module for detecting negation in clinical text, and extensively compare its performance across domains. Using four manually annotated corpora of clinical text, we show that negation detection performance suffers when there is no in-domain development (for manual methods) or training data (for machine learning-based methods). Various factors (e.g., annotation guidelines, named entity characteristics, the amount of data, and lexical and syntactic context) play a role in making generalizability difficult, but none completely explains the phenomenon. Furthermore, generalizability remains challenging because it is unclear whether to use a single source for accurate data, combine all sources into a single model, or apply domain adaptation methods. The most reliable means to improve negation detection is to manually annotate in-domain training data (or, perhaps, manually modify rules); this is a strategy for optimizing performance, rather than generalizing it. These results suggest a direction for future work in domain-adaptive and task-adaptive methods for clinical NLP.

Preserving knee function following osteoarthritis diagnosis: a sustainability theory and social ecology clinical commentary

To sustain natural systems, there must be an ongoing balance between environmental, social, and economic considerations. A key element of sustainability theory is to identify the most vulnerable surroundings. The most vulnerable knee tissue is the articular cartilage as it is the last line of osteoarthritis (OA) defense. This tissue has a poor capacity for healing. Based on sustainability theory and social ecology concepts we propose that several key factors contribute to knee function preservation. Factors include health history, genetic predisposition, personal behaviors, and socio-environmental factors in addition to local-regional-global physiological system function. Addressing only some of these factors or any one factor in isolation may lead to less than optimal treatment effectiveness. The purpose of this commentary is to introduce a medical, surgical and rehabilitation management approach for patients with knee OA that considers more than physical function improvement. This approach also considers social, emotional, and environmental factors to better ensure patient satisfaction, fulfilled expectations and successful outcomes. A clinical care pathway is presented for a 57-year-old patient with medial compartment knee OA who is contemplating early arthroplasty versus a knee function preservation treatment approach. Early arthroplasty refers to high revision likelihood based on a minimum 15 year prosthesis life-expectancy.

Incidence of contrast material-induced nephropathy after neuroendovascular procedures

PURPOSE

To report the incidence and risk factors for contrast material ( CM contrast material )-induced nephropathy ( CIN CM-induced nephropathy ) in patients with no history of chronic kidney disease and estimated glomerular filtration rate that exceeded 30 mL/min/1.73 m(2) after a relatively high dose of CM contrast material (≥250 mL) during neuroendovascular procedures.

MATERIALS AND METHODS

An institutional review board-approved retrospective chart review was performed for all patients who received a dose of CM contrast material 250 mL or greater while they underwent a neuroendovascular procedure between January 2011 and February 2013. The control group consisted of comparable patients who received a CM contrast material dose of 75-249 mL during the same period. Patients with pre-existing estimated glomerular filtration rate of 30 mL/min/1.73 m(2) or less or documented history of chronic kidney disease were excluded. CIN CM-induced nephropathy was defined as an increase in serum creatinine 50% above the baseline or an absolute increase of 0.3 mg/dL at either 24 or 48 hours after the procedure. Statistical analysis was performed with the Student t test, χ(2) analysis, and mixed-model analysis of variance.

RESULTS

Clinical characteristics between the control and high-dose group were similar for age (95% confidence interval [CI]: -3.69, 5.48; P = .70), sex (95% CI: 0.28, 0.43; P = .62), and ethnicity (95% CI: 0.42, 0.58; P = .47). The average volume of CM contrast material administered was 172 mL in the control group and 326 mL in the high-dose cohort (95% CI: 131.78, 175.05; P < .001). Of the 79 cases in the high-dose cohort, 36 (46%) received a CM contrast material dose between 250 and 299 mL, 29 (37%) received 300-399 mL, nine (11%) received 400-499 mL, and five (6%) received greater than 500 mL. By 48 hours, a statistically significant decrease in serum creatinine was seen in two of the four high-dose CM contrast material dose categories: 250-299 mL (decrease of 24%; [95% CI: 0.04, 0.36]; P = .003) and greater than 500 mL (decrease of 14% [95% CI: -0.33, 0.57]; P = .007). There were four cases (5%) of CIN CM-induced nephropathy : three (4%) at 24 hours and one (1%) at 48 hours. The comorbid rate of diabetes (25% vs 15% [95% CI: -0.01, 0.04]; P < .001) was found to be higher among those who developed CIN CM-induced nephropathy compared with those who did not within the high-dose cohort. No cases of CIN CM-induced nephropathy occurred in the control group.

CONCLUSION

Risk of developing CIN CM-induced nephropathy is relatively low in patients who undergo neuroendovascular procedures with CM contrast material doses of 250 mL or greater.

Affective disorders influence clinical outcomes after revision lumbar surgery in elderly patients with symptomatic adjacent-segment disease, recurrent stenosis, or pseudarthrosis

Object

Depression and persistent low-back pain (LBP) are common and disabling problems in elderly patients (> 65 years old). Affective disorders, such as depression and anxiety, are also common in elderly patients, with a prevalence ranging from 4% to 16%. Depressive symptoms are consistently associated with functional disability. To date, few studies have assessed the predictive value of baseline depression on outcomes in the setting of revision spine surgery in elderly patients. Therefore, in this study, the authors assessed the predictive value of preoperative depression on 2-year postoperative outcomes.

Methods

A total of 69 patients undergoing revision neural decompression and instrumented fusion for adjacent-segment disease (ASD, n = 28), pseudarthrosis (n = 17), or same-level recurrent stenosis (n = 24) were included in this study. Preoperative Zung Self-Rating Depression Scale (ZDS) scores were assessed for all patients. Preoperative and 2-year postoperative visual analog scale (VAS) scores for back pain (VAS-BP) and leg pain (VAS-LP) and the Oswestry Disability Index (ODI) were also assessed. The association between preoperative ZDS score and 2-year improvement in disability was assessed via multivariate regression analysis.

Results

Compared with preoperative status, 2-year postoperative VAS-BP was significantly improved after surgery for ASD (9 ± 2 vs 4.01 ± 2.56, respectively; p = 0.001), as were pseudarthrosis (7.41 ± 1 vs 5.0 ± 3.08, respectively; p = 0.02) and same-level recurrent stenosis (7 ± 2.00 vs 5.00 ± 2.34, respectively; p = 0.003). Two-year ODI was also significantly improved after surgery for ASD (29 ± 9 vs 23.10 ± 10.18, respectively; p = 0.001), as were pseudarthrosis (28.47 ± 5.85 vs 24.41 ± 7.75, respectively; p = 0.001) and same-level recurrent stenosis (30.83 ± 5.28 vs 26.29 ± 4.10, respectively; p = 0.003). Independent of other factors—age, body mass index, symptom duration, smoking, comorbidities, severity of preoperative pain, and disability—increasing preoperative ZDS score was significantly associated with lower 2-year improvement in disability (ODI) after revision surgery in elderly patients with symptomatic ASD, pseudarthrosis, or recurrent stenosis.

Conclusions

The extent of preoperative depression is an independent predictor of less functional improvement following revision lumbar surgery in elderly patients with symptomatic ASD, pseudarthrosis, or recurrent stenosis. Timely diagnosis and treatment of depression and somatic anxiety in this cohort of patients may contribute to improvement in postoperative functional status.

Relationship of thrombus length to number of stent retrievals, revascularization, and outcomes in acute ischemic stroke

PURPOSE

To study the relationship between intracranial thrombus length and number of stent retrievals, revascularization rates, and functional outcomes in stroke.

MATERIALS AND METHODS

Retrospective data were collected from consecutive cases of stroke treated with endovascular procedures at a single institution from April 2012-September 2013. Thrombus length was measured in the anterior cerebral circulation. Demographic and clinical details; involved vessels; and procedural details, including the number of devices used and number of retrievals used for each device, were recorded. Revascularization rates and 90-day functional outcomes were recorded.

RESULTS

Data regarding the length of thrombus in the anterior cerebral circulation were available for 28 patients. There was no significant association between thrombus length and number of stent retrievals (P = .3780), final thrombolysis in cerebral infarction (TICI) score (P = .4835), or 90-day modified Rankin Scale score (P = .4146). There was a significant difference (P = .0280) between number of retrievals and final TICI score, with lower number of retrieval passes corresponding to higher final TICI scores.

CONCLUSIONS

The data suggest no relationship between thrombus length and number of stent retrievals, final TICI score, or functional neurologic outcomes at 90 days in stent retrieval thrombectomy for acute ischemic stroke. These results do not support a predictive value for thrombus length quantification in the evaluation of stroke.