bluuebunny/crossref_metadata_2025_split huggingface dataset:
A long journey to short abbreviations: developing an open-source framework for clinical abbreviation recognition and disambiguation (CARD)
Authors: Wu Yonghui , Denny Joshua C , Trent Rosenbloom S , Miller Randolph A , Giuse Dario A , Wang Lulu , Blanquicett Carmelo , Soysal Ergin , Xu Jun , Xu Hua 
Published: August 2016

Objective: The goal of this study was to develop a practical framework for recognizing and disambiguating clinical abbreviations, thereby improving current clinical natural language processing (NLP) systems’ capability to handle abbreviations in clinical narratives.Methods: We developed an open-source framework for clinical abbreviation recognition and disambiguation (CARD) that leverages our previously developed methods, including: (1) machine learning based approaches to recognize abbreviations from a clinical corpus, (2) clustering-based semiautomated methods to generate possible senses of abbreviations, and (3) profile-based word sense disambiguation methods for clinical abbreviations. We applied CARD to clinical corpora from Vanderbilt University Medical Center (VUMC) and generated 2 comprehensive sense inventories for abbreviations in discharge summaries and clinic visit notes. Furthermore, we developed a wrapper that integrates CARD with MetaMap, a widely used general clinical NLP system.Results and Conclusion: CARD detected 27 317 and 107 303 distinct abbreviations from discharge summaries and clinic visit notes, respectively. Two sense inventories were constructed for the 1000 most frequent abbreviations in these 2 corpora. Using the sense inventories created from discharge summaries, CARD achieved an F1 score of 0.755 for identifying and disambiguating all abbreviations in a corpus from the VUMC discharge summaries, which is superior to MetaMap and Apache’s clinical Text Analysis Knowledge Extraction System (cTAKES). Using additional external corpora, we also demonstrated that the MetaMap-CARD wrapper improved MetaMap’s performance in recognizing disorder entities in clinical notes. The CARD framework, 2 sense inventories, and the wrapper for MetaMap are publicly available at https://sbmi.uth.edu/ccb/resources/abbreviation.htm. We believe the CARD framework can be a valuable resource for improving abbreviation identification in clinical NLP systems.
Using clinical data to predict high-cost performance coding issues associated with pressure ulcers: a multilevel cohort model
Authors: Padula William V , Gibbons Robert D , Pronovost Peter J , Hedeker Donald , Mishra Manish K , Makic Mary Beth F , Bridges John FP , Wald Heidi L , Valuck Robert J , Ginensky Adam J , Ursitti Anthony , Venable Laura Ruth , Epstein Ziv , Meltzer David O 
Published: August 2016

Objective: Hospital-acquired pressure ulcers (HAPUs) have a mortality rate of 11.6%, are costly to treat, and result in Medicare reimbursement penalties. Medicare codes HAPUs according to Agency for Healthcare Research and Quality Patient-Safety Indicator 3 (PSI-03), but they are sometimes inappropriately coded. The objective is to use electronic health records to predict pressure ulcers and to identify coding issues leading to penalties.
Materials and Methods: We evaluated all hospitalized patient electronic medical records at an academic medical center data repository between 2011 and 2014. These data contained patient encounter level demographic variables, diagnoses, prescription drugs, and provider orders. HAPUs were defined by PSI-03: stages III, IV, or unstageable pressure ulcers not present on admission as a secondary diagnosis, excluding cases of paralysis. Random forests reduced data dimensionality. Multilevel logistic regression of patient encounters evaluated associations between covariates and HAPU incidence.
Results: The approach produced a sample population of 21 153 patients with 1549 PSI-03 cases. The greatest odds ratio (OR) of HAPU incidence was among patients diagnosed with spinal cord injury (ICD-9 907.2: OR = 14.3; P &lt; .001), and 71% of spinal cord injuries were not properly coded for paralysis, leading to a PSI-03 flag. Other high ORs included bed confinement (ICD-9 V49.84: OR = 3.1, P &lt; .001) and provider-ordered pre-albumin lab (OR = 2.5, P &lt; .001).
Discussion: This analysis identifies spinal cord injuries as high risk for HAPUs and as being often inappropriately coded without paralysis, leading to PSI-03 flags. The resulting statistical model can be tested to predict HAPUs during hospitalization.
Conclusion: Inappropriate coding of conditions leads to poor hospital performance measures and Medicare reimbursement penalties.
Developing an evidence base of best practices for integrating computerized systems into the exam room: a systematic review
Authors: Patel Minal R , Vichich Jennifer , Lang Ian , Lin Jessica , Zheng Kai 
Published: August 2016

Objective: The introduction of health information technology systems, electronic health records in particular, is changing the nature of how clinicians interact with patients. Lack of knowledge remains on how best to integrate such systems in the exam room. The purpose of this systematic review was to (1) distill “best” behavioral and communication practices recommended in the literature for clinicians when interacting with patients in the presence of computerized systems during a clinical encounter, (2) weigh the evidence of each recommendation, and (3) rank evidence-based recommendations for electronic health record communication training initiatives for clinicians.Methods: We conducted a literature search of 6 databases, resulting in 52 articles included in the analysis. We extracted information such as study setting, research design, sample, findings, and implications. Recommendations were distilled based on consistent support for behavioral and communication practices across studies.Results: Eight behavioral and communication practices received strong support of evidence in the literature and included specific aspects of using computerized systems to facilitate conversation and transparency in the exam room, such as spatial (re)organization of the exam room, maintaining nonverbal communication, and specific techniques that integrate the computerized system into the visit and engage the patient. Four practices, although patient-centered, have received insufficient evidence to date.Discussion and Conclusion: We developed an evidence base of best practices for clinicians to maintain patient-centered communications in the presence of computerized systems in the exam room. Further work includes development and empirical evaluation of evidence-based guidelines to better integrate computerized systems into clinical care.
The Significance of Base Deficit in Acidemic Term Neonates
Authors: Knutzen L. , Svirko E. , Impey L. 
Published: August 2016

(Am J Obstet Gynecol. 2015;213(3):373.e1–e7)
A lack of oxygen during the intrapartum period is a well-known and significant factor leading to cerebral palsy and mortality in infants. The degree of risk can be estimated after delivery by examining pH levels in the umbilical artery. An arterial pH of <7.00 along with a base deficit of 12 mmol/L or higher is believed to be particularly significant in predicting morbidity. The authors of this study have attempted to evaluate this association, hypothesizing that the level of arterial base deficit does not have any extra predictive value in acidemic neonates beyond what can be learned from the arterial pH.
Umbilical Artery pH and Base Deficit in Obstetrics
Authors: Cahill A.G. 
Published: August 2016

(Am J Obstet Gynecol. 2015;213(3):257–258)
When a child is delivered, it is important to be able to find objective measures which can be obtained at birth to accurately inform an obstetrician as to whether the infant is healthy and if that infant has any increased risk factors for future morbidities. An example of such a marker is hypoxic ischemic encephalopathy, which serves as an indicator from the neonatal period for cerebral palsy. For many years, infant risk for hypoxic ischemic encephalopathy has been assessed by measuring pH at birth. However, many have questioned whether there might be better indicators, such as a large base deficit or lactate. Others have raised the equally important question of whether any of these indicators are in fact reliable.
Predictive Value of the sFlt-1:PlGF Ratio in Women With Suspected Preeclampsia
Authors: Zeisler H. , Llurba E. , Chantraine F. , Vatish M. , Cathrine Staff A. , Sennström M. , Olovsson M. , Brennecke S.P. , Stepan H. , Allegranza D. , Dilba P. , Schoedl M. , Hund M. , Verlohren S. 
Published: August 2016

(N Engl J Med. 2016;374:13–22)
Preeclampsia is a serious multisystem disorder affecting up to 5% of pregnancies worldwide. A reliable predictor of preeclampsia would be helpful in allowing health care providers to identify women at risk for developing the disorder. Serum levels of circulating maternal soluble fms-like tyrosine kinase 1 (sFlt-1) are known to be elevated in preeclampsia, while levels of placental growth factor (PlGF) are decreased. A high ratio of sFlt-1 to PlGF indicates an increased risk for preeclampsia and could potentially be a more reliable predictor than either of those factors alone. The authors of this study sought to evaluate the ratio as a predictive tool among women with suspected preeclampsia.
Sedative-hypnotic Binding to 11β-hydroxylase
Authors: Pejo Ervin , Zhou Xiaojuan , Husain S. Shaukat , Raines Douglas E. 
Published: August 2016

Abstract

Background
Etomidate potently suppresses adrenocortical steroid synthesis with potentially deleterious consequences by binding to 11β-hydroxylase and inhibiting its function. The authors hypothesized that other sedative-hypnotics currently in clinical use or under development (or their metabolites) might bind to the same site at clinically relevant concentrations. The authors tested this hypothesis by defining etomidate’s affinity for this site and the potencies with which other sedative-hypnotics (and their metabolites) inhibit etomidate binding.

Methods
3H-etomidate’s binding to adrenal membranes from Sprague-Dawley rats was characterized with a filtration assay, and its dissociation constant was defined using saturation and homologous ligand competition approaches. Half-inhibitory concentrations of sedative-hypnotics and metabolites were determined from the reduction in specific 3H-etomidate binding measured in the presence of ranging sedative-hypnotic and metabolite concentrations.

Results
Saturation and homologous competition studies yielded 3H-etomidate dissociation constants of 40 and 21 nM, respectively. Half-inhibitory concentrations of etomidate and cyclopropyl methoxycarbonyl metomidate (CPMM) differed significantly (26 vs. 143 nM, respectively; P &lt; 0.001), and those of the carboxylic acid (CA) metabolites etomidate-CA and CPMM-CA were greater than or equal to 1,000× higher than their respective parent hypnotics. The half-inhibitory concentration of dexmedetomidine was 2.2 µM, whereas those of carboetomidate, ketamine, and propofol were greater than or equal to 50 µM.

Conclusion
Etomidate’s in vitro dissociation constant for 11β-hydroxylase closely approximates its in vivo adrenocortical half-inhibitory concentration. CPMM produces less adrenocortical suppression than etomidate not only because it is metabolized faster but also because it binds to 11β-hydroxylase with lower affinity. Other sedative-hypnotics and metabolites bind to 11β-hydroxylase and inhibit etomidate binding only at suprahypnotic concentrations.
Enhanced Recovery Implementation in Major Gynecologic Surgeries
Authors: Modesitt Susan C. , Sarosiek Bethany M. , Trowbridge Elisa R. , Redick Dana L. , Shah Puja M. , Thiele Robert H. , Tiouririne Mohamed , Hedrick Traci L. 
Published: August 2016

OBJECTIVE:
To examine implementing an enhanced recovery after surgery (ERAS) protocol for women undergoing major gynecologic surgery at an academic institution and compare surgical outcomes before and after implementation.

METHODS:
Two ERAS protocols were developed: a full pathway using regional anesthesia for open procedures and a light pathway without regional anesthesia for vaginal and minimally invasive procedures. Enhanced recovery after surgery pathways included extensive preoperative counseling, carbohydrate loading and oral fluids before surgery, multimodal analgesia with avoidance of intravenous opioids, intraoperative goal-directed fluid resuscitation, and immediate postoperative feeding and ambulation. A before-and-after study design was used to compare clinical outcomes, costs, and patient satisfaction. Complications and risk-adjusted length of stay were drawn from the American College of Surgeons’ National Surgical Quality Improvement Program database.

RESULTS:
On the ERAS full protocol, 136 patients were compared with 211 historical controls and the median length of stay was reduced (2.0 compared with 3.0 days; P=.007) despite an increase in National Surgical Quality Improvement Program-predicted length of stay (2.5 compared with 2.0 days; P=.009). Reductions were seen in median intraoperative morphine equivalents (0.3 compared with 12.7 mg; P<.001), intraoperative (285 compared with 1,250 mL; P<.001) and total intravenous fluids (−917.5 compared with 1,410 mL; P<.001), immediate postoperative pain scores (3.7 compared with 5.0; P<.001), and total complications (21.3% compared with 40.2%; P=.004). On the ERAS light protocol, 249 patients were compared with 324 historical controls and demonstrated decreased intraoperative and postoperative morphine equivalents (0.0 compared with 13.0 mg; P<.001 and 15.0 compared with 23.6 mg; P<.001) and decreased intraoperative and overall net intravenous fluids (P<.001). Patient satisfaction scores showed a marked and significant improvement on focus questions regarding pain control, nurses keeping patients informed, and staff teamwork; 30-day total hospital costs were significantly decreased in both ERAS groups.

CONCLUSION:
Implementation of ERAS protocols in gynecologic surgery was associated with a substantial decrease in intravenous fluids and morphine administration coupled with reduction in length of stay for open procedures combined with improved patient satisfaction and decreased hospital costs.
Group Prenatal Care Compared With Traditional Prenatal Care
Authors: Carter Ebony B. , Temming Lorene A. , Akin Jennifer , Fowler Susan , Macones George A. , Colditz Graham A. , Tuuli Methodius G. 
Published: August 2016

OBJECTIVE:
To estimate the effect of group prenatal care on perinatal outcomes compared with traditional prenatal care.

DATA SOURCES:
We searched MEDLINE through PubMed, EMBASE, Scopus, Cumulative Index of Nursing and Allied Health literature, the Cochrane Database of Systematic Reviews, the Database of Abstracts of Reviews of Effects, the Cochrane Central Register of Controlled Trials, and ClinicalTrials.gov.

METHODS OF STUDY SELECTION:
We searched electronic databases for randomized controlled trials and observational studies comparing group care with traditional prenatal care. The primary outcome was preterm birth. Secondary outcomes were low birth weight, neonatal intensive care unit admission, and breastfeeding initiation. Heterogeneity was assessed using the Q test and I
2 statistic. Pooled relative risks (RRs) and weighted mean differences were calculated using random-effects models.

TABULATIONS, INTEGRATION, AND RESULTS:
Four randomized controlled trials and 10 observational studies met inclusion criteria. The rate of preterm birth was not significantly different with group care compared with traditional care (11 studies: pooled rates 7.9% compared with 9.3%, pooled RR 0.87, 95% confidence interval [CI] 0.70–1.09). Group care was associated with a decreased rate of low birth weight overall (nine studies: pooled rate 7.5% group care compared with 9.5% traditional care; pooled RR 0.81, 95% CI 0.69–0.96), but not among randomized controlled trials (four studies: 7.9% group care compared with 8.7% traditional care, pooled RR 0.92, 95% CI 0.73–1.16). There were no significant differences in neonatal intensive care unit admission or breastfeeding initiation.

CONCLUSION:
Available data suggest that women who participate in group care have similar rates of preterm birth, neonatal intensive care unit admission, and breastfeeding.
Outcomes and Postoperative Complications After Hysterectomies Performed for Benign Compared With Malignant Indications
Authors: Wallace Sumer K. , Fazzari Melissa J. , Chen Hui , Cliby William A. , Chalas Eva 
Published: August 2016

OBJECTIVE:
To compare complications and outcomes after hysterectomy for benign compared with malignant indications in the United States.

METHODS:
Women who underwent hysterectomy in the United States for either benign or malignant indications from January 2008 to December 2012 were retrospectively identified using the National Surgical Quality Improvement Program database. Patients were excluded if the procedure was not performed for primary gynecologic indications. Appropriate procedures were identified using Current Procedural Terminology and International Classification of Diseases, 9th Revision codes. Univariate and multivariable models for complication risk were estimated using logistic regression.

RESULTS:
We identified 59,525 eligible patients, with 49,331 (82.9%) hysterectomies performed for benign and 10,194 (17.1%) for malignant indications. All complications, including wound complications (2.5% benign compared with 5.5% malignant, P<.001), venous thromboembolism (0.33% compared with 1.7%, P<.001), urinary tract infection (2.7% compared with 3.2%, P=.009), sepsis (0.53% compared with 1.9%, P<.001), blood transfusion (2.6% compared with 11.5%, P<.001), death (0.02% compared with 0.10%, P<.001), unplanned readmission (1.8% compared with 4.5%, P<.001), and returns to the operating room (0.91% compared with 1.4%, P<.001), were significantly more common for malignant hysterectomies. The overall rate of complications for benign cases was 7.9% compared with a rate of 19.4% for malignant hysterectomy. The median operating time for laparoscopy in benign cases was significantly longer than for open or vaginal hysterectomy procedures (127 minutes compared with 105 or 94 minutes, respectively; P<.001). The median operating time in malignant cases was significantly longer than for benign cases (P<.001).

CONCLUSION:
Hysterectomies performed for gynecologic malignancies are associated with a more than twofold higher complication rate compared with those performed for benign conditions. Minimally invasive surgery is associated with a decreased complication rate compared with open surgery. These data can be used for patient counseling and surgical planning, determining physician and hospital costs of care, and considered when assigning value-based reimbursement.
Accuracy of Onsite Tests to Detect Asymptomatic Bacteriuria in Pregnancy
Authors: Rogozińska Ewelina , Formina Sandra , Zamora Javier , Mignini Luciano , Khan Khalid S. 
Published: August 2016

OBJECTIVE:To estimate the accuracy of onsite tests to detect asymptomatic bacteriuria among pregnant women.DATA SOURCES:We searched MEDLINE, EMBASE, Web of Science, Scopus, and Latin-American Literature from inception until June 2015 without language restrictions. The ClinicalTrials.gov register database was screened to identify any recently completed studies.METHODS OF STUDY SELECTION:Two independent reviewers selected studies that recruited asymptomatic pregnant women to evaluate the accuracy of onsite tests in detecting the presence of bacteria in the urine using urine culture as a reference standard.TABULATION, INTEGRATION, AND RESULTS:Women's characteristics, study design, urine sample collection, and handling were extracted along with the test accuracy data. Where possible, we pooled the data using a bivariate, hierarchical random-effects model. Of 1,360 screened references, 27 articles (13,641 women) with test accuracy data on nine tests met the inclusion criteria. The most commonly evaluated test was urine dipstick. The pooled sensitivity and specificity of nitrites detected by dipstick to detect asymptomatic bacteriuria were 0.55 (95% confidence interval [CI] 0.42–0.67) and 0.99 (95% CI 0.98–0.99), respectively. The Griess test to detect nitrites had a sensitivity of 0.65 (95% CI 0.50–0.78) and specificity of 0.99 (95% CI 0.98–1.00). Dipslide with Gram staining had a pooled sensitivity of 0.86 (95% CI 0.80–0.91) and specificity of 0.97 (95% CI 0.93–0.99).CONCLUSION:The specificity of onsite tests is high; however, the sensitivity is not with the result that they will fail to detect a substantial number of cases of asymptomatic bacteriuria.CLINICAL TRIAL REGISTRATION:PROSPERO International prospective register of systematic reviews, http://www.crd.york.ac.uk/PROSPERO/, CRD42015027905.
Prolonged Detection of Zika Virus RNA in Pregnant Women
Authors: Meaney-Delman Dana , Oduyebo Titilope , Polen Kara N.D. , White Jennifer L. , Bingham Andrea M. , Slavinski Sally A. , Heberlein-Larson Lea , St. George Kirsten , Rakeman Jennifer L. , Hills Susan , Olson Christine K. , Adamski Alys , Culver Barlow Lauren , Lee Ellen H. , Likos Anna M. , Muñoz Jorge L. , Petersen Emily E. , Dufort Elizabeth M. , Dean Amy B. , Cortese Margaret M. , Santiago Gilberto A. , Bhatnagar Julu , Powers Ann M. , Zaki Sherif , Petersen Lyle R. , Jamieson Denise J. , Honein Margaret A. ,   for the U.S. Zika Pregnancy Registry Prolonged Viremia Working Group
Published: August 2016

OBJECTIVE:
Zika virus infection during pregnancy is a cause of microcephaly and other fetal brain abnormalities. Reports indicate that the duration of detectable viral RNA in serum after symptom onset is brief. In a recent case report involving a severely affected fetus, Zika virus RNA was detected in maternal serum 10 weeks after symptom onset, longer than the duration of RNA detection in serum previously reported. This report summarizes the clinical and laboratory characteristics of pregnant women with prolonged detection of Zika virus RNA in serum that were reported to the U.S. Zika Pregnancy Registry.

METHODS:
Data were obtained from the U.S. Zika Pregnancy Registry, an enhanced surveillance system of pregnant women with laboratory evidence of confirmed or possible Zika virus infection. For this case series, we defined prolonged detection of Zika virus RNA as Zika virus RNA detection in serum by real-time reverse transcription-polymerase chain reaction (RT-PCR) 14 or more days after symptom onset or, for women not reporting signs or symptoms consistent with Zika virus disease (asymptomatic), 21 or more days after last possible exposure to Zika virus.

RESULTS:
Prolonged Zika virus RNA detection in serum was identified in four symptomatic pregnant women up to 46 days after symptom onset and in one asymptomatic pregnant woman 53 days postexposure. Among the five pregnancies, one pregnancy had evidence of fetal Zika virus infection confirmed by histopathologic examination of fetal tissue, three pregnancies resulted in live births of apparently healthy neonates with no reported abnormalities, and one pregnancy is ongoing.

CONCLUSION:
Zika virus RNA was detected in the serum of five pregnant women beyond the previously estimated timeframe. Additional real-time RT-PCR testing of pregnant women might provide more data about prolonged detection of Zika virus RNA and the possible diagnostic, epidemiologic, and clinical implications for pregnant women.