Multi-label natural language processing to identify diagnosis and procedure codes from MIMIC-III inpatient notes

In the United States, 25% or greater than 200 billion dollars of hospital spending accounts for administrative costs that involve services for medical coding and billing. With the increasing number of patient records, manual assignment of the codes performed is overwhelming, time-consuming and error-prone, causing billing errors. Natural language processing can automate the extraction of codes/labels from unstructured clinical notes, which can aid human coders to save time, increase productivity, and verify medical coding errors. Our objective is to identify appropriate diagnosis and procedure codes from clinical notes by performing multi-label classification. We used de-identified data of critical care patients from the MIMIC-III database and subset the data to select the ten (top-10) and fifty (top-50) most common diagnoses and procedures, which covers 47.45% and 74.12% of all admissions respectively. We implemented state-of-the-art Bidirectional Encoder Representations from Transformers (BERT) to fine-tune the language model on 80% of the data and validated on the remaining 20%. The model achieved an overall accuracy of 87.08%, an F1 score of 85.82%, and an AUC of 91.76% for top-10 codes. For the top-50 codes, our model achieved an overall accuracy of 93.76%, an F1 score of 92.24%, and AUC of 91%. When compared to previously published research, our model outperforms in predicting codes from the clinical text. We discuss approaches to generalize the knowledge discovery process of our MIMIC-BERT to other clinical notes. This can help human coders to save time, prevent backlogs, and additional costs due to coding errors.Comment: This is a shortened version of the Capstone Project that was accepted by the Faculty of Indiana University, in partial fulfillment of the requirements for the degree of Master of Science in Health Informatic

Global report on preterm birth and stillbirth (2 of 7): discovery science

<p>Abstract</p> <p>Background</p> <p>Normal and abnormal processes of pregnancy and childbirth are poorly understood. This second article in a global report explains what is known about the etiologies of preterm births and stillbirths and identifies critical gaps in knowledge. Two important concepts emerge: the continuum of pregnancy, beginning at implantation and ending with uterine involution following birth; and the multifactorial etiologies of preterm birth and stillbirth. Improved tools and data will enable discovery scientists to identify causal pathways and cost-effective interventions.</p> <p>Pregnancy and parturition continuum</p> <p>The biological process of pregnancy and childbirth begins with implantation and, after birth, ends with the return of the uterus to its previous state. The majority of pregnancy is characterized by rapid uterine and fetal growth without contractions. Yet most research has addressed only uterine stimulation (labor) that accounts for <0.5% of pregnancy.</p> <p>Etiologies</p> <p>The etiologies of preterm birth and stillbirth differ by gestational age, genetics, and environmental factors. Approximately 30% of all preterm births are indicated for either maternal or fetal complications, such as maternal illness or fetal growth restriction. Commonly recognized pathways leading to preterm birth occur most often during the gestational ages indicated: (1) inflammation caused by infection (22-32 weeks); (2) decidual hemorrhage caused by uteroplacental thrombosis (early or late preterm birth); (3) stress (32-36 weeks); and (4) uterine overdistention, often caused by multiple fetuses (32-36 weeks). Other contributors include cervical insufficiency, smoking, and systemic infections. Many stillbirths have similar causes and mechanisms. About two-thirds of late fetal deaths occur during the antepartum period; the other third occur during childbirth. Intrapartum asphyxia is a leading cause of stillbirths in low- and middle-income countries.</p> <p>Recommendations</p> <p>Utilizing new systems biology tools, opportunities now exist for researchers to investigate various pathways important to normal and abnormal pregnancies. Improved access to quality data and biological specimens are critical to advancing discovery science. Phenotypes, standardized definitions, and uniform criteria for assessing preterm birth and stillbirth outcomes are other immediate research needs.</p> <p>Conclusion</p> <p>Preterm birth and stillbirth have multifactorial etiologies. More resources must be directed toward accelerating our understanding of these complex processes, and identifying upstream and cost-effective solutions that will improve these pregnancy outcomes.</p

Unprecedented behaviour of chronic myeloid leukaemia

We report the occurrence of leukaemic infiltration of cervical spinal cord secondary to chronic myeloid leukaemia (CML) in a 31-year-old male patient. He presented with left upper limb monoplegia. On examination he had asymmetric quadriparesis, graded sensory loss and urinary retention. Diagnosis was suggested by magnetic resonance imaging. He responded dramatically to radiotherapy and corticosteroids treatment. Infiltration of the cervical spinal cord in a patient with CML has seldom been reported in literature till date, and hence we are reporting this case

Field, temperature and thickness dependent electron transport in 5,5′-(2,6-di-tert-butylanthracene-9,10-diyl)bis(2-p-tolyl-1,3,4-oxadiazole)

Charge transport in 5,5′-(2,6-di-tert-butylanthracene-9,10-diyl)bis(2-p-tolyl-1,3,4-oxadiazole) is investigated as a function of temperature and organic layer thickness. The thickness dependence of the current indicates towards the trap charge limited conduction (TCLC) with a field and temperature dependent mobility. The density of trap states has been found to be dependent on sample thickness. As the thickness has increased from 80 nm to 120 nm, trap energy has correspondingly increased from 78 meV to 130 meV. TCLC model with Poole Frenkel type field dependent mobility has been fitted into the data and has been found in excellent agreement. Temperature dependency of zero field mobility (μ0) and β has been estimated from the model

Field, temperature and thickness dependent electron transport in 5,5′-(2,6-di-tert-butylanthracene-9,10-diyl)bis(2-p-tolyl-1,3,4-oxadiazole)

Charge transport in 5,5′-(2,6-di-tert-butylanthracene-9,10-diyl)bis(2-p-tolyl-1,3,4-oxadiazole) is investigated as a function of temperature and organic layer thickness. The thickness dependence of the current indicates towards the trap charge limited conduction (TCLC) with a field and temperature dependent mobility. The density of trap states has been found to be dependent on sample thickness. As the thickness has increased from 80 nm to 120 nm, trap energy has correspondingly increased from 78 meV to 130 meV. TCLC model with Poole Frenkel type field dependent mobility has been fitted into the data and has been found in excellent agreement. Temperature dependency of zero field mobility (μ0) and β has been estimated from the model

Design and synthesis of novel anthracene derivatives as n-type emitters for electroluminescent devices: a combined experimental and DFT study

Six novel anthracene-oxadiazole derivatives, 4a (2-(4-(anthracen-9-yl)phenyl)-5-p-tolyl-1,3,4-oxadiazole), 4b (2-(4-(anthracen-9-yl)phenyl)-5-(4-tert-butylphenyl)-1,3,4-oxadiazole), 4c (2-(4-(anthracen-9-yl)phenyl)-5-(4-methoxyphenyl)-1,3,4-oxadiazole), 8a (2-(4-(anthracen-9-yl)phenyl)-5-m-tolyl-1,3,4-oxadiazole), 8b (2-(3-(anthracen-9-yl)phenyl)-5-(4-tert-butylphenyl)-1,3,4-oxadiazole) and 8c (2-(3-(anthracen-9-yl)phenyl)-5-(3,4,5-trimethoxyphenyl)-1,3,4-oxadiazole) have been synthesized and characterized for use as emitters in organic light emitting devices (OLEDs). They show good thermal stability (T-d, 297-364 degrees C) and glass transition temperatures (T-g) in the range of 82-98 degrees C, as seen from the thermo gravimetric analysis and differential scanning calorimetric studies. The solvatochromism phenomenon and electrochemical properties have been studied in detail using UV-Vis absorption, fluorescence spectroscopy and cyclic voltammetry. TD-DFT calculations have been carried out to understand the electrochemical and photophysical properties. The spatial structures of 4b and 8c are further confirmed by X-ray diffraction analysis. Un-optimized non-doped electroluminescent devices were fabricated using these anthracene derivatives as emitters with the following device configuration: ITO (120 nm)/alpha-NPD (30 nm)/4a-4c or 8a-8c (35 nm)/BCP (6 nm)/Alq(3) (28 nm)/LiF (1 nm)/Al (150 nm). Among all the six compounds, 8a displays the maximum brightness of 1728 cd m(-2) and current efficiency 0.89 cd A(-1). Furthermore, as an electron transporter, 8a exhibited superior performance (current efficiency is 11.7 cd A(-1)) than the device using standard Alq(3) (current efficiency is 8.69 cd A(-1)), demonstrating its high potential for employment in OLEDs. These results indicate that the new anthracene-oxadiazole derivatives could play an important role in the development of OLEDs

Chemical structure dependent electron transport in 9,10-bis(2-phenyl-1,3,4-oxadiazole) derivatives of anthracene

In this work, we present a detailed analysis on electron transport studies of 9,10-bis(2-phenyl-1,3,4-oxadiazole) derivatives of anthracene (OXD-PH, OXD-PTOL and OXD-OTOL). The effect of methyl substitution at ortho (OXD-OTOL) and para position (OXD-PTOL) on the phenyl ring on the electron transport properties was studied and the results were compared with the anthracene derivative without any substitution at the phenyl ring. Electron transport was found to be highly dependent on the methyl substitution and electron mobilities in OXD-PTOL and OXD-OTOL were found to be lower than in OXD-PH. Mobilities were also found to be different for OXD-PTOL and OXD-OTOL, which indicates that the substitution at different places did not have a similar effect on charge transport properties. Thickness dependent trap states were observed for all three molecules with thickness dependent electron mobilities. Electron mobility was found to increase in all three molecules with the decrease in thickness, which favors their use for organic electronic devices and all three molecules had a better electron transport in comparison to Alq(3). These results were explained by the DFT calculation which showed a dihedral structure. The dihedral angle was found to reduce in the anionic form of these molecules. Therefore, these molecules are likely to favor a proper stacking in the solid state for

Synthesis and characterization of 9,10-bis(2-phenyl-1,3,4-oxadiazole) derivatives of anthracene: Efficient n-type emitter for organic light-emitting diodes

With a general aim to make anthracene derivatives multifunctional (n-type emitter) and also study their suitability as electron transport layers for organic light emitting diodes (OLED), and with a more specific interest to understand the charge transport and packing pattern in the solid state due to the rotating side rings, we report the synthesis and characterization of six novel molecules (5–10) in which the 9 and 10 positions of anthracene have been directly substituted by phenyloxadiazole groups. We have carried out detailed studies of these molecules including photophysical, electrochemical, electroluminescent studies and solid state structure determination through crystallographic techniques. The electron affinity is very high, around 3.1–3.2 eV, and the ionization potential is around 5.9–6.0 eV, comparable to the more commonly used electron transport electroluminescent layer Alq3. The studies reveal that the new molecules being reported by us, in addition to the high thermal stability, are quite efficient in a two layer unoptimized device with the device structure ITO/α-NPD/5–10/LiF/Al and have an emission in pure green. They also show very high efficiency as electron transport layer in device structure ITO(120nm)/α-NPD(30nm)/Ir(ppy)3 doped CBP(35nm)/BCP(6nm)/5(28nm)/Al(150nm). From these studies we conclude that the anthracene derivatives also have considerable potential as multifunctional layers and as electron transport layers in OLED