Natural Language Processing for Information Extraction of Gastric Diseases and Its Application in Large-Scale Clinical Research

Background and Aims: The utility of clinical information from esophagogastroduodenoscopy (EGD) reports has been limited because of its unstructured narrative format. We developed a natural language processing (NLP) pipeline that automatically extracts information about gastric diseases from unstructured EGD reports and demonstrated its applicability in clinical research. Methods: An NLP pipeline was developed using 2000 EGD and associated pathology reports that were retrieved from a single healthcare center. The pipeline extracted clinical information, including the presence, location, and size, for 10 gastric diseases from the EGD reports. It was validated with 1000 EGD reports by evaluating sensitivity, positive predictive value (PPV), accuracy, and F1 score. The pipeline was applied to 248,966 EGD reports from 2010–2019 to identify patient demographics and clinical information for 10 gastric diseases. Results: For gastritis information extraction, we achieved an overall sensitivity, PPV, accuracy, and F1 score of 0.966, 0.972, 0.996, and 0.967, respectively. Other gastric diseases, such as ulcers, and neoplastic diseases achieved an overall sensitivity, PPV, accuracy, and F1 score of 0.975, 0.982, 0.999, and 0.978, respectively. The study of EGD data of over 10 years revealed the demographics of patients with gastric diseases by sex and age. In addition, the study identified the extent and locations of gastritis and other gastric diseases, respectively. Conclusions: We demonstrated the feasibility of the NLP pipeline providing an automated extraction of gastric disease information from EGD reports. Incorporating the pipeline can facilitate large-scale clinical research to better understand gastric diseases.

3D reconstructions of spinal segmental arteries using CT angiography: applications in minimally invasive spinal procedures

BACKGROUND AND PURPOSE

Injury to spinal segmental arteries may potentially occur during spinal surgery, particularly during anterior or minimally invasive approaches. Use of a noninvasive radiologic tool to evaluate these arteries before surgery may reduce this risk.

MATERIAL AND METHODS

We performed spinal CT angiography and reconstructed 3D images of segmental arteries in 41 patients. We classified the pathways and locations of the segmental arteries into 4 zones (A, B, C, and D) according to pedicle and vertebral endplates. We designated segmental arteries from T8 to L1 as "high-level segmental arteries" and those from L2 to L4, as "low-level segmental arteries." We compared the distribution of segmental arteries between these 2 groups. We also investigated anatomic variations of segmental arteries and the rate of occurrence of the artery of Adamkiewicz.

RESULTS

In all patients, 3D reconstruction images from spinal CT angiography clearly showed the pathways of segmental arteries on the vertebral bodies. Most of the segmental arteries passed the middle portion of the vertebral body (zones B and C). However, 51 of 738 segmental arteries (6.9%) had uncommon pathways (zones A and D), and segmental arteries from L2 to L4 had a higher incidence of uncommon pathways than higher level vertebrae (P < .05). We also observed 2 types of segmental artery anatomic variation, agenesis and dual supply.

CONCLUSIONS

We suggest that spinal CT angiography can help to precisely visualize the spinal segmental arteries and surrounding bony structures and can aid clinicians in deciding on optimal approaches for spinal surgery.

Impact of IL-1 receptor antagonist gene polymorphism on schizophrenia and bipolar disorder

OBJECTIVES

Variable levels of cytokines were observed in patients with schizophrenia and bipolar disorder, and an especially high level of interleukin-1 (IL-1) was detected in schizophrenia patients. It is known that IL-1 receptor antagonist (IL-1RA) binds to IL-1 receptors and inhibits the receptor binding of IL-1alpha and IL-1beta.

METHODS

In this study, the association between the variable number of tandem repeats polymorphism of the IL-1RA gene and schizophrenia (n=269) and bipolar disorder (n=83) was investigated.

RESULTS

The genotype distribution and allele frequency were significantly different between schizophrenic patients and the control group (P<0.05); however, there were no prominent differences between bipolar patients and the control group. The carriage rate for the IL1RN*2 allele was associated with higher risk of schizophrenia (odds ratio=2.24).

CONCLUSIONS

This study indicates that IL-1RA could be a candidate gene for susceptibility to schizophrenia.

Prolonged blood circulation of methotrexate by modulation of liposomal composition

Prolonged circulation by liposomal incorporation has been shown to enhance the therapeutic efficacy of drugs in many cases. The purpose of this study was to investigate whether the prolonged circulation of methotrexate (MTX) can be achieved by modulating the liposomal compositions. Various compositions of liposomes were prepared with 2:1 of phosphatidylcholine (PC) and cholesterol (CH) with or without distearoylphosphatidyl-ethanolamine-N-poly(ethyleneglycol) 2000 (DSPE-PEG). The MTX encapsulation efficiency depended on the type of PC used. It also appeared to increase by inclusion of DSPE-PEG. The size of liposomes decreased by the inclusion of DSPE-PEG. The inclusion of DSPE-PEG lowered the plasma-induced release of MTX from EggPC/CH and DPPC/CH liposomes, suggesting its enhancement effect on the liposomal stability. After intravenous injection to rats, the pharmacokinetics and biodistribution of MTX were significantly changed by liposomal incorporation and also by the composition of liposomes. The total body clearance of MTX incorporated in EggPC/CH, DPPC/CH, EggPC/CH/DSPE-PEG, and DPPC/CH/DSPE-PEG liposomes decreased 4.4-, 14.9-, 24.5-, and 53.1-fold, compared with that of free MTX. The ratio of MTX concentration in blood to liver and spleen after injection of DPPC/CH, EggPC/CH/DSPE-PEG, and DPPC/CH/DSPE-PEG liposomes was 5.4-, 8.5-, and 13.5-fold higher than that of EggPC/CH liposomes. Furthermore, the accumulation of MTX in the kidney, one of the organs in which MTX exhibits its toxicity, was significantly lowered by liposomal incorporation, especially by DSPE-PEG-containing liposomes. Taken together, DPPC/CH/DSPE-PEG liposomes most effectively prolonged the blood circulation, and reduced hepatosplenic and kidney uptake of MTX. DPPC/CH/DSPE-PEG liposomes may have potential as an efficient delivery system for MTX.

Phytoremediation of MTBE from a groundwater plume

The feasibility of phytoremediation to both remediate and hydraulically contain a methyl tert-butyl ether (MTBE)-contaminated groundwater plume was investigated in a three-phase study that included the following elements: (i) a laboratory bioreactor study that examined the fate and transport of 14C-radiolabeled MTBE in hybrid poplar trees, (ii) a novel approach for a mathematical modeling study that investigated the influence of deep-rooted trees on unsaturated and saturated groundwater flow, and (iii) a field study at a Houston site with MTBE-contaminated groundwater where hybrid poplar trees were planted. In the laboratory study, the predominant fate pathway was uptake and evapotranspiration of [14C]-MTBE from leaves and stems of poplar cuttings rooted in hydroponic solution. The modeling study demonstrates that phytohydraulic containment of MTBE in groundwater by deep-rooted trees can be achieved. The field study demonstrated significant groundwater uptake of groundwater by deep-rooted trees via direct measurement in the first three seasons. The use of vegetation may provide a cost-effective in-situ alternative for containment and remediation of MTBE-contaminated groundwater plumes.

High-level production of human growth hormone in Escherichia coli by a simple recombinant process

Procedures have been devised for producing in Escherichia coli high yields of purified recombinant human growth hormone (hGH), by utilizing N-terminal pentapeptide sequence of human tumor necrosis factor-alpha, histidine tag and enterokinase cleavage site as a fusion partner. The fusion protein was produced as a soluble protein at the beginning of gene expression, but progressively became insoluble in Escherichia coli cytoplasm. The insoluble protein was solubilized by simple alkaline pH shift and purified to near homogeneity by Ni(2+)-chelated affinity chromatography. Following specific enterokinase cleavage, the recombinant hGH was purified by one-step anion exchange chromatography. The ease and speed of this recombinant process, as well as the high productivity, makes it adaptable to the large-scale production of hGH. Moreover, the highly efficient fusion partner could be applied to the production of other therapeutically important proteins.

Growth-associated synthesis of recombinant human glucagon and human growth hormone in high-cell-density cultures of Escherichia coli

Synthesis of two recombinant proteins (human glucagon and human growth hormone) was investigated in fed-batch cultures at high cell concentrations of recombinant Escherichia coli. The glucose-limited growth was achieved without accumulation of metabolic by-products and hence the cellular environment is presumed invariable during growth and recombinant protein synthesis. Via exponential feeding in the two-phase fed-batch operation, the specific cell growth rate was successfully controlled at the desired rates and the fed-batch mode employed is considered appropriate for examining the correlation between the specific growth rate and the efficiency of recombinant product formation in the recombinant E. coli strains. The two recombinant proteins were expressed as fusion proteins and the concentration in the culture broth was increased to 15 g fusion growth hormone 1(-1) and 7 g fusion glucagon 1(-1). The fusion growth hormone was initially expressed as soluble protein but seemed to be gradually aggregated into inclusion bodies as the expression level increased, whereas the synthesized fusion glucagon existed as a cytoplasmic soluble protein during the whole induction period. The stressful conditions of cultivation employed (i.e., high-cell-density cultivation at low growth rate) may induce the increased production of various host-derived chaperones and thereby enhance the folding efficiency of synthesized heterologous proteins. The synthesis of the recombinant fusion proteins was strongly growth-dependent and more efficient at a higher specific growth rate. The mechanism linking specific growth rate with recombinant protein productivity is likely to be related to the change in cellular ribosomal content.

Enhanced production of human mini-proinsulin in fed-batch cultures at high cell density of Escherichia coli BL21(DE3)[pET-3aT2M2]

Synthesis of recombinant protein (human mini-proinsulin) is investigated in fed-batch cultures at high cell concentration of recombinant Escherichia coli BL21(DE3)[pET-3aT2M2]. Transcription of the recombinant gene is controlled by a T7 promoter system. The human mini-proinsulin is characterized by a C-chain peptide consisting of only nine amino acids, whereas the C-chain peptide of natural human proinsulin is made up of 35 amino acids. It is expressed in a fusion protein with a small fusion partner (a peptide with 18 amino acids) and finally aggregated into insoluble inclusion bodies in cytoplasm of recombinant E. coli. The fermentative production of this small fusion mini-proinsulin may be of great advantage in enhancing the yield of human insulin. To find an optimum induction strategy, effects of various key cultivation variables on the mini-proinsulin production are examined in high cell density fed-batch cultures. No general correlation is found between preinduction specific growth rate and recombinant protein synthesis, which confers a flexibility in choosing the feeding strategy of preinduction media for achieving the high cell density cultures. A culture temperature below 37 degrees C is unfavorable for recombinant gene expression, and the T7-based expression system is almost completely repressed at 30 degrees C. The nutrient glucose and yeast extract concentration in postinduction feed media is optimized by applying a statistical method for medium optimization, i.e. response surface methodology, and an effective amount of inducer molecule (IPTG) is determined to maximize the specific recombinant protein formation. The mini-proinsulin production in E. coli culture is significantly influenced by the volumetric feed rate of postinduction media, which is shown to be closely related to the plasmid copy number in the recombinant cell. Consequently, in a single-stage fed-batch process, the mini-proinsulin concentration is increased up to 7 g/L, approximately 62 wt % of which corresponds to mature human insulin. A two-stage fed-batch fermentation process, with recombinant cell growth occurring at a constant growth rate and constant cell concentration in a growth fermenter and mini-proinsulin production in an induction fermenter, is designed, and its efficacy in increasing volumetric productivity of mini-proinsulin is demonstrated.

Analysis of factors contributing to fertility decline in Korea

With the successful Korean national family planning program and rapid socioeconomic advancement since 1962, the contraceptive prevalence rate has risen from 9% in 1964 to 79% in 1991, with the corresponding total fertility rate (TFR) going from 6.0 in 1960 to 1.6 in 1988, which is considerably below the replacement fertility rate. The main purpose of this study is, therefore, to identify the structural and causal factors that contributed to the fall in fertility over the last 3 decades, in an effort to formulate future population policy directions and strategies. The 2 methods used for the study were: the standardization approach to examine the structural factors on fertility decline, and the bongaarts model to measure the effects of the proximate variables in the fertility decline. The study indicated that the fall in the crude birth rate and the general fertility rate for the periods of 1960-70 and 1980-90 were largely influenced by the decline in marital fertility which was triggered by the national family planning program initiated in 1962. The analysis based on the bongaarts model revealed that the 3 principal factors which exercised a strong influence on the fertility decline were the rise in age at marriage, the increase in induced abortion, and the increase in contraceptive use, but the influence of induced abortion has been decreasing in recent years. In general, the study results suggest that the main concerns of the national family planning program should be shifted from the past quantitative approach with emphasis on fertility reduction to a qualitative approach which stresses maternal and child health and other public health programs.

[The effect of patient teaching on compliance with sick role behavior of diabetic patients]

This study examined the effect of patient teaching on Compliance with sick role behavior in diabetic patients. The purpose was to improve diabetic patients Compliance by D.M. patient teaching. The study objectives were to determine the effect of patient teaching on Compliance with sick role behavior, and factors influencing compliance with sick role behavior of diabetic patients. The subjects, consisting of 52 diabetic patients diagnosed in the C. and other hospitals in K. city were divided into experimental and control groups. Data were gathered from July 25th to September 3rd, 1988 through interviews by questionnaires, measurement of blood sugar level by Reflux. D.M. Patient teaching was defined as informational intervention of social support by the nurse. A booklet representing patient education and questionnaires were developed by the investigator, and were tested for Content validity, and reliability by Item Analysis: Cronbachs alpha for any instrument to measure variables was patient Compliance .83, perceived health belief .65, diabetic knowledge .70. Analysis of data were done by paired t-test, t-test, Anova, Pearson correlation, and Stepwise multiple regression. The results of the study may be summarized as follows: 1. The effect of patient teaching on Compliance with sick role behavior, on diabetic Knowledge and health belief was Confirmed by significant differences between the experimental and the control group before and after the experiments. (P = 000 P = 006, P = 004).(ABSTRACT TRUNCATED AT 250 WORDS)

Side chain modified sterols as probes into insect molting hormone metabolism. II: synthesis of monofluorocholesterols

The hydroxylations of the cholesterol side chain at C-20, 22, and 25 are key terminal events in ecdysone biogenesis. We have prepared the C-20, C-22, C-24, and C-25 monofluorinated cholesterols as potential inhibitors of these hydroxylation events, and preliminary bioassay results in Manduca sexta are reported. The synthesis of [26(14)C]-20-fluorocholesterol is also described. Although the 20-, 22-, and 25-monofluorocholesterols do not appear to affect larval growth and development, the 24-fluoro isomer shows a moderate retardation of growth and a modest increase in mortality.