Use of general-purpose negation detection to augment concept indexing of medical documents: a quantitative study using the UMLS

OBJECTIVES

To test the hypothesis that most instances of negated concepts in dictated medical documents can be detected by a strategy that relies on tools developed for the parsing of formal (computer) languages-specifically, a lexical scanner ("lexer") that uses regular expressions to generate a finite state machine, and a parser that relies on a restricted subset of context-free grammars, known as LALR(1) grammars.

METHODS

A diverse training set of 40 medical documents from a variety of specialties was manually inspected and used to develop a program (Negfinder) that contained rules to recognize a large set of negated patterns occurring in the text. Negfinder's lexer and parser were developed using tools normally used to generate programming language compilers. The input to Negfinder consisted of medical narrative that was preprocessed to recognize UMLS concepts: the text of a recognized concept had been replaced with a coded representation that included its UMLS concept ID. The program generated an index with one entry per instance of a concept in the document, where the presence or absence of negation of that concept was recorded. This information was used to mark up the text of each document by color-coding it to make it easier to inspect. The parser was then evaluated in two ways: 1) a test set of 60 documents (30 discharge summaries, 30 surgical notes) marked-up by Negfinder was inspected visually to quantify false-positive and false-negative results; and 2) a different test set of 10 documents was independently examined for negatives by a human observer and by Negfinder, and the results were compared.

RESULTS

In the first evaluation using marked-up documents, 8,358 instances of UMLS concepts were detected in the 60 documents, of which 544 were negations detected by the program and verified by human observation (true-positive results, or TPs). Thirteen instances were wrongly flagged as negated (false-positive results, or FPs), and the program missed 27 instances of negation (false-negative results, or FNs), yielding a sensitivity of 95.3 percent and a specificity of 97.7 percent. In the second evaluation using independent negation detection, 1,869 concepts were detected in 10 documents, with 135 TPs, 12 FPs, and 6 FNs, yielding a sensitivity of 95.7 percent and a specificity of 91.8 percent. One of the words "no," "denies/denied," "not," or "without" was present in 92.5 percent of all negations.

CONCLUSIONS

Negation of most concepts in medical narrative can be reliably detected by a simple strategy. The reliability of detection depends on several factors, the most important being the accuracy of concept matching.

Suppression of hadrons with large transverse momentum in central Au+Au collisions at root square[s(NN)] = 130 GeV

Transverse momentum spectra for charged hadrons and for neutral pions in the range 1 GeV/c<p(T)<5 GeV/c have been measured by the PHENIX experiment at RHIC in Au+Au collisions at root square[s(NN)] = 130 GeV. At high p(T) the spectra from peripheral nuclear collisions are consistent with scaling the spectra from p+p collisions by the average number of binary nucleon-nucleon collisions. The spectra from central collisions are significantly suppressed when compared to the binary-scaled p+p expectation, and also when compared to similarly binary-scaled peripheral collisions, indicating a novel nuclear-medium effect in central nuclear collisions at RHIC energies.

Flow cytometry-based minisequencing: a new platform for high-throughput single-nucleotide polymorphism scoring

Single-nucleotide polymorphisms (SNPs) are the most abundant type of human genetic variation. These variable sites are present at high density in the genome, making them powerful tools for mapping and diagnosing disease-related alleles. We have developed a sensitive and rapid flow cytometry-based assay for the multiplexed analysis of SNPs based on polymerase-mediated primer extension, or minisequencing, using microspheres as solid supports. The new method involves subnanomolar concentrations of sample in small volumes ( approximately 10 microl) which can be analyzed at rates of one sample per minute or faster, without a wash step. Further, genomic analysis using multiplexing microsphere arrays (GAMMArrays), enables the simultaneous analysis of dozens, and potentially hundreds of SNPs per sample. We have tested the new method by genotyping the Glu69 variant from the HLA DPB1 locus, a SNP associated with chronic beryllium disease, as well as HLA DPA1 alleles using the multiplexed method. The results demonstrate the sensitivity and accuracy of flow cytometry-based minisequencing, a powerful new tool for genome- and global-scale SNP analysis.

Analysis of a circular derivative of Saccharomyces cerevisiae chromosome III: a physical map and identification and location of ARS elements

DNA was isolated from a circular derivative of chromosome III to prepare a library of recombinant plasmids enriched in chromosome III sequences. An ordered set of recombinant plasmids and bacteriophages carrying the contiguous 210-kilobase region of chromosome III between the HML and MAT loci was identified, and a complete restriction map was prepared with BamHI and EcoRI. Using the high frequency transformation assay and extensive subcloning, 13 ARS elements were mapped in the cloned region. Comparison of the physical maps of chromosome III from three strains revealed that the chromosomes differ in the number and positions of Ty elements and also show restriction site polymorphisms. A comparison of the physical map with the genetic map shows that meiotic recombination rates vary at least tenfold along the length of the chromosome.

Transcriptional response of human microglial cells to interferon-γ

Microglia, the resident macrophages in the central nervous system (CNS), play a pivotal role in innate and adaptive immune responses in the brain. The immune functions of microglia are regulated by cytokines, including interferon (IFN)-gamma, which is a major mediator of macrophage activation. We describe the transcriptional profile of human fetal microglial cells at 1, 6, and 24 h after IFN-gamma treatment. The results show a change in the expression of 405 genes including transcriptionally induced chemokines, IFN-gamma signaling factors, and major histocompatibility complex genes. Our results demonstrate that activation of microglia by IFN-gamma induces proinflammatory T-lymphocyte-related chemokine genes as well as genes involved in antigen presentation. As a result, signals for T-cell infiltration and antigen presentation are produced to allow for microglia-T-cell interactions that likely contribute to defense against invading pathogens. In sum, our results provide a foundation for the molecular mechanisms of the microglial response to IFN-gamma-a key to understanding cell-mediated immunity of the CNS.

Kinase domain mutations confer resistance to novel inhibitors targeting JAK2V617F in myeloproliferative neoplasms

The transforming JAK2V617F kinase is frequently associated with myeloproliferative neoplasms and thought to be instrumental for the overproduction of myeloid lineage cells. Several small molecule drugs targeting JAK2 are currently in clinical development for treatment in these diseases. We performed a high-throughput in vitro screen to identify point mutations in JAK2V617F that would be predicted to have potential clinical relevance and associated with drug resistance to the JAK2 inhibitor ruxolitinib (INCB018424). Seven libraries of mutagenized JAK2V617F cDNA were screened to specifically identify mutations in the predicted drug-binding region that would confer resistance to ruxolitinib, using a BaF3 cell-based assay. We identified five different non-synonymous point mutations that conferred drug resistance. Cells containing mutations had a 9- to 33-fold higher EC(50) for ruxolitinib compared with native JAK2V617F. Our results further indicated that these mutations also conferred cross-resistance to all JAK2 kinase inhibitors tested, including AZD1480, TG101348, lestaurtinib (CEP-701) and CYT-387. Surprisingly, introduction of the 'gatekeeper' mutation (M929I) in JAK2V617F affected only ruxolitinib sensitivity (fourfold increase in EC(50)). These results suggest that JAK2 inhibitors currently in clinical trials may be prone to resistance as a result of point mutations and caution should be exercised when administering these drugs.

Opioids for chronic low-back pain

BACKGROUND

The use of opioids in the long-term management of chronic low-back pain (LBP) appears to be increasing. Despite this trend, the benefits and risks of these medications remain unclear.

OBJECTIVES

To determine the efficacy of opioids in adults with chronic LBP.

SEARCH STRATEGY

We electronically searched CENTRAL, CINAHL and PsycINFO to May 2006; MEDLINE and EMBASE to May 2007. We supplemented our search by reviewing references in relevant systematic reviews and identified trials.

SELECTION CRITERIA

We included randomized or quasi-randomized controlled trials assessing the use of opioids (as monotherapy or in combination with other therapies) for longer than four weeks, in adults with chronic LBP. Studies were included if they compared non-injectable opioids to other treatments. Comparisons between opioids were excluded.

DATA COLLECTION AND ANALYSIS

Two authors independently assessed methodological quality and extracted data onto a pre-designed form. Results were statistically pooled using RevMan 4.2. We reported on pain and function using standardized mean difference (SMD) with 95% confidence interval (95% CI) and on side effects using absolute risk difference (RD) with 95% CI.

MAIN RESULTS

We included four trials. Three compared tramadol to placebo. Pooled results revealed that tramadol was more effective than placebo for pain relief, SMD 0.71 (95% CI 0.39 to 1.02), and improving function, SMD 0.17 (95% CI 0.04 to 0.30). The two most common side effects of tramadol were headaches, RD 9% (95% CI 6% to 12%) and nausea, RD 3% (95% CI 0% to 6%). One trial comparing opioids to another analgesic (naproxen) found opioids were statistically significant for relieving pain but not improving function. When re-calculated, the results were not statistically significant for either pain relief (SMD -0.58; 95% CI -1.42 to 0.26) or improving function (SMD -0.06; 95% CI -0.88 to 0.76) .

AUTHORS' CONCLUSIONS

Despite concerns surrounding the use of opioids for long-term management of chronic LBP, there remain few high-quality trials assessing their efficacy. The trials in this review, although achieving high internal validity scores, were characterized by a lack of generalizability, inadequate description of study populations, poor intention-to treat analysis, and limited interpretation of functional improvement. Based on our results, the benefits of opioids in clinical practice for the long-term management of chronic LBP remains questionable. Therefore, further high-quality studies that more closely simulate clinical practice are needed to assess the usefulness, and potential risks, of opioids for individuals with chronic LBP.

Simultaneous and coordinated rotational switching of all molecular rotors in a network

A range of artificial molecular systems has been created that can exhibit controlled linear and rotational motion. In the further development of such systems, a key step is the addition of communication between molecules in a network. Here, we show that a two-dimensional array of dipolar molecular rotors can undergo simultaneous rotational switching when applying an electric field from the tip of a scanning tunnelling microscope. Several hundred rotors made from porphyrin-based double-decker complexes can be simultaneously rotated when in a hexagonal rotor network on a Cu(111) surface by applying biases above 1 V at 80 K. The phenomenon is observed only in a hexagonal rotor network due to the degeneracy of the ground-state dipole rotational energy barrier of the system. Defects are essential to increase electric torque on the rotor network and to stabilize the switched rotor domains. At low biases and low initial rotator angles, slight reorientations of individual rotors can occur, resulting in the rotator arms pointing in different directions. Analysis reveals that the rotator arm directions are not random, but are coordinated to minimize energy via crosstalk among the rotors through dipolar interactions.

Endovascular repair of an aortoenteric fistula in a high-risk patient

PURPOSE

To describe the endovascular repair of an aortoenteric fistula in a high-risk patient.

METHODS AND RESULTS

A Vanguard tube stent-graft was deployed at the upper anastomotic suture line of a secondary aortoenteric fistula, successfully sealing the communication between the aorta and the third part of the duodenum without occlusion of the renal arteries.

CONCLUSIONS

Endovascular stent-graft repair of aortoenteric fistulae is possible, but further evaluation of this technique will determine its role in the management of this complication.

Suppressed pi(0) production at large transverse momentum in central Au+Au collisions at sqrt[s(NN)]=200 GeV

Transverse momentum spectra of neutral pions in the range 1<p(T)<10 GeV/c have been measured at midrapidity by the PHENIX experiment at BNL RHIC in Au+Au collisions at sqrt[s(NN)]=200 GeV. The pi(0) multiplicity in central reactions is significantly below the yields measured at the same sqrt[s(NN)] in peripheral Au+Au and p+p reactions scaled by the number of nucleon-nucleon collisions. For the most central bin, the suppression factor is approximately 2.5 at p(T)=2 GeV/c and increases to approximately 4-5 at p(T) approximately 4 GeV/c. At larger p(T), the suppression remains constant within errors. The deficit is already apparent in semiperipheral reactions and increases smoothly with centrality.

A systematic review and meta-analysis of the relative efficacy and safety of treatment regimens for HIV-associated cerebral toxoplasmosis: is trimethoprim-sulfamethoxazole a real option?

OBJECTIVES

The objective of this study was to perform a systematic review and meta-analysis of the literature to evaluate the efficacy and safety of therapies for cerebral toxoplasmosis in HIV-infected adults. The pyrimethamine plus sulfadiazine (P-S) combination is considered the mainstay therapy for cerebral toxoplasmosis and pyrimethamine plus clindamycin (P-C) is the most common alternative treatment. Although trimethoprim-sulfamethoxazole (TMP-SMX) has potential advantages, its use is infrequent.

METHODS

We searched PubMed and four other databases to identify randomized controlled trials (RCTs) and cohort studies. Two independent reviewers searched the databases, identified studies and extracted data. Risk ratios (RRs) were pooled across studies using random-effects models.

RESULTS

Nine studies were included (five RCTs, three retrospective cohort studies and one prospective cohort study). In comparison to P-S, treatment with P-C or TMP-SMX was associated with similar rates of partial or complete clinical response [P-C: RR 0.87; 95% confidence interval (CI) 0.70-1.08; TMP-SMX: RR 0.97; 95% CI 0.78-1.21], radiological response (P-C: RR 0.92; 95% CI 0.82-1.03), skin rash (P-C: RR 0.81; 95% CI 0.56-1.17; TMP-SMX: RR 0.17; 95% CI 0.02-1.29), gastrointestinal impairment (P-C: RR 5.16; 95% CI 0.66-40.11), and drug discontinuation because of adverse events (P-C: RR 0.32; 95% CI 0.07-1.47). Liver impairment was more frequent with P-S than P-C (P-C vs. P-S: RR 0.48; 95% CI 0.24-0.97).

CONCLUSIONS

The current evidence fails to identify a superior regimen in terms of relative efficacy or safety for the treatment of HIV-associated cerebral toxoplasmosis. Use of TMP-SMX as preferred treatment may be consistent with the available evidence and other real-world considerations. Larger comparative studies are needed.

Ferritin accumulation under iron scarcity in Drosophila iron cells

Ferritins are highly stable, multi-subunit protein complexes with iron-binding capacities that reach 4500 iron atoms per ferritin molecule. The strict dependence of cellular physiology on an adequate supply of iron cofactors has likely been a key driving force in the evolution of ferritins as iron storage molecules. The insect intestine has long been known to contain cells that are responsive to dietary iron levels and a specialized group of "iron cells" that always accumulate iron-loaded ferritin, even when no supplementary iron is added to the diet. Here, we further characterize ferritin localization in Drosophila melanogaster larvae raised under iron-enriched and iron-depleted conditions. High dietary iron intake results in ferritin accumulation in the anterior midgut, but also in garland (wreath) cells and in pericardial cells, which together filter the circulating hemolymph. Ferritin is also abundant in the brain, where levels remain unaltered following dietary iron chelation, a treatment that depletes ferritin from the aforementioned tissues. We attribute the stability of ferritin levels in the brain to the function of the blood-brain barrier that may shield this organ from systemic iron fluctuations. Most intriguingly, our dietary manipulations demonstrably iron-depleted the iron cells without a concomitant reduction in their production of ferritin. Therefore, insect iron cells may constitute an exception from the evolutionary norm with respect to iron-dependent ferritin regulation. It will be of interest to decipher both the physiological purpose served and the mechanism employed to untie ferritin regulation from cellular iron levels in this cell type.

Short course of steroids in home treatment of children with acute asthma

A double blind, randomised, placebo controlled study of the treatment of children with acute asthma at home showed that a three day course of prednisolone hastened improvement of both asthmatic symptoms and peak expiratory flow rates. Thus all asthmatic children who present with an acute attack should be considered for treatment with corticosteroids in addition to bronchodilators not only to prevent possible deterioration but also to speed recovery.

Treatment of traumatic false aneurysm of the thoracic aorta with endoluminal grafts

PURPOSE

Traumatic false aneurysms of the thoracic aorta presenting at a time remote from the original injury are a rare but complex problem. The treatment of a traumatic false aneurysm by endovascular techniques may offer many advantages over conventional open surgery.

METHODS AND RESULTS

Two male patients presented with traumatic false aneurysm of the thoracic aorta after being treated emergently for visceral injuries from a gunshot wound in one and an automobile accident in the other. In both cases, the aneurysm was situated so that only the T11 intercostal artery would be sacrificed by endoluminal exclusion. Commercially available endoluminal stent-grafts (Talent) were deployed successfully. Recovery in both patients was rapid and uneventful with no neurological sequelae. Spiral computed tomographic scans at 1 year indicated sustained aneurysm exclusion and satisfactory endograft position.

CONCLUSIONS

A customized endoluminal stent-graft can be used with great accuracy to exclude thoracic false aneurysms, avoiding the potential complexity and morbidity of an open thoracic approach.

Chronic hydrocephalus-induced hypoxia: increased expression of VEGFR-2+ and blood vessel density in hippocampus

Chronic hydrocephalus (CH) is a neurological disease characterized by increased cerebrospinal fluid volume and pressure that is often associated with impaired cognitive function. By and large, CH is a complex and heterogeneous cerebrospinal fluid (CSF) disorder where the exact site of brain insult is uncertain. Several mechanisms including neural compression, fiber stretch, and local or global hypoxia have been implicated in the underlying pathophysiology of CH. Specifically, the hippocampus, which plays a significant role in memory processing and is in direct contact with expanding CSF ventricles, may be involved. Using our model of chronic hydrocephalus, we quantified the density of vascular endothelial growth factor receptor 2 (VEGFR-2(+)) neurons, glial, endothelial cells, and blood vessels in hippocampal regions CA1, CA2-3, dentate gyrus and hilus using immunohistochemical and stereological methods. Density and %VEGFR-2(+) cell populations were estimated for CH animals (2-3 weeks vs. 12-16 weeks) and surgical controls (SC). Overall, we found approximately six- to eightfold increase in the cellular density of VEGFR-2(+) and more than double blood vessel density (BVd) in the hippocampus of CH compared with SC. There were no significant regional differences in VEGFR-2(+) cellular and BVd expression in the CH group. VEGFR-2(+) and BVds were significantly related to changes in CSF volume (P<or=0.05), and not intracranial pressure (ICP). The %VEGFR-2(+) was significantly greater in CH than SC (P<or=0.05), and was significantly correlated with BVd (P<or=0.05). These results showed that CH elicited a profound increase in VEGFR-2(+) in hippocampus that corresponded to increased BVd. It was unclear whether increased VEGFR-2(+) and blood vessel expression was related to focal compression alone or in combination with global ischemia/hypoxia conditions as previously described. These findings suggest that VEGFR-2 may play an adaptive role in angiogenesis after CH-induced hypoxia. Modulation of vascular endothelial growth factor/VEGFR-2(+) may be important in developing treatments for hypoxic conditions including hydrocephalus and other forms of cerebral ischemia.

Elliptic flow of identified hadrons in Au+Au collisions at sqrt sNN =200 GeV

The anisotropy parameter (v(2)), the second harmonic of the azimuthal particle distribution, has been measured with the PHENIX detector in Au+Au collisions at sqrt[s(NN)]=200 GeV for identified and inclusive charged particle production at central rapidities (|eta|<0.35) with respect to the reaction plane defined at high rapidities (|eta|=3-4 ). We observe that the v(2) of mesons falls below that of (anti)baryons for p(T)>2 GeV/c, in marked contrast to the predictions of a hydrodynamical model. A quark-coalescence model is also investigated.

The JAK2V617F oncogene requires expression of inducible phosphofructokinase/fructose-bisphosphatase 3 for cell growth and increased metabolic activity

Myeloproliferative neoplasms are characterized by overproduction of myeloid lineage cells with frequent acquisition of oncogenic JAK2V617F kinase mutations. The molecular mechanisms that regulate energy requirements in these diseases are poorly understood. Transformed cells tend to rely on fermentation instead of more efficient oxidative phosphorylation for energy production. Our data in JAK2V617F-transformed cells show that growth and metabolic activity were strictly dependent on the presence of glucose. Uptake of glucose and cell surface expression of the glucose transporter Glut1 required the oncogenic tyrosine kinase. Importantly, JAK2V617F as well as active STAT5 increased the expression of the inducible rate-limiting enzyme 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 3 (PFKFB3), which controls glycolytic flux through 6-phosphofructo-1-kinase. PFKFB3 was required for JAK2V617F-dependent lactate production, oxidative metabolic activity and glucose uptake. Targeted knockdown of PFKFB3 also limited cell growth under normoxic and hypoxic conditions and blocked in vivo tumor formation in mice. Overall, these data suggest that inducible PFKFB3 is required for increased growth, metabolic activity and is regulated through active JAK2 and STAT5. Novel therapies that specifically block PFKFB3 activity or expression would, therefore, be expected to inhibit JAK2/STAT5-dependent malignancies and related cancers.

Accurate Determination of the Neutron Skin Thickness of ^{208}Pb through Parity-Violation in Electron Scattering

We report a precision measurement of the parity-violating asymmetry A_{PV} in the elastic scattering of longitudinally polarized electrons from ^{208}Pb. We measure A_{PV}=550±16(stat)±8(syst) parts per billion, leading to an extraction of the neutral weak form factor F_{W}(Q^{2}=0.00616  GeV^{2})=0.368±0.013. Combined with our previous measurement, the extracted neutron skin thickness is R_{n}-R_{p}=0.283±0.071  fm. The result also yields the first significant direct measurement of the interior weak density of ^{208}Pb: ρ_{W}^{0}=-0.0796±0.0036(exp)±0.0013(theo)  fm^{-3} leading to the interior baryon density ρ_{b}^{0}=0.1480±0.0036(exp)±0.0013(theo)  fm^{-3}. The measurement accurately constrains the density dependence of the symmetry energy of nuclear matter near saturation density, with implications for the size and composition of neutron stars.