Automated Surgical Term Clustering: A Text Mining Approach for Unstructured Textual Surgery Descriptions.

High costs in health care and everlasting need for quality improvement in care delivery is increasingly becoming the motivating factor for novel predictive studies in health care informatics. Surgical services impact both the operating theatre costs and revenues and play critical role in care quality. Efficiency of such units relies extremely on effective operational planning and inventory management. A key ingredient to such planning activities is the structured and unstructured data available prior to the surgery day from the electronic health records and other information systems. Unstructured data, such as textual features of procedure description and notes, provide additional information while structured data alone is not sufficient. To effectively utilize textual information using text mining, textual features should be easily identifiable, i.e., without typographical errors and ad hoc abbreviations. While there exists numerous spelling correction and abbreviation identification tools, they are not suitable for the surgical medical text as they require a dictionary and cannot accommodate ad hoc words such as abbreviations. This study proposes a novel preprocessing framework for surgical text data to detect misspellings and abbreviations prior to the application of any text mining and predictive modeling. The proposed approach helps extract the most salient text features from the unstructured principal procedure and additional notes by effectively reducing the raw feature set dimension. The transformed (text) feature set thus improves subsequent prediction tasks in surgery units. We test and validate the proposed approach using datasets from multiple hospitals' surgical departments and benchmark feature sets.

Plant Responses to High Frequency Electromagnetic Fields.

High frequency nonionizing electromagnetic fields (HF-EMF) that are increasingly present in the environment constitute a genuine environmental stimulus able to evoke specific responses in plants that share many similarities with those observed after a stressful treatment. Plants constitute an outstanding model to study such interactions since their architecture (high surface area to volume ratio) optimizes their interaction with the environment. In the present review, after identifying the main exposure devices (transverse and gigahertz electromagnetic cells, wave guide, and mode stirred reverberating chamber) and general physics laws that govern EMF interactions with plants, we illustrate some of the observed responses after exposure to HF-EMF at the cellular, molecular, and whole plant scale. Indeed, numerous metabolic activities (reactive oxygen species metabolism, α- and ß-amylase, Krebs cycle, pentose phosphate pathway, chlorophyll content, terpene emission, etc.) are modified, gene expression altered (calmodulin, calcium-dependent protein kinase, and proteinase inhibitor), and growth reduced (stem elongation and dry weight) after low power (i.e., nonthermal) HF-EMF exposure. These changes occur not only in the tissues directly exposed but also systemically in distant tissues. While the long-term impact of these metabolic changes remains largely unknown, we propose to consider nonionizing HF-EMF radiation as a noninjurious, genuine environmental factor that readily evokes changes in plant metabolism.

Low-amplitude, high-frequency electromagnetic field exposure causes delayed and reduced growth in Rosa hybrida.

It is now accepted that plants perceive high-frequency electromagnetic field (HF-EMF). We wondered if the HF-EMF signal is integrated further in planta as a chain of reactions leading to a modification of plant growth. We exposed whole small ligneous plants (rose bush) whose growth could be studied for several weeks. We performed exposures at two different development stages (rooted cuttings bearing an axillary bud and 5-leaf stage plants), using two high frequency (900MHz) field amplitudes (5 and 200Vm(-1)). We achieved a tight control on the experimental conditions using a state-of-the-art stimulation device (Mode Stirred Reverberation Chamber) and specialized culture-chambers. After the exposure, we followed the shoot growth for over a one-month period. We observed no growth modification whatsoever exposure was performed on the 5-leaf stage plants. When the exposure was performed on the rooted cuttings, no growth modification was observed on Axis I (produced from the elongation of the axillary bud). Likewise, no significant modification was noted on Axis II produced at the base of Axis I, that came from pre-formed secondary axillary buds. In contrast, Axis II produced at the top of Axis I, that came from post-formed secondary buds consistently displayed a delayed and significant reduced growth (45%). The measurements of plant energy uptake from HF-EMF in this exposure condition (SAR of 7.2 10(-4)Wkg(-1)) indicated that this biological response is likely not due to thermal effect. These results suggest that exposure to electromagnetic field only affected development of post-formed organs.

Is hepato-imino diacetic acid scan a better imaging modality than abdominal ultrasound for diagnosing acute cholecystitis?

BACKGROUND: The role of hepato-imino diacetic acid scan (HIDA) in the diagnosis of acute cholecystitis remains controversial when compared with the more commonly used abdominal ultrasound (AUS). METHODS: The diagnostic imaging workup of 1,217 patients who presented to the emergency department at a single hospital with acute abdominal pain and suspicion of acute cholecystitis was reviewed to calculate the sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV) of AUS and HIDA. RESULTS: In patients undergoing both imaging modalities, HIDA had significantly higher sensitivity (90.7% vs 64.0%, P < .001) and specificity (71.4% vs 58.4%, P = .005) than AUS for the diagnosis of acute cholecystitis. Additionally, PPV and NPV of HIDA (56.2% and 95.0%, respectively) were higher than PPV and NPV of AUS (38.4% and 80.0%, respectively) when both imaging modalities were used for the same patient. CONCLUSION: In adults with acute abdominal pain, HIDA significantly increases the accuracy of the correct diagnosis.

Abdominal ultrasound versus hepato-imino diacetic acid scan in diagnosing acute cholecystitis--what is the real benefit?

BACKGROUND: Acute cholecystitis is one of the most common surgical problems, yet substantial debate remains over the utility of simple examination, abdominal ultrasound (AUS), or advanced imaging such as hepato-imino diacetic acid (HIDA) scan to support the diagnosis. MATERIALS AND METHODS: The preoperative diagnostic workup of patients who underwent cholecystectomy with histologically confirmed acute cholecystitis was reviewed to calculate the sensitivity of AUS, HIDA scan, or both. In addition, the sensitivity of the commonly described ultrasonographic findings was assessed. RESULTS: From 2010 through 2012, 406 patients among 9087 reviewed charts presented to the emergency department with acute upper abdominal pain and met inclusion criteria. 32.5% (N = 132) of patients underwent AUS only, 11.3% (N = 46) underwent HIDA scan only, and 56.2% (N = 228) had both studies performed for workup. 52.7% (N = 214) of patients had histopathologically confirmed acute cholecystitis. The sensitivities of AUS, HIDA, and AUS combined with HIDA for acute cholecystitis were 73.3% (95% confidence interval [CI] = 66.3%-79.5%), 91.7% (95% CI = 86.2%-95.5%), and 97.7% (95% CI = 93.4%-99.5%), respectively. Although of limited sensitivity, AUS findings of sonographic Murphy sign, gallbladder distension, and gallbladder wall thickening were associated with a diagnosis of acute cholecystitis. CONCLUSIONS: The sensitivity of AUS for diagnosing acute cholecystitis in patients with acute upper abdominal pain is limited. The addition of a HIDA scan in the diagnostic workup significantly improves sensitivity and can add valuable information in the appropriate clinical setting.

Where has all the message gone?

We provide a brief history of polyribosomes, ergosomes, prosomes, informosomes, maternal mRNA, stored mRNA, and RNP particles. Even though most published research focuses on total mRNA rather than polysomal mRNA and often assumes they are synonymous - i.e., if a functional mRNA is present, it must be translated - results from our laboratories comparing polysomal RNA and total mRNA in a range of "normal" issues show that some transcripts are almost totally absent from polysomes while others are almost entirely associated with polysomes. We describe a recent model from yeast showing various destinies for polysomal mRNA once it has been released from polysomes. The main points we want to emphasize are; a) when mRNA leaves polysomes to go to prosomes, P-bodies, stress granules, etc., it is not necessarily destined for degradation - it can be re-utilized; b) "normal" tissue, not just seeds and stressed tissue, contains functional non-polysomal mRNA; c) association of mRNA with different classes of polysomes affects their sub-cellular location and translatability; and d) drawbacks, misinterpretations, and false hopes arise from analysis of total mRNA rather than polysomal mRNA and from presuming that all polysomes are "created equal".

Human keratinocytes in culture exhibit no response when exposed to short duration, low amplitude, high frequency (900 MHz) electromagnetic fields in a reverberation chamber.

We exposed normal human epidermal keratinocytes to short duration, high frequency, and low amplitude electromagnetic fields, similar to that used by mobile phone technologies. We paid particular attention to the control of the characteristics of the electromagnetic environment generated within a mode stirred reverberation chamber (statistical homogeneity and isotropy of the field and SAR distribution). Two non-thermal exposure conditions were tested on the epidermal cells: 10-min exposure with a field amplitude of 8 V/m, and 30 min with 41 V/m. Corresponding specific absorption rates ranged from 2.6 to 73 mW/kg (continuous wave, 900 MHz carrier frequency). We collected RNA from cells subjected to these conditions and used it for a large-scale microarray screening of over 47000 human genes. Under these conditions, exposure of keratinocytes to the electromagnetic field had little effect; only 20 genes displayed significant modulation. The expression ratios were very small (close to 1.5-fold change), and none of them were shared by the two tested conditions. Furthermore, those assayed using polymerase chain reaction did not display significant expression modulation (overall mean of the exposed samples: 1.20 ± 0.18). In conclusion, the data presented here show that cultured keratinocytes are not significantly affected by EMF exposure.

Immunohistochemical localization of apyrase during initial differentiation and germination of pea seeds.

Localization of the 49-kDa apyrase (ATP diphosphohydrolase, EC3.6.1.5; DDBJ/EMBL/GenBank BAB40230) was investigated during early stages of germination of pea (Pisum sativum L. var. Alaska) at the organ, tissue, cellular, and sub-cellular level using light-microscopical immunohistochemistry. Whole mount tissues were immuno-reacted with anti-APY1 serum, pre-immune serum or anti-actin antibody for control. Antigen to the anti-APY1 serum was not detected until 16 h after sowing (26 h after start of imbibition), when the antigen was detected throughout the tissue, especially in the epidermis and cortex. At 35 h after sowing, the younger regions including the root tip and the tip of the stele were more strongly stained than the control. Both, epidermal and cortical cells of the epicotyl and root tip were stained. The stain was mainly localized in the cytoplasm and around nuclei in the apical meristem and the root tip, while vacuoles and cell walls were not stained. At 62 h, there was major staining in the plumule, hook, and elongating regions of the epicotyl and in the region between cotyledons and the epicotyl. After 84 h, lateral root primordia were stained. The pre-immune serum showed virtually no staining while the anti-actin antibody reacted solely with the cytoplasm. Since the antigen to the anti-APY1 serum was primarily found in the cytoplasm and around nuclei in elongating and differentiating tissues and labeling declined in mature tissues, it is suggested that apyrases may play a role in growth and development of tissues, for example, lateral roots.

A possible role for extra-cellular ATP in plant responses to high frequency, low amplitude electromagnetic field.

In parallel to evoking the accumulation of stress-related transcripts, exposure to low level 900 MHz EMF affected the levels of ATP, the main energy molecule of the cell. Its concentration dropped rapidly (27% after 30 min) in response to EMF exposure, along with a 18% decrease in the adenylate energy charge (AEC), a good marker of cell energy status. One could interpret this decrease in ATP and AEC in a classical way, i.e., as the result of an increase in cellular energy usage, but recent work brings exciting new insights in pointing out a signalling function for ATP, especially in the stress physiology context where it could trigger both reactive oxygen species and calcium movement (this latter being involved in plant responses to EMF exposure). In this addendum, we discuss our results within this new perspective for ATP function.

High frequency (900 MHz) low amplitude (5 V m-1) electromagnetic field: a genuine environmental stimulus that affects transcription, translation, calcium and energy charge in tomato.

Using an especially-designed facility, the Mode Stirred Reverberation Chamber, we exposed tomato plants (Lycopersicon esculentum Mill. VFN8) to low level (900 MHz, 5 V m(-1)) electromagnetic fields for a short period (10 min) and measured changes in abundance of three specific mRNA soon after exposure. Within minutes of electromagnetic stimulation, stress-related mRNA (calmodulin, calcium-dependent protein kinase and proteinase inhibitor) accumulated in a rapid, large and 3-phase manner typical of an environmental stress response. Accumulation of these transcripts into the polysomal RNA also took place (indicating that the encoded proteins were translated) but was delayed (indicating that newly-synthesized mRNA was not immediately recruited into polysomes). Transcript accumulation was maximal at normal Ca(2+) levels and was depressed at higher Ca(2+), especially for those encoding calcium-binding proteins. Removal of Ca(2+) (by addition of chelating agents or Ca(2+) channel blocker) led to total suppression of mRNA accumulation. Finally, 30 min after the electromagnetic treatment, ATP concentration and adenylate energy charge were transiently decreased, while transcript accumulation was totally prevented by application of the uncoupling reagent, CCCP. These responses occur very soon after exposure, strongly suggesting that they are the direct consequence of application of radio-frequency fields and their similarities to wound responses strongly suggests that this radiation is perceived by plants as an injurious stimulus.

Sequence, expression and tissue localization of a gene encoding a makorin RING zinc-finger protein in germinating rice (Oryza sativa L. ssp. Japonica) seeds.

The makorin (MKRN) RING finger protein gene family encodes proteins (makorins) with a characteristic array of zinc-finger motifs and which are present in a wide array of eukaryotes. In the present study, we analyzed the structure and expression of a putative makorin RING finger protein gene in rice (Oryza sativa L. ssp. Japonica cv. Nipponbare). From the analysis of the genomic (AP003543), mRNA (AK120250) and deduced protein (BAD61603) sequences of the putative MKRN gene of rice, obtained from GenBank, we found that it was indeed a bona fide member of the MKRN gene family. The rice MKRN cDNA encoded a protein with four C3H zinc-finger-motifs, one putative Cys-His zinc-finger motif, and one RING zinc-finger motif. The presence of this distinct motif organization and overall amino acid identity clearly indicate that this gene is indeed a true MKRN ortholog. We isolated RNA from embryonic axes of rice seeds at various stages of imbibition and germination and studied the temporal expression profile of MKRN by RT-PCR. This analysis revealed that MKRN transcripts were present at all the time points studied. It was at very low levels in dry seeds, increased slowly during imbibition and germination, and slightly declined in the seedling growth stage. After 6days of germination, an organ-dependent expression pattern of MKRN was observed: highest in roots and moderate in leaves. Similarly to MKRN transcripts, transcripts of cytoskeletal actin and tubulin were also detected in dry embryos, steadily increased during imbibition and germination and leveled off after 24h of germination. We studied the spatial expression profile of MKRN in rice tissues, by using a relatively fast, simple and effective non-radioactive mRNA in situ hybridization (NRISH) technique, which provided the first spatial experimental data that hints at the function of a plant makorin. This analysis revealed that MKRN transcripts were expressed in young plumules, lateral root primordia, leaf primordia, leaves and root tissues at many different stages of germination. The presence of MKRN transcripts in dry seeds, its early induction during germination and its continued spatiotemporal expression during early vegetative growth suggest that MKRN has an important role in germination, leaf and lateral root morphogenesis and overall development in rice.

Intercellular communication in plants: evidence for two rapidly transmitted systemic signals generated in response to electromagnetic field stimulation in tomato.

Exposing all of a wild-type tomato plant to electromagnetic radiation evoked rapid and substantial accumulation of basic leucine-zipper transcription factor (bZIP) mRNA in the terminal leaf (#4) with kinetics very similar to that seen in response to wounding, while in the abscisic acid (ABA) mutant (Sitiens), the response was more rapid, but transient. Submitting just the oldest leaf (#1) of a wild-type plant to irradiation evoked bZIP mRNA accumulation both locally in the exposed leaf and systemically in the unexposed (distant) leaf #4, although systemic accumulation was delayed somewhat. Accumulation of Pin2 mRNA was less than bZIP in both the exposed and distant leaves in wild type, but there was no delay in the systemic response. In Sitiens, bZIP mRNA accumulation was far less than in wild type in both local and distant leaves, while Pin2 mRNA accumulation was stronger in the exposed leaf, but totally prevented in the systemic leaf. In the jasmonic acid (JA) mutant (JL-5) and in wild-type plants treated with the ABA biosynthesis inhibitor, naproxen, responses were similar to those in the ABA mutant, while treatment of the exposed leaf with calcium antagonists totally abolished both local and systemic increases in bZIP transcript accumulation.

Plants Respond to GSM-Like Radiation.

In this article, we propose that an organism's general architecture is of primary importance for its ability to perceive electromagnetic radiation. Animals develop mainly as volumes for internal assimilation and appendages to increase their mobility, while plants develop as surfaces to optimize interaction with the environment. As a consequence, the proportion of cells directly interacting with EMF radiation at the organism/environment interface is much higher in plants than it is in animals, making them especially suited to study EMF effects on life.

Two Different Wound Signals Evoke Very Rapid, Systemic CMBP Transcript Accumulation in Tomato.

Flaming a tomato leaf evokes a variation potential; excising an unwounded leaf evokes an action potential; while excising a wounded leaf 90 sec after flame-wounding evokes an action potential superimposed on the variation potential. Furthermore, flaming one leaf induces rapid (15 min), systemic and biphasic accumulation of CMBP transcript, excising the unwounded leaf causes slower, monophasic transcript accumulation, while excising the wounded leaf after 90 sec has no effect on CMBP transcript accumulation in response to the flame-wound. We propose that both of these electrical signals, the flame-evoked variation potential and the cut-wound evoked action potential are capable of inducing CMBP transcript accumulation, although with somewhat different kinetics. Earlier work by others found the cut-wound had no effect on pin transcript accumulation, thus leaf excision could be used as a tool to determine whether transport of wound hormones out of the leaf could trigger pin gene expression. Here, however, leaf excision could not be used to prevent signal transmission, since excision itself evoked an electrical signal and transcript accumulation. Instead, the results show that two different electrical signals are involved in rapid, systemic CMBP mRNA accumulation and their effects are not additive implying they may share some common aspects.

Co-expression of an ethylene receptor gene, ERS1, and ethylene signaling regulator gene, CTR1, in Delphinium during abscission of florets.

We are trying to determine the mechanisms responsible for ethylene-induced floret abscission in cut flowers of Delphinium and recently identified an ethylene receptor gene, ERS1, and studied its response to ethylene treatment. In order to identify additional components of the ethylene response network in Delphinium, we performed 3' and 5' rapid amplification of cDNA ends (RACE) using the consensus sequence of the serine/threonine kinase domain of the ethylene signaling regulator gene (CTR1) involved in the constitutive triple response (CTR) to ethylene. The full-length cDNA (2754 nt) encoded a protein of 800 amino acids, which contained the expected serine/threonine kinase domain, the consensus ATP-binding site, and the serine/threonine kinase catalytic site. The protein had quite high (>50%) overall identity to CTR1 from Arabidopsis and tomato, and 70-75% identity in the catalytic site. The amount of mRNA encoding both CTR1 and ERS1 more than doubled within 6 h in cut florets incubated in the presence of exogenous ethylene. Similarly, the amount of ERS1 transcript doubled in florets within 6 d of harvesting, presumably in response to endogenous ethylene, while CTR1 mRNA increased to about 40% over the same period. However, in the presence of silver thiosulfate (STS), an ethylene inhibitor, the level of both transcripts remained essentially unchanged for the first 8 d before declining to very low levels. Florets on the control plants had almost completely abscised by 6 d, but the florets on STS-treated plants had not abscised by 20 d, by which time the flowers were almost dead. The data are consistent with the hypothesis that endogenous ethylene evokes the accumulation of both these transcripts (and their encoded proteins), thereby speeding up abscission and reducing the useful shelf life of the cut flowers.

Selection of candidate housekeeping controls in tomato plants using EST data.

Because the expression levels of housekeeping genes are relatively constant in most tissues, they are often useful controls when quantifying gene expression. We present an analytical method for identifying candidate housekeeping controls using expressed sequence tags (ESTs) from The Institute for Genomic Research Tomato Gene Index. We found relative expression levels for a collection of 127 transcripts and calculated the percentage of cDNA libraries that had expression levels (for a given transcript) within 2-fold through 10-fold ranges. When all libraries were considered together, the highest ranked housekeeping controls included transcripts for a DanJ-like protein, translationally controlled tumor protein, two alpha-tubulins, cyclophilin, and glyceraldehyde-3-phosphate dehydrogenase (GAPDH). For each organ (leaf, root, fruit, and flower), at least one transcript was found that occurred within a 2-fold range of expression in all respective libraries. These included transcripts for alpha-tubulin, DnaJ-like proteins, phosphoglycerate kinase, and GAPDH, although different transcripts appear better suited than others for different tissues. This analytical method is useful for identifying candidate housekeeping controls in particular tissues and at particular levels of expression and would be relevant for any species for which significant EST data exist.

Putative cis-elements in the promoter region of the carrot phenylalanine ammonia-lyase gene induced during anthocyanin synthesis.

Deletion mutants of the carrot phenylalanine ammonia-lyase gene promoter were used to survey cis-elements for their effect on expression of promoter activity by transient expression. Two putative cis-elements were required to give full activity, but a third might be the most important in regulation of the promoter by 2,4-dichlorophenoxyacetic acid.

Lysine-containing proteins in maize endosperm: a major contribution from cytoskeleton-associated carbohydrate-metabolizing enzymes.

We measured fresh weight, dry weight, total protein, and the amounts of several individual proteins during endosperm development in three varieties of maize ( Zea mays L.): W64A wild-type (WT) and opaque-2 (o2), and sweet corn (SW). By 28 days after pollination (DAP), fresh weight was much higher in WT and SW than in o2, but o2 had a higher dry weight and thus a much lower water content. By 28 DAP, protein concentration [mg (g tissue(-1))] was highest in o2 and lowest in WT, while the protein content (microg seed(-1)) was lowest in o2. The storage proteins, alpha- and gamma-zeins, were low initially, but by 28 DAP they comprised over 50% of the total protein in WT and SW, but only about 30% in o2. In all varieties, the cytoskeleton proteins, actin, tubulin and eEF1alpha, sedimented with the protein bodies at 30 g to 27,000 g in tissue homogenized in cytoskeleton-stabilizing buffer. Other cytoskeleton-associated proteins increased during development, including UDP-glucose starch glucosyltransferase (UDP-GSGT, EC 2.4.1.11), sucrose synthase 1 (SuSy-1, EC 2.4.1.13) and fructose-1,6 bisphosphate aldolase (FBA, EC 4.1.2.13). At 28 DAP, these cytoskeleton-associated proteins combined make up 27% (WT), 23% (SW) and 33% (o2) of the total protein. These proteins are all rather high (5-11%) in lysine, and so they contribute about 75% (WT), 67% (o2), and 51% (SW) of the total endosperm lysine. We conclude that efforts to elevate the levels of these proteins could make a significant contribution to the nutritional value of corn.