Building an abbreviation dictionary using a term recognition approach

MOTIVATION

Acronyms result from a highly productive type of term variation and trigger the need for an acronym dictionary to establish associations between acronyms and their expanded forms.

RESULTS

We propose a novel method for recognizing acronym definitions in a text collection. Assuming a word sequence co-occurring frequently with a parenthetical expression to be a potential expanded form, our method identifies acronym definitions in a similar manner to the statistical term recognition task. Applied to the whole MEDLINE (7 811 582 abstracts), the implemented system extracted 886 755 acronym candidates and recognized 300 954 expanded forms in reasonable time. Our method outperformed base-line systems, achieving 99% precision and 82-95% recall on our evaluation corpus that roughly emulates the whole MEDLINE.

AVAILABILITY AND SUPPLEMENTARY INFORMATION

The implementations and supplementary information are available at our web site: http://www.chokkan.org/research/acromine/

Improving chronological ordering of sentences extracted from multiple newspaper articles

It is necessary to determine a proper arrangement of extracted sentences to generate a well-organized summary from multiple documents. This paper describes our Multi-Document Summarization (MDS) system for TSC-3. It specifically addresses an approach to coherent sentence ordering for MDS. An impediment to the use of chronological ordering, which is widely used by conventional summarization system, is that it arranges sentences without considering the presupposed information of each sentence. We propose a method to improve chronological ordering by resolving precedent information of arranging sentences. Combining the refinement algorithm with topical segmentation and chronological ordering, we address our experiments and metrics to test the effectiveness of MDS tasks. Results demonstrate that the proposed method significantly improves chronological sentence ordering. At the end of the paper, we also report an outline/evaluation of important sentence extraction and redundant clause elimination integrated in our MDS system.

Effect of re-expansion after short-period lung collapse on pulmonary capillary permeability and pro-inflammatory cytokine gene expression in isolated rabbit lungs

BACKGROUND

Re-expansion pulmonary oedema is a rare complication caused by rapid re-expansion of a chronically collapsed lung. Several cases of pulmonary oedema associated with one-lung ventilation (OLV) have been reported recently. Elevated levels of pro-inflammatory cytokines in pulmonary oedema fluid are suggested to play important roles in its development. Activation of cytokines after re-expansion of collapsed lung during OLV has not been thoroughly investigated. Here we investigated the effects of re-expansion of the collapsed lung on pulmonary oedema formation and pro-inflammatory cytokine expression.

METHODS

Lungs isolated from female white Japanese rabbits were perfused and divided into a basal (BAS) group (n=7, baseline measurement alone), a control (CONT) group (n=9, ventilated without lung collapse for 120 min) and an atelectasis (ATEL) group (n=9, lung collapsed for 55 min followed by re-expansion and ventilation for 65 min). Pulmonary vascular resistance (PVR) and the coefficient of filtration (Kfc) were measured at baseline and 60 and 120 min. At the end of perfusion, bronchoalveolar lavage fluid/plasma protein ratio (B/P), wet/dry lung weight ratio (W/D) and mRNA expressions of tumour necrosis factor (TNF)-alpha, interleukin (IL)-1beta and myeloperoxidase (MPO) were determined.

RESULTS

TNF-alpha and IL-1beta mRNA were significantly up-regulated in lungs of the ATEL group compared with BAS and CONT, though no significant differences were noted in PVR, Kfc, B/P and W/D within and between groups. MPO increased at 120 min in CONT and ATEL groups.

CONCLUSION

Pro-inflammatory cytokines were up-regulated upon re-expansion and ventilation after short-period lung collapse, though no changes were noted in pulmonary capillary permeability.

Secoiridoid and iridoid glucosides from Syringa afghanica

Phytochemical investigation of the dried leaves of Syringa afghanica, has led to the isolation of nine secoiridoid glucosides, safghanosides A-H and 2"-epi-frameroside, as well as an iridoid glucoside, syringafghanoside along with nineteen known compounds. The structures were elucidated by spectroscopic and chemical means.

Characteristics of macrolide-resistant Mycoplasma pneumoniae strains isolated from patients and induced with erythromycin in vitro

Some patients with Mycoplasma pneumoniae infection are clinically resistant to antibiotics such as erythromycin, clarithromycin, or clindamycin. We isolated M. pneumoniae from such patients and found that one of three isolates showed a point mutation in the 23S rRNA gene. Furthermore, 141 EM-sensitive clinical isolates of M. pneumoniae were cultured in broth medium containing 100 microg/ml of erythromycin (EM). Among 11 EM-resistant strains that grew in the medium, point mutations in the 23S rRNA were found in 3 strains at A2063G, 5 strains at A2064G and 3 strains at A2064C. The relationship between the point mutation pattern of these EM-resistant strains and their resistance phenotypes to several macrolide antibiotics was investigated.

Role of potassium channels in isoflurane- and sevoflurane-induced attenuation of hypoxic pulmonary vasoconstriction in isolated perfused rabbit lungs

BACKGROUND

Although potassium channels are thought to be responsible for the initiation of hypoxic pulmonary vasoconstriction (HPV), their role in the HPV-inhibitory effect of volatile anesthetics is unclear. The current study tested if the HPV-inhibitory effect of isoflurane and sevoflurane can be affected by changing the potassium-channel opening status with specific potassium-channel inhibitors in isolated rabbit lungs.

METHODS

Isolated rabbit lungs were divided into eight groups (n = 6 each in isoflurane groups and n = 8 in sevoflurane groups): those receiving no inhibitor treatment = control-isoflurane and control-sevoflurane groups; those treated with an adenosine triphosphate-sensitive potassium (K(ATP))-channel inhibitor, glibenclamide = glibenclamide-isoflurane and glibenclamide-sevoflurane groups; those treated with a high-conductance calcium-activated potassium (K(Ca))-channel inhibitor, iberiotoxin = iberiotoxin-isoflurane and iberiotoxin-sevoflurane groups; and those treated with a voltage-sensitive potassium (Kv)-channel inhibitor, 4-aminopyridine = 4-aminopyridine-isoflurane and 4-aminopyridine-sevoflurane groups. The effect of anesthetic on HPV was tested by exposure of the lungs to isoflurane at a concentration of 0, 0.5, 1, or 2 minimum alveolar concentration, or to sevoflurane at a concentration of 0, 0.5, 1, or 1.62 minimum alveolar concentration. The relation between anesthetic concentrations and the HPV response was analyzed by the Wagner equation.

RESULTS

The inhibition of Kv channels by 4-aminopyridine and K(Ca) channels by iberiotoxin augmented the HPV response. The isoflurane-induced attenuation of HPV was attenuated by voltage-sensitive potassium-channel inhibition with 4-aminopyridine, potentiated by K(Ca)-channel inhibition with iberiotoxin, but not affected by K(ATP)-channel inhibition with glibenclamide. The sevoflurane-induced attenuation of HPV was not affected by any of the potassium-channel inhibitors.

CONCLUSIONS

Isoflurane may modulate the HPV response partially through K(Ca) and Kv channels, but sevoflurane may attenuate the HPV response through other pathways rather than through the currently investigated potassium channels in isolated rabbit lungs.

A cryptic melibiose transporter gene possessing a frameshift from Citrobacter freundii

Wild-type Citrobacter freundii cannot grow on melibiose as a sole source of carbon. The melibiose transporter gene melB was cloned from a C. freundii mutant M4 that could utilize melibiose as a sole carbon source. Although the cloned melB gene is closely similar to the melB genes of other bacteria, it is cryptic because of a frameshift mutation. Site-directed mutagenesis was used to construct a functional melB gene by deleting one nucleotide, resulting in the production of an active melibiose transporter. The active MelB transporter could utilize Na(+) and H(+) as coupling cations to melibiose transport. The amino acid sequence of the C. freundii MelB was found to be most similar to those of Salmonella typhimurium and Escherichia coli MelB. These facts are consistent with the phylogenetic relationship of bacteria and the cation coupling properties of the melibiose transporters.

Interaction of the Unc-51-like kinase and microtubule-associated protein light chain 3 related proteins in the brain: possible role of vesicular transport in axonal elongation

We identified two mammalian ULK1 (Unc-51-like kinase involved in neurite extension) binding proteins by yeast two-hybrid screening. Both proteins showed high structural similarity to microtubule-associated protein (MAP) light chain 3 (LC3). One is identical to the Golgi-associated ATPase Enhancer of 16 kDa (GATE-16), an essential factor for intra-Golgi transport [39]. The other is identical to the gamma 2-subunit of GABA-A receptor associated protein (GABARAP) which has a possible role in receptor transport [46]. Using the yeast two-hybrid system and the in vitro GST pull-down assay, we found that the N-terminal proline/serine rich (PS) domain of ULK1 (amino acid 287-416) is required for ULK1-GATE-16 and ULK1-GABARAP protein interactions. However, the kinase activity of ULK1 affected neither ULK1-GATE-16 nor ULK1-GABARAP interaction. Immunohistochemical analysis using ULK1 and GABARAP antibodies showed that the ULK1 and the GABARAP proteins co-localized to many kind of neurons such as pyramidal cells of the hippocampus, mitral cells of the olfactory bulb, and Purkinje cells of the cerebellum. In HeLa cells, endogenous ULK1 and tagged GABARAP showed punctate structures in the cytosol, and were colocalized. These results suggest that the interaction of ULK1 and GABARAP is important to vesicle transport and axonal elongation in mammalian neurons.

[Home infusion therapy system from a resident's point of view]

We started a new home infusion therapy system in July 1999. The home infusion therapy system is made up of doctors, nursing stations, and pharmacies in the community. We coordinate these parties before patient discharge from our hospital and support them when the patient needs hospitalization (for example, he or she develops pneumonia). This report discusses past experiences and future issue.

Temperature rule for the speed of sound in water: a chemical kinetics model

Water forms three-dimensional polymeric structures due to the influence of hydrogen bonds and is fundamentally different from other substances. One of the simplest ways to analyze the structure of water in any system, such as hydration, is to measure the degree of compressibility, which can be determined from the speed of sound, by making use of the physical laws established by Newton and later perfected by Laplace. Although the speed of sound is strongly dependent on the temperature of a liquid, Laplace's equation does not refer to temperature in any of its terms. It is necessary, therefore, to determine the degree of temperature dependency. However, only approximate expressions of a fifth-order polynomial have been reported so far in the literature. In this paper, a universal method for describing the speed of sound from the perspective of physicochemical reaction kinetics is presented. It is shown that the speed of sound U [ms(-1)] changes with temperature T [K] according to a thermodynamically-derived formula given as U= exp(-A/T-BlnT+C) and that the motion and propagation phenomena of sound energy can also be regarded as chemical reactions.

Chemiluminescence underestimates nitric oxide concentration in the presence of potent inhalation anaesthetics

We investigated the effect of potent inhalation anaesthetics on nitric oxide (NO) concentration measured by the chemiluminescence method. We found that the NO concentration was increasingly underestimated with increasing concentrations of halothane, isoflurane, enflurane and sevoflurane (r2 = 0.918-0.997, P < 0.01). Statistical analysis showed that the four inhalation agents at the same concentration produced a similar error in the measured NO concentration. In the presence of a fixed concentration of sevoflurane (5.0%), isoflurane (5.2%), enflurane (4.5%) or halothane (6.1%), the rate of reduction in the measured NO concentration increased in proportion to the NO concentration (r2 = 0.909-0.982, P < 0.01). No direct chemical interaction between the potent inhalation agents and NO was detected by gas chromatography-mass spectrometry. We conclude that NO concentration can be underestimated when measured by the chemiluminescence method in the presence of potent inhalation agents. This underestimation may result from emission absorption and/or the quenching phenomenon, but is not attributable to a chemical reaction between the inhalation agent and NO.

Molecular cloning and characterization of a transcriptional activator gene, amyR, involved in the amylolytic gene expression in Aspergillus oryzae

A gene, designated amyR, coding for a transcriptional activator involved in amylolytic gene expression has been cloned from Aspergillus oryzae by screening for a clone that enabled to reverse the reduced expression of the alpha-amylase gene (amyB) promoter. amyR encodes 604 amino acid residues of a putative DNA-binding protein carrying a zinc binuclear cluster motif (Zn(II)2Cys6) belonging to the GAL4 family of transcription factors. The amyR gene disruptants showed a significant restricted growth on starch medium and produced little of the amylolytic enzymes including alpha-amylase and glucoamylase compared with a non-disruptant, indicating that amyR is a transcriptional activator gene involved in starch/maltose-induced efficient expression of the amylolytic genes in A. oryzae. In addition, sequencing analysis found that amyR, agdA (encoding alpha-glucosidase), and amyA (encoding alpha-amylase), are clustered on a 12-kb DNA fragment of the largest chromosome in A. oryzae, and that amyR is about 1.5 kb upstream of agdA and transcribed in the opposite direction. Furthermore, transcriptional analysis revealed that the amyR gene was expressed in the presence of glucose comparable to the level in the presence of maltose, while the amylolytic genes were transcribed at high levels only in the presence of maltose.

Effects of aldehyde dehydrogenase and acetyl-CoA synthetase on acetate formation in sake mash

To reveal the mechanism of the production of acetate by sake yeast (Saccharomyces cerevisiae), the expression of genes encoding aldehyde dehydrogenase (ALD), acetyl-CoA synthetase (ACS) and acetyl-CoA hydrolase (ACH), which are related to acetate production, was investigated. Northern blot analysis using total RNA of sake yeast isolated from sake mash revealed that all of the tested genes, ACS1, ACS2, ALD2/3, ALD4, ALD6 and ACH1, were transcribed during sake fermentation. Transcription of ALD2/3 was detected only in the early stage of sake fermentation. A static culture of sake yeast in hyperosmotic media including 1 M sorbitol or 20% glucose resulted in high acetate production and increased transcription of ALD2/3. This is the same result as reported in an aerobic condition, and induction of ALD2/3 seemed to be one reason for high acetate production at high glucose concentration during fermentation. Overexpression of ACS2 resulted in low acetate production both during small-scale sake fermentation and in a static liquid culture. On the other hand, over-expression of ACS1 did not change acetate productivity significantly in a static culture. These results indicate that ALD2/3 and ACS2 play important roles for acetate production during sake fermentation.

Mouse ULK2, a novel member of the UNC-51-like protein kinases: unique features of functional domains

The UNC-51 serine/threonine kinase of C. elegans plays an essential role in axonal elongation, and unc-51 mutants exhibit uncoordinated movements. We have previously identified mouse and human cDNAs encoding UNC-51-like kinase (ULK1). Here we report the identification and characterization of the second murine member of this kinase family, ULK2. Mouse ULK2 cDNA encodes a putative polypeptide of 1033 aa which has an overall 52% and 33% amino acid identity to ULK1 and UNC-51, respectively. ULKs and UNC-51 share a typical domain structure of an amino-terminal kinase domain, a central proline/serine rich (PS) domain, and a carboxy-terminal (C) domain. Northern blot analysis showed that ULK2 mRNA is widely expressed in adult tissues. In situ hybridization analysis indicated that ULK2 mRNA is ubiquitously localized in premature as well as mature neurons in developing nervous system. ULK2 gene was mapped to mouse chromosome 11B1.3 and rat chromosome 10q23 by FISH. HA-tagged ULK2 expressed in COS7 cells had an apparent molecular size of approximately 150 kDa and was autophosphorylated in vitro. Truncation mutants suggested that the autophosphorylation occurs in the PS domain. Although expression of ULK2 failed to rescue unc-51 mutant of C. elegans, a series of ULK2/UNC-51 chimeric kinases revealed that function of the kinase and PS domains are conserved among species, while the C domain acts in a species-specific manner. These results suggest that ULK2 is involved in a previously uncharacterized signaling pathway in mammalian cells.

Identification of a new variable sequence in the P1 cytadhesin gene of Mycoplasma pneumoniae: evidence for the generation of antigenic variation by DNA recombination between repetitive sequences

A Mycoplasma pneumoniae cytadhesin P1 gene with novel nucleotide sequence variation has been identified. Four clinical strains of M. pneumoniae were found to carry this type of P1 gene. This new P1 gene is similar to the known group II P1 genes but possesses novel sequence variation of approximately 300 bp in the RepMP2/3 region. The position of the new variable region is distant from the previously reported variable regions known to differ between group I and II P1 genes. Two sequences closely homologous to this new variable region were found within the repetitive sequences outside the P1 gene of the M. pneumoniae M129 genome. This suggests that the new P1 gene was generated by DNA recombination between repetitive sequences and the P1 gene locus. The finding of this new type of P1 gene supports the hypothesis that the repetitive sequences of the M. pneumoniae genome serve as a reservoir to generate antigenic variation of the cytadhesin P1 gene.

Deconvolution of chemiluminescent emission curve associated with phagocytosis into three logarithmic normal distributions

The chemiluminescent emission reaction dependence on the activity of phagocytosis is well known. However, this method is not used to diagnostically in clinical assessment because the relationship between phagocytizing activity and chemiluminescent intensity has not been clearly established. Therefore, we attempted to analyze quantitatively the chemiluminescent emission curve by the phagocytosis of leukocytes. Mathematical assessment of the emission curve with respect to time was performed by fitting the curve to several regression models using the unweighed non-linear least squares method. A triple logarithmic normal distribution model provided a reasonable goodness of fit to the measured emission curve. The first component, about 5% of the calculated total counts, was assumed to arise from monocytes activity, the second component, about 20% from eosinocytes activity and the third component, up to 75%, from neutrophils activity. This method seems promising as a means for assaying whole blood without the need for pretreatment and for the providing a valid index that is independent of the technical differences between laboratories.

Chromosomal DNA patterns and gene stability of Pichia pastoris

We have clearly resolved four chromosomal bands from four Pichia pastoris (Komagataella pastoris) strains by using contour-clamped homogeneous electric field gel electrophoresis. The size of the P. pastoris chromosomal bands ranged from 1.7 Mb to 3.5 Mb and total genome size was estimated to be 9.5 Mb to 9.8 Mb; however, chromosome-length polymorphisms existed among four strains. Thirteen cloned genes isolated from strain GTS115 were assigned to the separated chromosomes, revealing that different hybridization patterns were observed in the AOX2 and URA3 genes among strains. P. pastoris is frequently used as an efficient host for heterologous gene expressions. We analysed chromosomal stability of strain GTS115-derived recombinant cell expressing human serum albumin during serial cultivation under the condition of vegetative and non-selective growth. No chromosomal rearrangements were observed and the expression constructs integrated into the his4 locus on chromosome I were very stable even at 83 generations, suggesting that stable expression would be carried out even in large-scale fermentation.

Mutants of Citrobacter freundii that transport and utilize melibiose

We have isolated mutants of Citrobacter freundii that can grow on melibiose. Inducible alpha-galactosidase activity and melibiose transport activity were detected in the mutant cells but not in the wild-type cells. We detected a DNA region which hybridized with melB (the gene for the melibiose transporter) DNA of Escherichia coli in the chromosomal DNA of wild-type C. freundii. Protons, but not sodium ions, were found to be the coupling cations for melibiose (and methyl-beta-D-thiogalactoside) transport in the mutant cells.

[Mycoplasma pneumoniae detection from throat swab by two-step polymerase chain reaction]

Two-step polymerase chain reaction (PCR) with primers designated against 16S rRNA gene of Mycoplasma pneumoniae for diagnosis of infection was evaluated in comparison with the conventional single-step PCR and culture methods. The two-step PCR method showed specific amplification of M. pneumoniae DNA and higher sensitivity (1.5 fg/assay) than the single-step PCR method. With the two-step PCR method, 76 of 322 throat swabs (23.6%) from patients with acute respiratory complaints gave positive results whereas 20.2% were positive in the culture method. Seven of 13 samples which were negative in the single-step PCR method but positive in either serological or the culture method showed positive results by the two-step PCR method. In addition, 5 samples which were weakly positive in the single-step PCR method showed distinctly positive results in the two-step PCR. These results indicate that the two-step PCR method is a useful tool for detection of M. pneumoniae in clinical specimens, although it requires a relatively sophisticated in technique.

HRA model for hypercholesterolemia based on a longitudinal health database

To evaluate the risk factors for hypercholesterolemia, we examined 4,371 subjects (3,207 males and 1,164 females) who received medical checkups more than twice at an AMHTS in Tokyo during the period from 1976 through 1991; and whose serum total cholesterol was under 250 mg/dl. The mean follow-up duration was 6.6 years. A self-registering questionnaire was administered at the time of the health checkup. The endpoint of this study was the onset of hypercholesterolemia when the level of serum total cholesterol was 250 mg/dl and over. We compared two prognosis groups (normal and hypercholesterol) in terms of age, examination findings and lifestyle. After assessing each variable, we employed Cox's proportional hazards model analysis to determine the factors related to the occurrence of hypercholesterolemia. According to proportional hazards model analysis, total cholesterol, triglyceride and smoking at the beginning, and hypertension during the observation period were selected in males; and total cholesterol at the beginning and age were selected in females to determine the factors related to the occurrence of hypercholesterolemia.