MScanner: a classifier for retrieving Medline citations

Background  

Keyword searching through PubMed and other systems is the standard means of retrieving information from Medline. However, ad-hoc retrieval systems do not meet all of the needs of databases that curate information from literature, or of text miners developing a corpus on a topic that has many terms indicative of relevance. Several databases have developed supervised learning methods that operate on a filtered subset of Medline, to classify Medline records so that fewer articles have to be manually reviewed for relevance. A few studies have considered generalisation of Medline classification to operate on the entire Medline database in a non-domain-specific manner, but existing applications lack speed, available implementations, or a means to measure performance in new domains.     

The physiological effects and metabolic alterations caused by the expression of Rhizobium etli pyruvate carboxylase in Escherichia coli

Oxaloacetate (OAA) plays an important role in the tricarboxylic acid cycle and for the biosynthesis of a variety of cellular compounds. Some microorganisms, such as Rhizobium etli and Corynebacterium glutamicum, are able to synthesize OAA during growth on glucose via either of the enzymes pyruvate carboxylase (PYC) or phosphoenolpyruvate carboxylase (PPC). Other microorganisms, including Escherichia coli, synthesize OAA during growth on glucose only via PPC because they lack PYC. In this study we have examined the effect that the R. etli PYC has on the physiology of E. coli. The expressed R. etli PYC was biotinylated by the native biotin holoenzyme synthase of E. coli and displayed kinetic properties similar to those reported for alpha4 PYC enzymes from other sources. R. etli PYC was able to restore the growth of an E. coli ppc null mutant in minimal glucose medium, and PYC expression caused increased carbon flow towards OAA in wild-type E. coli cells without affecting the glucose uptake rate or the growth rate. During aerobic glucose metabolism, expression of PYC resulted in a 56% increase in biomass yield and a 43% decrease in acetate yield. During anaerobic glucose metabolism, expression of PYC caused a 2.7-fold increase in succinate concentration, making it the major product by mass. The increase in succinate came mainly at the expense of lactate formation. However, in a mutant lacking lactate dehydrogenase activity, expression of PYC resulted in only a 1.7-fold increase in succinate concentration. The decreased enhancement of succinate formation in the /dh mutant was hypothesized to be due to accumulation of pyruvate and NADH, metabolites that affect the interconversion of the active and inactive form of the enzyme pyruvate formate-lyase.     

Female Choice in the Synchronously Waving Fiddler Crab Uca annulipes

In the fiddler crab, Uca annulipes, males attract receptive females into their burrows by waving their greatly enlarged major claw. We have previously shown that males clustered around a female wave in close synchrony. Females may have a preference for leading signals and synchronised waving may arise as an epiphenomenon of competition between males to signal first. Indeed, the males in clusters that females approach and visit in their burrows are more likely to produce leading waves than are their neighbours. Here we document two other differences in the waving behaviour of visited males and their neighbours. First, visited males complete the downward component of the wave more rapidly than their neighbours. Second, the interval between the end of one wave and the start of the next is shorter for visited males. How can waving be synchronous if visited males wave faster than their neighbours? While only 9% (40/431) of waves by neighbours did not overlap those of the visited male, 22% (110/501) of visited male waves did not overlap the wave of a focal neighbour (111 visited male-neighbour dyads). Hence, while overlapping waves are nearly synchronous, visited males produce additional, ‘nonoverlapping’ waves that result in a higher wave rate than that of their neighbours.     

Lamp-1 is upregulated in human glioblastoma cell lines induced to undergo apoptosis

Lysosome-associated membrane protein (LAMP)-1, one of the major protein components of the lysosomal membrane, is upregulated in the human glioblastoma cell lines, U-373 MG and LN-Z308, which undergo cisplatin-induced apoptosis. These human brain tumor cell lines demonstrated apoptosis in response to cisplatin/nifedipine treatment. Both cell lines demonstrated an apoptotic response by more than one criterion. Apoptosis was demonstrated by DNA fragmentation techniques such as DNA laddering, ApopTag in situ labeling, and an ELISA-based method of detecting liberated oligosomes. These cells also had characteristic morphologic changes and upregulation of bax consistent with apoptosis. LAMP-1 expression at the protein and mRNA level was examined and found to increase with cisplatin/nifedipine treatment. LAMP-1 expression was examined using indirect immunofluorescent staining, Northern blot analysis and Western blot analysis. The finding of an augmentation of LAMP-1 in these cells induced to die is enigmatic. These findings raise the possibility of LAMP-1 involvement in the apoptotic process.     

Use of a permanent magnetic field to inhibit the development of canine osteoarthritis

This study was designed to determine the potential of a permanent magnetic field to inhibit the progression of osteoarthritis (OA) in a canine model. The magnetic field was created by 72 domino-sized ceramic magnets with surface field strength of 1100 G (0.11 T). The magnetic field strength at the surface of the mattress was 450-500 G (45-50 mT) and was equally distributed over the mattress surface. Eighteen animals had closed resection of their right stifle anterior cruciate ligament. Their kennel floors were covered in one of three ways: no floor mattress (OA) (N = 6); a floor mattress with domino-sized ceramic pieces placed between two layers of foam (sham control OA-MAT) (N = 6); or a floor mattress with domino-sized ceramic permanent magnets placed between two layers of foam (OA-MAT-MAG) (N = 6). Animals were kept in their cages except for 4 h of exercise each day. The left stifle of six animals served as the normal control. The stifle joints were examined at 12 weeks for synovial effusion, gross anatomic appearance, microscopic anatomic appearance (Mankin score), and metalloproteinase (MMP)-1 and -3. Macroscopically, the OA-MAT-MAG group appeared to have less synovitis, less synovial effusion, less disruption of the cartilage surface, and less cartilage ulceration than did the OA group or the control mattress group. The mean Mankin score for the OA-MAT-MAG group was less than that for the OA group (4.2 +/- 0.8 vs. 6.7 +/- 0.3; P <.05) and the control mattress group (4.2 +/- 0.8 vs. 5.2 +/- 0.8; P >.05), but greater than that for the normal left group (4.2 +/- 0.8 vs. 1.0 +/- 0.4; P <.05). These scores show a trend of improvement for OA-MAT-MAG group but the difference with the sham control OA-MAT group was not statistically significant. In immunohistochemical studies, the OA-MAT-MAG group cartilage was stained less heavily for MMP-1 and MMP-3 than were the OA group cartilage and the control mattress group cartilage, but did not differ significantly in MMP-1 and MMP-3 from the normal left group cartilage. The OA-MAT-MAG group did not differ from the normal left group in MMP-3 as determined by Western blot analysis. The study suggests that OA of the medial femoral condyle developed in a canine model exposed to a magnetic field may be inhibited beyond the benefit provided by mattress. Further studies are needed to delineate more precisely the effect of the magnetic field in reducing the severity of OA.     

Renal urologic anomalies presenting in adult identical twins

Two sets of identical adult twins recently presented to our hospital. In one case, the patients demonstrated (ipsilateral) renal agenesis. In the other, the patients presented approximately one year apart with symptomatic (ipsilateral) ureteropelvic junction obstructions. Although the literature suggests a few reports of this type in the pediatric and newborn population, the authors are unaware of similar reports in adults.