Graph comparison by log-odds score matrices with application to protein topology analysis

A TOPS diagram is a simplified description of the topology of a protein using a graph where nodes are alpha-helices and beta-strands, and edges correspond to chirality relations and parallel or antiparallel bonds between strands. We present a matching algorithm between two TOPS diagrams where the likelihood of a match is measured according to previously known matches between complete 3D structures. This totally new 3D training is recorded on transition matrices that count the likelihood that a given TOPS feature, or combination thereof, is replaced by another feature on homologs. The new algorithm outperforms existing ones on a benchmark database. Some biologically significant examples are discussed as well. The method can be used whenever frequencies of edge relationship matches are known, as it is the case for several biopolymer structures.

Epicardial adipose tissue is an independent predictor of coronary atherosclerotic burden

INTRODUCTION

Epicardial adipose tissue (EAT) may play an active role in the development of coronary artery disease (CAD). The aim of this work was to study the relations between EAT, abdominal visceral fat (AVF), and coronary atherosclerotic burden as assessed by multislice computed tomography (MSCT).

POPULATION AND METHODS

Two hundred fifteen patients without known CAD referred to 64-SCT during a 6-months period were included. All patients underwent a standardized protocol including quantification of AVF, EAT, coronary artery calcification (CAC), and coronary angiography by MSCT.

RESULTS

Two hundred fifteen patients, with mean age of 58 ± 11 years, in which 61% were males, with mean body mass index (BMI) of 28 ± 4 kg/m(2) were included. EAT volume was directly associated with male sex, age, BMI, abdominal circumference, AVF, number of coronary segments with atherosclerotic plaques (p<0.01 for all), number of segments with significant stenoses, and presence of metabolic syndrome components (p<0.05). CAC increased by 14.7% per additional 10 ml of EAT volume. Adjusting for age, gender, and AVF changed this increase to 7.5%. After adjusting for all considered confounders, there was still an independent association, with a CAC increase of 3.7% per additional 10 ml of EAT. A significant interaction was found between EAT volume and gender and between EAT volume and obesity: an increase of EAT was associated with an increase of additional 8% of CAC in men, and additional increase of 5% in non-obese individuals (p<0.001 for both).

CONCLUSION

EAT volume positively relates to coronary atherosclerotic burden, as assessed by CAC; this correlation was shown to be independent of AVF.

In vivo anti-inflammatory effect and toxicological screening of Maytenus heterophylla and Maytenus senegalensis extracts

Maytenus heterophylla (Eckl & Zeyh.) Robson and Maytenus senegalensis (Lam). Exell are two African medicinal plants used to treat painful and inflammatory diseases. We evaluated the in vivo (per os) anti-inflammatory activity of M. heterophylla leaf, stem and root extracts and of M. senegalensis leaf and stem extracts. Additionally, we assessed their in vivo acute and sub-acute toxicities. Anti-inflammatory activities of ethanol extracts were determined in Wistar albino rats, by the carrageenan-induced paw oedema method. Acute and sub-acute toxicity screening of the extracts was evaluated in adult male CD-6 mice. Leaf extracts of M. heterophylla and M. senegalensis exhibited significant anti-inflammatory activity (120 mg/kg, per os), reducing oedema by 51% and 35%, respectively. While M. heterophylla extracts at 1200 mg/kg have shown to be non-toxic, M. senegalensis extracts indicated some toxicity. Our results show a significant anti-inflammatory effect of both M. heterophylla and M. senegalensis leaf extracts in a local model of acute inflammation and suggest the absence of acute and sub-acute toxicity signs of the M. heterophylla leaf extract (but not of M. senegalensis). Ongoing studies will surely shed some light into the mechanism of action of this active extract and establish its chemical fingerprint.

Unexpected angiographic and visual findings after clipping of a carotid-ophthalmic aneurysm

A 56-year-old woman underwent surgery for a ruptured carotid-ophthalmic artery aneurysm. Intraoperative visual inspection confirmed that the ophthalmic artery was left intact. She had no light perception on the operated side right after surgery. Angiography one week after surgery confirmed exclusion of the aneurysm, no filling of the proximal portion of the ophthalmic artery, and a very faint filling of its distal orbital part. She gradually recovered from this deficit and 9 months after surgery she is capable of counting fingers. At this time angiography displayed filling of all the portions of the ophthalmic artery, absence of recruitment of collateral blood supply, and exclusion of the aneurysm as before. Surgical manipulation seems to either have induced vasospasm or thrombosis of the ophthalmic artery. Regression of vasospasm or secondary recanalization of the thrombus without development of collateral blood supply may account for the gradual improvement of vision. A risk of monocular blindness is associated with the surgical treatment of para-clinoid aneurysms. Nevertheless, when it occurs, a perspective of recovery may exist if certain etiologies are involved.

Topical Imiquimod Treatment of Lentigo Maligna

Lentigo maligna (LM) is the in situ phase of lentigo maligna melanoma, which may progress to invasive melanoma if left untreated. It mainly occurs on sun-exposed areas of elderly patients. The lesions can be large and conventional surgery can be difficult, particularly on the face. Recent reports indicate that topical imiquimod 5% cream is effective in the treatment of LM. It may be an alternative when surgery or other classical treatments are not possible in elderly patients. We describe an 80-year-old Caucasian woman with a 10-year history of a histologically verified extensive LM of the face. She was treated with imiquimod 5% cream once daily. After four months it showed complete clinical response. One year after the treatment the patient was still free from recurrence.

Demonstration of serum albumin (ALB) polymorphism in wild rabbits, Oryctolagus cuniculus, by means of isoelectric focusing

Genetic polymorphism of serum albumin was demonstrated by isoelectric focusing in wild rabbit populations from Portugal and England. Gene frequencies were estimated to be (1) ALB*1 = 0.47, ALB*2 = 0.49, ALB*3 = 0.04, in Portugal, and (2) ALB*1 = 0.60 and ALB*2 = 0.40, in England. One hundred Portuguese domestic rabbits of mixed breeds were all of ALB 1 type.

Functionalization of atomic force microscope tips by dielectrophoretic assembly of Gd(2)O(3):Eu(3+) nanorods

An atomic force microscopy (AFM) tip has been coated with photoluminescent Eu(3+)-doped Gd(2)O(3) nanorods using a dielectrophoresis technique, which preserves the red emission of the nanorods (quantum yield 0.47). The performance of the modified tips has been tested by using them for regular topography imaging in tapping and contact modes. Both a regular AFM standard grid and a patterned surface (of an organic-inorganic methacrylate Zr-based oxo-cluster and poly(oxyethylene)/siloxane hybrid) have been used. Similar depth values have been measured using a conventional silicon tip and the nanorod-modified tip. The tips before and after use exhibit similar SEM images and photoluminescence spectra and, thus, seem to be stable under working conditions. These tips should find applications in scanning near-field optical microscopy and other scanning techniques.

Perceptually stable regions for arbitrary polygons

Zou and Yan have recently developed a skeletonization algorithm of digital shapes based on a regularity/singularity analysis; they use the polygon whose vertices are the boundary pixels of the image to compute a constrained Delaunay triangulation (CDT) in order to find local symmetries and stable regions. Their method has produced good results but it is slow since its complexity depends on the number of contour pixels. This paper presents an extension of their technique to handle arbitrary polygons, not only polygons of short edges. Consequently, not only can we achieve results as good as theirs for digital images, but we can also compute skeletons of polygons of any number of edges. Since we can handle polygonal approximations of figures, the skeletons are more resilient to noise and faster to process.

[Primary angiitis of the central nervous system: an infrequent form of presentation]

INTRODUCTION

Primary angiitis of the central nervous system (CNS) is a rare disease. Clinical signs and symptoms include headache and cognitive disorders associated to multifocal neurological deficits. A definitive diagnosis can only be achieved by means of a cerebromeningeal biopsy.

CASE REPORT

We describe the case of a 15-year-old male who first reported lower back pain and progressive paresis of the right lower limb, later followed by laterocollis on the right side. Magnetic resonance (MR) scanning of the brain and spinal cord revealed a pseudotumoral lesion in the right cerebellum and two lesions in the spinal cord. Dexamethasone was administered and surgical resection of the cerebellar lesion was performed. Following surgery, the patient received corticoid treatment with progressive withdrawal. Full clinical recovery of the patient was achieved. A year later, the same patient was admitted to hospital again because of headaches and diplopia. A new MR brain scan showed a right frontotemporal lesion. Dexamethasone was administered and the patient recovered. Thirteen months later, he reported dysarthria and right-side hemiparesis. An MR brain scan revealed the presence of a number of bilateral lesions in the white matter. Results of a lumbar puncture showed lymphocytic pleocytosis and raised protein levels in cerebrospinal fluid. The laminae from the cerebromeningeal biopsy were reviewed and the results confirmed the hypothetical diagnosis of angiitis of the CNS. Treatment was established with intravenous cyclophosphamide in association with oral prednisone.

CONCLUSIONS

Primary angiitis of the CNS is an infrequent disease and its pathogenesis remains unknown. The definitive diagnosis of these patients is histological. It courses spontaneously and generally has a fatal outcome. Treatment, which consists in an association of cyclophosphamide and prednisone, must be started as early as possible.

Transitory gliosis in the CA3 hippocampal region in rats fed on a ketogenic diet

The ketogenic diet (KD) is a high-fat, low-protein and low-carbohydrate diet included as medical practice against seizure disorders, particularly in children refractory to conventional anti-epileptic drug treatment. However, the molecular basis of its therapeutic effect remains unclear. Considering the growing evidence for the importance of glial cells for neuronal development, survival and plasticity, we investigated astrocyte protein markers from KD fed rats, in different regions of hippocampus, a brain structure commonly involved in seizure disorders. We found a transitory increment in GFAP in the CA3 hippocampal region, but not in the CA1 or dentate gyrus (DG). This change was not accompanied by changes in S100B content or glutamine synthetase activity. In order to evaluate possible hippocampal involvement we investigated spatial-cognitive behavior using the water-maze task. No changes were observed. This transitory gliosis in CA3 could be related to, or precede, other associated changes proposed to be involved in the attenuation of seizure disorders. These data reinforce the importance of hippocampal astrocytes as cell targets during KD feeding.

The epidemiology of moderate and severe injuries in a Nicaraguan community: a household-based survey

Although injuries constitute a major public health problem worldwide, the magnitude and nature of this problem is difficult to establish in low-income settings due to the lack of valid and representative data. In Nicaragua, several parallel studies have been carried out attempting to assess levels and patterns of injury using various sources of information. The objective of this study was to describe the magnitude and profile of moderate and severe injuries in a well-defined community in Nicaragua. The study was conducted using a household-based survey design. Randomized cluster sampling provided information from 10,797 households (63,886 inhabitants). The outcomes included fatal and non-fatal injuries registered during a recall period of 6 weeks. Seven percent of all injuries were classified as moderate or severe. The estimated annual incidence rate of moderate/severe injuries was 27.6 per 1000 [95% confidence intervals (CI): 26.4-29.2], while the mortality and impairment rates were 108.9 (95% CI: 83.5-134.4) and 95.3 (95% CI: 71.4-119.2) per 100,000 inhabitants, respectively. Home and traffic areas were the main environments associated with injury occurrence. The most affected groups were the elderly, children and males. No differences were found between urban and rural areas. Only 9% of all cases, including minor injuries, sought hospital treatment. The main causes of non-fatal injuries were falls, traffic and cuts, whereas fatalities were largely associated with intentional injuries. For every death due to injury, there was one permanent disability, 25 moderate/severe injuries and 354 minor injuries. This study provides a broad description of injury magnitudes and patterns in a defined Nicaraguan community, and demonstrates the aggregate injury pyramid of the same community. It also identifies the issue of severity and concludes with a recommendation to apply different criteria of severity. Our results support the call for a careful evaluation of injury data sources and severity scores when planning injury prevention programmes.

A family of metrics for biopolymers based on counting independent sets

We introduce a new family of metrics for graphs of fixed size, based on counting-independent sets. Our definition is simpler and easier to calculate than the edge ideal metric family defined by Llabrés and Rosselló without loosing any of its abstract properties. We contrast them on some examples with graphs that represent protein secondary and three-dimensional (3D) structures. We conclude that although the edge ideal metrics are faster to calculate on some sparse graphs, in general, the independent set metrics are more tractable.

Tracing the origin of the most common thiopurine methyltransferase (TPMT) variants: preliminary data from the patterns of haplotypic association with two CA repeats

Thiopurine methyltransferase (TPMT) is an essential enzyme for normal metabolism of thiopurine drugs. In humans TPMT activity is largely dependent upon genetic variation at the TPMT locus, with TPMT*3A and TPMT*3C being the most frequent mutant alleles associated with reduced activity. TPMT*3C is a widespread allele reaching the highest frequencies in Africans, whereas TPMT*3A is virtually restricted to Caucasian descendent populations. To estimate the time of origin of these two alleles, we analyzed the levels of diversity at two CA repeats flanking the TPMT gene. In accordance to its pattern of geographical distribution, the study of the decay in linkage disequilibrium over time indicated that TPMT*3A was the younger allele. The estimated age was 5700 years, which coincides with the Neolithic, a period characterized by major population expansion that could have been responsible for the spread of TPMT*3A from its place of origin, maybe a western Eurasian population. TPMT*3C was found to have arisen earlier, roughly 14000 years ago, which could explain the worldwide dispersal of TPMT*3C.

Occupational injuries identified by an emergency department based injury surveillance system in Nicaragua

OBJECTIVES

To identify and describe the work related injuries in both the formal and informal work sectors captured in an emergency department based injury surveillance system in Managua, Nicaragua.

SETTING

Urban emergency department in Managua, Nicaragua serving 200-300 patients per day.

METHODS

Secondary analysis from the surveillance system data. All cases indicating an injury while working and seen for treatment at the emergency department between 1 August 2001 and 31 July 2002 were included. There was no exclusion based on place of occurrence (home, work, school), age, or gender.

RESULTS

There were 3801 work related injuries identified which accounted for 18.6% of the total 20 425 injures captured by the surveillance system. Twenty seven work related fatalities were recorded, compared with the 1998 International Labor Organization statistic of 25 occupational fatalities for all of Nicaragua. Injuries occurring outside of a formal work location accounted for more than 60% of the work related injuries. Almost half of these occurred at home, while 19% occurred on the street. The leading mechanisms for work related injuries were falls (30%), blunt objects (28%), and stabs/cuts (23%). Falls were by far the most severe mechanism in the study, causing 37% of the work related deaths and more than half of the fractures.

CONCLUSIONS

Occupational injuries are grossly underreported in Nicaragua. This study demonstrated that an emergency department can be a data source for work related injuries in developing countries because it captures both the formal and informal workforce injuries. Fall prevention initiatives could significantly reduce the magnitude and severity of occupational injuries in Managua, Nicaragua.

Mg,Al layered double hydroxides with intercalated indomethacin: Synthesis, characterization, and pharmacological study

Magnesium aluminium layered double hydroxides (LDH) with a molar Mg/Al ratio of 2.0 have been prepared with intercalated indomethacin following two routes: reconstruction from a previously calcined Mg(2)Al-CO(3) LDH, and coprecipitation from the corresponding chlorides. The solids have been characterized by powder X-ray diffraction, FTIR, and (13)C CP/MAS NMR spectroscopies and thermal stability (differential thermal analysis and thermogravimetric analysis). Intercalation of the drug is attained by both routes; however, while coprecipitation leads to a single layered structure, contamination with another layered MgAl-CO(3) phase occurs by the reconstruction method. The amount of drug intercalated, as well as the height of the gallery, are larger by the coprecipitation than by the reconstruction one. The data obtained support a somewhat tilted, upwards orientation of the drug molecules forming an interdigited bilayer, in the case of the sample prepared by coprecipitation, with the carboxylate groups pointing towards the hydroxyl layers. However, in the case of the sample prepared by reconstruction, the molecules are forming a tilted, upwards monolayer. The solids prepared are stable up to 250 degrees C. Pharmacological studies in vivo show that intercalation of the drug in the LDH reduces the ulcerating damage of the drug.

Controlling hydrolysis and dispersion of AlN powders in aqueous media

Aqueous suspensions of aluminum nitride (AlN) powders have been prepared in the presence of different surface-active agents, namely, H3PO4 and an anionic surfactant, to avoid the hydrolysis of AlN powders and to enhance dispersion. The most determinant parameters to the hydrolysis process (DeltapH and time of contact) and the stabilization of AlN particles in water (surface crystallinity, surface chemical modification, and surface ionic charge) were seen to be strongly dependent on the acidic agent. The H3PO4 treatment was effective against hydrolysis of AlN due to the formation of a phosphate-based protection layer on the particles' surface, and, although it keeps the pH of the suspension below 4, it does not guarantee a good dispersion. The individual adsorption of the anionic surfactant at the surface of AlN particles suspensions did not completely suppress the hydrolysis but it did enhance the degree of dispersion. A proper combination of the two types of surface-active agents enabled the preparation of AlN aqueous suspensions of relatively low viscosity and high AlN concentration, which can be a good starting point for aqueous-based colloidal shaping techniques or for freeze granulation or spray drying to obtain suitable granulate powder characteristics for dry-pressing technologies. An adsorption mechanism of the surface-active agents onto the particles' surface is proposed and supported by NMR and FT-IR analyses.

alpha1-Antitrypsin null alleles: evidence for the recurrence of the L353fsX376 mutation and a novel G-->A transition in position +1 of intron IC affecting normal mRNA splicing

alpha1-Antitrypsin (PI) deficiency is a common autosomal recessive disorder associated with emphysema and liver disease, which may result from a wide spectrum of mutations causing a reduction of serum levels (deficient alleles) or a total lack of circulating protein (null alleles). We report two different alleles associated with the absence of isoelectric focusing banding patterns in Portuguese patients with emphysema. The first allele, Q0(ourém), results from the recurrence of the defining mutation of the Q0(mattawa) variant (L353fsX376) on a M3 normal background. The second allele, Q0(porto), has a novel G-->A mutation at position +1 of the intron IC (IVS1C+1G-->A), which restricts mononuclear phagocyte transcripts to mRNA species resulting from the direct splice of exon IA to exon II. The absence of this normal splice alternative in the liver, where PI is primarily synthesized, provides a basis for the pathogenic effects of this mutation.

High-resolution heteronuclear correlation spectra between 31P and 27Al in microporous aluminophosphates

A solid-state nuclear magnetic resonance (NMR) experiment, which provides high-resolution two-dimensional heteronuclear correlation (HETCOR) spectra between 27Al and 31P, is described. The first part of the experiment uses triple-quantum or quintuple-quantum magic-angle spinning (MQMAS) NMR of spin-5/2 nuclei (27Al) to produce an isotropic echo that is unaffected by the second-order quadrupolar broadening. The magnetization is then transferred to the spin-1/2 (31P) nuclei via cross-polarization (CP), resulting in isotropic resolution in both spectral dimensions. To illustrate its usefulness, this method (referred to as MQHETCOR) is applied to two important microporous framework aluminophosphates, hydrated VPI-5 and AIPO4-40.

Localization of a recessive juvenile cataract mutation to proximal chromosome 7 in mice

OBJECTIVE

To localize the chromosomal position of a novel cataract mutation (juvenile recessive cataract; jrc) in mice.

METHODS

A mapping population was developed by crossing cataract males (albino MH) to wild-type females (black C57BL/6J). F1 females were backcrossed to albino MH males with cataracts.

RESULTS

The results were consistent with a model of a single autosomal recessive gene [153 cataract, 169 wild-type; chi2 = 0.8, 1 degree of freedom (d.f.), p > 0.35]. Linkage with the albino (tyrosinase; Tyr) locus was evident (chi2 = 61.5, 1 d.f., p < 0.0001), implicating chromosome 7 as the location of jrc. Recombination percentages (+/- SE) between jrc and D7Mit340 (1.2 cM location), D7Mit227 (16.0 cM) and D7Mit270 (18.0 cM) were 17.1 +/- 2.1, 3.7 +/- 1.1 and 6.2 +/- 1.3%, respectively. Multi-point mapping determined that the most likely order of these loci is D7Mit340 - jrc - D7Mit227 - D7Mit270 - Tyr. Although animals with the mutant phenotype appeared to have little or no sense of sight, their growth was not different (p >0.20) from that of normal mice.

CONCLUSION

The jrc mutation model may be useful in the study of the genetics of cataracts in other animal species, including humans.

Pyrochlore-type tin niobate

A single crystal of Sn(1.59)Nb(1.84)O(6.35) was grown at 1273 K from a mixture of sodium niobate and tin(II) chloride. The structure is of pyrochlore type A(2)B(2)O(7). The tin is partially oxidized to tin(IV) and competes with niobium for the occupation of site B. The stereoactivity of the Sn(2+) lone pair induces displacement of tin towards the O atoms of the tunnel.

Ab initio structure determination of a small-pore framework sodium stannosilicate

The structure of a small-pore framework sodium stannosilicate Na(2)SnSi(3)O(9).2H(2)O (AV-10) has been determined ab initio from powder X-ray diffraction data (XRD). The unit cell is orthorhombic (space group C222(1), Z = 4) with cell dimensions a = 7.9453(5), b = 10.3439(7), c = 11.6252(7) A, V = 955 A(3). The structure of AV-10 is composed of corner sharing SnO(6) octahedra and SiO(4) tetrahedra, forming a three-dimensional framework structure. The SiO(4) tetrahedra form helix chains along [001] interconnected by SnO(6) octahedra. The SnO(6) octahedra are isolated by SiO(4) tetrahedra and, thus, there are no Sn-O-Sn linkages. AV-10 has been characterized by chemical analysis, powder XRD, scanning electron microscopy, (29)Si, (119)Sn, single- and (FAM) triple-quantum (23)Na MAS NMR spectroscopy, thermogravimetry (TGA), and nitrogen adsorption isotherms. The zeolitic water of AV-10 is reversibly lost. The dehydrated material has been studied in situ by powder XRD, TGA, and, in particular, triple-quantum (23)Na MAS NMR.