CysView: protein classification based on cysteine pairing patterns

CysView is a web-based application tool that identifies and classifies proteins according to their disulfide connectivity patterns. It accepts a dataset of annotated protein sequences in various formats and returns a graphical representation of cysteine pairing patterns. CysView displays cysteine patterns for those records in the data with disulfide annotations. It allows the viewing of records grouped by connectivity patterns. CysView's utility as an analysis tool was demonstrated by the rapid and correct classification of scorpion toxin entries from GenPept on the basis of their disulfide pairing patterns. It has proved useful for rapid detection of irrelevant and partial records, or those with incomplete annotations. CysView can be used to support distant homology between proteins. CysView is publicly available at http://research.i2r.a-star.edu.sg/CysView/.

Generic classification for the Gasteruptiinae (Hymenoptera: Gasteruptiidae) based on a cladistic analysis, with the description of two new Neotropical genera and the revalidation of Plutofoenus Kieffer

Gasteruptiinae is the largest Gasteruptiidae subfamily, with circa 400 species that have been grouped into the worldwide Gasteruption Latreille. Based on a cladistic analysis with 43 morphological characters, 40 ingroup taxa representing all biogeographic regions, and seven outgroups (four Hyptiogastrinae, two Aulacidae and one Evaniidae), I confirm the monophyly of Gasteruptiinae and Gasteruption and recognize three exclusively Neotropical small genera: Plutofoenus Kieffer (revalidated) (southern South America), Spinolafoenus Macedo n. gen. (Chile) and Trilobitofoenus Macedo n. gen. (Central and South America). Gasteruption, supported by four synapomorphies, remains the most speciose genus in the subfamily. The four Gasteruptiinae genera are keyed and described. Seven species are keyed and described or redescribed: Plutofoenus chaeturus (Schletterer) n. comb., P. edwardsi Turner, P. paraguayensis (Schrottky), Spinolafoenus ruficornis (Spinola) n. comb., Trilobitofoenus alvarengai Macedo n. sp., T. plaumanni Macedo n. sp. and T. sericeus (Cameron) n. comb. (lectotype designated).

EULAR/PRINTO/PRES criteria for Henoch-Schonlein purpura, childhood polyarteritis nodosa, childhood Wegener granulomatosis and childhood Takayasu arteritis: Ankara 2008. Part II: Final classification criteria

Objectives To validate the previously proposed classification criteria for Henoch-Schonlein purpura (HSP), childhood polyarteritis nodosa (c-PAN), c-Wegener granulomatosis (c-WG) and c-Takayasu arteritis (c-TA). Methods Step 1: retrospective/prospective webdata collection for children with HSP, c-PAN, c-WG and c-TA with age at diagnosis <= 18 years. Step 2: blinded classification by consensus panel of a representative sample of 280 cases. Step 3: statistical (sensitivity, specificity, area under the curve and.-agreement) and nominal group technique consensus evaluations. Results 827 patients with HSP, 150 with c-PAN, 60 with c-WG, 87 with c-TA and 52 with c-other were compared with each other. A patient was classified as HSP in the presence of purpura or petechiae (mandatory) with lower limb predominance plus one of four criteria: (1) abdominal pain; (2) histopathology (IgA); (3) arthritis or arthralgia; (4) renal involvement. Classification of c-PAN required a systemic inflammatory disease with evidence of necrotising vasculitis OR angiographic abnormalities of medium-/small-sized arteries (mandatory criterion) plus one of five criteria: (1) skin involvement; (2) myalgia/muscle tenderness; (3) hypertension; (4) peripheral neuropathy; (5) renal involvement. Classification of c-WG required three of six criteria: (1) histopathological evidence of granulomatous inflammation; (2) upper airway involvement; (3) laryngo-tracheo-bronchial involvement; (4) pulmonary involvement (x-ray/CT); (5) antineutrophilic cytoplasmic antibody positivity; (6) renal involvement. Classification of c-TA required typical angiographic abnormalities of the aorta or its main branches and pulmonary arteries (mandatory criterion) plus one of five criteria: (1) pulse deficit or claudication; (2) blood pressure discrepancy in any limb; (3) bruits; (4) hypertension; (5) elevated acute phase reactant. Conclusion European League Against Rheumatism/Paediatric Rheumatology International Trials Organisation/Paediatric Rheumatology European Society propose validated classification criteria for HSP, c-PAN, c-WG and c-TA with high sensitivity/specificity.

Normal and anomalous classification of category exemplars in schizophrenia

Background Schizophrenia has been associated with semantic memory impairment and previous studies report a difficulty in accessing semantic category exemplars (Moelter et al. 2005 Schizophr Res 78:209–217). The anterior temporal cortex (ATC) has been implicated in the representation of semantic knowledge (Rogers et al. 2004 Psychol Rev 111(1):205–235). We conducted a high-field (4T) fMRI study with the Category Judgment and Substitution Task (CJAST), an analogue of the Hayling test. We hypothesised that differential activation of the temporal lobe would be observed in schizophrenia patients versus controls. Methods Eight schizophrenia patients (7M : 1F) and eight matched controls performed the CJAST, involving a randomised series of 55 common nouns (from five semantic categories) across three conditions: semantic categorisation, anomalous categorisation and word reading. High-resolution 3D T1-weighted images and GE EPI with BOLD contrast and sparse temporal sampling were acquired on a 4T Bruker MedSpec system. Image processing and analyses were performed with SPM2. Results Differential activation in the left ATC was found for anomalous categorisation relative to category judgment, in patients versus controls. Conclusions We examined semantic memory deficits in schizophrenia using a novel fMRI task. Since the ATC corresponds to an area involved in accessing abstract semantic representations (Moelter et al. 2005), these results suggest schizophrenia patients utilise the same neural network as healthy controls, however it is compromised in the patients and the different ATC activity might be attributable to weakening of category-to-category associations.

Mild myocardial infarction - A classification problem in epidemiologic studies

In studies assessing the trends in coronary events, such as the World Health Organization (WHO) MONICA Project (multinational MONItoring of trends and determinants of CArdiovascular disease), the main emphasis has been on coronary deaths and non-fatal definite myocardial infarctions (MI). It is, however, possible that the proportion of milder MIs may be increasing because of improvements in treatment and reductions in levels of risk factors. We used the MI register data of the WHO MONICA Project to investigate several definitions for mild non-fatal MIs that would be applicable in various settings and could be used to assess trends in milder coronary events. Of 38 populations participating in the WHO MONICA MI register study, more than half registered a sufficiently wide spectrum of events that it was possible to identify subsets of milder cases. The event rates and case fatality rates of MI are clearly dependent on the spectrum of non-fatal MIs, which are included. On clinical grounds we propose that the original MONICA category ''non-fatal possible MI'' could bt:divided into two groups: ''non fatal probable MI'' and ''prolonged chest pain.'' Non-fatal probable MIs are cases, which in addition to ''typical symptoms'' have electrocardiogram (EGG) or enzyme changes suggesting cardiac ischemia, but not severe enough to fulfil the criteria for non-fatal definite MI In more than half of the MONICA Collaborating Centers, the registration of MI covers these milder events reasonably well. Proportions of non-fatal probable MIs vary less between populations than do proportions of non fatal possible MIs. Also rates of non-fatal probable MI are somewhat more highly correlated with rates of fatal events and non-fatal definite MI. These findings support the validity of the category of non-fatal probable MI. In each center the increase in event rates and the decrease in case-fatality due to the inclusion of non-fatal probable MI was lar er for women than men. For the WHO MONICA Project and other epidemiological studies the proposed category of non-fatal probable MIs can be used for assessing trends in rates of milder MI. Copyright (C) 1997 Elsevier Science Inc.

Updated Clinical Classification of Pulmonary Hypertension

The aim of a clinical classification of pulmonary hypertension (PH) is to group together different manifestations of disease sharing similarities in pathophysiologic mechanisms, clinical presentation, and therapeutic approaches. In 2003, during the 3rd World Symposium on Pulmonary Hypertension, the clinical classification of PH initially adopted in 1998 during the 2nd World Symposium was slightly modified. During the 4th World Symposium held in 2008, it was decided to maintain the general architecture and philosophy of the previous clinical classifications. The modifications adopted during this meeting principally concern Group 1, pulmonary arterial hypertension (PAH). This subgroup includes patients with PAH with a family history or patients with idiopathic PAH with germline mutations (e. g., bone morphogenetic protein receptor-2, activin receptor-like kinase type 1, and endoglin). In the new classification, schistosomiasis and chronic hemolytic anemia appear as separate entities in the subgroup of PAH associated with identified diseases. Finally, it was decided to place pulmonary venoocclusive disease and pulmonary capillary hemangiomatosis in a separate group, distinct from but very close to Group 1 (now called Group 1`). Thus, Group 1 of PAH is now more homogeneous. (J Am Coll Cardiol 2009;54:S43-54) (C) 2009 by the American College of Cardiology Foundation

Effect of the Novel Thienopyridine Prasugrel Compared With Clopidogrel on Spontaneous and Procedural Myocardial Infarction in the Trial to Assess Improvement in Therapeutic Outcomes by Optimizing Platelet Inhibition With Prasugrel-Thrombolysis in Myocardial Infarction 38 An Application of the Classification System From the Universal Definition of Myocardial Infarction

Background-Prasugrel is a novel thienopyridine that reduces new or recurrent myocardial infarctions (MIs) compared with clopidogrel in patients with acute coronary syndrome undergoing percutaneous coronary intervention. This effect must be balanced against an increased bleeding risk. We aimed to characterize the effect of prasugrel with respect to the type, size, and timing of MI using the universal classification of MI. Methods and Results-We studied 13 608 patients with acute coronary syndrome undergoing percutaneous coronary intervention randomized to prasugrel or clopidogrel and treated for 6 to 15 months in the Trial to Assess Improvement in Therapeutic Outcomes by Optimizing Platelet Inhibition With Prasugrel-Thrombolysis in Myocardial Infarction (TRITON-TIMI 38). Each MI underwent supplemental classification as spontaneous, secondary, or sudden cardiac death (types 1, 2, and 3) or procedure related (Types 4 and 5) and examined events occurring early and after 30 days. Prasugrel significantly reduced the overall risk of MI (7.4% versus 9.7%; hazard ratio [HR], 0.76; 95% confidence interval [CI], 0.67 to 0.85; P < 0.0001). This benefit was present for procedure-related MIs (4.9% versus 6.4%; HR, 0.76; 95% CI, 0.66 to 0.88; P = 0.0002) and nonprocedural (type 1, 2, or 3) MIs (2.8% versus 3.7%; HR, 0.72; 95% CI, 0.59 to 0.88; P = 0.0013) and consistently across MI size, including MIs with a biomarker peak >= 5 times the reference limit (HR. 0.74; 95% CI, 0.64 to 0.86; P = 0.0001). In landmark analyses starting at 30 days, patients treated with prasugrel had a lower risk of any MI (2.9% versus 3.7%; HR, 0.77; P = 0.014), including nonprocedural MI (2.3% versus 3.1%; HR, 0.74; 95% CI, 0.60 to 0.92; P = 0.0069). Conclusion-Treatment with prasugrel compared with clopidogrel for up to 15 months in patients with acute coronary syndrome undergoing percutaneous coronary intervention significantly reduces the risk of MIs that are procedure related and spontaneous and those that are small and large, including new MIs occurring during maintenance therapy. (Circulation. 2009; 119: 2758-2764.)

Short-term specialized enteral diet fails to attenuate malnutrition impairment of experimental open wound acute healing

Objective: We assessed the effect of enteral refeeding on the morphology, gene expression, and contraction of acute open wounds in previously malnourished rats using two different enteral diets. Methods: Adult male isogenic Lewis rats divided into two groups (eutrophic, n = 30; and previously malnourished, 12-15% body weight loss, n = 27) were subjected to cutaneous dorsal wounds and gastrostomy. Control rats received a standard oral diet (AIN-93M chow) plus enteral saline solution. Subject rats received chow plus a standard enteral diet or an enteral diet enriched with arginine and antioxidants. On post-trauma days 7 and 14, wound granulation tissue samples were collected for morphologic analysis using hematoxylin and eosin and picrosirius stain or immunohistochemistry slides and real-time polymerase chain reaction for collagen I and III gene expression. Wound contraction was also evaluated by comparing wound images from days 0,7, and 14. Results: Malnourished control rats had increased intensity and duration of wound inflammation, impaired increase of fibroblast cells contingent on post-trauma days 7 to 14, decreased expression of collagen III, and less wound contraction compared with eutrophic control rats. A specialized enteral diet did not improve wound healing of malnourished rats but did promote wound contraction at post-trauma day 7 in eutrophic rats. Conclusion: Short-term enteral refeeding, even with a specialized diet, failed to protect previously wounded malnourished rats from a prolonged inflammatory phase and impaired healing. (C) 2010 Elsevier Inc. All rights reserved.

Involvement of Astroglial Fibroblast Growth Factor-2 and Microglia in the Nigral 6-OHDA Parkinsonism and a Possible Role of Glucocorticoid Hormone on the Glial Mediated Local Trophism and Wound Repair

We have observed in previous studies that 6-hydroxydopamine (6-OHDA)-induced lesions in the nigrostriatal dopamine (DA) system promote increases of the astroglial basic fibroblast growth factor (FGF-2, bFGF) synthesis in the ascending DA pathways, event that could be modified by adrenosteroid hormones. Here, we first evaluated the changes of microglial reactivity in relation to the FGF-2-mediated trophic responses in the lesioned nigrostriatal DA system. 6-OHDA was injected into the left side of the rat substantia nigra. The OX42 immunohistochemistry combined with stereology showed the time course of the microglial activation. The OX42 immunoreactivity (IR) was already increased in the pars compacta of the substantia nigra (SNc) and ventral tegmental area (VTA) 2 h after the 6-OHDA injection, peaked on day 7, and remained increased on the 14th day time-interval. In the neostriatum, OX42 immunoreactive (ir) microglial profiles increased at 24 h, peaked at 72 h, was still increased at 7 days but not 14 days after the 6-OHDA injection. Two-colour immunofluorescence analysis of the tyrosine hydroxylase (TH) and OX42 IRs revealed the presence of small patches of TH IR within the activated microglia. A decreased FGF-2 IR was seen in the cytoplasm of DA neurons of the SNc and VTA as soon as 2 h after 6-OHDA injection. The majority of the DA FGF-2 ir cells of these regions had disappeared 72 h after neurotoxin. The astroglial FGF-2 IR increased in the SNc and VTA, which peaked on day 7. Two-colour immunofluorescence and immunoperoxidase analyses of the FGF-2 and OX42 IRs revealed no FGF-2 IR within the reactive or resting microglia. Second, we have evaluated in a series of biochemical experiments whether adrenocortical manipulation can interfere with the nigral lesion and the state of local astroglial reaction, looking at the TH and GFAP levels respectively. Rats were adrenalectomized (ADX) and received a nigral 6-OHDA stereotaxical injection 2 days later and sacrificed up to 3 weeks after the DA lesion. Western blot analysis showed time-dependent decrease and elevation of TH and GFAP levels, respectively, in the lesioned versus contralateral midbrain sides, events potentiated by ADX and worsened by corticosterone replacement. ADX decreased the levels of FGF-2 protein (23 kDa isoform) in the lesioned side of the ventral midbrain compared contralaterally. The results indicate that reactive astroglia, but not reactive microglia, showed an increased FGF-2 IR in the process of DA cell degeneration induced by 6-OHDA. However, interactions between these glial cells may be relevant to the mechanisms which trigger the increased astroglial FGF-2 synthesis and thus may be related to the trophic state of DA neurons and the repair processes following DA lesion. The findings also gave further evidence that adrenocortical hormones may regulate astroglial-mediated trophic mechanisms and wound repair events in the lesioned DA system that may be relevant to the progression of Parkinson`s disease.

Assessment of immediate conservative breast surgery reconstruction: A classification system of defects revisited and an algorithm for selecting the appropriate technique

Background: Although various techniques have been used for breast conservation surgery reconstruction, there are few studies describing a logical approach to reconstruction of these defects. The objectives of this study were to establish a classification system for partial breast defects and to develop a reconstructive algorithm. Methods: The authors reviewed a 7-year experience with 209 immediate breast conservation surgery reconstructions. Mean follow-up was 31 months. Type I defects include tissue resection in smaller breasts (bra size A/B), including type IA, which involves minimal defects that do not cause distortion; type III, which involves moderate defects that cause moderate distortion; and type IC, which involves large defects that cause significant deformities. Type II includes tissue resection in medium-sized breasts with or without ptosis (bra size C), and type III includes tissue resection in large breasts with ptosis (bra size D). Results: Eighteen percent of patients presented type I, where a lateral thoracodorsal flap and a latissimus dorsi flap were performed in 68 percent. Forty-five percent presented type II defects, where bilateral mastopexy was performed in 52 percent. Thirty-seven percent of patients presented type III distortion, where bilateral reduction mammaplasty was performed in 67 percent. Thirty-five percent of patients presented complications, and most were minor. Conclusions: An algorithm based on breast size in relation to tumor location and extension of resection can be followed to determine the best approach to reconstruction. The authors` results have demonstrated that the complications were similar to those in other clinical series. Success depends on patient selection, coordinated planning with the oncologic surgeon, and careful intraoperative management.