QuMinS: fast and scalable querying, mining and summarizing multi-modal databases

Given a large image set, in which very few images have labels, how to guess labels for the remaining majority? How to spot images that need brand new labels different from the predefined ones? How to summarize these data to route the user’s attention to what really matters? Here we answer all these questions. Specifically, we propose QuMinS, a fast, scalable solution to two problems: (i) Low-labor labeling (LLL) – given an image set, very few images have labels, find the most appropriate labels for the rest; and (ii) Mining and attention routing – in the same setting, find clusters, the top-'N IND.O' outlier images, and the 'N IND.R' images that best represent the data. Experiments on satellite images spanning up to 2.25 GB show that, contrasting to the state-of-the-art labeling techniques, QuMinS scales linearly on the data size, being up to 40 times faster than top competitors (GCap), still achieving better or equal accuracy, it spots images that potentially require unpredicted labels, and it works even with tiny initial label sets, i.e., nearly five examples. We also report a case study of our method’s practical usage to show that QuMinS is a viable tool for automatic coffee crop detection from remote sensing images.

Electroconvulsive Therapy in Brazil After the "Psychiatric Reform" A Public Health Problem-Example From a University Service

Objectives: The Brazilian public health system does not provide electroconvulsive therapy (ECT), which is limited to a few academic services. National mental health policies are against ECT. Our objectives were to analyze critically the public policies toward ECT and present the current situation using statistics from the Institute of Psychiatry of the University of Sao Paulo (IPq-HCFMUSP) and summary data from the other 13 ECT services identified in the country. Methods: Data regarding ECT treatment at the IPq-HCFMUSP were collected from January 2009 to June 2010 (demographical, number of sessions, and diagnoses). All the data were analyzed using SPSS 19, Epic Info 2000, and Excel. Results: During this period, 331 patients were treated at IPq-HCFMUSP: 221 (67%) were from Sao Paulo city, 50 (15.2%) from Sao Paulo's metropolitan area, 39 (11.8%) from Sao Paulo's countryside, and 20 (6.1%) from other states; 7352 ECT treatments were delivered-63.0% (4629) devoted entirely via the public health system (although not funded by the federal government); the main diagnoses were a mood disorder in 86.4% and schizophrenia in 7.3% of the cases. Conclusions: There is an important lack of public assistance for ECT, affecting mainly the poor and severely ill patients. The university services are overcrowded and cannot handle all the referrals. The authors press for changes in the mental health policies.

A large Cervidae Holocene accumulation in Eastern Brazil: an example of extreme taphonomical control in a cave environment

A remarkable cervid bone accumulation occurs at a single passage (named Cervid Passage; CP) at Lapa Nova, a maze cave in eastern Brazil. CP lies away from cave entrances, is a typical pitfall passage and contains bone remains of at least 121 cervids, besides few bats, peccaries and rodents remains. There is no evidence of water (or sediment) flow at the site and in general bones lack post depositional alterations and display anatomical proximity, suggesting that the majority of the remains found inside CP (mainly cervids) are due to animals that after entering the cave got trapped in the site. Observations suggest that two entrances could have provided access to cervids (and the few other animals, besides bats), either by falling inside the cave or by entering by their own free will. Once inside the cave, the maze pattern would make route finding difficult, and of all passage intersections, only the one leading to CP would result in a non-return situation, starving the animal to death. Radiocarbon dates suggest that animal entrapment occurred during at least 5 thousand years, during the Holocene. The reasons why mainly cervids were found are unknown but they are probably related to the biology of this group coupled with the fact that caves provide several specific taphonomic processes that may account for a strong bias in bone accumulation. Indeed, the frequent occurrence of Cervidae in both the fossil and sub-fossil record in Brazilian caves may be related to an overall high faunal abundance or may suggest that these animals were especially prone to enter caves, perhaps in search of nutrients (as cave saltpetre) or water.

Expression of Mitochondrial Non-coding RNAs (ncRNAs) Is Modulated by High Risk Human Papillomavirus (HPV) Oncogenes

The study of RNA and DNA oncogenic viruses has proved invaluable in the discovery of key cellular pathways that are rendered dysfunctional during cancer progression. An example is high risk human papillomavirus (HPV), the etiological agent of cervical cancer. The role of HPV oncogenes in cellular immortalization and transformation has been extensively investigated. We reported the differential expression of a family of human mitochondrial non-coding RNAs (ncRNAs) between normal and cancer cells. Normal cells express a sense mitochondrial ncRNA (SncmtRNA) that seems to be required for cell proliferation and two antisense transcripts (ASncmtRNAs). In contrast, the ASncmtRNAs are down-regulated in cancer cells. To shed some light on the mechanisms that trigger down-regulation of the ASncmtRNAs, we studied human keratinocytes (HFK) immortalized with HPV. Here we show that immortalization of HFK with HPV-16 or 18 causes down-regulation of the ASncmtRNAs and induces the expression of a new sense transcript named SncmtRNA-2. Transduction of HFK with both E6 and E7 is sufficient to induce expression of SncmtRNA-2. Moreover, E2 oncogene is involved in down-regulation of the ASncmtRNAs. Knockdown of E2 in immortalized cells reestablishes in a reversible manner the expression of the ASncmtRNAs, suggesting that endogenous cellular factors(s) could play functions analogous to E2 during non-HPV-induced oncogenesis.

Characterization of a thermostable extracellular tannase produced under submerged fermentation by Aspergillus ochraceus

Background: Tannases are enzymes that may be used in different industrial sectors as, for example, food and pharmaceutical. They are obtained mainly from microorganisms, as filamentous fungi. However, the diversity of fungi stays poorly explored for tannase production. In this article, Aspergillus ochraceus is presented as a new source of tannase with interesting features for biotechnological applications. Results: Extracellular tannase production was induced when the fungus was cultured in Khanna medium with tannic acid as carbon source. The extracellular tannase was purified 9-fold with 2% recovery and a single band corresponding to 85 kDa was observed in SDS-PAGE. The native apparent molecular mass was estimated as 112 kDa. Optima of temperature and pH were 40 degrees C and 5.0, respectively. The enzyme was fully stable from 40 degrees C to 60 degrees C during 1 hr. The activity was enhanced by Mn2+ (33-39%) and NH4+ (15%). The purified tannase hydrolyzed tannic acid and methyl gallate with Km of 0.76 mM and 0.72 mM, respectively, and Vmax of 0.92 U/mg protein and 0.68 U/mg protein, respectively. The analysis of a partial sequence of the tannase encoding gene showed an open read frame of 567 bp and a sequence of 199 amino acids were predicted. TLC analysis revealed the presence of gallic acid as a tannic acid hydrolysis product. Conclusion: The extracellular tannase produced by A. ochraceus showed distinctive characteristics such as monomeric structure and activation by Mn2+, suggesting a new kind of fungal tannases with biotechnological potential. Further, it was the first time that a partial gene sequence for A. ochraceus tannase was described.

The uncertain consequences of transferring bacterial strains between laboratories - rpoS instability as an example

Abstract Background Microbiological studies frequently involve exchanges of strains between laboratories and/or stock centers. The integrity of exchanged strains is vital for archival reasons and to ensure reproducible experimental results. For at least 50 years, one of the most common means of shipping bacteria was by inoculating bacterial samples in agar stabs. Long-term cultures in stabs exhibit genetic instabilities and one common instability is in rpoS. The sigma factor RpoS accumulates in response to several stresses and in the stationary phase. One consequence of RpoS accumulation is the competition with the vegetative sigma factor σ70. Under nutrient limiting conditions mutations in rpoS or in genes that regulate its expression tend to accumulate. Here, we investigate whether short-term storage and mailing of cultures in stabs results in genetic heterogeneity. Results We found that samples of the E. coli K-12 strain MC4100TF exchanged on three separate occasions by mail between our laboratories became heterogeneous. Reconstruction studies indicated that LB-stabs exhibited mutations previously found in GASP studies in stationary phase LB broth. At least 40% of reconstructed stocks and an equivalent proportion of actually mailed stock contained these mutations. Mutants with low RpoS levels emerged within 7 days of incubation in the stabs. Sequence analysis of ten of these segregants revealed that they harboured each of three different rpoS mutations. These mutants displayed the classical phenotypes of bacteria lacking rpoS. The genetic stability of MC4100TF was also tested in filter disks embedded in glycerol. Under these conditions, GASP mutants emerge only after a 3-week period. We also confirm that the intrinsic high RpoS level in MC4100TF is mainly due to the presence of an IS1 insertion in rssB. Conclusions Given that many E. coli strains contain high RpoS levels similar to MC4100TF, the integrity of such strains during transfers and storage is questionable. Variations in important collections may be due to storage-transfer related issues. These results raise important questions on the integrity of bacterial archives and transferred strains, explain variation like in the ECOR collection between laboratories and indicate a need for the development of better methods of strain transfer.

Birth defects in newborns and stillborns: an example of the Brazilian reality

Abstract Background This study constitutes a clinical and genetic study of all newborn and stillborn infants with birth defects seen in a period of one year in a medical school hospital located in Brazil. The aims of this study were to estimate the incidence, causes and consequences of the defects. Methods For all infants we carried out physical assessment, photographic records, analysis of medical records and collection of additional information with the family, besides the karyotypic analysis or molecular tests in indicated cases. Result The incidence of birth defects was 2.8%. Among them, the etiology was identified in 73.6% (ci95%: 64.4-81.6%). Etiology involving the participation of genetic factors single or associated with environmental factors) was more frequent 94.5%, ci95%: 88.5-98.0%) than those caused exclusively by environmental factors (alcohol in and gestational diabetes mellitus). The conclusive or presumed diagnosis was possible in 85% of the cases. Among them, the isolated congenital heart disease (9.5%) and Down syndrome (9.5%) were the most common, followed by gastroschisis (8.4%), neural tube defects (7.4%) and clubfoot (5.3%). Maternal age, parental consanguinity, exposure to teratogenic agents and family susceptibility were some of the identified risk factors. The most common observed consequences were prolonged hospital stays and death. Conclusions The current incidence of birth defects among newborns and stillbirths of in our population is similar to those obtained by other studies performed in Brazil and in other underdeveloped countries. Birth defects are one of the major causes leading to lost years of potential life. The study of birth defects in underdeveloped countries should continue. The identification of incidence, risk factors and consequences are essential for planning preventive measures and effective treatments.

Fine-tuning of defensive behaviors in the dorsal periaqueductal gray by atypical neurotransmitters

This paper presents an up-to-date review of the evidence indicating that atypical neurotransmitters such as nitric oxide (NO) and endocannabinoids (eCBs) play an important role in the regulation of aversive responses in the periaqueductal gray (PAG). Among the results supporting this role, several studies have shown that inhibitors of neuronal NO synthase or cannabinoid receptor type 1 (CB1) receptor agonists cause clear anxiolytic responses when injected into this region. The nitrergic and eCB systems can regulate the activity of classical neurotransmitters such as glutamate and γ-aminobutyric acid (GABA) that control PAG activity. We propose that they exert a ‘fine-tuning’ regulatory control of defensive responses in this area. This control, however, is probably complex, which may explain the usually bell-shaped dose-response curves observed with drugs that act on NO- or CB1-mediated neurotransmission. Even if the mechanisms responsible for this complex interaction are still poorly understood, they are beginning to be recognized. For example, activation of transient receptor potential vanilloid type-1 channel (TRPV1) receptors by anandamide seems to counteract the anxiolytic effects induced by CB1 receptor activation caused by this compound. Further studies, however, are needed to identify other mechanisms responsible for this fine-tuning effect.

Effects of low-salinity and high-turbidity waters one mpirical ocean colour algorithms: an example for Southwestern Atlantic waters

The spectral reflectance of the sea surface recorded using ocean colour satellite sensors has been used to estimate chlorophyll-a concentrations for decades. However, in bio-optically complex coastal waters, these estimates are compromised by the presence of several other coloured components besides chlorophyll, especially in regions affected by low-salinity waters. The present work aims to (a) describe the influence of the freshwater plume from the La Plata River on the variability of in situ remote sensing reflectance and (b) evaluate the performance of operational ocean colour chlorophyll algorithms applied to Southwestern Atlantic waters, which receive a remarkable seasonal contribution from La Plata River discharges. Data from three oceanographic cruises are used, in addition to a historical regional bio-optical dataset. Deviations found between measured and estimated concentrations of chlorophyll-a are examined in relation to surface water salinity and turbidity gradients to investigate the source of errors in satellite estimates of pigment concentrations. We observed significant seasonal variability in surface reflectance properties that are strongly driven by La Plata River plume dynamics and arise from the presence of high levels of inorganic suspended solids and coloured dissolved materials. As expected, existing operational algorithms overestimate the concentration of chlorophyll-a, especially in waters of low salinity (S<33.5) and high turbidity (Rrs(670)>0.0012 sr−1). Additionally, an updated version of the regional algorithm is presented, which clearly improves the chlorophyll estimation in those types of coastal environment. In general, the techniques presented here allow us to directly distinguish the bio-optical types of waters to be considered in algorithm studies by the ocean colour community.

Development of heat sink device by using topology optimization

Small scale fluid flow systems have been studied for various applications, such as chemical reagent dosages and cooling devices of compact electronic components. This work proposes to present the complete cycle development of an optimized heat sink designed by using Topology Optimization Method (TOM) for best performance, including minimization of pressure drop in fluid flow and maximization of heat dissipation effects, aiming small scale applications. The TOM is applied to a domain, to obtain an optimized channel topology, according to a given multi-objective function that combines pressure drop minimization and heat transfer maximization. Stokes flow hypothesis is adopted. Moreover, both conduction and forced convection effects are included in the steady-state heat transfer model. The topology optimization procedure combines the Finite Element Method (to carry out the physical analysis) with Sequential Linear Programming (as the optimization algorithm). Two-dimensional topology optimization results of channel layouts obtained for a heat sink design are presented as example to illustrate the design methodology. 3D computational simulations and prototype manufacturing have been carried out to validate the proposed design methodology.

Layer-by-Layer assembled cobalt ferrite nanoparticles for chemical sensing

Ultra-thin (thicknesses of 50-90 nm) nanocomposite films of cobalt ferrite nanoparticles (np-CoFe2O4, 18 nm in diameter) and polyelectrolytes (doped polyaniline-PANI, poly-3,4-ethylenedioxy thiophene: polystyrene sulfonic acid-PEDOT:PSS, and sulfonated lignin-SL) are assembled layer-by-layer onto interdigitated microelectrodes aiming at to create novel nanostructured sensoactive materials for liquid media chemical sensors. The nanocomposites display a distinctive globular morphology with nanoparticles densely-packed while surrounded by polyelectrolytes. Due to the presence of np-CoFe2O4 the nanocomposites display low electrical conductivity according to impedance data. On the other hand, this apparent shortcoming turns such nanocomposites much more sensitive to the presence of ions in solution than films made exclusively of conducting polyelectrolytes. For example, the electrical resistance of np-CoFe2O4/PEDOT:PSS and PANI/SL/np-CoFe2O4/SL architectures has a 10-fold decrease when they are immersed in 20 mmol. L-1 NaCl solution. Impedance spectra fitted with the response of an equivalent circuit model suggest that the interface created between nanoparticles and polyelectrolytes plays a major role on the nanocomposites electrical/dielectrical behavior. Since charge transport is sensitive to nanoparticle-polyelectrolyte interfaces as well as to the physicochemical conditions of the environment, the np-CoFe2O4-based nanocomposites can be used as sensing elements in chemical sensors operated under ac regime and room temperature.