A novel approach for protein subcellular location prediction using amino acid exposure

BACKGROUND: Proteins perform their functions in associated cellular locations. Therefore, the study of protein function can be facilitated by predictions of protein location. Protein location can be predicted either from the sequence of a protein alone by identification of targeting peptide sequences and motifs, or by homology to proteins of known location. A third approach, which is complementary, exploits the differences in amino acid composition of proteins associated to different cellular locations, and can be useful if motif and homology information are missing. Here we expand this approach taking into account amino acid composition at different levels of amino acid exposure. RESULTS: Our method has two stages. For stage one, we trained multiple Support Vector Machines (SVMs) to score eukaryotic protein sequences for membership to each of three categories: nuclear, cytoplasmic and extracellular, plus extra category nucleocytoplasmic, accounting for the fact that a large number of proteins shuttles between those two locations. In stage two we use an artificial neural network (ANN) to propose a category from the scores given to the four locations in stage one. The method reaches an accuracy of 68% when using as input 3D-derived values of amino acid exposure. Calibration of the method using predicted values of amino acid exposure allows classifying proteins without 3D-information with an accuracy of 62% and discerning proteins in different locations even if they shared high levels of identity. CONCLUSIONS: In this study we explored the relationship between residue exposure and protein subcellular location. We developed a new algorithm for subcellular location prediction that uses residue exposure signatures. Our algorithm uses a novel approach to address the multiclass classification problem. The algorithm is implemented as web server 'NYCE' and can be accessed at http://cbdm.mdc-berlin.de/~amer/nyce

Aesthetic markers in the voice of radio professionals

Voice is one of the most essential means of expression in human experience and a valuable tool for communication. Its sound characteristics are most relevant in contexts such as social communication and particularly the radio, where the practice of communication is treated at a professional level and the need to captivate a public-listener through the vocal resources is identified. Therefore, this study intended to find if there are specific vocal qualities that contribute to a better or worse appreciation of vocal aesthetic of the radio professional concerning experienced radio listeners.info:eu-repo/semantics/publishedVersio

mBISON: Finding miRNA target over-representation in gene lists from ChIP-sequencing data

BACKGROUND: Over-representation of predicted miRNA targets in sets of genes regulated by a given transcription factor (e.g. as defined by ChIP-sequencing experiments) helps to identify biologically relevant miRNA targets and is useful to get insight into post-transcriptional regulation. FINDINGS: To facilitate the application of this approach we have created the mBISON web-application. mBISON calculates the significance of over-representation of miRNA targets in a given non-ranked gene set. The gene set can be specified either by a list of genes or by one or more ChIP-seq datasets followed by a user-defined peak-gene association procedure. mBISON is based on predictions from TargetScan and uses a randomization step to calculate False-Discovery-Rates for each miRNA, including a correction for gene set specific properties such as 3'UTR length. The tool can be accessed from the following web-resource: http://cbdm.mdc-berlin.de/~mgebhardt/cgi-bin/mbison/home . CONCLUSION: mBISON is a web-application that helps to extract functional information about miRNAs from gene lists, which is in contrast to comparable applications easy to use by everyone and can be applied on ChIP-seq data directly

Bilateral Hipoglossal Nerve Palsy In Necrotizing Otitis Externa

[No abstract available]734576Benecke Jr., J.A., Management of osteomyelitis of the skull base (1989) Laryngoscope, 99 (12), pp. 1220-1223Boringa, J.B., Hoekstra, O.S., Roos, J.W., Bertelsmann, F.W., Multiple cranial nerve palsy after otitis externa: A case report (1995) Clin Neurol Neurosurg, 97, pp. 332-335Rubin, J., Yu, V.L., Malignant external otitis: Insights into pathogenesis, clinical manifestations and therapy (1998) Am J Med, 85, pp. 391-39

Tandem Thio-Michael Addition/Remote Lactone Activation of 5-Hydroxymethylfurfural-Derived δ-Lactone-Fused Cyclopentenones

Funding Information: We thank the Fundação para a Ciência e a Tecnologia (SFRH/BD/120829/2016, SFRH/BD/148211/2019, UIDB/04138/2020, UIDP/04138/2020, PTDC/QUI‐QOR/32008/2017 and GHTM‐UID/04413/2020). The project leading to this application has received funding from the European Union's Horizon 2020 research and innovation programme under grant agreement No 951996. J. A. S. C. thanks the Fundação para a Ciência e a Tecnologia (FCT) for Scientific Employment Stimulus 2020/02383/CEECIND. Publisher Copyright: © 2022 The Authors. ChemSusChem published by Wiley-VCH GmbH.The creation of structurally diverse chemical entities from fairly simple biorefinery products remains a challenge. In this work 5-hydroxymethylfurfural (HMF) was identified as a key synthon for preparing highly complex cyclopentenones (CP) via tandem 1,4-addition/elimination/remote lactone activation to external O- and N-nucleophiles in δ-lactone-fused-CPs hotspots. This scaffold was also reactive enough to be incorporated into model cysteine-peptides in low concentrations, paving the way to a potential translation generating complexity in the synthesis of small peptides. The new enones also exhibited activity against intraerythrocytic Plasmodium falciparum (IC50=1.32 μm).publishersversionpublishe

Climate Indicators and the Impact on Morbidity and Mortality of Acute Respiratory Infections

The fire incidences in Campo Grande have been a serious environmental problem. Therefore, this study is aimed at studying the trend of acute respiratory infections (IRA) from the year 2011 to 2017 and to correlate it with precipitation, wind speed, relative humidity, maximum and minimum temperatures, surface ozone concentration, optical depth, index of clarity and the number of outbreaks of fires. IRA records were obtained through DATASUS; the record of burn outbreaks at the National Institute for Space Research and the ozone concentration at the Federal University of Mato Grosso do Sul. There exists a positive and significant correlation between the number of burn outbreaks, wind velocity, ozone concentration, and optical depth with rates of hospitalizations for IRA. Also, a negative correlation exists between precipitation parameters, relative humidity, maximum and minimum temperatures. These results show the intensity of the problem and the great impact on the respiratory health of the population as well as on the economy due to increase in the number of hospitalizations and days of treatment

Agricultural intensification can help protect the Amazon Forest and reduce global warming / Protecting the Amazon forest and reducing global warming via agricultural intensification

The Amazon basin includes 550 M ha covered with rainforests, with 60% of this area being in Brazil. Conversion of rainforest for soybean production raises concerns about the degree to which Brazil can reconcile production and environmental goals. Here we investigated the degree to which intensification could help Brazil produce more soybean without further encroachment of the Amazon Forest. Our analysis shows that continuation of current trends in soybean yield and area would lead to conversion of additional 5.7 M ha of forests and savannas during the next 15 years, with an associated 2550 Mt of CO2eq released into the atmosphere. In contrast, acceleration of yield improvement, coupled with expansion of soybean area only in areas currently used for livestock production, would allow Brazil to achieve similar economic benefits without deforestation and with substantially lower global climate warming