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Additional file 1: Table S1. of Characterization of background noise in capture-based targeted sequencing data

Gahee Park, Joo Park, Seung-Ho Shin, Hyo-Jeong Jeon, Nayoung Kim, Yeon Kim, Hyun-Tae Shin, Eunjin Lee, Kwang Lee, Dae-Soon Son, Woong-Yang Park & Donghyun Park
Findings and methods from studies charactering artifactual substitutions in sequencing data. (DOCX 29 kb)

Additional file 10: Table S8. of Long noncoding RNA expression profiles in sub-lethal heat-treated hepatoma carcinoma cells

Qingsong Deng, Shihan Chen, Chunchuan Fu, Jiayun Jiang, Mengda Zou, Yunhua Tan, Xiaofei Wang, Feng Xia, Kai Feng, Kuansheng Ma & Ping Bie
Target prediction summary. (XLS 2 kb)

Exploring general-purpose protein features for distinguishing enzymes and non-enzymes within the twilight zone

Yasser Ruiz-Blanco, Guillermin Agüero-Chapin, Enrique García-Hernández, Orlando Álvarez, Agostinho Antunes & James Green
Abstract Background Computational prediction of protein function constitutes one of the more complex problems in Bioinformatics, because of the diversity of functions and mechanisms in that proteins exert in nature. This issue is reinforced especially for proteins that share very low primary or tertiary structure similarity to existing annotated proteomes. In this sense, new alignment-free (AF) tools are needed to overcome the inherent limitations of classic alignment-based approaches to this issue. We have recently introduced...

Additional file 3: of Exploring general-purpose protein features for distinguishing enzymes and non-enzymes within the twilight zone

Yasser Ruiz-Blanco, Guillermin Agüero-Chapin, Enrique García-Hernández, Orlando Álvarez, Agostinho Antunes & James Green
Experiments leading to the selection of the SVM and kernel parameters. (PDF 310 kb)

Competing for space in an already crowded market: a mixed methods study of why an online community of practice (CoP) for alcohol harm reduction failed to generate interest amongst the group of public health professionals at which it was aimed

Ruth Ponsford, Jennifer Ford, Helena Korjonen, Emma Hughes, Asha Keswani, Triantafyllos Pliakas & Matt Egan
Abstract Background Improving mechanisms for knowledge translation (KT) and connecting decision-makers to each other and the information and evidence they consider relevant to their work remains a priority for public health. Virtual communities of practices (CoPs) potentially offer an affordable and flexible means of encouraging connection and sharing of evidence, information and learning among the public health community in ways that transgress traditional geographical, professional, institutional and time boundaries. The suitability of online CoPs in...

Additional file 1: Table S1. of Competing for space in an already crowded market: a mixed methods study of why an online community of practice (CoP) for alcohol harm reduction failed to generate interest amongst the group of public health professionals at which it was aimed

Ruth Ponsford, Jennifer Ford, Helena Korjonen, Emma Hughes, Asha Keswani, Triantafyllos Pliakas & Matt Egan
Combined findings from surveys of UK Health Forum alcohol group members who subscribed or did not subscribe to the Community of Practice (CoP). (DOCX 39 kb)

Additional file 2: of Exploring general-purpose protein features for distinguishing enzymes and non-enzymes within the twilight zone

Yasser Ruiz-Blanco, Guillermin Agüero-Chapin, Enrique García-Hernández, Orlando Álvarez, Agostinho Antunes & James Green
Supplementary figures (Figure SI-I and SI-2) and Tables (Table SI-1 to Table SI-13). Figure SI-1 Dot plot of the pairwise amino acid identity matrix expressed in percentage (colour bar) for the D&D dataset. (A) Global all-vs-all sequence alignments using the Needleman-Wunsch (NW) algorithm (B) Local all-vs-all sequence alignments using the Smith-Waterman (SW) algorithm. Figure SI-2 Structural diversity summary of the D&D dataset according to SCOP database. Table SI-1 Compendium of structural and chemical-physical amino acid...

Additional file 1: of Exploring general-purpose protein features for distinguishing enzymes and non-enzymes within the twilight zone

Yasser Ruiz-Blanco, Guillermin Agüero-Chapin, Enrique García-Hernández, Orlando Álvarez, Agostinho Antunes & James Green
Different families of AF protein predictors implemented in ProtDCal and TI2BioP. (PDF 136 kb)

Epidemiology of taeniosis/cysticercosis in Europe, a systematic review: Western Europe

Minerva Laranjo-González, Brecht Devleesschauwer, Chiara Trevisan, Alberto Allepuz, Smaragda Sotiraki, Annette Abraham, Mariana Afonso, Joachim Blocher, Luís Cardoso, José Correia Da Costa, Pierre Dorny, Sarah Gabriël, Jacinto Gomes, María Gómez-Morales, Pikka Jokelainen, Miriam Kaminski, Brane Krt, Pascal Magnussen, Lucy Robertson, Veronika Schmidt, Erich Schmutzhard, G. Smit, Barbara Šoba, Christen Stensvold, Jože Starič … & Veronique Dermauw
Abstract Background Taenia solium and Taenia saginata are zoonotic parasites of public health importance. Data on their occurrence in humans and animals in western Europe are incomplete and fragmented. In this study, we aimed to update the current knowledge on the epidemiology of these parasites in this region. Methods We conducted a systematic review of scientific and grey literature published from 1990 to 2015 on the epidemiology of T. saginata and T. solium in humans...

Additional file 5: Table S4. of Epidemiology of taeniosis/cysticercosis in Europe, a systematic review: Western Europe

Minerva Laranjo-González, Brecht Devleesschauwer, Chiara Trevisan, Alberto Allepuz, Smaragda Sotiraki, Annette Abraham, Mariana Afonso, Joachim Blocher, Luís Cardoso, José Correia Da Costa, Pierre Dorny, Sarah Gabriël, Jacinto Gomes, María Gómez-Morales, Pikka Jokelainen, Miriam Kaminski, Brane Krt, Pascal Magnussen, Lucy Robertson, Veronika Schmidt, Erich Schmutzhard, G. Smit, Barbara Šoba, Christen Stensvold, Jože Starič … & Veronique Dermauw
Identified taeniosis cases in case reports in western Europe (1990–2015). Table S5. Aggregated taeniosis cases reported in authorities’ reports, epidemiological bulletins, and national registries in western Europe (1990–2015). Table S6. Aggregated taeniosis cases reported at hospital/laboratory level in western Europe (1990–2015). Table S7. Taeniosis prevalence data reported in epidemiological studies (1990–2015). Table S8. Taeniosis estimates published in western Europe (1990–2015). Table S9. Identified human cysticercosis cases in case reports in western Europe (1990–2015). Table S10....

Additional file 4: Table S3. of Epidemiology of taeniosis/cysticercosis in Europe, a systematic review: Western Europe

Minerva Laranjo-González, Brecht Devleesschauwer, Chiara Trevisan, Alberto Allepuz, Smaragda Sotiraki, Annette Abraham, Mariana Afonso, Joachim Blocher, Luís Cardoso, José Correia Da Costa, Pierre Dorny, Sarah Gabriël, Jacinto Gomes, María Gómez-Morales, Pikka Jokelainen, Miriam Kaminski, Brane Krt, Pascal Magnussen, Lucy Robertson, Veronika Schmidt, Erich Schmutzhard, G. Smit, Barbara Šoba, Christen Stensvold, Jože Starič … & Veronique Dermauw
List of references included in the review made available through local sources. (XLSX 39 kb)

Additional file 6: Figure S2. of Phylogenetic classification of bony fishes

Ricardo Betancur-R, Edward Wiley, Gloria Arratia, Arturo Acero, Nicolas Bailly, Masaki Miya, Guillaume Lecointre & Guillermo OrtĂ­
High resolution image of Figure 2. (PDF 4040 kb)

Additional file 5: Figure S1. of Phylogenetic classification of bony fishes

Ricardo Betancur-R, Edward Wiley, Gloria Arratia, Arturo Acero, Nicolas Bailly, Masaki Miya, Guillaume Lecointre & Guillermo OrtĂ­
High resolution image of Figure 1. (PDF 1120 kb)

Minocycline modulates NFκB phosphorylation and enhances antimicrobial activity against Staphylococcus aureus in mesenchymal stromal/stem cells

Alberto Guerra, Warren Rose, Peiman Hematti & W. Kao
Abstract Background Mesenchymal stromal/stem cells (MSCs) have demonstrated pro-healing properties due to their anti-inflammatory, angiogenic, and even antibacterial properties. We have shown previously that minocycline enhances the wound healing phenotype of MSCs, and MSCs encapsulated in poly(ethylene glycol) and gelatin-based hydrogels with minocycline have antibacterial properties against Staphylococcus aureus (SA). Here, we investigated the signaling pathway that minocycline modulates in MSCs which results in their enhanced wound healing phenotype and determined whether preconditioning MSCs with...

Additional file 3: Figure S3. of Minocycline modulates NFÎşB phosphorylation and enhances antimicrobial activity against Staphylococcus aureus in mesenchymal stromal/stem cells

Alberto Guerra, Warren Rose, Peiman Hematti & W. Kao
Showing colony forming abilities of SA after 6 hours of coculture with media controls, MSCs with or without anti-IL-6, and MSCs pretreated with minocycline with or without anti-IL-6. (JPG 146 kb)

Additional file 3: Table S2. of Epidemiology of taeniosis/cysticercosis in Europe, a systematic review: Western Europe

Minerva Laranjo-González, Brecht Devleesschauwer, Chiara Trevisan, Alberto Allepuz, Smaragda Sotiraki, Annette Abraham, Mariana Afonso, Joachim Blocher, Luís Cardoso, José Correia Da Costa, Pierre Dorny, Sarah Gabriël, Jacinto Gomes, María Gómez-Morales, Pikka Jokelainen, Miriam Kaminski, Brane Krt, Pascal Magnussen, Lucy Robertson, Veronika Schmidt, Erich Schmutzhard, G. Smit, Barbara Šoba, Christen Stensvold, Jože Starič … & Veronique Dermauw
List of references included in the review retrieved through online international databases. (XLSX 30 kb)

Additional file 2: Figure S2. of Minocycline modulates NFÎşB phosphorylation and enhances antimicrobial activity against Staphylococcus aureus in mesenchymal stromal/stem cells

Alberto Guerra, Warren Rose, Peiman Hematti & W. Kao
Showing expression of IL6 in MSCs when cultured alone or with SA with and without minocycline pretreatment. (JPG 171 kb)

A deep convolutional neural network approach to single-particle recognition in cryo-electron microscopy

Yanan Zhu, Qi Ouyang & Youdong Mao
Abstract Background Single-particle cryo-electron microscopy (cryo-EM) has become a mainstream tool for the structural determination of biological macromolecular complexes. However, high-resolution cryo-EM reconstruction often requires hundreds of thousands of single-particle images. Particle extraction from experimental micrographs thus can be laborious and presents a major practical bottleneck in cryo-EM structural determination. Existing computational methods for particle picking often use low-resolution templates for particle matching, making them susceptible to reference-dependent bias. It is critical to develop a...

Additional file 1: Figure S1. of Minocycline modulates NFÎşB phosphorylation and enhances antimicrobial activity against Staphylococcus aureus in mesenchymal stromal/stem cells

Alberto Guerra, Warren Rose, Peiman Hematti & W. Kao
Showing proliferation of MSCs after 24 hours of minocycline treatment in a dose-dependent manner. (JPG 103 kb)

Additional file 1: Figure S1. of A deep convolutional neural network approach to single-particle recognition in cryo-electron microscopy

Yanan Zhu, Qi Ouyang & Youdong Mao
The feature maps of the convolutional and subsampling layers from a typical particle image of KLH learned by our CNN. Figure S2. (a) and (b) show a comparison of the results obtained before and after additional selection using standard deviation of the KLH dataset, respectively. (c) and (d) show a comparison of the results obtained before and after additional selection using standard deviation of the 19S, respectively. Figure S3. (a) and (b) show a comparison...

NoGOA: predicting noisy GO annotations using evidences and sparse representation

Guoxian Yu, Chang Lu & Jun Wang
Abstract Background Gene Ontology (GO) is a community effort to represent functional features of gene products. GO annotations (GOA) provide functional associations between GO terms and gene products. Due to resources limitation, only a small portion of annotations are manually checked by curators, and the others are electronically inferred. Although quality control techniques have been applied to ensure the quality of annotations, the community consistently report that there are still considerable noisy (or incorrect) annotations....

Mental health differences between German gay and bisexual men and population-based controls

Frank Sattler, Gabriele Franke & Hanna Christiansen
Abstract Background International studies have revealed that gay and bisexual men present more mental health problems than the general male population. Furthermore, there is evidence that minority stress predicts mental health problems in gay and bisexual men. The aim of the present study is to provide initial data on mental health differences in Germany and to analyze the effect of minority stress. Methods Mental health data on n = 1903 German gay and bisexual men and n = 958...

Additional file 1 of NoGOA: predicting noisy GO annotations using evidences and sparse representation

Guoxian Yu, Chang Lu & Jun Wang
Supplementary file of â NoGOA: predicting noisy GO annotations using evidences and sparse representationâ This PDF file includes additional experimental results mentioned in the main text. (PDF 1300 kb)

Additional file 1: Table S1. of Mental health differences between German gay and bisexual men and population-based controls

Frank Sattler, Gabriele Franke & Hanna Christiansen
Used mental health subscales. (DOCX 31 kb)

Additional file 6: Table S4. of An integrated computational-experimental approach reveals Yersinia pestis genes essential across a narrow or a broad range of environmental conditions

Nicola Senior, Kalesh Sasidharan, Richard Saint, Andrew Scott, Mitali Sarkar-Tyson, Philip Ireland, Helen Bullifent, Z. Rong Yang, Karen Moore, Petra Oyston, Timothy Atkins, Helen Atkins, Orkun Soyer & Richard Titball
Overlap between experimentally identified and computationally predicted essential genes. Lines 1â 54 details genes that are predicted to be essential in all computationally tested media (100% essentiality score) and are also experimentally identified to be an essential gene under the BAB broth medium. Lines 55â 78 details genes that are predicted to be essential in all computationally tested media (100% essentiality score) but not experimentally identified to be an essential gene under the BAB broth...

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