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Additional file 1: Table S1. of Insertion and deletion polymorphisms of the ancient AluS family in the human genome

Maria Kryatova, Jared Steranka, Kathleen Burns & Lindsay Payer
Comparison of subfamily classification of Alu polymorphisms (nâ =â 52) using multiple established methods. (XLSX 14 kb)

Additional file 13: Figure S10. of Amelioration of amyloid-β-induced deficits by DcR3 in an Alzheimer’s disease model

Yi-Ling Liu, Wei-Ting Chen, Yu-Yi Lin, Po-Hung Lu, Shie-Liang Hsieh & Irene Cheng
Illustration of the quantification method of microglia or YM1 around each plaque in Fig. 5b and Additional file 10: Figure S8. Plaque areas were circled to determine the centers. The circles were then enlarged 10 μm in radius from the center, which was considered to be the region of interest for measuring the microglia or secreted YM1 coverage. (PDF 11009 kb)

Additional file 12: Table S3. of Amelioration of amyloid-β-induced deficits by DcR3 in an Alzheimerâ s disease model

Yi-Ling Liu, Wei-Ting Chen, Yu-Yi Lin, Po-Hung Lu, Shie-Liang Hsieh & Irene Cheng
List of the C3 cytokine array data. (PDF 24088 kb)

Identification of anti-HBV activities in Paeonia suffruticosa Andr. using GRP78 as a drug target on Herbochip®

Iao-Fai Lam, Min Huang, Margaret Chang, Pei-Wun Yao, Yu-Ting Chou, Sim-Kun Ng, Ying-Lin Tsai, Yu-Chang Lin, Yun-Feng Zhang, Xiao-Yuan Yang & Yiu-Kay Lai
Abstract Background Herbochip® technology is a high throughput drug screening platform in a reverse screening manner, in which potential chemical leads in herbal extracts are immobilized and drug target proteins can be used as probes for screening process [BMC Complementary and Alternative Medicine (2015) 15:146]. While herbal medicines represent an ideal reservoir for drug screenings, here a molecular chaperone GRP78 is demonstrated to serve as a potential target for antiviral drug discovery. Methods We cloned...

MOESM3 of Identification of anti-HBV activities in Paeonia suffruticosa Andr. using GRP78 as a drug target on HerbochipÂŽ

Iao-Fai Lam, Min Huang, Margaret Chang, Pei-Wun Yao, Yu-Ting Chou, Sim-Kun Ng, Ying-Lin Tsai, Yu-Chang Lin, Yun-Feng Zhang, Xiao-Yuan Yang & Yiu-Kay Lai
Additional file 3. The ARRIVE Guidelines Checklist.

Additional file 11: Figure S9. of Amelioration of amyloid-β-induced deficits by DcR3 in an Alzheimer’s disease model

Yi-Ling Liu, Wei-Ting Chen, Yu-Yi Lin, Po-Hung Lu, Shie-Liang Hsieh & Irene Cheng
Identifying protein expression patterns in primary microglia lysates and CM. (a) DcR3 promoted more YM1 secretion in the Aβ treated primary microglia culture according to the immunoblotting analysis. GAPDH was used as a loading control. (b) The changes in pro-MMP9 levels in the cytokine array analysis. (PDF 554 kb)

MOESM2 of Identification of anti-HBV activities in Paeonia suffruticosa Andr. using GRP78 as a drug target on HerbochipÂŽ

Iao-Fai Lam, Min Huang, Margaret Chang, Pei-Wun Yao, Yu-Ting Chou, Sim-Kun Ng, Ying-Lin Tsai, Yu-Chang Lin, Yun-Feng Zhang, Xiao-Yuan Yang & Yiu-Kay Lai
Additional file 2. Ethics approval document of Ducklings experiments.

Additional file 10: Figure S8. of Amelioration of amyloid-β-induced deficits by DcR3 in an Alzheimer’s disease model

Yi-Ling Liu, Wei-Ting Chen, Yu-Yi Lin, Po-Hung Lu, Shie-Liang Hsieh & Irene Cheng
DcR3 induced more M2a microglia surrounded plaques and more YM1 expression in vivo. (a) The representative confocal images were labeled with M2a activated microglia marker (YM1, green) and Aβ (6E10, red) in the mouse brain slices. Scale bar: 20 μm. (N = 13-14 slices per genotype) (b) Quantification of the YM1 positive signal intensity surrounded plaques. The quantification method for Fig. 5b and Additional file 10: Figure S8 is showen in Additional file 13: Figure S10. ***P ≤ 0.001 vs....

MOESM1 of Identification of anti-HBV activities in Paeonia suffruticosa Andr. using GRP78 as a drug target on HerbochipÂŽ

Iao-Fai Lam, Min Huang, Margaret Chang, Pei-Wun Yao, Yu-Ting Chou, Sim-Kun Ng, Ying-Lin Tsai, Yu-Chang Lin, Yun-Feng Zhang, Xiao-Yuan Yang & Yiu-Kay Lai
Additional file 1. Minimum Standards of Reporting Checklist.

Additional file 1: of Predictors of delayed culture conversion among Ugandan patients

Daniel Atwine, Patrick Orikiriza, Ivan Taremwa, Arnold Ayebare, Suzan Logoose, Juliet Mwanga-Amumpaire, Amina Jindani & Maryline Bonnet
Dataset. (CSV 14.4kb)

Predictors of delayed culture conversion among Ugandan patients

Daniel Atwine, Patrick Orikiriza, Ivan Taremwa, Arnold Ayebare, Suzan Logoose, Juliet Mwanga-Amumpaire, Amina Jindani & Maryline Bonnet
Abstract Background Estimates of month-2 culture conversion, a proxy indicator of tuberculosis (TB) treatment efficacy in phase-2 trials can vary by culture-type and geographically with lower rates reported among African sites. The sub-study aimed at comparing TB detection rates of different culture media, within and across rifampicin-based regimens (R10, 15 and 20 mg/Kg) over a 6-month treatment follow-up period, and to establish predictors of month-2 culture non-conversion among HIV-negative TB patients enrolled at RIFATOX trial site...

Severe type 1 upgrading leprosy reaction in a renal transplant recipient: a paradoxical manifestation associated with deficiency of antigen-specific regulatory T-cells?

Ana Vieira, Maria Trindade, FlĂĄvio De Paula, Neusa Sakai-Valente, Alberto JosĂŠ Da Silva Duarte, Francine Lemos & Gil Benard
Abstract Background Due to its chronic subclinical course and large spectrum of manifestations, leprosy often represents a diagnostic challenge. Even with proper anti-mycobacteria treatment, leprosy follow up remains challenging: almost half of leprosy patients may develop reaction episodes. Leprosy is an infrequent complication of solid organ transplant recipients. This case report illustrates the challenges in diagnosing and managing leprosy and its reactional states in a transplant recipient. Case presentation A 53-year-old man presented 34 months after...

Semaphorin-Plexin signaling influences early ventral telencephalic development and thalamocortical axon guidance

Manuela Mitsogiannis, Graham Little & Kevin Mitchell
Abstract Background Sensory processing relies on projections from the thalamus to the neocortex being established during development. Information from different sensory modalities reaching the thalamus is segregated into specialized nuclei, whose neurons then send inputs to cognate cortical areas through topographically defined axonal connections. Developing thalamocortical axons (TCAs) normally approach the cortex by extending through the subpallium; here, axonal navigation is aided by distributed guidance cues and discrete cell populations, such as the corridor neurons...

Prevention of cervical cancer in HIV-seropositive women from developing countries: a systematic review protocol

Witness Mapanga, Ahmed Elhakeem, Shingairai Feresu, Fresier Maseko & Tsungai Chipato
Abstract Background Over 85% of cervical cancer cases and deaths occur in developing countries. HIV-seropositive women are more likely to develop precancerous lesions that lead to cervical cancer than HIV-negative women. However, the literature on cervical cancer prevention in seropositive women in developing countries has not been reviewed. The aim of this study is to systematically review cervical cancer prevention modalities available for HIV-seropositive women in developing countries. Methods/design This protocol was developed by following...

Additional file 3: of Prevention of cervical cancer in HIV-seropositive women from developing countries: a systematic review protocol

Witness Mapanga, Ahmed Elhakeem, Shingairai Feresu, Fresier Maseko & Tsungai Chipato
Quality assessment form. This form will be used for grading the quality of studies included in the review. It is a modified/amended version of the Newcastle-Ottawa Quality Assessment Scale. (DOCX 21 kb)

Additional file 1: of Severe type 1 upgrading leprosy reaction in a renal transplant recipient: a paradoxical manifestation associated with deficiency of antigen-specific regulatory T-cells?

Ana Vieira, Maria Trindade, Flávio De Paula, Neusa Sakai-Valente, Alberto José Da Silva Duarte, Francine Lemos & Gil Benard
Strategy and methods for the Treg measurements. (DOC 1009 kb)

Microbiota-activated CD103+ DCs stemming from microbiota adaptation specifically drive γδT17 proliferation and activation

Chris Fleming, Yihua Cai, Xuan Sun, Venkatakrishna Jala, Feng Xue, Samantha Morrissey, Yu-Ling Wei, Yueh-Hsiu Chien, Huang-Ge Zhang, Bodduluri Haribabu, Jian Huang & Jun Yan
Abstract Background IL-17-producing γδT cells (γδT17) promote autoinflammatory diseases and cancers. Yet, γδT17 peripheral regulation has not been thoroughly explored especially in the context of microbiota-host interaction. The potent antigen-presenting CD103+ dendritic cell (DC) is a key immune player in close contact with both γδT17 cells and microbiota. This study presents a novel cellular network among microbiota, CD103+ DCs, and γδT17 cells. Methods Immunophenotyping of IL-17r−/− mice and IL-17r−/− IRF8−/− mice were performed by ex...

Additional file 2: of Prevention of cervical cancer in HIV-seropositive women from developing countries: a systematic review protocol

Witness Mapanga, Ahmed Elhakeem, Shingairai Feresu, Fresier Maseko & Tsungai Chipato
Data extraction form. This form will be used to extract relevant data such as exposure and outcome and statistics from the included studies. (DOCX 18 kb)

Additional file 1: of Prevention of cervical cancer in HIV-seropositive women from developing countries: a systematic review protocol

Witness Mapanga, Ahmed Elhakeem, Shingairai Feresu, Fresier Maseko & Tsungai Chipato
Full-text screening form. This form will be used for the screening of potentially eligible studies to be included in the review. (DOCX 15 kb)

The PINK1 p.I368N mutation affects protein stability and ubiquitin kinase activity

Maya Ando, Fabienne Fiesel, Roman Hudec, Thomas Caulfield, Kotaro Ogaki, Paulina Górka-Skoczylas, Dariusz Koziorowski, Andrzej Friedman, Li Chen, Valina Dawson, Ted Dawson, Guojun Bu, Owen Ross, Zbigniew Wszolek & Wolfdieter Springer
Abstract Background Mutations in PINK1 and PARKIN are the most common causes of recessive early-onset Parkinson’s disease (EOPD). Together, the mitochondrial ubiquitin (Ub) kinase PINK1 and the cytosolic E3 Ub ligase PARKIN direct a complex regulated, sequential mitochondrial quality control. Thereby, damaged mitochondria are identified and targeted to degradation in order to prevent their accumulation and eventually cell death. Homozygous or compound heterozygous loss of either gene function disrupts this protective pathway, though at different...

Additional file 6 of The PINK1 p.I368N mutation affects protein stability and ubiquitin kinase activity

Maya Ando, Fabienne Fiesel, Roman Hudec, Thomas Caulfield, Kotaro Ogaki, Paulina Górka-Skoczylas, Dariusz Koziorowski, Andrzej Friedman, Li Chen, Valina Dawson, Ted Dawson, Guojun Bu, Owen Ross, Zbigniew Wszolek & Wolfdieter Springer
Figure S2. Expression of PINK1-V5 WT and p.I368N mutation at different levels in HeLa cells. (A) HeLa cells were transfected with PINK1 siRNA and with different amounts (0.5 or 1 μg per well of a 12-well plate) of V5 empty vector, PINK1-V5 WT or p.I368N, as indicated. Cells were left untreated or incubated with 10 μM CCCP for 4 h and lysates were analyzed on WB with anti-V5 and PINK1 antibodies. GAPDH was used as a loading control....

Additional file 1: of Microbiota-activated CD103+ DCs stemming from microbiota adaptation specifically drive γδT17 proliferation and activation

Chris Fleming, Yihua Cai, Xuan Sun, Venkatakrishna Jala, Feng Xue, Samantha Morrissey, Yu-Ling Wei, Yueh-Hsiu Chien, Huang-Ge Zhang, Bodduluri Haribabu, Jian Huang & Jun Yan
Includes supplemental experimental procedures and five figures. (DOCX 2846 kb)

Moderate alkali-thermophilic ethanologenesis by locally isolated Bacillus licheniformis from Pakistan employing sugarcane bagasse: a comparative aspect of aseptic and non-aseptic fermentations

Qurat-Ul-Ain Ahmad, Shang-Tian Yang, Maleeha Manzoor & Javed Qazi
Abstract Background Biofuels obtained from first-generation (1G) sugars-starch streams have been proven unsustainable as their constant consumption is not only significantly costly for commercial scale production systems, but it could potentially lead to problems associated with extortionate food items for human usage. In this regard, biofuelsâ production in alkali-thermophilic environs from second-generation (2G) bio-waste would not only be markedly feasible, but these extreme conditions might be able to sustain aseptic fermentations without spending much for...

Additional file 5: Figure S1. of The PINK1 p.I368N mutation affects protein stability and ubiquitin kinase activity

Maya Ando, Fabienne Fiesel, Roman Hudec, Thomas Caulfield, Kotaro Ogaki, Paulina Górka-Skoczylas, Dariusz Koziorowski, Andrzej Friedman, Li Chen, Valina Dawson, Ted Dawson, Guojun Bu, Owen Ross, Zbigniew Wszolek & Wolfdieter Springer
Reduced full-length PINK1 levels in p.I368N mutant fibroblasts upon treatment with valinomycin. (A) Representative confocal IF images of control and two PINK1 p.I368N fibroblasts showing mitochondrial localization but greatly reduced levels of the mutant protein. Cells were left untreated (-) or treated with 10 μM CCCP for 6 days (+) and stained with antibodies against PINK1 (green) and TOM20 (mitochondria, red). Nuclei were counterstained with Hoechst (blue). Scale bars represent 10 μm. (B) Subcellular fractionation of WT control...

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