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OVERVIEW: If you're in your late 30s, 40s, or 50s and wondering why weight loss feels harder than ever — this episode is for you. You're not broken, and it's not just “getting older.” The truth is, midlife brings real physiological shifts that impact your metabolism, hormones, energy, and fat loss. In this episode, I'm breaking down exactly why weight loss becomes more difficult in midlife — and what you can do about it. From declining muscle mass and metabolic slowdowns to hormonal fluctuations during perimenopause, I'll explain what's really happening in your body. Plus, I'll introduce you to my signature framework: the Three Phases of Transformation — Repair, Rebuild, and Results — and how this process helps my clients overcome plateaus, balance their hormones, and finally see progress that lasts. Why midlife weight gain is not your fault — and how to work with your body, not against it How aging impacts your metabolism and what you can do to restore it The hormone shifts that stall fat loss (estrogen, progesterone, cortisol, thyroid) An overview of my 3-phase coaching framework: Repair, Rebuild, and Results Here's the thing—there's nothing wrong with wanting to figure things out on your own, but if you're tired of trial and error and want a proven, structured plan designed for YOU, it might be time to stop spinning your wheels and get the support you deserve. RESOURCES: Click here to schedule your FREE alignment call to see if my 1:1 coaching program is a good fit for you: https://app.acuityscheduling.com/schedule/7de98067/appointment/18062930/calendar/4677043?appointmentTypeIds%5B%5D=18062930 Click Here to learn more about my 1:1 coaching program https://metabolicfix.purfitstudio.com/one Take My PHASE ASSESSMENT QUIZ HERE: https://www.metabolicfix.com/phase-quiz Follow Ashley on Instagram: @ashley_fillmore1 Join Ashley's FREE Facebook Group: https://www.facebook.com/groups/635528110302527Email us at: customer.success@purfitstudio.com Want to see which one of my programs is the best for you? Take my Services Quiz: https://www.metabolicfix.com/services-quiz Take my FREE Metabolic Damage Quiz here: https://metabolicfix.purfitstudio.com/md-quiz

Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2023.04.18.537310v1?rss=1 Authors: Stamatiou, K., Huguet, F., Spanos, C., Rappsilber, J., Vagnarelli, P. Abstract: Background: The proliferation antigen Ki-67 has been widely used in clinical settings for cancer staging for many years but investigations on its biological functions have lagged. Recently, Ki-67 was shown to regulate both the composition of the chromosome periphery and chromosome behaviour in mitosis as well as to play a role in heterochromatin organisation and gene transcription. However, a role for Ki-67 in regulating cell cycle progression has never been reported. The progress towards understanding Ki-67 function have been limited by the tools available to deplete the protein coupled to its abundance and fluctuation during the cell cycle. Results: Here we have used an auxin-inducible degron tag (AID) to achieve a rapid and homogeneous degradation of Ki-67 in HCT116 cells. This system, coupled with APEX2 proteomics and phospho-proteomics approaches, allowed us to show for the first time that Ki-67 plays a role during DNA replication. In its absence, DNA replication is severely delayed, the replication machinery is unloaded, causing DNA damage that is not sensed by the canonical pathways and dependant on HUWE1 ligase. This leads to replication and sister chromatids cohesion defects, but it also triggers an interferon response mediated by the cGAS/STING pathway in all the cell lines tested. Conclusions: We have unveiled a new function of Ki-67 in DNA replication and genome maintenance that is independent of its previously known role in mitosis and gene regulation. Copy rights belong to original authors. Visit the link for more info Podcast created by Paper Player, LLC

Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2023.04.13.536748v1?rss=1 Authors: Boileau, C., Deforges, S., Peret, A., Scavarda, D., Bartholomei, F., Giles, A., Partouche, N., Gautron, J., Viotti, J., Janowitz, H., Penchet, G., Marchal, C., Lagarde, S., Trebuchon, A., Villeneuve, N., Rumi, J., Marissal, T., Khazipov, R., Khalilov, I., Martineau, F., Marechal, M., Lepine, A., Milh, M., Figarella-Branger, D., Dougy, E., Tong, S., Appay, R., Baudouin, S., Mercer, A., Smith, J. B., Danos, O., Porter, R., Mulle, C., Crepel, V. Abstract: Objective: Temporal lobe epilepsy (TLE) is characterized by recurrent seizures generated in the limbic system, particularly in the hippocampus. In TLE, recurrent mossy fiber sprouting from dentate gyrus granule cells (DGCs) creates an aberrant epileptogenic network between DGCs which operates via ectopically expressed GluK2/GluK5-containing kainate receptors (KARs). TLE patients are often resistant to anti-seizure medications and suffer significant comorbidities; hence there is an urgent need for novel therapies. Previously we have shown that GluK2 knockout mice are protected from seizures. This study aims at providing evidence that downregulating KARs in the hippocampus using gene therapy reduces chronic epileptic discharges in TLE. Methods: We combined molecular biology and electrophysiology in rodent models of TLE and in hippocampal slices surgically resected from patients with drug-resistant TLE. Results: Here we confirmed the translational potential of KAR suppression using a non-selective KAR antagonist that markedly attenuated Interictal-like Epileptiform Discharges (IEDs) in TLE patient-derived hippocampal slices. An adeno-associated virus (AAV) serotype-9 vector expressing anti-grik2 miRNA was designed to specifically downregulate GluK2 expression. Direct delivery of AAV9-anti grik2 miRNA into the hippocampus of TLE mice led to a marked reduction in seizure activity. Transduction of TLE patient hippocampal slices reduced levels of GluK2 protein and, most importantly, significantly reduced IEDs. Interpretation: Our gene silencing strategy to knock down aberrant GluK2 expression demonstrates inhibition of chronic seizure in a mouse TLE model and IEDs in cultured slices derived from TLE patients. These results provide proof-of-concept for a gene therapy approach targeting GluK2 KARs for drug-resistant TLE patients. Copy rights belong to original authors. Visit the link for more info Podcast created by Paper Player, LLC

Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2023.04.04.535566v1?rss=1 Authors: Aguilar-Bravo, B., Arino, S., Blaya, D., Pose, E., Martinez Garcia de la Torre, R. A., Latasa, M. U., Martinez-Sanchez, C., Zanatto, L., Sererols-Vinas, L., Cantallops, P., Affo, S., Coll, M., Thillen, X., Dubuquoy, L., Avila, M. A., Argemi, J. M., Lamas Paz, A., Nevzorova, Y. A., Cubero, J., Bataller, R., Lozano, J. J., Gines, P., Mathurin, P., Sancho-Bru, P. Abstract: Background and Aims: Loss of hepatocyte identity is associated with impaired liver function in alcohol-related hepatitis (AH). In this context, hepatocyte dedifferentiation gives rise to cells with a hepatobiliary (HB) phenotype expressing biliary and hepatocytes markers and showing immature features. However, the mechanisms and the impact of hepatocyte dedifferentiation in liver disease are poorly understood. Methods: HB cells and ductular reaction (DR) cells were quantified and microdissected from liver biopsies from patients with alcohol-related liver disease (ALD). Hepatocyte-specific overexpression or deletion of CXCR4, and CXCR4 pharmacological inhibition were assessed in mouse liver injury. Patient-derived and mouse organoids were generated to assess plasticity. Results: Here we show that HB and DR cells are increased in patients with decompensated cirrhosis and AH, but only HB cells correlate with poor liver function and patients outcome. Transcriptomic profiling of HB cells revealed the expression of biliary-specific genes and a mild reduction of hepatocyte metabolism. Functional analysis identified pathways involved in hepatocyte reprogramming, inflammation, stemness and cancer gene programs. CXCR4 pathway was highly enriched in HB cells, and correlated with disease severity and hepatocyte dedifferentiation. In vitro, CXCR4 was associated with biliary phenotype and loss of hepatocyte features. Liver overexpression of CXCR4 in chronic liver injury decreased hepatocyte specific gene expression profile and promoted liver injury. CXCR4 deletion or its pharmacological inhibition ameliorated hepatocyte dedifferentiation and reduced DR and fibrosis progression. Conclusions: This study shows the association of hepatocyte dedifferentiation with disease progression and poor outcome in AH. Moreover, the transcriptomic profiling of HB cells revealed CXCR4 as a new driver of hepatocyte-to-biliary reprogramming and as a potential therapeutic target to halt hepatocyte dedifferentiation in AH. Copy rights belong to original authors. Visit the link for more info Podcast created by Paper Player, LLC

Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2023.03.07.531564v1?rss=1 Authors: Ester, L., Cabrita, I., Ventzke, M., Christodoulou, M., Fabretti, F., Benzing, T., Habbig, S., Schermer, B. Abstract: Background: Mutations in genes encoding nuclear pore proteins (NUPs) cause steroid-resistant nephrotic syndrome (SRNS) and focal and segmental glomerulosclerosis (FSGS). The mechanisms of how NUP deficiency may cause podocyte dysfunction and failure of the kidney filtration barrier are elusive. The tightly controlled activity of the transcriptional effectors of the evolutionarily conserved Hippo pathway YAP and TAZ is essential for podocyte homeostasis. Here we analyze the role of NUPs in controlling YAP/TAZ nuclear import and activity in podocytes. Methods: We used quantitative label-free mass spectrometry to characterize the YAP/TAZ interactomes in podocytes, particularly identifying NUP interactions. Moreover, we specifically studied NUP205 in controlling YAP/TAZ nuclear import and YAP/TAZ-dependent target gene expression. Results: Here we identify the disease-causing nuclear pore proteins NUP107, NUP133, NUP205, and XPO5 as components of YAP and TAZ protein complexes in podocytes. We demonstrate that NUP205 is essential for YAP/TAZ nuclear import. The nuclear interaction of YAP/TAZ with TEAD1 and their transcriptional activity were dependent on NUP205 expression. Furthermore, we identify a feedback regulatory mechanism that controls YAP activity depending on TAZ-mediated NUP205 expression. Conclusion: This study links the disease protein NUP205 with the activity of the transcriptional regulators and Hippo effectors YAP and TAZ and suggests a pathogenic role of YAP/TAZ-deregulation in podocytes in patients with NUP205 mutations. Moreover, this study suggests an important role of YAP/TAZ signaling in human FSGS. Copy rights belong to original authors. Visit the link for more info Podcast created by Paper Player, LLC

Check Out My Clients' Results Here! Download my free manifestation workbook below: https://www.vegangoddessfitness.com/hot-girl-summer-cookbook1632431724760 Apply to work with me HERE (1:1 vegan fitness coaching) Add me on Instagram

This was such a fun episode to record (both for the podcast and for YouTube) I'll give you my take on popular diet trends as a certified nutrition coach who has coached hundreds of vegan and plant based women. Check Out My Clients' Results Here! Download my free 1-week meal plan below: https://www.vegangoddessfitness.com/w... Apply to work with me HERE (1:1 vegan fitness coaching) Add me on Instagram

Join Finish Strong 21 Day Challenge Now! Check Out My Clients' Results Here! Download my free 1-week meal plan below: https://www.vegangoddessfitness.com/w... Apply to work with me HERE (1:1 vegan fitness coaching) Add me on Instagram

The pressure you put on yourself to achieve a result by a specific timeline is robbing you of having any fun on this journey. If you desire ease, effortlessness, strength, and real happiness, you may be doing yourself a big disservice by adding all this extra pressure. Not just that, but we are setting ourselves up for failure by believing that our happiness is waiting for us once we achieve our results... listen to the episode for more! Join Finish Strong 21 Day Challenge Now! https://www.vegangoddessfitness.com/joinnow Check Out My Clients' Results Here! Download my free 1-week meal plan below: https://www.vegangoddessfitness.com/w... Apply to work with me HERE (1:1 vegan fitness coaching) Add me on Instagram

It’s time for another one of our infamous and patented Care/Don’t Care Podcasts, with your talent: the astounding Eugene S. Robinson, along with... WAIT!!! — Breaking: This week's Care/Don’t Care Podcast has been cancelled due to unforeseen circumstances and Eugene has come to the rescue! Today, we are airing ‘The Eugene S. Robinson Show Stomper!’ right here on Bloody Elbow Presents – so you can still get your MMA Podcast fix, while hearing all of Eugene’s reactions to UFC 261. Overall, this 13-bout card saw 6 exciting 1st Rd finishes, 2 fantastic subs, and 7 phenomenal KO/TKO’s – including our 3 title fights, along with 4 decisions - 1 split. Rounding things out, bonuses for putting forth POTN efforts went to Rose Namajunas & Kamaru Usman; FOTN honors went to Aori Qileng vs. Jeff Molina. What a night of fights we have to share with you, join Eugene to discuss all the action... UFC 261 RESULTS: Here’s a look at the UFC 261: ‘USMAN VS MASVIDAL 2’ RESULTS & UPDATED FIGHT RECORDS: ESPN+ MAIN PPV CARD | SAT. APR. 24 13. UFC Welterweight Championship - Kamaru Usman (19-1) DEF Jorge Masvidal (35-15) - KO/TKO, Right Cross at 1:02 of Rd 2, Total 6:02 12. Women’s UFC Strawweight Championship - Rose Namajunas (10-4) DEF Weili Zhang (21-2) - KO/TKO, Head Kick at 1:18 of Rd 1 11. Women’s UFC Flyweight Championship - Valentina Shevchenko (21-3) DEF Jéssica Andrade (21-9) - KO/TKO, Elbows from Crucifix at 3:19 of Rd 2/5, Total 8:19 10. 185lbs Uriah Hall (17-9) DEF Chris Weidman (15-6) - KO/TKO, BROKEN LEG at 0:17 of Rd 1 9. 205lbs Anthony Smith (35-16) DEF Jimmy Crute (12-2) - KO/TKO, Dr. Stoppage-Leg Injury at 5:00 of Rd 1 ESPN/ESPN+ PRELIMS 8. 170lbs Randy Brown (13-4) DEF Alex Oliveira (22-10) - SUB, One-Arm Rear Naked Choke at 2:50 of Rd 1 7. 170lbs Dwight Grant (11-2) DEF Stefan Sekulić (12-4) - DEC, SPLIT 6. 185lbs Brendan Allen (16-4) DEF Karl Roberson (9-4) - SUB, Heel Hook at 4:55 of Rd 1 5. 145lbs Pat Sabatini (14-3) DEF Tristan Connelly (14-7) - DEC, Unanimous ESPN+/UFC Fight Pass EARLY PRELIMS 4. 135lbs Danaa Batgerel (9-2) DEF Kevin Natividad (9-3) - KO/TKO, Counter, Left Hook at 0:50 of Rd 1 3. 155lbs Rodrigo Vargas (12-4) DEF Zhu Rong (17-4) - DEC, Unanimous 2. 125lbs Jeff Molina (9-2) DEF Qileng Aori (18-8) - DEC, Unanimous 1. 115lbs Ariane Carnelossi (13-2) DEF Na Liang (15-5) - KO/TKO to G&P from Guard at 1:28 of Rd 2, Total 6:28 Be sure to follow Eugene for more MMA ramblings & observations: On twitter @EugeneSRobinson, on Insta @MrSleep3, PAY here at his Patreon IF you wish: www.patreon.com/thestomp... Check him out at ozy.com & listen to his ‘Ozy Confidential’ Podcast. Give the live video broadcast of ‘The Show Stomper! Podcast’ a “thumbs up”, subscribe and share on The Stomper YT page at: https://youtu.be/fEXhnYOVifE, OR: Give the premium video production of the show a “like” and share on The Stomper’s Facebook: https://www.facebook.com/stompville/ OR: Listen to premium audio on his... * SoundCloud at: https://soundcloud.com/user-914736745, * Spotify: https://open.spotify.com/show/353qdjKsABTte8zQVZCwyd?si=OJjhBfBfTYyYiSZSE5RV0g, * iTunes & Apple TV: https://itunes.apple.com/us/podcast/eugene-s-robinson-show-stomper/id1340723629?mt=2, * iHeartRadio: https://www.iheart.com/podcast/269-eugene-s-robinson-show-sto-30674882/, * OverCast: https://overcast.fm/itunes1340723629/eugene-s-robinson-show-stomper, * PlayerFM: https://player.fm/series/eugene-s-robinson-show-stomper, TuneIn: https://tunein.com/podcasts/Sports--Recreation-Podcasts/Eugene-S-Robinson-Show-Stomper-p1190934/, * Stitcher: https://www.stitcher.com/podcast/the-eugene-s-robinson-show-stomper?refid=stpr, * or blubrry: https://www.blubrry.com/eugene_s_robinson_show_stomper/ – and now also on Amazon Music: https://music.amazon.com/podcasts/31b526af-ea19-4022-ba38-202b583cf8d3/Eugene-S-Robinson-Show-Stomper

Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2020.11.17.387811v1?rss=1 Authors: Kang, K., Chong, H., Ning, K. Abstract: Motivation: Microbial community samples and sequencing data have been accumulated at a speed faster than ever, with tens of thousands of samples been sequenced each year. Mining such a huge amount of multi-source heterogeneous data is becoming more and more difficult. Among several sample mining bottlenecks, efficient and accurate search of samples is one of the most prominent: Faced with millions of samples in the data repository, traditional sample comparison and search approaches fall short in speed and accuracy. Results: Here we proposed Meta-Prism 2.0, a microbial community sample search method based on smart pair-wise sample comparison, which pushed the time and memory efficiency to a new limit, without the compromise of accuracy. Based on memory-saving data structure, time-saving instruction pipeline, and boost scheme optimization, Meta-Prism 2.0 has enabled ultra-fast, accurate and memory-efficient search among millions of samples. Meta-Prism 2.0 has been put to test on several datasets, with largest containing one million samples. Results have shown that firstly, as a distance-based method, Meta-Prism 2.0 is not only faster than other distance-based methods, but also faster than unsupervised methods. Its 0.00001s per sample pair search speed, as well as 8GB memory needs for searching against one million samples, have enabled it to be the most efficient method for sample comparison. Additionally, Meta-Prism 2.0 could achieve the comparison accuracy and search precision that are comparable or better than other contemporary methods. Thirdly, Meta-Prism 2.0 can precisely identify the original biome for samples, thus enabling sample source tracking. Conclusion: In summary, Meta-Prism 2.0 can perform accurate searches among millions of samples with very low memory cost and fast speed, enabling knowledge discovery from samples at a massive scale. It has changed the traditional resource-intensive sample comparison and search scheme to a cheap and effective procedure, which could be conducted by researchers everyday even on a laptop, for insightful sample search and knowledge discovery. Meta-Prism 2.0 could be accessed at: https://github.com/HUST-NingKang-Lab/Meta-Prism-2.0. Copy rights belong to original authors. Visit the link for more info

Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2020.11.09.374140v1?rss=1 Authors: Klasberg, S., Schmidt, A. H., Lange, V., Schöfl, G. Abstract: Background: High resolution HLA genotyping of donors and recipients is a crucially important prerequisite for haematopoetic stem-cell transplantation and relies heavily on the quality and completeness of immunogenetic reference sequence databases of allelic variation. Results: Here, we report on DR2S, an R package that leverages the strengths of two sequencing technologies - the accuracy of next-generation sequencing with the read length of third-generation sequencing technologies like PacBio's SMRT sequencing or ONT's nanopore sequencing - to reconstruct fully-phased high-quality full-length haplotype sequences. Although optimised for HLA and KIR genes, DR2S is applicable to all loci with known reference sequences provided that full-length sequencing data is available for analysis. In addition, DR2S integrates supporting tools for easy visualisation and quality control of the reconstructed haplotype to ensure suitability for submission to public allele databases. Conclusions: DR2S is a largely automated workflow designed to create high-quality fully-phased reference allele sequences for highly polymorphic gene regions such as HLA or KIR. It has been used by biologists to successfully characterise and submit more than 500 HLA alleles and more than 500 KIR alleles to the IPD-IMGT/HLA and IPD-KIR databases. Copy rights belong to original authors. Visit the link for more info

Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2020.11.01.363960v1?rss=1 Authors: Gregory, A. C., Gerhardt, K., Zhong, Z.-P., Bolduc, B., Temperton, B., Konstantinidis, K. T. C., Sullivan, M. B. Abstract: Background: Microbes and their viruses are hidden engines driving Earth's ecosystems from the oceans and soils to humans and bioreactors. Though gene marker approaches can now be complemented by genome-resolved studies of inter- (macrodiversity) and intra- (microdiversity) population variation, analytical tools to do so remain scattered or under-developed. Results: Here we introduce MetaPop, an open-source bioinformatic pipeline that provides a single interface to analyze and visualize microbial and viral community metagenomes at both the macro- and micro-diversity levels. Macrodiversity estimates include population abundances and - and {beta}-diversity. Microdiversity calculations include identification of single nucleotide polymorphisms, novel codon-constrained linkage of SNPs, nucleotide diversity ({pi} and {theta}) and selective pressures (pN/pS and Tajima's D) within and fixation indices (FST) between populations. MetaPop will also identify genes with distinct codon usage. Following rigorous validation, we applied MetaPop to the gut viromes of autistic children that underwent fecal microbiota transfers and their neurotypical peers. The macrodiversity results confirmed our prior findings for viral populations (microbial shotgun metagenomes were not available), that diversity did not significantly differ between autistic and neurotypical children. However, by also quantifying microdiversity, MetaPop revealed lower average viral nucleotide diversity ({pi}) in autistic children. Analysis of the percentage of genomes detected under positive selection was also lower among autistic children, suggesting that higher viral {pi} in neurotypical children may be beneficial because it allows populations to better 'bet hedge' in changing environments. Further, comparisons of microdiversity pre- and post-FMT in the autistic children revealed that the delivery FMT method (oral versus rectal) may influence viral activity and engraftment of microdiverse viral populations, with children who received their FMT rectally having higher microdiversity post-FMT. Overall, these results show that analyses at the macro-level alone can miss important biological differences. Conclusions: These findings suggest that standardized population and genetic variation analyses will be invaluable for maximizing biological inference, and MetaPop provides a convenient tools package to explore the dual impact of macro- and micro-diversity across microbial communities. Copy rights belong to original authors. Visit the link for more info

Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2020.10.27.357459v1?rss=1 Authors: Caponegro, M. D., Oh, K., Madeira, M., Radin, D., Sterge, N., Moffitt, R. A., Tsirka, S. E. Abstract: Background: Myeloid involvement in High Grade Gliomas, such as Glioblastoma, has become apparent and detrimental to disease outcomes. There is great interest in characterizing the HGG tumor microenvironment to understand how neoplastic lesions are supported, and to devise novel therapeutic targets. The tumor microenvironment of the central nervous system is unique as it contains neural and specialized glial cells, including the resident myeloid cells, microglia. Glioma-associated microglia and peripherally infiltrating monocytes/macrophages (GAM) accumulate within the neoplastic lesion where they facilitate tumor growth and drive immunosuppression. A longstanding limitation has been the ability to accurately differentiate microglia and macrophage roles in pathology, and identify the consequences of the spatial organization of these cells. Results: Here we characterize the tumor-stroma border and identify peripheral glioma-associated microglia (PGAM) at the tumor leading edge as a unique subpopulation of GAM. Using data mining and analyses of samples derived from both murine and human sources, we show that PGAM exhibit a pro-inflammatory and chemotactic phenotype that is associated with peripheral monocyte recruitment, poorly enhancing radiomic features, and decreased overall survival. Conclusions: PGAM act as a unique subset of GAM, at the tumor-stroma interface, corresponding to disease outcomes. We propose the application of a novel gene signature to identify these cells, and suggest that PGAM constitute a cellular target of the TME. Copy rights belong to original authors. Visit the link for more info

Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2020.10.19.345389v1?rss=1 Authors: BRIERE, G., Darbo, E., Thebault, P., Uricaru, R. Abstract: Background Facing the diversity of omic data and the difficulty of selecting one result over all those produced by several methods, consensus strategies have the potential to reconcile multiple inputs and to produce robust results. Results Here, we introduce ClustOmics, a generic consensus clustering tool that we use in the context of cancer subtyping. ClustOmics relies on a non-relational graph database, which allows for the simultaneous integration of both multiple omic data and results from various clustering methods. This new tool conciliates input clusterings, regardless of their origin, their number, their size or their shape. ClustOmics implements an intuitive and flexible strategy, based upon the idea of evidence accumulation clustering. It computes co-occurrences of pairs of samples in input clusters and uses this score as a similarity measure to reorganise data into consensus clusters. Conclusion We applied ClustOmics to multi-omic disease subtyping on real TCGA cancer data from ten different cancer types. We showed that ClustOmics is robust to heterogeneous qualities of input partitions, smoothing and reconciling preliminary predictions into high quality consensus clusters, both from a computational and a biological point of view. In this regard, ClustOmics is not meant to compete with other integrative tools, but rather to make profit from their various predictions when no gold-standard metric is available to assess their significance. Availability ClustOmics' source code, released under MIT licence, as well as the results obtained on TCGA cancer data are available on Github: https://github.com/galadrielbriere/ClustOmics. Copy rights belong to original authors. Visit the link for more info

Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2020.10.12.318808v1?rss=1 Authors: R Melo Costa, V., Pfeuffer, J., Louloupi, A., V Orom, U. A., Piro, R. M. Abstract: Background: Introns are generally removed from primary transcripts to form mature RNA molecules in a post-transcriptional process called splicing. An efficient splicing of primary transcripts is an essential step in gene expression and its misregulation is related to numerous human diseases. Thus, to better understand the dynamics of this process and the perturbations that might be caused by aberrant transcript processing it is important to quantify splicing efficiency. Results: Here, we introduce SPLICE-q, a fast and user-friendly Python tool for genome-wide SPLICing Efficiency quantification. It supports studies focusing on the implications of splicing efficiency in transcript processing dynamics. SPLICE-q uses aligned reads from strand-specific RNA-seq to quantify splicing efficiency for each intron individually and allows the user to select different levels of restrictiveness concerning the introns' overlap with other genomic elements such as exons of other genes. We applied SPLICE-q to globally assess the dynamics of intron excision in yeast and human nascent RNA-seq. We also show its application using total RNA-seq from a patient-matched prostate cancer sample. Conclusions: Our analyses illustrate that SPLICE-q is suitable to detect a progressive increase of splicing efficiency throughout a time course of nascent RNA-seq and it might be useful when it comes to understanding cancer progression beyond mere gene expression levels. SPLICE-q is available at: github.com/vrmelo/SPLICE-q . Copy rights belong to original authors. Visit the link for more info

Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2020.09.24.311720v1?rss=1 Authors: Stamboulian, M., Doak, T. G., Ye, Y. Abstract: Background: Recent advances in genome and metagenome sequencing have dramatically enriched the collection of genomes of bacterial species related to human health and diseases. In metagenomic studies phylogenetic trees are commonly used to depict, describe, and compare the bacterial members of the community under study. The most accurate tree-building algorithms now use large sets of marker genes taken from across genomes. However, many of the current bacterial genomes were assembled from metagenomic datasets (i.e., metagenome assembled genomes, MAGs), and often contain missing information. It is therefore important to study how well the phylogeny approach performs on such genomes. Further, phylogeny methods are not perfect and it is important to know how reliable an inferred tree is. Results: Here we examined the impact of incompleteness of the genomes on the tree reconstruction, and we showed that phylogeny approaches including RAxML (which handles missing data explicitly) and FastTree generally performed well on simulated collection of 400 genomes with missing information. As RAxML is computationally prohibitive for the much larger collections of gut genomes, we chose FastTree to build a unified tree of human-gut associated bacterial species (referred to as gut tree), including more than 3000 genomes, most of which are incomplete. We developed two downstream applications of the gut tree: peptide-centric analysis of metaproteomics datasets; and taxonomic characterization of metagenomic sequences. In both applications, the gut tree provided the basis for quantification of species composition at various taxonomic resolutions. Conclusions: The gut tree presented in this study provides a useful framework for taxonomic profiling of human gut microbiome. Including MAGs in the tree provides more comprehensive representation of microbial species diversity associated with human gut, important for studying the taxonomic composition of gut microbiome. Availability and Implementation: The tree construction pipeline and downstream applications of the gut tree are freely available at https://github.com/mgtools/guttree. Copy rights belong to original authors. Visit the link for more info

Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2020.09.16.299495v1?rss=1 Authors: Hart, R., Prlic, A. Abstract: Motivation Access to biological sequence data, such as genome, transcript, or protein sequence, is at the core of many bioinformatics analysis workflows. The National Center for Biotechnology Information (NCBI), Ensembl, and other sequence database maintainers provide methods to access sequences through network connections. For many users, the convenience and currency of remotely managed data are compelling, and the network latency is non-consequential. However, for high-throughput and clinical applications, local sequence collections are essential for performance, stability, privacy, and reproducibility. Results Here we describe SeqRepo, a novel system for building a local, high-performance, non-redundant collection of biological sequences. SeqRepo enables clients to use primary database identifiers and several digests to identify sequences and sequence alises. SeqRepo provides a native Python interface and a REST interface, which can run locally and enables access from other programming languages. SeqRepo also provides an alternative REST interface based on the GA4GH refget protocol. SeqRepo provides fast random access to sequence slices. We provide results that demonstrate that a local SeqRepo sequence collection yields significant performance benefits of up to 1300-fold over remote sequence collections. In our use case for a variant validation and normalization pipeline, SeqRepo improved throughput 50-fold relative to use with remote sequences. SeqRepo may be used with any species or sequence type. Regular snapshots of Human sequence collections are available. It is often convenient or necessary to use a computed digest as a sequence identifier. For example, a digest-based identifier may be used to refer to proprietary reference genomes or segments of a graph genome, for which conventional identifiers will not be available. Here we also introduce a convention for the application of the SHA-512 hashing algorithm with Base64 encoding to generate URL-safe identifiers. This convention, sha512t24u, combines a fast digest mechanism with a space-efficient representation that can be used for any object. Our report includes an analysis of timing and collision probabilities for sha512t24u. SeqRepo enables clients to use sha512t24u as identifiers, thereby seamlessly integrating public and private sequence sets. Availability SeqRepo is released under the Apache License 2.0 and is available on github and PyPi. Docker images and database snapshots are also available. See https://github.com/biocommons/biocommons.seqrepo . Copy rights belong to original authors. Visit the link for more info

Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2020.09.02.271098v1?rss=1 Authors: Sulit, A. K. L., Kolisnik, T., Frizelle, F. A., Purcell, R., Schmeier, S. Abstract: Background: The identification of functional processes taking place in microbiome communities augment traditional microbiome taxonomic studies, giving a more complete picture of interactions taking place within the community. While there are applications that perform functional annotation on metagenome or metatranscriptomes, very few of these are able to link taxonomic identity to function and are limited by their input types or databases used. Results: Here we present MetaFunc, a workflow which takes input reads, and from these 1) identifies species present in the microbiome sample and 2) provides gene ontology (GO) annotations associated with the species identified. MetaFunc can also provide a differential abundance analysis step comparing species between sample conditions. In addition, MetaFunc allows mapping of reads to a host genome, and separates these reads, before proceeding with the microbiome analyses. From the host reads, MetaFunc is able to identify host genes, perform differential gene expression analysis, and gene-set enrichment analysis. A final correlation analysis between microbial species and host genes can also be performed. Finally, MetaFunc builds an R shiny application that allows users to view and interact with the microbiome results. In this paper we show how MetaFunc can be applied to metatranscriptomic datasets of colorectal cancer. Conclusion: MetaFunc is a one-stop shop microbiome analysis pipeline that can identify taxonomies and their respective functional contributions in a microbiome sample through GO annotations. It can also analyse host reads in a microbiome sample, providing information on host gene expression, and allowing for correlations between the microbiome and host genes. MetaFunc comes with a user-friendly R shiny application that allows for easier visualisation and exploration of its results. MetaFunc is freely available through https://gitlab.com/schmeierlab/workflows/metafunc.git. Copy rights belong to original authors. Visit the link for more info

In this episode Lauren + Abby recap the latest news from the past week including the pro races over the weekend, a new signing for ON + a handful of new announcements from World Athletics. Things We Talked About Sign up for the Run With Rivs Challenge here 1 year to Tokyo... Again - NY Times Article Big Friendly 3 - Results Here Diamond League Monaco will take place on August 14th Watch The Bowerman Intersquad IV here Angel Piccirillo joins Little Wing! Read announcement here Joe Klecker has signed with On Running Cross Country Maybe Being Added to the 2024 Olympic Games in Paris RAF Faces Ban from World Athletics if they don't pay fines World Athletics Amends Shoe Technology Rule ----- The Hand Off: For The Long Run Episode 92 with Alexi Pappas - Listen on iTunes here ----- Thanks to Momentous for supporting the Up + Running Podcast. Save 25% off of your first order at livemomentous.com with you sign up for a subscription and the code "UPRUNNING25". Join us for our Fall Training Group starting 8/10 and save $25 off your registration when you use code "UPRUNNINGPODCAST". Learn more and sign up HERE Follow Up + Running on IG @uprunning.co Follow Lauren on IG @laurenfloris77 Follow Abby on IG @abbycstanley

Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2020.08.03.233825v1?rss=1 Authors: Wozniak, T., Sajek, M., Jaruzelska, J., Sajek, M. P. Abstract: Motivation The function of RNA molecules is mainly determined by their secondary structure. Addressing that issue requires creation of appropriate bioinformatic tools that enable alignment of multiple RNA molecules to determine functional domains and/or classify RNA families. The existing tools for RNA multiple alignment that use structural information are relatively slow. Therefore, providing a rapid tool for multiple structural alignment may improve classification of the known RNAs and reveal the function of the newly discovered ones. Results Here, we developed an extremely fast Python based RNAlign2D tool. It converts RNA sequence and structure to pseudo-amino acid sequence and uses customizable pseudo-amino acid substitution matrix to align RNA secondary structures and sequences using MUSCLE. It is suitable for RNAs containing modified nucleosides and/or pseudoknots. Our approach is compatible with virtually all protein aligners. Availability and implementation RNAlign2D is available from https://github.com/tomaszwozniakihg/rnalign2d. It has been tested on Linux and MacOSX. Supplementary information Supplementary data are available at Bioinformatics online. Copy rights belong to original authors. Visit the link for more info

Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2020.07.23.214536v1?rss=1 Authors: Bedre, R. H., Avila, C. A., Mandadi, K. Abstract: Motivation: Use of high-throughput sequencing (HTS) has become indispensable in life science research. Raw HTS data contains several sequencing artifacts, and as a first step it is imperative to remove the artifacts for reliable downstream bioinformatics analysis. Although there are multiple stand-alone tools available that can perform the various quality control steps separately, availability of an integrated tool that can allow one-step, automated quality control analysis of HTS datasets will significantly enhance handling large number of samples parallelly. Results: Here, we developed HTSeqQC, a stand-alone, flexible, and easy-to-use software for one-step quality control analysis of raw HTS data. HTSeqQC can evaluate HTS data quality and perform filtering and trimming analysis in a single run. We evaluated the performance of HTSeqQC for conducting batch analysis of HTS datasets with 322 sample datasets with an average ~ 1M (paired end) sequence reads per sample. HTSeqQC accomplished the QC analysis in ~3 hours in distributed mode and ~31 hours in shared mode, thus underscoring its utility and robust performance. Availability and implementation: HTSeqQC software, Docker image and Nextflow template are available for download at https://github.com/reneshbedre/HTSeqQC and graphical user interface (GUI) is available at CyVerse Discovery Environment (DE) (https://cyverse.org/ ). Documentation available at https://reneshbedre.github.io/blog/htseqqc.html and https://cyverse-htseqqc-cyverse-tutorial.readthedocs-hosted.com/en/latest/ (for CyVerse). Copy rights belong to original authors. Visit the link for more info

This week we rank and draft our favorite Sandra Bullock movies. We cover everything from Speed and the Net to Ocean’s 8 which we haven’t seen yet. Bullock has been in everything from comedies to thrillers and we had some fun discussing them all. Check the Results Here. Listen to It | iTunes | Google … Continue reading "Episode 090 – Favorite Sandra Bullock Movies"

It’s Comic Con week and to celebrate we’re drafting and ranking and discussing comic book movies outside of the DC/Marvel super hero genre. So we’re talking indie comics and non-supies. There’s probably a lot of movies out there that you didn’t even know were comic book based. Check the Results Here.  Listen to It | … Continue reading "Episode 089 – Comic Book Movies (No Supies)"

This week we rank and draft our favorite movies of the Romance/Love Story genre. We’re joined by Mike’s friend from work, Kristin. This list is all over the place. I think had you didn’t know the theme, you’d be hard pressed to guess it. Happy Valentine’s Day. Results Here. Listen to It Listen to them … Continue reading "Episode 067 Fav Love Stories/Romance Movies"

We rank and draft our favorite TV shows and miniseries from 2017. There’s a little bit of everything here – comedy, drama, real life, and more.  Results Here. Listen to It Listen to them all iTunes Google Play Stitcher

Background: Aneuploidy, a karyotype deviating from multiples of a haploid chromosome set, affects the physiology of eukaryotes. In humans, aneuploidy is linked to pathological defects such as developmental abnormalities, mental retardation or cancer, but the underlying mechanisms remain elusive. There are many different types and origins of aneuploidy, but whether there is a uniform cellular response to aneuploidy in human cells has not been addressed so far. Results: Here we evaluate the transcription profiles of eleven trisomic and tetrasomic cell lines and two cell lines with complex aneuploid karyotypes. We identify a characteristic aneuploidy response pattern defined by upregulation of genes linked to endoplasmic reticulum, Golgi apparatus and lysosomes, and downregulation of DNA replication, transcription as well as ribosomes. Strikingly, complex aneuploidy elicits the same transcriptional changes as trisomy. To uncover the triggers of the response, we compared the profiles with transcription changes in human cells subjected to stress conditions. Interestingly, we found an overlap only with the response to treatment with the autophagy inhibitor bafilomycin A1. Finally, we identified 23 genes whose expression is significantly altered in all aneuploids and which may thus serve as aneuploidy markers. Conclusions: Our analysis shows that despite the variability in chromosome content, aneuploidy triggers uniform transcriptional response in human cells. A common response independent of the type of aneuploidy might be exploited as a novel target for cancer therapy. Moreover, the potential aneuploidy markers identified in our analysis might represent novel biomarkers to assess the malignant potential of a tumor.

Background: A key issue for safe and reproducible gene therapy approaches is the autologous and tissue-specific expression of transgenes. Tissue-specific expression in vivo is either achieved by transfer vectors that deliver the gene of interest into a distinct cell type or by use of tissue-specific expression cassettes. Here we present the generation of non-viral, episomally replicating vectors that are able to replicate in a tissue specific manner thus allowing tissue specific transgene expression in combination with episomal replication. The episomal replication of the prototype vector pEPI-1 and its derivatives depends exclusively on a transcription unit starting from a constitutively active promoter extending into the scaffold/matrix attachment region (S/MAR). Results: Here, we exchanged the constitutive promoter in the pEPI derivative pEPito by the tumor specific alpha fetoprotein (AFP) or the muscle specific smooth muscle 22 (SM22) promoter leading to specific transgene expression in AFP positive human hepatocellular carcinoma (HUH7) and in a SM22 positive cell line, respectively. The incorporation of the hCMV enhancer element into the expression cassette further boosted the expression levels with both promoters. Tissue specific-replication could be exemplary proven for the smooth muscle protein 22 (SM22) promoter in vitro. With the AFP promoter-driven pEPito vector hepatocellular carcinoma-specific expression could be achieved in vivo after systemic vector application together with polyethylenimine as transfection enhancer. Conclusions: In this study we present an episomal plasmid system designed for tissue specific transgene expression and replication. The human AFP-promoter in combination with the hCMV enhancer element was demonstrated to be a valuable tissue-specific promoter for targeting hepatocellular carcinomas with non-viral gene delivery system, and tissue specific replication could be shown in vitro with the muscle specific SM22 promoter. In combination with appropriate delivery systems, the tissue specific pEPito vector system will allow higher tissue-specificity with less undesired side effects and is suitable for long term transgene expression in vivo within gene therapeutical approaches.

Background: Fueled by rapid progress in high-throughput sequencing, the size of public sequence databases doubles every two years. Searching the ever larger and more redundant databases is getting increasingly inefficient. Clustering can help to organize sequences into homologous and functionally similar groups and can improve the speed, sensitivity, and readability of homology searches. However, because the clustering time is quadratic in the number of sequences, standard sequence search methods are becoming impracticable. Results: Here we present a method to cluster large protein sequence databases such as UniProt within days down to 20%-30% maximum pairwise sequence identity. kClust owes its speed and sensitivity to an alignment-free prefilter that calculates the cumulative score of all similar 6-mers between pairs of sequences, and to a dynamic programming algorithm that operates on pairs of similar 4-mers. To increase sensitivity further, kClust can run in profile-sequence comparison mode, with profiles computed from the clusters of a previous kClust iteration. kClust is two to three orders of magnitude faster than clustering based on NCBI BLAST, and on multidomain sequences of 20%-30% maximum pairwise sequence identity it achieves comparable sensitivity and a lower false discovery rate. It also compares favorably to CD-HIT and UCLUST in terms of false discovery rate, sensitivity, and speed. Conclusions: kClust fills the need for a fast, sensitive, and accurate tool to cluster large protein sequence databases to below 30% sequence identity. kClust is freely available under GPL at ftp://toolkit.lmb.uni-muenchen.de/pub/kClust/.

Background: Genome-wide association studies (GWAS) with metabolic traits and metabolome-wide association studies (MWAS) with traits of biomedical relevance are powerful tools to identify the contribution of genetic, environmental and lifestyle factors to the etiology of complex diseases. Hypothesis-free testing of ratios between all possible metabolite pairs in GWAS and MWAS has proven to be an innovative approach in the discovery of new biologically meaningful associations. The p-gain statistic was introduced as an ad-hoc measure to determine whether a ratio between two metabolite concentrations carries more information than the two corresponding metabolite concentrations alone. So far, only a rule of thumb was applied to determine the significance of the p-gain. Results: Here we explore the statistical properties of the p-gain through simulation of its density and by sampling of experimental data. We derive critical values of the p-gain for different levels of correlation between metabolite pairs and show that B/(2*alpha) is a conservative critical value for the p-gain, where a is the level of significance and B the number of tested metabolite pairs. Conclusions: We show that the p-gain is a well defined measure that can be used to identify statistically significant metabolite ratios in association studies and provide a conservative significance cut-off for the p-gain for use in future association studies with metabolic traits.

Background: Genome-wide association studies (GWAS) have provided a large set of genetic loci influencing the risk for many common diseases. Association studies typically analyze one specific trait in single populations in an isolated fashion without taking into account the potential phenotypic and genetic correlation between traits. However, GWA data can be efficiently used to identify overlapping loci with analogous or contrasting effects on different diseases. Results: Here, we describe a new approach to systematically prioritize and interpret available GWA data. We focus on the analysis of joint and disjoint genetic determinants across diseases. Using network analysis, we show that variant-based approaches are superior to locus-based analyses. In addition, we provide a prioritization of disease loci based on network properties and discuss the roles of hub loci across several diseases. We demonstrate that, in general, agonistic associations appear to reflect current disease classifications, and present the potential use of effect sizes in refining and revising these agonistic signals. We further identify potential branching points in disease etiologies based on antagonistic variants and describe plausible small-scale models of the underlying molecular switches. Conclusions: The observation that a surprisingly high fraction (>15%) of the SNPs considered in our study are associated both agonistically and antagonistically with related as well as unrelated disorders indicates that the molecular mechanisms influencing causes and progress of human diseases are in part interrelated. Genetic overlaps between two diseases also suggest the importance of the affected entities in the specific pathogenic pathways and should be investigated further.

Background: With the advance of genome sequencing technologies, phenotyping, rather than genotyping, is becoming the most expensive task when mapping genetic traits. The need for efficient selective phenotyping strategies, i.e. methods to select a subset of genotyped individuals for phenotyping, therefore increases. Current methods have focused either on improving the detection of causative genetic variants or their precise genomic location separately. Results: Here we recognize selective phenotyping as a Bayesian model discrimination problem and introduce SPARE (Selective Phenotyping Approach by Reduction of Entropy). Unlike previous methods, SPARE can integrate the information of previously phenotyped individuals, thereby enabling an efficient incremental strategy. The effective performance of SPARE is demonstrated on simulated data as well as on an experimental yeast dataset. Conclusions: Using entropy reduction as an objective criterion gives a natural way to tackle both issues of detection and localization simultaneously and to integrate intermediate phenotypic data. We foresee entropy-based strategies as a fruitful research direction for selective phenotyping.

Background: The episomal replication of the prototype vector pEPI-1 depends on a transcription unit starting from the constitutively expressed Cytomegalovirus immediate early promoter (CMV-IEP) and directed into a 2000 bp long matrix attachment region sequence (MARS) derived from the human beta-interferon gene. The original pEPI-1 vector contains two mammalian transcription units and a total of 305 CpG islands, which are located predominantly within the vector elements necessary for bacterial propagation and known to be counterproductive for persistent long-term transgene expression. Results: Here, we report the development of a novel vector pEPito, which is derived from the pEPI-1 plasmid replicon but has considerably improved efficacy both in vitro and in vivo. The pEPito vector is significantly reduced in size, contains only one transcription unit and 60% less CpG motives in comparison to pEPI-1. It exhibits major advantages compared to the original pEPI-1 plasmid, including higher transgene expression levels and increased colony-forming efficiencies in vitro, as well as more persistent transgene expression profiles in vivo. The performance of pEPito-based vectors was further improved by replacing the CMV-IEP with the human CMV enhancer/human elongation factor 1 alpha promoter (hCMV/EF1P) element that is known to be less affected by epigenetic silencing events. Conclusions: The novel vector pEPito can be considered suitable as an improved vector for biotechnological applications in vitro and for non-viral gene delivery in vivo.

Background: The German Dementia Competence Network (DCN) has established procedures for standardized multicenter acquisition of clinical, biological and imaging data, for centralized data management, and for the evaluation of new treatments. Methods: A longitudinal cohort study was set up for patients with mild cognitive impairment (MCI), patients with mild dementia and control subjects. The aims were to establish the diagnostic, differential diagnostic and prognostic power of a range of clinical, laboratory and imaging methods. Furthermore, 2 clinical trials were conducted with patients suffering from MCI and mild to moderate Alzheimer's Disease (AD). These trials aimed at evaluating the efficacy and safety of the combination of galantamine and memantine versus galantamine alone. Results: Here, we report on the scope and projects of the DCN, the methods that were employed, the composition and flow within the diverse groups of patients and control persons and on the clinical and neuropsychological baseline characteristics of the group of 2,113 subjects who participated in the observational and clinical trials. Conclusion: These data have an impact on the procedures for the early and differential clinical diagnosis of dementias, the current standard treatment of AD as well as on future clinical trials in AD. Copyright (C) 2009 S. Karger AG, Basel

Background: Introducing point mutations into bacterial chromosomes is important for further progress in studies relying on functional genomics, systems- and synthetic biology, and for metabolic engineering. For many investigations, chromosomal systems are required rather than artificial plasmid based systems. Results: Here we describe the introduction of a single point mutation into the Escherichia coli chromosome by site-directed mutagenesis without leaving any selection marker. We used Red (R)/ET (R) Recombination in combination with rpsL counter-selection to introduce a single point mutation into the E. coli MG1655 genome, one of the widely used bacterial model strains in systems biology. The method we present is rapid and highly efficient. Since single-stranded synthetic oligonucleotides can be used for recombination, any chromosomal modification can be designed. Conclusion: Chromosomal modifications performed by rpsL counter-selection may also be used for other bacteria that contain an rpsL homologue, since Red (R)/ET (R) Recombination has been applied to several enteric bacteria before.

Background: Production of interferon (IFN)-gamma is key to efficient anti-tumor immunity. The present study was set out to investigate effects of IFN. on the release of the potent pro-angiogenic mediator IL-8 by human A549 lung carcinoma cells. Methods: A549 cells were cultured and stimulated with interleukin (IL)-1 beta alone or in combination with IFN gamma. IL-8 production by these cells was analyzed with enzyme linked immuno sorbent assay (ELISA). mRNA-expression was analyzed by real-time PCR and RNase protection assay (RPA), respectively. Expression of inhibitor-kappa B alpha, cellular IL-8, and cyclooxygenase-2 was analyzed by Western blot analysis. Results: Here we demonstrate that IFN gamma efficiently reduced IL-8 secretion under the influence of IL-1 beta. Surprisingly, real-time PCR analysis and RPA revealed that the inhibitory effect of IFN gamma on IL-8 was not associated with significant changes in mRNA levels. These observations concurred with lack of a modulatory activity of IFN gamma on IL-1 beta-induced NF-kappa B activation as assessed by cellular I kappa B levels. Moreover, analysis of intracellular IL-8 suggests that IFN gamma modulated IL-8 secretion by action on the posttranslational level. In contrast to IL-8, IL-1 beta-induced cyclooxygenase-2 expression and release of IL-6 were not affected by IFN gamma indicating that modulation of IL-1 beta action by this cytokine displays specificity. Conclusion: Data presented herein agree with an angiostatic role of IFN gamma as seen in rodent models of solid tumors and suggest that increasing T helper type I (Th1)-like functions in lung cancer patients e.g. by local delivery of IFN gamma may mediate therapeutic benefit via mechanisms that potentially include modulation of pro-angiogenic IL-8.

Background: Using suitable error models for gene expression measurements is essential in the statistical analysis of microarray data. However, the true probabilistic model underlying gene expression intensity readings is generally not known. Instead, in currently used approaches some simple parametric model is assumed (usually a transformed normal distribution) or the empirical distribution is estimated. However, both these strategies may not be optimal for gene expression data, as the non-parametric approach ignores known structural information whereas the fully parametric models run the risk of misspecification. A further related problem is the choice of a suitable scale for the model (e. g. observed vs. log-scale). Results: Here a simple semi-parametric model for gene expression measurement error is presented. In this approach inference is based an approximate likelihood function (the extended quasi-likelihood). Only partial knowledge about the unknown true distribution is required to construct this function. In case of gene expression this information is available in the form of the postulated (e.g. quadratic) variance structure of the data. As the quasi-likelihood behaves (almost) like a proper likelihood, it allows for the estimation of calibration and variance parameters, and it is also straightforward to obtain corresponding approximate confidence intervals. Unlike most other frameworks, it also allows analysis on any preferred scale, i.e. both on the original linear scale as well as on a transformed scale. It can also be employed in regression approaches to model systematic (e.g. array or dye) effects. Conclusions: The quasi-likelihood framework provides a simple and versatile approach to analyze gene expression data that does not make any strong distributional assumptions about the underlying error model. For several simulated as well as real data sets it provides a better fit to the data than competing models. In an example it also improved the power of tests to identify differential expression.