| 1. |
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| 2. |
- Elsik, Christine G., et al.
(author)
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The Genome Sequence of Taurine Cattle : A Window to Ruminant Biology and Evolution
- 2009
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In: Science. - : American Association for the Advancement of Science (AAAS). - 0036-8075 .- 1095-9203. ; 324:5926, s. 522-528
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Journal article (peer-reviewed)abstract
- To understand the biology and evolution of ruminants, the cattle genome was sequenced to about sevenfold coverage. The cattle genome contains a minimum of 22,000 genes, with a core set of 14,345 orthologs shared among seven mammalian species of which 1217 are absent or undetected in noneutherian (marsupial or monotreme) genomes. Cattle-specific evolutionary breakpoint regions in chromosomes have a higher density of segmental duplications, enrichment of repetitive elements, and species-specific variations in genes associated with lactation and immune responsiveness. Genes involved in metabolism are generally highly conserved, although five metabolic genes are deleted or extensively diverged from their human orthologs. The cattle genome sequence thus provides a resource for understanding mammalian evolution and accelerating livestock genetic improvement for milk and meat production.
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| 3. |
- Aldred, Jason, et al.
(author)
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Continuous Subcutaneous Foslevodopa/Foscarbidopa in Parkinson's Disease: Safety and Efficacy Results From a 12-Month, Single-Arm, Open-Label, Phase 3 Study.
- 2023
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In: Neurology and Therapy. - 2193-8253 .- 2193-6536. ; 12:6, s. 1937-1958
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Journal article (peer-reviewed)abstract
- Foslevodopa/foscarbidopa, a soluble formulation of levodopa/carbidopa (LD/CD) prodrugs for the treatment of Parkinson's disease (PD), is administered as a 24-hour/day continuous subcutaneous infusion (CSCI) with a single infusion site. The efficacy and safety of foslevodopa/foscarbidopa versus oral immediate-release LD/CD was previously demonstrated in patients with PD in a 12-week, randomized, double-blind, phase 3 trial (NCT04380142). We report the results of a separate 52-week, open-label, phase 3 registrational trial (NCT03781167) that evaluated the safety/tolerability and efficacy of 24-hour/day foslevodopa/foscarbidopa CSCI in patients with advanced PD.Male and female patients with levodopa-responsive PD and≥2.5hours of "Off" time/day received 24-hour/day foslevodopa/foscarbidopa CSCI at individually optimized therapeutic doses (approximately 700-4250mg of LD per 24hours) for 52weeks. The primary endpoint was safety/tolerability. Secondary endpoints included changes from baseline in normalized "Off" and "On" time, percentage of patients reporting morning akinesia, Movement Disorder Society Unified Parkinson's Disease Rating Scale (MDS-UPDRS), Parkinson's Disease Sleep Scale-2 (PDSS-2), 39-item Parkinson's Disease Questionnaire (PDQ-39), and EuroQol 5-dimension questionnaire (EQ-5D-5L).Of 244 enrolled patients, 107 discontinued, and 137 completed treatment. Infusion site events were the most common adverse events (AEs). AEs were mostly nonserious (25.8% of patients reported serious AEs) and mild/moderate in severity. At week 52, "On" time without troublesome dyskinesia and "Off" time were improved from baseline (mean [standard deviation (SD)] change in normalized "On" time without troublesome dyskinesia, 3.8 [3.3] hours; normalized "Off" time, -3.5 [3.1] hours). The percentage of patients experiencing morning akinesia dropped from 77.7% at baseline to 27.8% at week 52. Sleep quality (PDSS-2) and quality of life (PDQ-39 and EQ-5D-5L) also improved.Foslevodopa/foscarbidopa has the potential to provide a safe and efficacious, individualized, 24-hour/day, nonsurgical alternative for patients with PD.ClinicalTrials.gov identifier NCT03781167.
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| 4. |
- Baldwin, Scott A., et al.
(author)
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Intraclass correlation associated with therapists : estimates and applications in planning psychotherapy research
- 2011
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In: Cognitive Behaviour Therapy. - : Routledge, Taylor and Francis Group. - 1650-6073 .- 1651-2316. ; 40:1, s. 15-33
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Journal article (peer-reviewed)abstract
- It is essential that outcome research permit clear conclusions to be drawn about the efficacy of interventions. The common practice of nesting therapists within conditions can pose important methodological challenges that affect interpretation, particularly if the study is not powered to account for the nested design. An obstacle to the optimal design of these studies is the lack of data about the intraclass correlation coefficient (ICC), which measures the statistical dependencies introduced by nesting. To begin the development of a public database of ICC estimates, the authors investigated ICCs for a variety outcomes reported in 20 psychotherapy outcome studies. The magnitude of the 495 ICC estimates varied widely across measures and studies. The authors provide recommendations regarding how to select and aggregate ICC estimates for power calculations and show how researchers can use ICC estimates to choose the number of patients and therapists that will optimize power. Attention to these recommendations will strengthen the validity of inferences drawn from psychotherapy studies that nest therapists within conditions.
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| 5. |
- Chiang, Ivy Kim-Ni, et al.
(author)
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SoxF factors induce Notch1 expression via direct transcriptional regulation during early arterial development
- 2017
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In: Development. - : COMPANY OF BIOLOGISTS LTD. - 0950-1991 .- 1477-9129. ; 144:14, s. 2629-2639
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Journal article (peer-reviewed)abstract
- Arterial specification and differentiation are influenced by a number of regulatory pathways. While it is known that the Vegfa-Notch cascade plays a central role, the transcriptional hierarchy controlling arterial specification has not been fully delineated. To elucidate the direct transcriptional regulators of Notch receptor expression in arterial endothelial cells, we used histone signatures, DNaseI hypersensitivity and ChIP-seq data to identify enhancers for the human NOTCH1 and zebrafish notch1b genes. These enhancerswere able to direct arterial endothelial cell-restricted expression in transgenic models. Genetic disruption of SoxF binding sites established a clear requirement for members of this group of transcription factors (SOX7, SOX17 and SOX18) to drive the activity of these enhancers in vivo. Endogenous deletion of the notch1b enhancer led to a significant loss of arterial connections to the dorsal aorta in Notch pathway-deficient zebrafish. Loss of SoxF function revealed that these factors are necessary for NOTCH1 and notch1b enhancer activity and for correct endogenous transcription of these genes. These findings position SoxF transcription factors directly upstream of Notch receptor expression during the acquisition of arterial identity in vertebrates.
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| 6. |
- Grazioli, Véronique S, et al.
(author)
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Protective behavioral strategies and future drinking behaviors : effect of drinking intentions
- 2015
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In: Psychology of Addictive Behaviors. - : American Psychological Association (APA). - 0893-164X .- 1939-1501. ; 29:2, s. 355-364
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Journal article (peer-reviewed)abstract
- Alcohol use is common among United States and Swedish high school students and is related to negative consequences. Whereas drinking intentions are associated with future drinking behaviors, the use of protective behavioral strategies (PBS) is associated with decreased alcohol-related harm among young adults. The interactive effect of PBS and drinking intentions in predicting alcohol outcomes has not been examined. Further, because most PBS studies have been conducted among U.S. college students, PBS research among other populations is needed. The aims of this study were to evaluate longitudinally (a) the relationships between drinking intentions, PBS and alcohol outcomes, and (b) the moderating roles of drinking intentions and country in these relationships among United States and Swedish high school drinkers. Data were collected at baseline, 6- and 12-month follow-ups on 901 Swedish and 288 U.S. high school drinkers. Drinking intentions were associated with more alcohol use and consequences, and use of certain PBS was related to fewer alcohol-related consequences over time. Additionally, the negative prospective relationship between use of PBS and alcohol use, but not alcohol-related consequences, was moderated by intentions, such that the relationship was stronger among participants endorsing high drinking intentions. Country did not moderate these relationships. These results provide initial support for the generalizability of PBS college research to United States and Swedish high school students and suggest that interventions targeting the use of PBS may be most effective among high school drinkers endorsing high drinking intentions.
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| 7. |
- Indukuri, Rajitha
(author)
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Estrogen receptor beta transcriptional regulation: A potential mechanism for colon cancer prevention
- 2021
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Doctoral thesis (other academic/artistic)abstract
- Colorectal cancer (CRC) is the third leading cause of death from cancer in both men andwomen in the Western world. Improved screening efforts, surveillance, and treatment havereduced CRC mortality in older patients. However, the incidence is increasing in young adults,even in the absence of CRC family history. This may indicate an influence of increasingobesity, changed dietary patterns, and lifestyle factors. The progression of CRC is a multistepprocedure that takes 10-15 years, thus offering a time to implement preventative measures andearly detection. There is a critical need to develop more effective preventive therapies due tothe risks posed by current prevention therapies. The best CRC prophylactic agent should beboth safe and suitable to use for a long time (1).In preclinical studies, estrogen has been shown to protect from CRC, and substantial evidencesuggests it is through estrogen receptor beta (ERβ). Natural ERβ selective agonists have beentested in phase II clinical trials to treat menopause symptoms and proven to be safe and welltolerated with no side effects (2, 3). Thus, selective activation of ERβ with selective agonists,which do not activate estrogen receptor alpha (ERα), is a potential clinical approach inpreventing adenomatous polyps progression into CRC. However, the mechanism of thesebeneficial ERβ effects is not well understood, and there is a significant knowledge gap in thisarea.The overall aim of this thesis was to identify the mechanistic background of the intestinal ERβmediated antitumorigenic effects in the colon and further to explore ERβ as a preventativeapproach in CRC. One specific aim was to determine whether ERβ present specifically in colonepithelium is responsible for protecting from CRC, which is addressed in Paper I. Tounderstand the impact of ERβ in protecting from colitis-associated CRC (CA-CRC), we haveinduced colitis in intestinal-specific ERβ knockout mice of both sexes. The loss of intestinalERβ aggravated CA-CRC in a sex-dependent manner. The incidence of tumors increased inmales, while in females, the size of the tumors was enhanced. We identified that ERβ attenuatestumor necrosis factor alpha (TNFα) induced epithelial cell damage and modulates theregulation of key nuclear factor-κB (NFκB) members. As a direct consequence, ERβ was foundto reduce inflammation and to control intestinal crypt cell proliferation.Another aim was to explore transcriptional regulation by ERβ through mapping of chromatinbinding sites and interaction with NFκB, which is studied in Paper II and IV. Commonly usedERβ antibodies have been shown to be unspecific towards ERβ; this study used a validatedERβ antibody to map genome-wide ERβ binding sites in colon cancer cells. We observed thatthe presence of ERβ also modulated the regulatory chromatin mark H3K27AC in potentialenhancers of transcriptional regulation, Wnt signaling, and cell proliferation. Further, motifanalysis indicated a novel ERβ colon-specific cross-talk with TCF, and KLF motifs supporteda interaction between β-catenin/TCF and ERβ. We found that ERβ binds and regulates severalimportant tumor suppressors and oncogenes in CRC cells, such as CST5 and LRP6, consistentwith its proposed antitumorigenic activity. We also revealed the p65 cistrome in CRC cell lines and showed that ERβ alters the p65 chromatin binding in a cell-type-dependent manner. Wefound that ERβ chromatin binding sites were enriched among circadian clock genes and alsothat ERβ modulates p65 binding to core clock genes in CRC cells, indicating potential crosstalk between ERβ and circadian clock gene regulation.The final aim was to investigate the impact of ERβ, and estrogen signaling in high-fat diet(HFD) induced inflammation in colon, explored in paper III. We fed mice with an HFD for 13weeks and treated them with estrogenic ligands for the last three weeks prior to sacrifice. Thecolon transcriptome showed predominant sex differences, and selective activation of ERβreduced macrophage infiltration and epithelial cell proliferation induced by HFD. Wedemonstrated that ERβ opposes HFD-induced dysregulation of core circadian clock genes invivo, further strengthening the role of ERβ in circadian rhythm.Taken together, these results highlight the chemopreventive potential of ERβ in CRC in bothsexes. The identified cross-talk with TNFα/NFκB pathway, Wnt signaling, regulating genesinvolved circadian clock, and tumorigenesis reflected ERβ protection/antitumor activityagainst CRC progression and development (as illustrated in Figure 1).
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| 8. |
- Rouhimoghadam, Milad, et al.
(author)
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Tamoxifen-Induced Apoptosis of MCF-7 Cells via GPR30/PI3K/MAPKs Interactions : Verification by ODE Modeling and RNA Sequencing
- 2018
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In: Frontiers in Physiology. - : Frontiers Media S.A.. - 1664-042X. ; 9
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Journal article (peer-reviewed)abstract
- Tamoxifen (Nolvadex) is one of the most widely used and effective therapeutic agent for breast cancer. It benefits nearly 75% of patients with estrogen receptor (ER)-positive breast cancer that receive this drug. Its effectiveness is mainly attributed to its capacity to function as an ER antagonist, blocking estrogen binding sites on the receptor, and inhibiting the proliferative action of the receptor-hormone complex. Although, tamoxifen can induce apoptosis in breast cancer cells via upregulation of pro-apoptotic factors, it can also promote uterine hyperplasia in some women. Thus, tamoxifen as a multifunctional drug could have different effects on cells based on the utilization of effective concentrations or availability of specific co-factors. Evidence that tamoxifen functions as a GPR30 (G-Protein Coupled Receptor 30) agonist activating adenylyl cyclase and EGFR (Epidermal Growth Factor Receptor) intracellular signaling networks, provides yet another means of explaining the multi-functionality of tamoxifen. Here ordinary differential equation (ODE) modeling, RNA sequencing and real time qPCR analysis were utilized to establish the necessary data for gene network mapping of tamoxifen-stimulated MCF7 cells, which express the endogenous ER and GPR30. The gene set enrichment analysis and pathway analysis approaches were used to categorize transcriptionally upregulated genes in biological processes. Of the 2,713 genes that were significantly upregulated following a 48 h incubation with 250 mu M tamoxifen, most were categorized as either growth-related or pro-apoptotic intermediates that fit into the Tp53 and/or MAPK signaling pathways. Collectively, our results display that the effects of tamoxifen on the breast cancer MCF-7 cell line are mediated by the activation of important signaling pathways including Tp53 and MAPKs to induce apoptosis.
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| 9. |
- Thompson, Luke R., et al.
(author)
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A communal catalogue reveals Earth's multiscale microbial diversity
- 2017
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In: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 551:7681, s. 457-463
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Journal article (peer-reviewed)abstract
- © 2017 Macmillan Publishers Limited, part of Springer Nature. All rights reserved. Our growing awareness of the microbial world's importance and diversity contrasts starkly with our limited understanding of its fundamental structure. Despite recent advances in DNA sequencing, a lack of standardized protocols and common analytical frameworks impedes comparisons among studies, hindering the development of global inferences about microbial life on Earth. Here we present a meta-analysis of microbial community samples collected by hundreds of researchers for the Earth Microbiome Project. Coordinated protocols and new analytical methods, particularly the use of exact sequences instead of clustered operational taxonomic units, enable bacterial and archaeal ribosomal RNA gene sequences to be followed across multiple studies and allow us to explore patterns of diversity at an unprecedented scale. The result is both a reference database giving global context to DNA sequence data and a framework for incorporating data from future studies, fostering increasingly complete characterization of Earth's microbial diversity.
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| 10. |
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- 2019
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Journal article (peer-reviewed)
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