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Hubbard TJP, Aken BL, Beal K, Ballester B, Caccamo M, Chen Y, Clarke L, Coates G, Cunningham F, Cutts T, Down T, Dyer SC, Fitzgerald S, Fernandez-Banet J, Graf S, Haider S, Hammond M, Herrero J, Holland R, Howe K, Howe K, Johnson N, Kahari A, Keefe D, Kokocinski F, Kulesha E, Lawson D, Longden I, Melsopp C, Megy K, Meidl P, Ouverdin B, Parker A, Prlic A, Rice S, Rios D, Schuster M, Sealy I, Severin J, Slater G, Smedley D, Spudich G, Trevanion S, Vilella A, Vogel J, White S, Wood M, Cox T, Curwen V, Durbin R, Fernandez-Suarez XM, Flicek P, Kasprzyk A, Proctor G, Searle S, Smith J, Ureta-Vidal A, Birney E. Ensembl 2007. Nucleic Acids Res 2006; 35:D610-7. [PMID: 17148474 PMCID: PMC1761443 DOI: 10.1093/nar/gkl996] [Citation(s) in RCA: 657] [Impact Index Per Article: 34.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The Ensembl (http://www.ensembl.org/) project provides a comprehensive and integrated source of annotation of chordate genome sequences. Over the past year the number of genomes available from Ensembl has increased from 15 to 33, with the addition of sites for the mammalian genomes of elephant, rabbit, armadillo, tenrec, platypus, pig, cat, bush baby, common shrew, microbat and european hedgehog; the fish genomes of stickleback and medaka and the second example of the genomes of the sea squirt (Ciona savignyi) and the mosquito (Aedes aegypti). Some of the major features added during the year include the first complete gene sets for genomes with low-sequence coverage, the introduction of new strain variation data and the introduction of new orthology/paralog annotations based on gene trees.
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Research Support, Non-U.S. Gov't |
19 |
657 |
2
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Hubbard TJP, Aken BL, Ayling S, Ballester B, Beal K, Bragin E, Brent S, Chen Y, Clapham P, Clarke L, Coates G, Fairley S, Fitzgerald S, Fernandez-Banet J, Gordon L, Graf S, Haider S, Hammond M, Holland R, Howe K, Jenkinson A, Johnson N, Kahari A, Keefe D, Keenan S, Kinsella R, Kokocinski F, Kulesha E, Lawson D, Longden I, Megy K, Meidl P, Overduin B, Parker A, Pritchard B, Rios D, Schuster M, Slater G, Smedley D, Spooner W, Spudich G, Trevanion S, Vilella A, Vogel J, White S, Wilder S, Zadissa A, Birney E, Cunningham F, Curwen V, Durbin R, Fernandez-Suarez XM, Herrero J, Kasprzyk A, Proctor G, Smith J, Searle S, Flicek P. Ensembl 2009. Nucleic Acids Res 2008; 37:D690-7. [PMID: 19033362 PMCID: PMC2686571 DOI: 10.1093/nar/gkn828] [Citation(s) in RCA: 650] [Impact Index Per Article: 38.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The Ensembl project (http://www.ensembl.org) is a comprehensive genome information system featuring an integrated set of genome annotation, databases, and other information for chordate, selected model organism and disease vector genomes. As of release 51 (November 2008), Ensembl fully supports 45 species, and three additional species have preliminary support. New species in the past year include orangutan and six additional low coverage mammalian genomes. Major additions and improvements to Ensembl since our previous report include a major redesign of our website; generation of multiple genome alignments and ancestral sequences using the new Enredo-Pecan-Ortheus pipeline and development of our software infrastructure, particularly to support the Ensembl Genomes project (http://www.ensemblgenomes.org/).
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Research Support, Non-U.S. Gov't |
17 |
650 |
3
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Flicek P, Aken BL, Beal K, Ballester B, Caccamo M, Chen Y, Clarke L, Coates G, Cunningham F, Cutts T, Down T, Dyer SC, Eyre T, Fitzgerald S, Fernandez-Banet J, Gräf S, Haider S, Hammond M, Holland R, Howe KL, Howe K, Johnson N, Jenkinson A, Kähäri A, Keefe D, Kokocinski F, Kulesha E, Lawson D, Longden I, Megy K, Meidl P, Overduin B, Parker A, Pritchard B, Prlic A, Rice S, Rios D, Schuster M, Sealy I, Slater G, Smedley D, Spudich G, Trevanion S, Vilella AJ, Vogel J, White S, Wood M, Birney E, Cox T, Curwen V, Durbin R, Fernandez-Suarez XM, Herrero J, Hubbard TJP, Kasprzyk A, Proctor G, Smith J, Ureta-Vidal A, Searle S. Ensembl 2008. Nucleic Acids Res 2007; 36:D707-14. [PMID: 18000006 PMCID: PMC2238821 DOI: 10.1093/nar/gkm988] [Citation(s) in RCA: 371] [Impact Index Per Article: 20.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
The Ensembl project (http://www.ensembl.org) is a comprehensive genome information system featuring an integrated set of genome annotation, databases and other information for chordate and selected model organism and disease vector genomes. As of release 47 (October 2007), Ensembl fully supports 35 species, with preliminary support for six additional species. New species in the past year include platypus and horse. Major additions and improvements to Ensembl since our previous report include extensive support for functional genomics data in the form of a specialized functional genomics database, genome-wide maps of protein–DNA interactions and the Ensembl regulatory build; support for customization of the Ensembl web interface through the addition of user accounts and user groups; and increased support for genome resequencing. We have also introduced new comparative genomics-based data mining options and report on the continued development of our software infrastructure.
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Research Support, Non-U.S. Gov't |
18 |
371 |
4
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Haider S, Knöfler M. Human tumour necrosis factor: physiological and pathological roles in placenta and endometrium. Placenta 2008; 30:111-23. [PMID: 19027157 DOI: 10.1016/j.placenta.2008.10.012] [Citation(s) in RCA: 241] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/28/2008] [Revised: 10/10/2008] [Accepted: 10/16/2008] [Indexed: 12/20/2022]
Abstract
The cytokine tumour necrosis factor alpha (TNF) is a well known member of the TNF superfamily consisting of at least 18 ligands and 29 different receptors involved in numerous cellular processes. TNF signals through two distinct receptors TNFR1 and TNFR2 thereby controlling expression of cytokines, immune receptors, proteases, growth factors and cell cycle genes which in turn regulate inflammation, survival, apoptosis, cell migration, proliferation and differentiation. Since expression of TNF was discovered in amnion and placenta many studies demonstrated the presence of the cytokine and its receptors in the diverse human reproductive tissues. Whereas TNF has been implicated in ovulation, corpus luteum formation and luteolysis, this review focuses on the functions of TNF in human placental, endometrial and decidual cell types of normal tissues and also discusses its role in endometrial and gestational diseases. Physiological levels of the cytokine could be important for balancing cell fusion and apoptotic shedding of villous trophoblasts and to limit trophoblast invasion into maternal decidua. Regulation of the TNF/TNFR system by steroid hormones also suggests a role in uterine function including menstrual cycle-dependent destruction and regeneration of endometrial tissue. Aberrant levels of TNF, however, are associated with diverse reproductive diseases such as amniotic infections, recurrent spontaneous abortions, preeclampsia, preterm labour or endometriosis. Hence, concentrations, receptor distribution and length of stimulation determine whether TNF has beneficial or adverse effects on female reproduction and pregnancy.
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Review |
17 |
241 |
5
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Wiegand PN, Nathwani D, Wilcox MH, Stephens J, Shelbaya A, Haider S. Clinical and economic burden of Clostridium difficile infection in Europe: a systematic review of healthcare-facility-acquired infection. J Hosp Infect 2012; 81:1-14. [PMID: 22498638 DOI: 10.1016/j.jhin.2012.02.004] [Citation(s) in RCA: 227] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2011] [Accepted: 02/07/2012] [Indexed: 10/28/2022]
Abstract
PubMed, EMBASE and conference abstracts were reviewed systematically to determine the clinical and economic burden associated with Clostridium difficile infection (CDI) acquired and treated in European healthcare facilities. Inclusion criteria were: published in the English language between 2000 and 2010, and study population of at least 20 patients with documented CDI acquired/treated in European healthcare facilities. Data collection was completed by three unblinded reviewers using the Cochrane Handbook and PRISMA statement. The primary outcomes were mortality, recurrence, length of hospital stay (LOS) and cost related to CDI. In total, 1138 primary articles and conference abstracts were identified, and this was narrowed to 39 and 30 studies, respectively. Data were available from 14 countries, with 47% of studies from UK institutions. CDI mortality at 30 days ranged from 2% (France) to 42% (UK). Mortality rates more than doubled from 1999 to 2004, and continued to rise until 2007 when reductions were noted in the UK. Recurrent CDI varied from 1% (France) to 36% (Ireland); however, recurrence definitions varied between studies. Median LOS ranged from eight days (Belgium) to 27 days (UK). The incremental cost of CDI was £4577 in Ireland and £8843 in Germany, after standardization to 2010 prices. Country-specific estimates, weighted by sample size, ranged from 2.8% to 29.8% for 30-day mortality and from 16 to 37 days for LOS. CDI burden in Europe was most commonly described using 30-day mortality, recurrence, LOS and cost data. The continued spread of CDI and resultant healthcare burden underscores the need for judicious use of antibiotics.
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Systematic Review |
13 |
227 |
6
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Choudhry H, Albukhari A, Morotti M, Haider S, Moralli D, Smythies J, Schödel J, Green CM, Camps C, Buffa F, Ratcliffe P, Ragoussis J, Harris AL, Mole DR. Tumor hypoxia induces nuclear paraspeckle formation through HIF-2α dependent transcriptional activation of NEAT1 leading to cancer cell survival. Oncogene 2015; 34:4482-90. [PMID: 25417700 PMCID: PMC4430310 DOI: 10.1038/onc.2014.378] [Citation(s) in RCA: 184] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2014] [Revised: 09/29/2014] [Accepted: 10/10/2014] [Indexed: 12/18/2022]
Abstract
Activation of cellular transcriptional responses, mediated by hypoxia-inducible factor (HIF), is common in many types of cancer, and generally confers a poor prognosis. Known to induce many hundreds of protein-coding genes, HIF has also recently been shown to be a key regulator of the non-coding transcriptional response. Here, we show that NEAT1 long non-coding RNA (lncRNA) is a direct transcriptional target of HIF in many breast cancer cell lines and in solid tumors. Unlike previously described lncRNAs, NEAT1 is regulated principally by HIF-2 rather than by HIF-1. NEAT1 is a nuclear lncRNA that is an essential structural component of paraspeckles and the hypoxic induction of NEAT1 induces paraspeckle formation in a manner that is dependent upon both NEAT1 and on HIF-2. Paraspeckles are multifunction nuclear structures that sequester transcriptionally active proteins as well as RNA transcripts that have been subjected to adenosine-to-inosine (A-to-I) editing. We show that the nuclear retention of one such transcript, F11R (also known as junctional adhesion molecule 1, JAM1), in hypoxia is dependent upon the hypoxic increase in NEAT1, thereby conferring a novel mechanism of HIF-dependent gene regulation. Induction of NEAT1 in hypoxia also leads to accelerated cellular proliferation, improved clonogenic survival and reduced apoptosis, all of which are hallmarks of increased tumorigenesis. Furthermore, in patients with breast cancer, high tumor NEAT1 expression correlates with poor survival. Taken together, these results indicate a new role for HIF transcriptional pathways in the regulation of nuclear structure and that this contributes to the pro-tumorigenic hypoxia-phenotype in breast cancer.
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research-article |
10 |
184 |
7
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da Motta LL, Ledaki I, Purshouse K, Haider S, De Bastiani MA, Baban D, Morotti M, Steers G, Wigfield S, Bridges E, Li JL, Knapp S, Ebner D, Klamt F, Harris AL, McIntyre A. The BET inhibitor JQ1 selectively impairs tumour response to hypoxia and downregulates CA9 and angiogenesis in triple negative breast cancer. Oncogene 2017; 36:122-132. [PMID: 27292261 PMCID: PMC5061082 DOI: 10.1038/onc.2016.184] [Citation(s) in RCA: 117] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2015] [Revised: 03/22/2016] [Accepted: 04/15/2016] [Indexed: 12/16/2022]
Abstract
The availability of bromodomain and extra-terminal inhibitors (BETi) has enabled translational epigenetic studies in cancer. BET proteins regulate transcription by selectively recognizing acetylated lysine residues on chromatin. BETi compete with this process leading to both downregulation and upregulation of gene expression. Hypoxia enables progression of triple negative breast cancer (TNBC), the most aggressive form of breast cancer, partly by driving metabolic adaptation, angiogenesis and metastasis through upregulation of hypoxia-regulated genes (for example, carbonic anhydrase 9 (CA9) and vascular endothelial growth factor A (VEGF-A). Responses to hypoxia can be mediated epigenetically, thus we investigated whether BETi JQ1 could impair the TNBC response induced by hypoxia and exert anti-tumour effects. JQ1 significantly modulated 44% of hypoxia-induced genes, of which two-thirds were downregulated including CA9 and VEGF-A. JQ1 prevented HIF binding to the hypoxia response element in CA9 promoter, but did not alter HIF expression or activity, suggesting some HIF targets are BET-dependent. JQ1 reduced TNBC growth in vitro and in vivo and inhibited xenograft vascularization. These findings identify that BETi dually targets angiogenesis and the hypoxic response, an effective combination at reducing tumour growth in preclinical studies.
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research-article |
8 |
117 |
8
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Dryden M, Baguneid M, Eckmann C, Corman S, Stephens J, Solem C, Li J, Charbonneau C, Baillon-Plot N, Haider S. Pathophysiology and burden of infection in patients with diabetes mellitus and peripheral vascular disease: focus on skin and soft-tissue infections. Clin Microbiol Infect 2015. [PMID: 26198368 DOI: 10.1016/j.cmi.2015.03.024] [Citation(s) in RCA: 96] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Diabetes mellitus affects 284 million adults worldwide and is increasing in prevalence. Accelerated atherosclerosis in patients with diabetes mellitus contributes an increased risk of developing cardiovascular diseases including peripheral vascular disease (PVD). Immune dysfunction, diabetic neuropathy and poor circulation in patients with diabetes mellitus, especially those with PVD, place these patients at high risk for many types of typical and atypical infections. Complicated skin and soft-tissue infections (cSSTIs) are of particular concern because skin breakdown in patients with advanced diabetes mellitus and PVD provides a portal of entry for bacteria. Patients with diabetes mellitus are more likely to be hospitalized with cSSTIs and to experience related complications than patients without diabetes mellitus. Patients with PVD requiring lower extremity bypass are also at high risk of surgical site and graft infections. Methicillin-resistant Staphylococcus aureus (MRSA) is a frequent causative pathogen in cSSTIs, and may be a significant contributor to surgical site infections, especially in patients who are colonized with MRSA on hospital admission. Patients with cSSTIs and diabetes mellitus or PVD experience lower clinical success rates than patients without these comorbidities, and may also have a longer length of hospital stay and higher risk of adverse drug events. Clinicians should be vigilant in recognizing the potential for infection with multi-drug-resistant organisms, especially MRSA, in these populations and initiating therapy with appropriate antibiotics.
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Review |
10 |
96 |
9
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Drgona L, Khachatryan A, Stephens J, Charbonneau C, Kantecki M, Haider S, Barnes R. Clinical and economic burden of invasive fungal diseases in Europe: focus on pre-emptive and empirical treatment of Aspergillus and Candida species. Eur J Clin Microbiol Infect Dis 2014; 33:7-21. [PMID: 24026863 PMCID: PMC3892112 DOI: 10.1007/s10096-013-1944-3] [Citation(s) in RCA: 93] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2013] [Accepted: 07/29/2013] [Indexed: 11/23/2022]
Abstract
Invasive fungal diseases (IFDs) have been widely studied in recent years, largely because of the increasing population at risk. Aspergillus and Candida species remain the most common causes of IFDs, but other fungi are emerging. The early and accurate diagnosis of IFD is critical to outcome and the optimisation of treatment. Rapid diagnostic methods and new antifungal therapies have advanced disease management in recent years. Strategies for the prevention and treatment of IFDs include prophylaxis, and empirical and pre-emptive therapy. Here, we review the available primary literature on the clinical and economic burden of IFDs in Europe from 2000 to early 2011, with a focus on the value and outcomes of different approaches.
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Review |
11 |
93 |
10
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Choudhry H, Albukhari A, Morotti M, Haider S, Moralli D, Smythies J, Schödel J, Green CM, Camps C, Buffa F, Ratcliffe P, Ragoussis J, Harris AL, Mole DR. Tumor hypoxia induces nuclear paraspeckle formation through HIF-2α dependent transcriptional activation of NEAT1 leading to cancer cell survival. Oncogene 2015; 34:4546. [PMID: 26289678 PMCID: PMC7609283 DOI: 10.1038/onc.2014.431] [Citation(s) in RCA: 86] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Correction to: Oncogene (2015) 34, 4482–4490; doi:10.1038/onc.2014.378; published online 24 November 2014. Following the online publication of this article, the authors have noticed a misspelt surname: S Hider should read S Haider. There is also an addition to the acknowledgements to read ‘This study makes use of data generated by the Molecular Taxonomy of Breast Cancer International Consortium, which was funded by Cancer Research UK and the British Columbia Cancer Agency Branch’. The corrected article appears in this issue. The authors would like to apologise for any inconvenience this may cause.
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Published Erratum |
10 |
86 |
11
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Cappello P, Blaser H, Gorrini C, Lin DCC, Elia AJ, Wakeham A, Haider S, Boutros PC, Mason JM, Miller NA, Youngson B, Done SJ, Mak TW. Role of Nek2 on centrosome duplication and aneuploidy in breast cancer cells. Oncogene 2013; 33:2375-84. [PMID: 23708664 DOI: 10.1038/onc.2013.183] [Citation(s) in RCA: 80] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2012] [Revised: 04/04/2013] [Accepted: 04/04/2013] [Indexed: 11/09/2022]
Abstract
Breast cancer is the most common solid tumor and the second most common cause of death in women. Despite a large body of literature and progress in breast cancer research, many molecular aspects of this complex disease are still poorly understood, hindering the design of specific and effective therapeutic strategies. To identify the molecules important in breast cancer progression and metastasis, we tested the in vivo effects of inhibiting the functions of various kinases and genes involved in the regulation/modulation of the cytoskeleton by downregulating them in mouse PyMT mammary tumor cells and human breast cancer cell lines. These kinases and cytoskeletal regulators were selected based on their prognostic values for breast cancer patient survival. PyMT tumor cells, in which a selected gene was stably knocked down were injected into the tail veins of mice, and the formation of tumors in the lungs was monitored. One of the several genes found to be important for tumor growth in the lungs was NIMA-related kinases 2 (Nek2), a cell cycle-related protein kinase. Furthermore, Nek2 was also important for tumor growth in the mammary fat pad. In various human breast cancer cell lines, Nek2 knockdown induced aneuploidy and cell cycle arrest that led to cell death. Significantly, the breast cancer cell line most sensitive to Nek2 depletion was of the triple negative breast cancer subtype. Our data indicate that Nek2 has a pivotal role in breast cancer growth at primary and secondary sites, and thus may be an attractive and novel therapeutic target for this disease.
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Research Support, Non-U.S. Gov't |
12 |
80 |
12
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Dorner TE, Luger E, Tschinderle J, Stein KV, Haider S, Kapan A, Lackinger C, Schindler KE. Association between nutritional status (MNA®-SF) and frailty (SHARE-FI) in acute hospitalised elderly patients. J Nutr Health Aging 2014; 18:264-9. [PMID: 24626753 DOI: 10.1007/s12603-013-0406-z] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
OBJECTIVE This study aimed to explore the association between the impaired nutritional status and frailty in acute hospitalised elderly patients by using two tools, the MNA®-SF (Mini Nutritional Assessment® short-form) and the SHARE-FI (Frailty Instrument for Primary Care of the Survey of Health, Ageing and Retirement in Europe). DESIGN Cross-sectional study. SETTING Acute hospitalised, community-dwelling elderly patients were recruited at internal medicine wards in Vienna, Austria. PARTICIPANTS 133 men (39%) and women (61%) aged 74 (65-97) years. MEASUREMENTS MNA®-SF was used to investigate malnutrition (<7 points) and patients at risk of malnutrition (8 to 11 points). By using the SHARE-FI, subjects were classified as frail, pre-frail or robust. A factor analysis was applied to identify overlaps between the MNA®-SF and SHARE-FI items. Internal consistency of different dimensions was assessed by using Cronbach's Alpha. RESULTS Malnutrition or risk of malnutrition was found in 76.7% of the total sample and in 46.8% of robust, in 69.0% of pre-frail, and in 93.0% of frail participants. Frailty or prefrailty was found in 75.9% of the total sample and in 45.1% of the subjects with no risk of malnutrition, in 80.9% of subjects at risk of malnutrition, and in 94.1% of malnourished patients. The two used tools show overlaps in three dimensions: (1) nutrition problems, (2) mobility problems and (3) anthropometric items with a moderate to strong internal consistency (Cronbach's Alpha of 0.670, 0.834 and 0.946, respectively). 64.7% of the total sample (79.5% of frail and 87.9% of malnourished subjects) would participate in a home-based muscle training and nutritional intervention program. CONCLUSIONS This study underlines the association and the overlap between frailty and impaired nutritional status. There is a high readiness to participate in a program to tackle the problems associated with malnutrition and frailty, especially in those, who would benefit most from it.
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11 |
72 |
13
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Mihmanli I, Besirli K, Kurugoglu S, Atakir K, Haider S, Ogut G, Numan F, Canturk E, Sayin AG. Cephalic vein and hemodialysis fistula: surgeon's observation versus color Doppler ultrasonographic findings. JOURNAL OF ULTRASOUND IN MEDICINE : OFFICIAL JOURNAL OF THE AMERICAN INSTITUTE OF ULTRASOUND IN MEDICINE 2001; 20:217-222. [PMID: 11270525 DOI: 10.7863/jum.2001.20.3.217] [Citation(s) in RCA: 71] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
The aim of this study was to evaluate whether preoperative color Doppler ultrasonography improves immediate success rates of arteriovenous fistulas for dialysis. One hundred twenty-four patients with chronic renal failure underwent color Doppler ultrasonographic examination of both arms, including the cephalic vein, before arteriovenous fistula construction. Patients were randomly divided into 2 groups: A and B. In group A, there were 52 patients, and the surgeon planned to construct arteriovenous fistulas depending only on physical examination. In group B, which comprised 72 patients, surgeons performed arteriovenous fistula construction on sites labeled by color Doppler ultrasonography. In group A, of 52 patients who had surgery for arteriovenous fistula construction, 13 had fistulas that did not function. Among these 13 patients, 8 were found to have chronic thrombotic changes in the cephalic vein on color Doppler ultrasonography, and 5 had none of these changes. When we checked the color Doppler ultrasonographic findings, we noted that these 5 patients had decreased volume flow in the radial artery. On the whole, the arteriovenous fistulas worked in 39 patients (75%) and did not function in 13 patients (25%). In group B, surgeons followed the color Doppler ultrasonographic results. Of 72 patients who underwent the procedure, 68 patients (94.4%) had functioning fistulas, whereas 4 (5.6%) had fistulas that did not work. These 4 patients were found to have low volume flow in the radial artery. When both groups were compared by chi2 analysis, the difference was statistically significant (P = .002). Group B, in which patients were preoperatively evaluated by color Doppler ultrasonography, had a high success rate. We found that color Doppler ultrasonography is very helpful as a noninvasive procedure for this evaluation. Although many surgical clinics still perform arteriovenous fistula construction without the aid of color Doppler ultrasonographic findings, we think that the use of color Doppler ultrasonography should be emphasized before surgeons proceed with arteriovenous fistula construction.
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Clinical Trial |
24 |
71 |
14
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Prutsch N, Fock V, Haslinger P, Haider S, Fiala C, Pollheimer J, Knöfler M. The role of interleukin-1β in human trophoblast motility. Placenta 2012; 33:696-703. [PMID: 22710193 PMCID: PMC3432868 DOI: 10.1016/j.placenta.2012.05.008] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/29/2012] [Revised: 05/10/2012] [Accepted: 05/21/2012] [Indexed: 02/07/2023]
Abstract
The pleiotropic cytokine interleukin-1β (IL-1β) can promote physiological cell migration, as well as cancer cell invasion and metastasis. Its role in human trophoblast invasion, however, has not been satisfactorily answered since direct, indirect as well as no effects on trophoblast motility have been published. Therefore, the role of IL-1β has been re-evaluated by exclusively using human primary trophoblast model systems. Immunofluorescence of first trimester placentae indicated IL-1 receptor 1 (IL-1R1) protein expression in first trimester villous cytotrophoblasts (vCTB) and extravillous trophoblasts (EVT). The latter expressed higher mRNA levels of the receptor as shown by comparative gene chip data of vCTB and EVT. Similarly, Western blot analyses and immunofluorescence revealed a time- and differentiation-dependent increase of IL-1R1 in primary EVT seeded on fibronectin. IL-1β dose-dependently elevated migration of isolated first trimester EVT through fibronectin-coated transwells, which was inhibited in the presence of IL-1R antagonist (IL-1Ra), whereas proliferation of these cells was not affected. Similarly, the interleukin did not alter proliferation of vCTB and cell column trophoblasts in floating villi of early pregnancy, but promoted migration in villous explant cultures seeded on collagen I. Western blot analyses of supernatants of primary EVT and first trimester villous explant cultures revealed IL-1β induced secretion of urokinase plasminogen activator (uPA), plasminogen activator inhibitor (PAI)-1 and PAI-2, which was diminished upon combined IL-1β/IL-1Ra treatment. In conclusion, these data suggest that IL-1β directly promotes trophoblast motility of first trimester EVT involving the uPA/PAI system.
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Research Support, Non-U.S. Gov't |
13 |
70 |
15
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Haider S, Hrbek A, Xu Y. Magneto-acousto-electrical tomography: a potential method for imaging current density and electrical impedance. Physiol Meas 2008; 29:S41-50. [DOI: 10.1088/0967-3334/29/6/s04] [Citation(s) in RCA: 64] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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17 |
64 |
16
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Leisser C, Saleh L, Haider S, Husslein H, Sonderegger S, Knöfler M. Tumour necrosis factor-alpha impairs chorionic gonadotrophin beta-subunit expression and cell fusion of human villous cytotrophoblast. Mol Hum Reprod 2006; 12:601-9. [PMID: 16896069 DOI: 10.1093/molehr/gal066] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Growth factors expressed at the fetal-maternal interface modulate hormone expression of placental trophoblasts. The aim of this study was to investigate the effects of different cytokines on hCG subunit mRNA expression in differentiating villous cytotrophoblasts. Quantitative real-time PCR revealed a 1.8- and 6.9-fold increase of hCG-alpha and hCG-beta mRNA levels, respectively, between 36 and 60 h of term trophoblast syncytialization. Compared with controls, neither interleukin (IL)-1beta, IL-2, IL-4, IL-6, IL-10, IL-13 and IL-15 nor tumour necrosis factor (TNF)-alpha significantly altered hCG-alpha mRNA expression. Similarly, the ILs did not affect hCG-beta transcript levels. In contrast, TNF-alpha suppressed hCG-beta mRNA 3.8- and 1.8-fold at 36 and 60 h of term trophoblast differentiation. Accordingly, hCG secretion was impaired by TNF-alpha but not by the different ILs. Moreover, TNF-alpha reduced luciferase expression of reporter plasmids harbouring the proximal hCG-beta5 promoter to 35 and 77%, respectively, in primary term trophoblasts and trophoblastic SHGPL-5 cells. In addition, counting of nuclei in syncytialized, desmoplakin-negative areas revealed a 1.9-fold reduction of term trophoblast fusion in the presence of TNF-alpha. Similarly, floating explant cultures prepared from first trimester-denuded villi recovered the syncytium 2.8-fold less efficiently during 72 h of cytokine treatment. Concomitantly, TNF-alpha impaired induction of endogenous and secreted hCG-beta protein levels in these cultures. The data suggest that TNF-alpha decreases hCG-beta mRNA and protein expression by reducing gene transcription and trophoblast cell fusion. Suppression of these processes by TNF-alpha could partly explain the adverse effects of the cytokine on placental function and pregnancy outcome.
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Journal Article |
19 |
60 |
17
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Majkut J, Sgobba M, Holohan C, Crawford N, Logan AE, Kerr E, Higgins CA, Redmond KL, Riley JS, Stasik I, Fennell DA, Van Schaeybroeck S, Haider S, Johnston PG, Haigh D, Longley DB. Differential affinity of FLIP and procaspase 8 for FADD's DED binding surfaces regulates DISC assembly. Nat Commun 2014; 5:3350. [PMID: 24577104 PMCID: PMC3942653 DOI: 10.1038/ncomms4350] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2013] [Accepted: 01/30/2014] [Indexed: 01/05/2023] Open
Abstract
Death receptor activation triggers recruitment of FADD, which via its death effector domain (DED) engages the DEDs of procaspase 8 and its inhibitor FLIP to form death-inducing signalling complexes (DISCs). The DEDs of FADD, FLIP and procaspase 8 interact with one another using two binding surfaces defined by α1/α4 and α2/α5 helices, respectively. Here we report that FLIP has preferential affinity for the α1/α4 surface of FADD, whereas procaspase 8 has preferential affinity for FADD's α2/α5 surface. These relative affinities contribute to FLIP being recruited to the DISC at comparable levels to procaspase 8 despite lower cellular expression. Additional studies, including assessment of DISC stoichiometry and functional assays, suggest that following death receptor recruitment, the FADD DED preferentially engages FLIP using its α1/α4 surface and procaspase 8 using its α2/α5 surface; these tripartite intermediates then interact via the α1/α4 surface of FLIP DED1 and the α2/α5 surface of procaspase 8 DED2.
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research-article |
11 |
59 |
18
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52 |
55 |
19
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Ahmad N, Haider S, Jagannathan S, Anaissie E, Driscoll JJ. MicroRNA theragnostics for the clinical management of multiple myeloma. Leukemia 2013; 28:732-8. [PMID: 24714346 DOI: 10.1038/leu.2013.262] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2013] [Accepted: 08/27/2013] [Indexed: 02/07/2023]
Abstract
Theragnostics represent cutting-edge, multi-disciplinary strategies that combine diagnostics with therapeutics in order to generate personalized therapies that improve patient outcome. In oncology, the approach is aimed at more accurate diagnosis of cancer, optimization of patient selection to identify those most likely to benefit from a specific therapy and to generate effective therapeutics that enhance patient survival. MicroRNAs (miRNAs) are master regulators of the human genome that orchestrate myriad cellular pathways to control growth during physiologic and pathologic conditions. Compelling evidence shows that miRNA deregulation promotes events linked to tumor initiation, metastasis and drug resistance as seen in multiple myeloma (MM), an invariably fatal hematologic malignancy. miRNAs are readily detected in body fluids, for example, serum, plasma, urine, as well as circulating tumor cells to demonstrate their potential as readily accessible, non-invasive diagnostic and prognostic biomarkers and potential therapeutics. Specific miRNAs are aberrantly expressed early in myelomagenesis and may more readily detect high-risk disease than current methods. Although only recently discovered miRNAs have rapidly advanced from preclinical studies to evaluation in human clinical trials. The development of miRNA theragnostics should provide widely applicable tools for the targeted delivery of personalized medicines to improve the outcome of patients with MM.
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Review |
12 |
54 |
20
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Raza A, Charagh S, Abbas S, Hassan MU, Saeed F, Haider S, Sharif R, Anand A, Corpas FJ, Jin W, Varshney RK. Assessment of proline function in higher plants under extreme temperatures. PLANT BIOLOGY (STUTTGART, GERMANY) 2023; 25:379-395. [PMID: 36748909 DOI: 10.1111/plb.13510] [Citation(s) in RCA: 53] [Impact Index Per Article: 26.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2023] [Accepted: 01/30/2023] [Indexed: 06/18/2023]
Abstract
Climate change and abiotic stress factors are key players in crop losses worldwide. Among which, extreme temperatures (heat and cold) disturb plant growth and development, reduce productivity and, in severe cases, lead to plant death. Plants have developed numerous strategies to mitigate the detrimental impact of temperature stress. Exposure to stress leads to the accumulation of various metabolites, e.g. sugars, sugar alcohols, organic acids and amino acids. Plants accumulate the amino acid 'proline' in response to several abiotic stresses, including temperature stress. Proline abundance may result from de novo synthesis, hydrolysis of proteins, reduced utilization or degradation. Proline also leads to stress tolerance by maintaining the osmotic balance (still controversial), cell turgidity and indirectly modulating metabolism of reactive oxygen species. Furthermore, the crosstalk of proline with other osmoprotectants and signalling molecules, e.g. glycine betaine, abscisic acid, nitric oxide, hydrogen sulfide, soluble sugars, helps to strengthen protective mechanisms in stressful environments. Development of less temperature-responsive cultivars can be achieved by manipulating the biosynthesis of proline through genetic engineering. This review presents an overview of plant responses to extreme temperatures and an outline of proline metabolism under such temperatures. The exogenous application of proline as a protective molecule under extreme temperatures is also presented. Proline crosstalk and interaction with other molecules is also discussed. Finally, the potential of genetic engineering of proline-related genes is explained to develop 'temperature-smart' plants. In short, exogenous application of proline and genetic engineering of proline genes promise ways forward for developing 'temperature-smart' future crop plants.
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Review |
2 |
53 |
21
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Haider S, Nafziger D, Gutierrez JA, Brar I, Mateo N, Fogle J. Progressive multifocal leukoencephalopathy and idiopathic CD4+lymphocytopenia: a case report and review of reported cases. Clin Infect Dis 2000; 31:E20-2. [PMID: 11049808 DOI: 10.1086/318120] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
Abstract
Progressive multifocal leukoencephalopathy (PML) is a well recognized demyelinating neurological disorder caused by JC virus. Idiopathic CD4(+) lymphocytopenia (ICL) is a syndrome first described by the Centers for Disease Control and Prevention as a CD4(+) count <300 cells/mm(3) or a CD4(+) count that is <20% of the total T cell count on 2 occasions, with no evidence of human immunodeficiency virus (HIV) infection on testing, and absence of any defined immunodeficiency or therapy that depresses the levels of CD4(+) T cells. To the best of our knowledge, this is the third reported case of PML and ICL, and also the first reported case of the use of cidofovir to treat PML in a patient not infected with human immunodeficiency virus.
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Case Reports |
25 |
52 |
22
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Upadhyaya N, Haider S. Germinal vesicle breakdown in oocytes of catfish, Mystus vittatus (Bloch): relative in vitro effectiveness of estradiol-17 beta, androgens, corticosteroids, progesterone, and other pregnene derivatives. Gen Comp Endocrinol 1986; 63:70-6. [PMID: 3770447 DOI: 10.1016/0016-6480(86)90183-8] [Citation(s) in RCA: 50] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
The relative in vitro effectiveness of estradiol-17 beta, androgen, corticosteroids, progesterone, and other pregnene derivatives on germinal vesicle breakdown (GVBD) using folliculated oocytes of an Indian catfish Mystus vittatus was investigated. 17 alpha,20 beta-Dihydroxyprogesterone was found to be the most effective maturation-inducing steroid (MIS). Estradiol-17 beta and testosterone were not effective but androsterone was found to be fairly effective in final oocyte maturation. Deoxycorticosterone (DOC), hydrocortisone, progesterone, and 17 alpha-hydroxyprogesterone were also effective at their higher concentrations. Among 5 beta-reduced pregnenes, all but 5 beta-pregnene-3 alpha-ol-20-one could induce oocyte maturation. The significance of these findings in relation to the progestagens as natural MIS and the present controversial position of another Indian catfish Heteropneustes fossilis is discussed in the light of available literature.
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39 |
50 |
23
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Vujic A, Robinson EL, Ito M, Haider S, Ackers-Johnson M, See K, Methner C, Figg N, Brien P, Roderick HL, Skepper J, A Ferguson-Smith, Foo RS. Experimental heart failure modelled by the cardiomyocyte-specific loss of an epigenome modifier, DNMT3B. J Mol Cell Cardiol 2015; 82:174-83. [PMID: 25784084 DOI: 10.1016/j.yjmcc.2015.03.007] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/08/2014] [Revised: 03/06/2015] [Accepted: 03/09/2015] [Indexed: 12/18/2022]
Abstract
Differential DNA methylation exists in the epigenome of end-stage failing human hearts but whether it contributes to disease progression is presently unknown. Here, we report that cardiac specific deletion of Dnmt3b, the predominant DNA methyltransferase in adult mouse hearts, leads to an accelerated progression to severe systolic insufficiency and myocardial thinning without a preceding hypertrophic response. This was accompanied by widespread myocardial interstitial fibrosis and myo-sarcomeric disarray. By targeted candidate gene quantitative RT-PCR, we discovered an over-activity of cryptic splice sites in the sarcomeric gene Myh7, resulting in a transcript with 8 exons missing. Moreover, a region of differential methylation overlies the splice site locus in the hearts of the cardiac-specific conditional knockout (CKO) mice. Although abundant and complex forms of alternative splice variants have been reported in diseased hearts and the contribution of each remains to be understood in further detail, our results demonstrate for the first time that a link may exist between alternative splicing and the cardiac epigenome. In particular, this gives the novel evidence whereby the loss of an epigenome modifier promotes the development and progression of heart disease.
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10 |
45 |
24
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Abstract
Rats fed on a restricted feeding (RF) schedule of 4 h day-1 to produce a 15-20% reduction in body weight were killed before (starved) and after (fed) the presentation of food on the sixth day to compare 5-hydroxytryptamine (5-HT; serotonin) metabolism and synthesis rate in the hypothalamus with freely feeding (FF) controls. The RF rats showed lower 5-HT concentration and synthesis rate than FF controls. Restricted feeding did not decrease tryptophan concentration in the hypothalamus. However, RF-fed rats had lower tryptophan concentration than RF starved rats. 5-HIAA concentration was comparable in RF fed rats and FF controls but higher in RF starved rats. Possible implications of the findings in the pathogenesis of the food deprivation/starvation-related disease anorexia nervosa are discussed.
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29 |
42 |
25
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Kapan A, Stefanac S, Sandner I, Haider S, Grabovac I, Dorner T. Use of Electronic Cigarettes in European Populations: A Narrative Review. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2020; 17:E1971. [PMID: 32192139 PMCID: PMC7142603 DOI: 10.3390/ijerph17061971] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Revised: 03/10/2020] [Accepted: 03/12/2020] [Indexed: 12/28/2022]
Abstract
The increasing popularity of electronic cigarettes in past decades has aroused public health concern. This study aims to review the literature on the prevalence of e-cigarette use among the general adult and young populations in Europe. We searched Medline and Google Scholar from September 2019, and included "prevalence of e-cigarettes", "electronic cigarettes" or "e-cigarettes", and "electronic nicotine delivery system" or "vaping". The prevalence of current e-cigarette use ranged from 0.2% to 27%, ever-use ranged from 5.5% to 56.6% and daily use ranged from 1% to 2.9%. Current smokers of conventional cigarettes showed the highest prevalence for the use of e-cigarettes, ranging from 20.4% to 83.1%, followed by ex-smokers, with ranges from 7% to 15%. The following socio-demographic factors were associated with a higher chance of using e-cigarettes: male sex and younger age groups; results for economic status were inconclusive. In European countries, there is a higher prevalence of e-cigarette use among males, adolescents and young adults, smokers of conventional cigarettes, and former smokers.
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Review |
5 |
40 |