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Alessandra Livigni, Laura O'Hara, Marta E Polak, Tim Angus, Derek W Wright, Lee B Smith, Tom C Freeman
A major endeavor of systems biology is the construction of graphical and computational models of biological pathways as a means to better understand their structure and function. Here, we present a protocol for a biologist-friendly graphical modeling scheme that facilitates the construction of detailed network diagrams, summarizing the components of a biological pathway (such as proteins and biochemicals) and illustrating how they interact. These diagrams can then be used to simulate activity flow through a pathway, thereby modeling its dynamic behavior...
April 2018: Nature Protocols
Mohamed Omar, Maximilian Petri, Nael Hawi, Christian Krettek, Jörg Eberhard, Emmanouil Liodakis
PURPOSE: The aim of this study was to assess the diagnostic accuracy of swab polymerase chain reaction (PCR) compared with tissue culture as the current gold standard. METHODS: Forty-one consecutive patients were prospectively enrolled undergoing revision arthroplasty due to septic and aseptic reasons. Infection classification was done according to the criteria of the Musculoskeletal Infection Society. Intraoperatively, tissue samples of the periprosthetic membrane were collected for culture analysis, and swabs were taken from the accessible implant surface to perform 16S ribosomal RNA PCR...
January 2018: Journal of Orthopaedic Surgery
Petri Kemppainen, Arild Husby
Genome wide association studies have contributed immensely to our understanding of the genetic basis of complex traits. One major conclusion arising from these studies is that most traits are controlled by many loci of small effect, confirming the infinitesimal model of quantitative genetics. A popular approach to test for polygenic architecture involves so called 'chromosome partitioning' where phenotypic variance explained by each chromosome is regressed on the size of the chromosome. First developed for humans, this has now been repeatedly used in other species, but there has been no evaluation of the suitability of this method in species that can differ in their genome characteristics such as number and size of chromosomes...
March 14, 2018: Molecular Ecology Resources
Ram Dixit, Sabine Petry
No abstract text is available yet for this article.
March 15, 2018: Molecular Biology of the Cell
Jeff Sperinde, Weidong Huang, Aki Vehtari, Ahmed Chenna, Pirkko-Liisa Kellokumpu-Lehtinen, John Winslow, Petri Bono, Yolanda Lie, Christos J Petropoulos, Jodi Marie Weidler, Heikki Joensuu
PURPOSE: Expression of p95HER2 (p95), a truncated form of the HER2 receptor, which lacks the trastuzumab binding site but retains kinase activity, has been reported as a prognostic biomarker for poor outcomes in trastuzumab-treated HER2-positive metastatic breast cancer. The impact of p95 expression on trastuzumab treatment efficacy in early HER2-positive breast cancer is less clear. In the current study, p95 was tested as a predictive marker of trastuzumab treatment benefit in the HER2-positive subset of the FinHer adjuvant phase III trial...
March 13, 2018: Clinical Cancer Research: An Official Journal of the American Association for Cancer Research
Ulla Lantto, Sallamaaria Kettunen, Terhi Tapiainen, Petri Koivunen, Matti Uhari, Marjo Renko
OBJECTIVES: To compare the long-term morbidity of patients with periodic fever, aphthous stomatitis, pharyngitis, and adenitis (PFAPA) syndrome treated by tonsillectomy (TE) in childhood to that of matched controls. METHODS: We identified 132 PFAPA patients from the medical records treated by TE in 1987-2007 in Oulu University Hospital, Finland. Altogether 119 patients participated the follow-up study and 94 were clinically examined on average 9.0 years after TE...
February 27, 2018: Clinical and Experimental Rheumatology
Lijuan Yan, Petri Penttinen, Anu Mikkonen, Kristina Lindström
We investigated bacterial community dynamics in response to used motor oil contamination and perennial crop cultivation by 16S rRNA gene amplicon sequencing in a 4-year field study. Actinobacteria, Proteobacteria, Chloroflexi, Acidobacteria, and Gemmatimonadetes were the major bacterial phyla, and Rhodococcus was the most abundant genus. Initially, oil contamination decreased the overall bacterial diversity. Actinobacteria, Betaproteobacteria, and Gammaproteobacteria were sensitive to oil contamination, exhibiting clear succession with time...
March 12, 2018: Environmental Science and Pollution Research International
Ralph A H Stewart, Dominika Szalewska, Amanda Stebbins, Hussein R Al-Khalidi, John G H Cleland, Andrzej Rynkiewicz, Mark H Drazner, Harvey D White, Daniel B Mark, Ambuj Roy, Dragana Kosevic, Miroslaw Rajda, Marek Jasinski, Chua Yeow Leng, Wiwun Tungsubutra, Patrice Desvigne-Nickens, Eric J Velazquez, Mark C Petrie
Background: In patients with ischaemic left ventricular dysfunction, coronary artery bypass surgery (CABG) may decrease mortality, but it is not known whether CABG improves functional capacity. Objective: To determine whether CABG compared with medical therapy alone (MED) increases 6 min walk distance in patients with ischaemic left ventricular dysfunction and coronary artery disease amenable to revascularisation. Methods: The Surgical Treatment in Ischemic Heart disease trial randomised 1212 patients with ischaemic left ventricular dysfunction to CABG or MED...
2018: Open Heart
Rahul Aggarwal, Jackson Steinkamp, Nicholas Chiu, Benjamin Petrie, Haares Mirzan
Optimal blood pressure (BP) targets for different populations, especially diabetics, remain uncertain after conflicting data on intensive management. We assessed whether a <120 mm Hg systolic target is beneficial and whether certain patient populations differ in response. Individual patient data of 14 094 patients from 2 randomized control trials was pooled. Seven thousand forty patients were assigned to an intensive target of <120 mm Hg and 7054 patients to a standard target of <140 mm Hg in an intention-to-treat analysis...
March 12, 2018: Hypertension
Kevin W George, Mitchell Thompson, Joonhoon Kim, Edward E K Baidoo, George Wang, Veronica Teixeira Benites, Christopher J Petzold, Leanne Jade G Chan, Suzan Yilmaz, Petri Turhanen, Paul D Adams, Jay D Keasling, Taek Soon Lee
Isopentenyl pyrophosphate (IPP) toxicity presents a challenge in engineered microbial systems since its formation is unavoidable in terpene biosynthesis. In this work, we develop an experimental platform to study IPP toxicity in isoprenol-producing Escherichia coli. We first characterize the physiological response to IPP accumulation, demonstrating that elevated IPP levels are linked to growth inhibition, reduced cell viability, and plasmid instability. We show that IPP toxicity selects for pathway "breakage", using proteomics to identify a reduction in phosphomevalonate kinase (PMK) as a probable recovery mechanism...
March 9, 2018: Metabolic Engineering
Heather deBoer, Matthew Andrews, Stephanie Cudd, Ellie Leung, Alana Petrie, Soo Chan Carusone, Kelly K O'Brien
PURPOSE: To investigate the role of physical therapy in HIV care from the perspective of people living with HIV and health care professionals with expertise in HIV care. METHODS: We conducted a qualitative descriptive study using semistructured interviews (with health care professionals) and focus groups (with people living with HIV). We purposively sampled health care professionals and recruited people living with HIV in collaboration with an HIV-specialty hospital...
March 13, 2018: Disability and Rehabilitation
Lino Polese, Alice Bressan, Edoardo Savarino, Massimo Vecchiato, Angelo Turoldo, Annachiara Frigo, Giacomo Carlo Sturniolo, Nicolò De Manzini, Roberto Petri, Stefano Merigliano
PURPOSE: The study aimed to evaluate the QoL in patients who underwent elective surgery for uncomplicated diverticulitis using a recently developed diverticulitis quality of life questionnaire (DV-QoL). METHODS: All consecutive patients who underwent surgery for uncomplicated diverticulitis or who were hospitalized and treated conservatively for acute uncomplicated diverticulitis episodes in three referral centers, in a 5-year period, were included in the study...
March 10, 2018: International Journal of Colorectal Disease
Otavio Berwanger, Eliana Vieira Santucci, Pedro Gabriel Melo de Barros E Silva, Isabella de Andrade Jesuíno, Lucas Petri Damiani, Lilian Mazza Barbosa, Renato Hideo Nakagawa Santos, Ligia Nasi Laranjeira, Flávia de Mattos Egydio, Juliana Aparecida Borges de Oliveira, Frederico Toledo Campo Dall Orto, Pedro Beraldo de Andrade, Igor Ribeiro de Castro Bienert, Carlos Eduardo Bosso, José Armando Mangione, Carisi Anne Polanczyk, Amanda Guerra de Moraes Rego Sousa, Renato Abdala Karam Kalil, Luciano de Moura Santos, Andrei Carvalho Sposito, Rafael Luiz Rech, Antônio Carlos Sobral Sousa, Felipe Baldissera, Bruno Ramos Nascimento, Roberto Rocha Corrêa Veiga Giraldez, Alexandre Biasi Cavalcanti, Sabrina Bernardez Pereira, Luiz Alberto Mattos, Luciana Vidal Armaganijan, Hélio Penna Guimarães, José Eduardo Moraes Rego Sousa, John Hunter Alexander, Christopher Bull Granger, Renato Delascio Lopes
Importance: The effects of loading doses of statins on clinical outcomes in patients with acute coronary syndrome (ACS) and planned invasive management remain uncertain. Objective: To determine if periprocedural loading doses of atorvastatin decrease 30-day major adverse cardiovascular events (MACE) in patients with ACS and planned invasive management. Design, Setting, and Participants: Multicenter, double-blind, placebo-controlled, randomized clinical trial conducted at 53 sites in Brazil among 4191 patients with ACS evaluated with coronary angiography to proceed with a percutaneous coronary intervention (PCI) if anatomically feasible...
March 11, 2018: JAMA: the Journal of the American Medical Association
Dominick DePhilippis, Nancy M Petry, Marcel O Bonn-Miller, Sarah B Rosenbach, James R McKay
BACKGROUND: In 2011, the Department of Veterans Affairs launched an initiative to expand patients' access to contingency management (CM) for the treatment of substance use disorders, particularly stimulant use disorder. This study evaluates the uptake and effectiveness of the VA initiative by presenting data on participation in coaching, fidelity to key components of the CM protocol, and clinical outcomes (CM attendance and substance use). METHODS: Fifty-five months after the first VA stations began offering CM to patients in June 2011, 94 stations had made CM available to 2060 patients...
February 16, 2018: Drug and Alcohol Dependence
Yama Dixit, David A Hodell, Alena Giesche, Sampat K Tandon, Fernando Gázquez, Hari S Saini, Luke C Skinner, Syed A I Mujtaba, Vikas Pawar, Ravindra N Singh, Cameron A Petrie
Today the desert margins of northwest India are dry and unable to support large populations, but were densely occupied by the populations of the Indus Civilization during the middle to late Holocene. The hydroclimatic conditions under which Indus urbanization took place, which was marked by a period of expanded settlement into the Thar Desert margins, remains poorly understood. We measured the isotopic values (δ18 O and δD) of gypsum hydration water in paleolake Karsandi sediments in northern Rajasthan to infer past changes in lake hydrology, which is sensitive to changing amounts of precipitation and evaporation...
March 9, 2018: Scientific Reports
Petar M Seferović, Mark C Petrie, Gerasimos S Filippatos, Stefan D Anker, Giuseppe Rosano, Johann Bauersachs, Walter J Paulus, Michel Komajda, Francesco Cosentino, Rudolf A de Boer, Dimitrios Farmakis, Wolfram Doehner, Ekaterini Lambrinou, Yuri Lopatin, Massimo F Piepoli, Michael J Theodorakis, Henrik Wiggers, John Lekakis, Alexandre Mebazaa, Mamas A Mamas, Carsten Tschöpe, Arno W Hoes, Jelena P Seferović, Jennifer Logue, Theresa McDonagh, Jillian P Riley, Ivan Milinković, Marija Polovina, Dirk J van Veldhuisen, Mitja Lainscak, Aldo P Maggioni, Frank Ruschitzka, John J V McMurray
The coexistence of type 2 diabetes mellitus (T2DM) and heart failure (HF), either with reduced (HFrEF) or preserved ejection fraction (HFpEF), is frequent (30-40% of patients) and associated with a higher risk of HF hospitalization, all-cause and cardiovascular (CV) mortality. The most important causes of HF in T2DM are coronary artery disease, arterial hypertension and a direct detrimental effect of T2DM on the myocardium. T2DM is often unrecognized in HF patients, and vice versa, which emphasizes the importance of an active search for both disorders in the clinical practice...
March 8, 2018: European Journal of Heart Failure
Elina Virtanen, Hanna Seppälä, Ilkka Helanterä, Pia Laine, Irmeli Lautenschlager, Lars Paulin, Laura Mannonen, Petri Auvinen, Eeva Auvinen
BACKGROUND: BK polyomavirus (BKPyV) infection is a common asymptomatic viral infection in the general population. Severe complications are seen in immunocompromised individuals, such as polyomavirus-associated nephropathy (PyVAN) in renal transplant recipients. Information on BKPyV microRNA expressions is scarce, although polyomavirus-encoded microRNAs have been shown to control viral replication and assist in immune evasion. Whereas the pathogenic role of rearrangements in JC polyomavirus has been well established, little is known about BKPyV rearrangements in PyVAN...
February 12, 2018: Journal of Clinical Virology: the Official Publication of the Pan American Society for Clinical Virology
Anni Hartikainen, Pasi Yli-Pirilä, Petri Tiitta, Ari Leskinen, Miika Kortelainen, Jürgen Orasche, Jürgen Schnelle-Kreis, Kari Lehtinen, Ralf Zimmermann, Jorma Jokiniemi, Olli Sippula
Residential wood combustion (RWC) emits high amounts of volatile organic compounds (VOCs) into ambient air, leading to formation of secondary organic aerosol (SOA) and various health and climate effects. In this study, the emission factors of VOCs from a logwood-fired modern masonry heater were measured using a Proton-Transfer-Reactor Time-of-Flight Mass Spectrometer (PTR-ToF-MS). Next, the VOCs were aged in a 29 m3 Teflon chamber equipped with UV black lights, where dark and photochemical atmospheric conditions were simulated...
March 8, 2018: Environmental Science & Technology
Claudine Boiziau, Macha Nikolski, Elodie Mordelet, Justine Aussudre, Karina Vargas-Sanchez, Klaus G Petry
Multiple sclerosis is characterized by inflammatory lesions dispersed throughout the central nervous system (CNS) leading to severe neurological handicap. Demyelination, axonal damage, and blood brain barrier alterations are hallmarks of this pathology, whose precise processes are not fully understood. In the experimental autoimmune encephalomyelitis (EAE) rat model that mimics many features of human multiple sclerosis, the phage display strategy was applied to select peptide ligands targeting inflammatory sites in CNS...
March 7, 2018: Inflammation
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