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1.
Mol Ecol ; 32(9): 2174-2185, 2023 05.
Article in English | MEDLINE | ID: mdl-36756702

ABSTRACT

The genetic consequences of the subdivision of populations are regarded as significant to long-term evolution, and research has shown that the scale and speed at which this is now occurring is critically reducing the adaptive potential of most species which inhabit human-impacted landscapes. Here, we provide a rare and, to our knowledge, the first analysis of this process while it is happening and demonstrate a method of evaluating the effect of mitigation measures such as fauna crossings. We did this by using an extensive genetic data set collected from a koala population which was intensely monitored during the construction of linear transport infrastructure which resulted in the subdivision of their population. First, we found that both allelic richness and effective population size decreased through the process of population subdivision. Second, we predicted the extent to which genetic drift could impact genetic diversity over time and showed that after only 10 generations the resulting two subdivided populations could experience between 12% and 69% loss in genetic diversity. Lastly, using forward simulations we estimated that a minimum of eight koalas would need to disperse from each side of the subdivision per generation to maintain genetic connectivity close to zero but that 16 koalas would ensure that both genetic connectivity and diversity remained unchanged. These results have important consequences for the genetic management of species in human-impacted landscapes by showing which genetic metrics are best to identify immediate loss in genetic diversity and how to evaluate the effectiveness of any mitigation measures.


Subject(s)
Genetic Variation , Phascolarctidae , Animals , Humans , Phascolarctidae/genetics , Ecosystem , Conservation of Natural Resources/methods , Genetic Drift , Genetics, Population
2.
J Prev Alzheimers Dis ; 9(4): 801-808, 2022.
Article in English | MEDLINE | ID: mdl-36281685

ABSTRACT

BACKGROUND: Performance of cognitively complex "instrumental activities of daily living" (IADL) has previously been related to amyloid deposition in preclinical Alzheimer's disease. OBJECTIVES: We aimed to investigate the relationship between IADL performance and cerebral tau accumulation in cognitively normal older adults. DESIGN: Cross-sectional. SETTING: Data was collected in the Anti-Amyloid Treatment in Asymptomatic Alzheimer's (A4) and Longitudinal Evaluation of Amyloid Risk and Neurodegeneration (LEARN) studies. PARTICIPANTS: Participants (n = 447, age 71.9±4.9 years, 57.5% female) who underwent tau positron emission tomography were selected from the A4 and LEARN studies. MEASUREMENTS: IADL performance was measured using the self- and study partner-reported versions of the Alzheimer's Disease Cooperative Study Activities of Daily Living - Prevention Instrument (ADCS ADL-PI). We also investigated discordance between participants and their study partners. Cross-sectional associations between entorhinal and inferior temporal tau (independent variables) and ADCS ADL-PI total scores, item-level scores and discordance (dependent variables) were investigated in linear and logistic regressions. Analyses were adjusted for age, sex and education and a tau by amyloid interaction was also included. RESULTS: Participants and their study partners reported high levels of IADL performance. Entorhinal and inferior temporal tau were related to study partner but not to self-reported total ADCS ADL-PI scores. The association was not retained after adjustment for global cerebral amyloid burden. At the item level, greater entorhinal tau was associated with study partner-reported difficulties remembering important dates (odds ratio (OR) = 1.24, 95% confidence interval (95%CI) = [1.06, 1.45], p = 0.008) and difficulties remembering the details of TV programs and movies (OR = 1.32, 95%CI = [1.08, 1.61], p = 0.007). Greater inferior temporal tau was associated with self-reported difficulties managing to find personal belongings (OR = 1.23, 95%CI = [1.04, 1.46], p = 0.018) and study partner-reported difficulties remembering the details of TV programs and movies (OR = 1.39, 95%CI = [1.11, 1.75], p = 0.005). Discordance between participant and study partner-report was more likely with greater entorhinal (OR = 1.18, 95%CI = [1.05, 1.33], p = 0.005) and inferior temporal tau burden (OR = 1.29, 95%CI = [1.10, 1.51], p = 0.002). DISCUSSION: We found a cross-sectional relationship between study partner-reported everyday functioning and tau in cognitively normal older adults. Participants were more likely to self-report difficulties differently from their study partners when tau burden was higher. This may hint at an altered early-disease awareness of functional changes and underscores the importance of self-report of IADL functioning in addition to collateral report by a study partner.


Subject(s)
Alzheimer Disease , Humans , Female , Aged , Male , tau Proteins , Activities of Daily Living , Positron-Emission Tomography , Amyloid
3.
Health Policy Open ; 3: 100059, 2022 Dec.
Article in English | MEDLINE | ID: mdl-37383567

ABSTRACT

States retain significant power over key components of Affordable Care Act implementation. Using data from the US Census from 2010 to 2018, we examine how states' decisions to either establish state-run marketplaces or to default to the federal marketplace influenced the distribution of health insurance types within states. We find, somewhat counterintuitively, that state-based marketplaces are associated with greater change in enrollment for Medicaid compared to the federal marketplace. These findings confirm that, at least until 2018, the most significant increases in insurance coverage resulting from the ACA were in public insurance, rather than private insurance. We explore a number of possible explanations to help explain these findings, raising important questions about the efficacy of the individual mandate (a key mechanism in legislative efforts to reduce the numbers of uninsured), the related administrative burdens associated with state and federal marketplaces, and, equally as important, differential access to Medicaid entitlements among citizens living in different states-access that hinges not only or always on Medicaid expansion, but also and perhaps more importantly, on policy decisions about insurance marketplaces.

4.
Int J Infect Dis ; 116: 157-165, 2022 Mar.
Article in English | MEDLINE | ID: mdl-34929356

ABSTRACT

BACKGROUND: COVID-19 transmission and disease dynamics in sub-Saharan Africa are not well understood. Our study aims to provide insight into COVID-19 epidemiology in Malawi by estimating SARS-CoV-2 prevalence and immunity after SARS-CoV-2 infection in a hospital-based setting. METHODS: We conducted a hospital-based, convenience sampling, cross-sectional survey for SARS-CoV-2 in Lilongwe, Malawi. Participants answered a questionnaire and were tested for SARS-CoV-2 by enzyme-linked immunosorbent assay and real-time reverse-transcription polymerase chain reaction (RT-PCR). A surrogate virus neutralization test (sVNT) was performed in seropositive samples to estimate immunity. Poisson regression was used to assess SARS-CoV-2 point prevalence association with demographic and behavioral variables. FINDINGS: The study included 930 participants. We found a combined point prevalence of 10.1%. Separately analyzed, RT-PCR positivity was 2.0%, and seropositivity was 9.3%. Of tested seropositive samples, 90.1% were sVNT positive. We found a high rate (45.7%) of asymptomatic SARS-CoV-2 infection. SARS-CoV-2 point prevalence was significantly associated with being a healthcare worker. INTERPRETATION: Our study suggests that official data underestimate COVID-19 transmission. Using sVNTs to estimate immunity in Malawi is feasible and revealed considerable post-infection immunity in our cohort. Subclinical infection and transmission are probably a game-changer in surveillance, mitigation and vaccination strategies.


Subject(s)
COVID-19 , SARS-CoV-2 , COVID-19/epidemiology , Cross-Sectional Studies , Hospitals , Humans , Malawi/epidemiology , Prevalence
5.
Diabet Med ; 38(6): e14382, 2021 06.
Article in English | MEDLINE | ID: mdl-33245572

ABSTRACT

AIMS: To explore perceptions of useful routine consultations with diabetologists from the perspective of adults with type 1 diabetes, including preferences for discussing psychosocial issues. METHODS: We conducted semi-structured interviews in 2018/2019 with 33 people with type 1 diabetes (age 22-75 years, 20 men and 13 women, median diabetes duration 25 years) recruited from two diabetes clinics in the capital region of Denmark. Interviews were audio recorded, transcribed verbatim and analysed using thematic text condensation. RESULTS: Achieving a useful consultation was perceived as a shared responsibility between people with diabetes and diabetologists. Participants' perspectives of what constitutes a useful consultation and expectations for both consultation and diabetologist varied in relation to perceptions of (1) the interaction between the person with diabetes and diabetologist, including being prepared, being honest, experiencing good rapport and preferring a partnership with the diabetologist or 'keeping it clinical' and (2) the diabetologist's approach to diabetes care, including providing up-to-date knowledge and listening and showing understanding. CONCLUSIONS: Both content and style of diabetes consultations need to be adapted to the individual person with type 1 diabetes. People with diabetes have an important role in expressing their needs and preferences related to both content and style. Diabetologists need to be aware of and attentive to the many individual needs and expectations among people with diabetes, including the desire and need to discuss psychosocial issues. Dialogue tools for preparation and in consultations may enable people with diabetes to voice their needs and expectations and diabetologists to juggle these diversities.


Subject(s)
Diabetes Mellitus, Type 1/therapy , Physician-Patient Relations , Physicians , Qualitative Research , Referral and Consultation/organization & administration , Adult , Aged , Female , Humans , Male , Middle Aged , Young Adult
6.
Arq. bras. med. vet. zootec. (Online) ; 72(5): 1997-2001, Sept.-Oct. 2020. ilus
Article in English | LILACS, VETINDEX | ID: biblio-1131557

ABSTRACT

A literatura atual discute múltiplas modalidades de imagem para acompanhar o processo de cicatrização da origem do ligamento suspensor do boleto (LSB) em equinos, mas nenhuma pode garantir que eles possuam fibras colágenas com calibre suficiente para suportar o retorno ao exercício. Já as técnicas morfológicas e bioquímicas, bem como a análise de birrefringência, podem ser mais apropriadas para caracterizar o processo de cicatrização e avaliar a eficiência do tratamento. O objetivo deste artigo é descrever procedimento simples que possibilita a coleta de amostras teciduais de boa qualidade e em sentido longitudinal, por biópsia em equinos em estação. Após antissepsia local, sedação e bloqueio do nervo palmar lateral no aspecto medial do osso acessório do carpo (OAC), o membro foi colocado em suspensão com o carpo flexionado em 90º; a agulha de biópsia guiada por ultrassom foi introduzida em sentido distoproximal, 11 a 13cm distal ao OAC, ângulo de 20º em relação ao LSB, até a região de sua origem. O equipamento foi disparado e coletou-se a amostra tecidual. Essa técnica possibilitou a coleta de fragmentos de boa qualidade para análise histológica e de birrefringência, sem reações adversas, podendo ser usada em modelos experimentais ou na prática clínica.(AU)


Subject(s)
Animals , Round Ligaments/diagnostic imaging , Horses , Image-Guided Biopsy/veterinary
7.
Acta Naturae ; 11(2): 68-76, 2019.
Article in English | MEDLINE | ID: mdl-31413882

ABSTRACT

The anti-HIV activity of a new humic substance-derived preparation has been studied in individual pools of immune cells (CD4+ T lymphocytes, macrophages, dendritic cells). Near-complete inhibition of the HIV infection (by more than 90%) was achieved by treating each of the abovementioned cell types with non-toxic concentrations of the preparation. The inhibitory effect demonstrates the possibility of preventing the depletion of a significant portion of functionally important immune cells. A comparative study of infection inhibition in individual cell pools has allowed us to reveal the differences in the preparation's effectiveness in each of the cell populations. A R5-tropic HIV-1 infection in macrophages exhibited maximum sensitivity to the preparation: 90% and 50% inhibition of the infection were observed in the presence of concentrations as low as 1.4 and 0.35 µg/ml, respectively. A 15- and 19-fold higher concentration was required to achieve the same extent of inhibition in dendritic cells infected with the same strain. The effectiveness of the drug in CD4 + T lymphocytes is quite comparable to its effectiveness in macrophages. The drug is universally effective for both the T- and M-tropic variants of HIV-1.

8.
Paediatr Respir Rev ; 32: 30-35, 2019 Nov.
Article in English | MEDLINE | ID: mdl-31427159

ABSTRACT

Clinicians and other decision makers in healthcare use results from clinical trials to inform practice. Interpretation of clinical trial results can be challenging, as weaknesses in trial design, data collection, analysis or reporting, can compromise the usefulness of results. A good working knowledge of clinical trial design is essential to expertly interpret and determine the validity and generalizability of the results. This manuscript will give a brief overview of clinical trial design including the strengths and limitations of various approaches. The focus will be on confirmatory clinical trials.


Subject(s)
Clinical Trials as Topic , Research Design , Adaptive Clinical Trials as Topic , Equivalence Trials as Topic , Humans , Randomized Controlled Trials as Topic
9.
Rev Sci Instrum ; 89(9): 092803, 2018 Sep.
Article in English | MEDLINE | ID: mdl-30278754

ABSTRACT

Time-resolved diffraction has become a vital tool for probing dynamic responses to an applied stimulus. Such experiments traditionally use hardware solutions to histogram measured data into their respective bin. We will show that a major advantage of event-based data acquisition, which time-stamps measured diffraction data with 100 ns accuracy, is much preferred over hardware histogramming of the data by enabling postprocessing for advanced custom binning using a software solution. This approach is made even more powerful by coupling measured diffraction data with metadata about the applied stimuli and material response. In this work, we present a time-filter approach that leverages the power of event-based diffraction collection to reduce stroboscopic data measured over many hours into equally weighted segments that represent subsets of the response to a single cycle of the applied stimulus. We demonstrate this approach by observing ferroelectric/ferroelastic domain wall motion during electric field cycling of BaTiO3. The developed approach can readily be expanded to investigate other dynamic phenomena using complex sample environments.

10.
J Appl Microbiol ; 124(4): 990-1000, 2018 Apr.
Article in English | MEDLINE | ID: mdl-28921812

ABSTRACT

AIMS: The aim of this study was to identify the most efficient sampling method for quantitative PCR-based detection of airborne human norovirus (NoV). METHODS AND RESULTS: A comparative experiment was conducted in an aerosol chamber using aerosolized murine norovirus (MNV) as a surrogate for NoV. Sampling was performed using a nylon (NY) filter in conjunction with four kinds of personal samplers: Gesamtstaubprobenahme sampler (GSP), Triplex-cyclone sampler (TC), 3-piece closed-faced Millipore cassette (3P) and a 2-stage NIOSH cyclone sampler (NIO). In addition, sampling was performed using the GSP sampler with four different filter types: NY, polycarbonate (PC), polytetrafluoroethylene (PTFE) and gelatine (GEL). The sampling efficiency of MNV was significantly influenced by both sampler and filter type. The GSP sampler was found to give significantly (P < 0·05) higher recovery of aerosolized MNV than 3P and NIO. A higher recovery was also found for GSP compared with TC, albeit not significantly. Finally, recovery of aerosolized MNV was significantly (P < 0·05) higher using NY than PC, PTFE and GEL filters. CONCLUSIONS: The GSP sampler combined with a nylon filter was found to be the best method for personal filter-based sampling of airborne NoV. SIGNIFICANCE AND IMPACT OF THE STUDY: The identification of a suitable NoV air sampler is an important step towards studying the association between exposure to airborne NoV and infection.


Subject(s)
Aerosols/analysis , Air Microbiology , Environmental Monitoring/methods , Norovirus/isolation & purification , Environmental Monitoring/instrumentation , Humans , Norovirus/classification , Norovirus/genetics
11.
Mol Psychiatry ; 23(3): 759-766, 2018 03.
Article in English | MEDLINE | ID: mdl-28607458

ABSTRACT

Some studies suggest that prenatal infection increases risk of autism spectrum disorders (ASDs). This study was undertaken in a prospective cohort in Norway to examine whether we could find evidence to support an association of the prenatal occurrence of fever, a common manifestation of infection, with ASD risk. Prospective questionnaires provided maternal exposure data; case status was established from clinical assessments and registry linkages. In a large, prospectively ascertained cohort of pregnant mothers and their offspring, we examined infants born ⩾32 weeks for associations between fever exposure in each trimester and ASD risk using logistic regression. Maternal exposure to second-trimester fever was associated with increased ASD risk, adjusting for presence of fever in other trimesters and confounders (adjusted odds ratio (aOR), 1.40; 95% confidence interval, 1.09-1.79), with a similar, but nonsignificant, point estimate in the first trimester. Risk increased markedly with exposure to three or more fever episodes after 12 weeks' gestation (aOR, 3.12; 1.28-7.63). ASD risk appears to increase with maternal fever, particularly in the second trimester. Risk magnified dose dependently with exposure to multiple fevers after 12 weeks' gestation. Our findings support a role for gestational maternal infection and innate immune responses to infection in the pathogenesis of at least some cases of ASD.


Subject(s)
Autism Spectrum Disorder/etiology , Autistic Disorder/etiology , Adult , Female , Fever/complications , Genetic Linkage , Gestational Age , Humans , Immunity, Innate/immunology , Infant , Infant, Newborn , Infections/complications , Male , Maternal Exposure , Mothers , Norway , Odds Ratio , Pregnancy , Pregnancy Trimester, Second/physiology , Prenatal Exposure Delayed Effects , Prospective Studies , Registries , Risk Factors , Surveys and Questionnaires
12.
Anaesthesia ; 72(11): 1388-1397, 2017 Nov.
Article in English | MEDLINE | ID: mdl-28872662

ABSTRACT

Inhalation of aerosolised medications are the mainstay of treatment for a number of chronic lung diseases and have several advantages over systemically-administered medications. These include more rapid onset of action for drugs such as ß-adrenergic agonists when compared with oral medication, high luminal doses for inhaled antibiotics when used to treat endobronchial infection, and an improved therapeutic index compared with systemic delivery for these and other classes of drugs such as corticosteroids. The use of aerosolised drugs to treat patients whose tracheas are intubated is less well established, in part because systemic delivery via the intravenous route can be a simpler alternative for many drugs. Consequently, research in this area is largely limited to a number of in vitro studies and very few clinical trials. Unfortunately, a lack of focus in this area has resulted in a number of practices which at best are ineffective, and at worst dangerous for the patient. Although there have been some attempts to re-invigorate research in order to improve delivery systems, current devices are, to a great extent, based on long-standing technology developed more than 50 years ago. In this review, we explore current knowledge and provide guidance as to when and how the inhaled route may be of value when treating patients whose tracheas are intubated, and we set out the challenges facing those attempting to advance the topic. We conclude by reviewing current areas of interest that may lead to more effective and widespread use of aerosols in the treatment of intubated patients.


Subject(s)
Aerosols , Noninvasive Ventilation/methods , Pharmaceutical Preparations/administration & dosage , Respiration, Artificial/methods , Administration, Inhalation , Adolescent , Child , Child, Preschool , Humans , Infant , Nebulizers and Vaporizers
13.
Leukemia ; 31(12): 2752-2760, 2017 12.
Article in English | MEDLINE | ID: mdl-28439110

ABSTRACT

An increasing number of variants of unknown significance are being identified in leukemia patients with the application of deep sequencing and these include CSF3R cytoplasmic mutations. Previous studies have demonstrated oncogenic potential of certain CSF3R truncation mutations prior to internalization motifs. However, the oncogenic potential of truncating the more distal region of CSF3R cytoplasmic domain as well as cytoplasmic missense mutations remains uncharacterized. Here we identified that CSF3R distal cytoplasmic truncation mutations (Q793-Q823) also harbored leukemogenic potential. Mechanistically, these distal cytoplasmic truncation mutations demonstrated markedly decreased receptor degradation, probably owing to loss of the de-phosphorylation domain (residues N818-F836). Furthermore, all truncations prior to Q823 demonstrated increased expression of the higher molecular weight CSF3R band, which is shown to be essential for the receptor surface expression and the oncogenic potential. We further demonstrated that sufficient STAT5 activation is essential for oncogenic potential. In addition, CSF3R K704A demonstrated transforming capacity due to interruption of receptor ubiquitination and degradation. In summary, we have expanded the region of the CSF3R cytoplasmic domain in which truncation or missense mutations exhibit leukemogenic capacity, which will be useful for evaluating the relevance of CSF3R mutations in patients and helpful in defining targeted therapy strategies.


Subject(s)
Cell Transformation, Neoplastic/genetics , Mutation, Missense , Protein Domains/genetics , Receptors, Colony-Stimulating Factor/genetics , Sequence Deletion , Alleles , Animals , Cell Line , Humans , Leukemia, Myeloid, Acute/genetics , Mice , Myeloproliferative Disorders/genetics , Phosphorylation , Proteolysis , Receptors, Colony-Stimulating Factor/chemistry , STAT5 Transcription Factor/metabolism
14.
Water Res ; 112: 110-119, 2017 04 01.
Article in English | MEDLINE | ID: mdl-28153697

ABSTRACT

Exposure to bioaerosols can pose a health risk to workers at wastewater treatment plants (WWTPs) and to habitants of their surroundings. The main objective of this study was to examine the presence of harmful microorganisms in the air emission from a new type of hospital WWTP employing advanced wastewater treatment technologies. Air particle measurements and sampling of inhalable bacteria, endotoxin and noroviruses (NoVs) were performed indoor at the WWTP and outside at the WWTP ventilation air exhaust, downwind of the air exhaust, and upwind of the WWTP. No significant differences were seen in particle and endotoxin concentrations between locations. Bacterial concentrations were comparable or significantly lower in the exhaust air than inside the WWTP and in the upwind reference. Bacterial isolates were identified using matrix-assisted laser desorption-ionization time-of-flight mass spectrometry. In total, 35 different bacterial genera and 64 bacterial species were identified in the air samples. Significantly higher genus and species richness was found with an Andersen Cascade Impactor compared with filter-based sampling. No pathogenic bacteria were found in the exhaust air. Streptomyces was the only bacterium found in the air both inside the WWTP and at the air emission, but not in the upwind reference. NoV genomes were detected in the air inside the WWTP and at the air exhaust, albeit in low concentrations. As only traces of NoV genomes could be detected in the exhaust air they are unlikely to pose a health risk to surroundings. Hence, we assess the risk of airborne exposure to pathogenic bacteria and NoVs from the WWTP air emission to surroundings to be negligible. However, as a slightly higher NoV concentration was detected inside the WWTP, we cannot exclude the possibility that exposure to airborne NoVs can pose a health risk to susceptible to workers inside the WWTP, although the risk may be low.


Subject(s)
Air Microbiology , Wastewater/microbiology , Bacteria/isolation & purification , Norovirus , Vehicle Emissions
15.
Pediatr Pulmonol ; 52(3): 319-323, 2017 Mar.
Article in English | MEDLINE | ID: mdl-28221736

ABSTRACT

BACKGROUND: Ciprofloxacin (CIP) is frequently used when treating cystic fibrose (CF) patients with intermittent Pseudomonas aeruginosa (P. aeruginosa) lung colonization. However, approximately 20% of the patients progress to chronic infection despite early intervention. The aim of this study, was to investigate the pharmacokinetics of CIP, to evaluate if CYP3A4-related metabolism is involved and to find the optimal dose needed to eradicate intermittently colonizing bacteria in the lungs of CF patients. Methods An open-label, prospective pharmacokinetic study was performed. Twenty-two adult CF-patients were each given 500 mg CIP orally. One blood sample was taken at t = 0, and the following 12 hr, nine blood samples were collected. The optimal dose and interval was then calculated by Monte Carlo simulation. CYP3A4-activity was mesured using the Erythromycin Breath Test (ERMBT). Results A 14-fold variation in AUC for the 500 mg CIP (median 473.5 µg/ml × min), and a 30-fold variation in Cmax for CIP (median 2 µg/ml) was found. For CYP3A4-activity the variation was 8-fold. No correlation was found between the CYP3A4-activity and CIP-concentrations. The probability of eradicating intermittent P. aeruginosa colonization in the lungs of CF patients was found to be 57% (3 doses/day), when 500 mg CIP was given. It was calculated to be 89% (2 doses/day) and 94% (3 doses/day), respectivly if 750 mg CIP had been given. Conclusion A large pharmacokinetic difference of CIP in CF patiens was found, not explained by CYP3A4 variation. CIP should be given at 750 mg two or three times daily to adult CF patients with intermittently colonization. Pediatr Pulmonol. 2017;52:319-323. © 2016 Wiley Periodicals, Inc.


Subject(s)
Anti-Bacterial Agents/pharmacokinetics , Ciprofloxacin/pharmacokinetics , Cystic Fibrosis/drug therapy , Pseudomonas Infections/drug therapy , Adult , Anti-Bacterial Agents/administration & dosage , Anti-Bacterial Agents/analysis , Breath Tests , Ciprofloxacin/administration & dosage , Ciprofloxacin/analysis , Cytochrome P-450 CYP3A/physiology , Dose-Response Relationship, Drug , Female , Humans , Male , Middle Aged , Prospective Studies , Pseudomonas aeruginosa , Sweat/chemistry , Young Adult
16.
Pac Symp Biocomput ; 22: 485-496, 2017.
Article in English | MEDLINE | ID: mdl-27897000

ABSTRACT

Cancer metabolism differs remarkably from the metabolism of healthy surrounding tissues, and it is extremely heterogeneous across cancer types. While these metabolic differences provide promising avenues for cancer treatments, much work remains to be done in understanding how metabolism is rewired in malignant tissues. To that end, constraint-based models provide a powerful computational tool for the study of metabolism at the genome scale. To generate meaningful predictions, however, these generalized human models must first be tailored for specific cell or tissue sub-types. Here we first present two improved algorithms for (1) the generation of these context-specific metabolic models based on omics data, and (2) Monte-Carlo sampling of the metabolic model ux space. By applying these methods to generate and analyze context-specific metabolic models of diverse solid cancer cell line data, and primary leukemia pediatric patient biopsies, we demonstrate how the methodology presented in this study can generate insights into the rewiring differences across solid tumors and blood cancers.


Subject(s)
Models, Biological , Neoplasms/metabolism , Algorithms , Cell Line, Tumor , Child , Computational Biology , Humans , Leukemia/metabolism , Metabolic Networks and Pathways , Monte Carlo Method , Neoplasms/genetics , Proteomics
17.
J Virol ; 90(11): 5231-5245, 2016 06 01.
Article in English | MEDLINE | ID: mdl-26984721

ABSTRACT

UNLABELLED: A fraction of HIV-1 patients are able to generate broadly neutralizing antibodies (bNAbs) after 2 to 4 years of infection. In rare occasions such antibodies are observed close to the first year of HIV-1 infection but never within the first 6 months. In this study, we analyzed the neutralization breadth of sera from 157 antiretroviral-naive individuals who were infected for less than 1 year. A range of neutralizing activities was observed with a previously described panel of six recombinant viruses from five different subtypes (M. Medina-Ramirez et al., J Virol 85:5804-5813, 2011, http://dx.doi.org/10.1128/JVI.02482-10). Some sera were broadly reactive, predominantly targeting envelope epitopes within the V2 glycan-dependent region. The neutralization breadth was positively associated with time postinfection (P = 0.0001), but contrary to what has been reported for chronic infections, no association with the viral load was observed. Notably, five individuals within the first 6 months of infection (two as early as 77 and 96 days postinfection) showed substantial cross-neutralization. This was confirmed with an extended panel of 20 Env pseudoviruses from four different subtypes (two in tier 3, 14 in tier 2, and four in tier 1). Sera from these individuals were capable of neutralizing viruses from four different subtypes with a geometric mean 50% infective dose (ID50) between 100 and 800. These results indicate that induction of cross-neutralizing responses, albeit rare, is achievable even within 6 months of HIV-1 infection. These observations encourage the search for immunogens able to elicit this kind of response in preventive HIV-1 vaccine approaches. IMPORTANCE: There are very few individuals able to mount broadly neutralizing activity (bNA) close to the first year postinfection. It is not known how early in the infection cross-neutralizing responses can be induced. In the present study, we show that bNAbs, despite being rare, can be induced much earlier than previously thought. The identification of HIV-1-infected patients with these activities within the first months of infection and characterization of these responses will help in defining new immunogen designs and neutralization targets for vaccine-mediated induction of bNAbs.


Subject(s)
Antibodies, Neutralizing/blood , Antibodies, Neutralizing/immunology , Epitopes/immunology , HIV Antibodies/blood , HIV Infections/immunology , HIV-1/immunology , Adult , Cross-Sectional Studies , Epitope Mapping , Epitopes/chemistry , Female , HIV Antibodies/immunology , HIV Infections/virology , HIV-1/physiology , Humans , Male , Neutralization Tests , Polysaccharides/immunology , Time Factors , Viral Load
18.
J Hosp Infect ; 92(4): 378-84, 2016 Apr.
Article in English | MEDLINE | ID: mdl-26905662

ABSTRACT

BACKGROUND: Viruses cause a major proportion of human infections, especially gastroenteritis and respiratory infections in children and adults. Indirect transmission between humans via environmental surfaces may play a role in infections, but methods to investigate this have been sparse. AIM: To validate and test efficient and reliable procedures to detect multiple human pathogenic viruses on surfaces. METHODS: The study was divided into two parts. In Part A, six combinations of three different swabs (consisting of cotton, foamed cotton, or polyester head) and two different elution methods (direct lysis or immersion in alkaline glycine buffer before lysis) were tested for efficient recovery of human norovirus GII.7 and mengovirus from artificially contaminated surfaces. In Part B we determined the detection limit for norovirus GI.1 and GII.3 using the best procedure found in Part A linked with a commercial multiplex real-time quantitative polymerase chain reaction detection assay. FINDINGS: Combining the polyester swab with direct lysis allowed recovery down to 100 and 10 genome copies/cm(2) of norovirus GI.1 and GII.3, respectively. This procedure resulted in the significant highest recovery of both norovirus and mengovirus, whereas no differences in amplification efficiencies were observed between the different procedures. CONCLUSION: The results indicate that it is possible to detect low concentrations of virus on environmental surfaces. We therefore suggest that a polyester swab, followed by direct lysis, combined with a multiplex qPCR detection assay is an efficient screening tool that merits study of different respiratory and gastrointestinal viruses on environment surfaces.


Subject(s)
Environmental Microbiology , Norovirus/isolation & purification , Specimen Handling/methods , Virology/methods , Viruses/isolation & purification , Humans , Mengovirus/isolation & purification
19.
Br J Clin Pharmacol ; 81(2): 246-55, 2016 Feb.
Article in English | MEDLINE | ID: mdl-26407011

ABSTRACT

AIM: Pridopidine, a new oral drug for treatment of patients with motor symptoms associated with Huntington's Disease (HD) is currently under development. In steady-state conditions, pridopidine elimination is mediated primarily through renal excretion. This study evaluated single dose and steady-state pharmacokinetics (PK) of a daily dose of pridopidine in subjects with mild and moderate renal impairment and matched healthy subjects. METHODS: Subjects with mild renal impairment (n = 12), moderate impairment (n = 12), or their matched healthy controls (n = 25) participated in this study. Subjects received a single dose of pridopidine (45 mg) on day 1 and a multiple dose cycle of 45 mg once daily on days 5-18. Blood and urine samples were collected on days 1 and 18 for PK analysis. RESULTS: Mild renal impairment did not affect the PK of pridopidine whilst an increase in exposure was seen in subjects with moderate renal impairment. Subjects with moderate impairment showed reduced plasma clearance (by 44%) and had 68% higher AUC (90% CI 1.22, 2.30) and 26% higher Cmax (90% CI 1.02, 1.56) values than those with normal renal function at steady-state. Pridopidine was safe and well tolerated in healthy subjects and in subjects with mild and moderate renal impairment. CONCLUSIONS: Mild renal impairment has no impact on exposure to pridopidine while moderately impaired renal function resulted in higher pridopidine concentrations.


Subject(s)
Huntington Disease/drug therapy , Kidney Diseases , Piperidines/pharmacokinetics , Adolescent , Adult , Aged , Cytochrome P-450 CYP2D6/genetics , Dose-Response Relationship, Drug , Female , Germany , Humans , Huntington Disease/complications , Kidney Diseases/blood , Kidney Diseases/complications , Kidney Diseases/urine , Kidney Function Tests , Male , Middle Aged , Piperidines/blood , Piperidines/urine , Severity of Illness Index , Young Adult
20.
Mol Psychiatry ; 21(2): 261-9, 2016 Feb.
Article in English | MEDLINE | ID: mdl-25824300

ABSTRACT

Myalgic encephalomyelitis/chronic fatigue syndrome is an unexplained debilitating disorder that is frequently associated with cognitive and motor dysfunction. We analyzed cerebrospinal fluid from 32 cases, 40 subjects with multiple sclerosis and 19 normal subjects frequency-matched for age and sex using a 51-plex cytokine assay. Group-specific differences were found for the majority of analytes with an increase in cases of CCL11 (eotaxin), a chemokine involved in eosinophil recruitment. Network analysis revealed an inverse relationship between interleukin 1 receptor antagonist and colony-stimulating factor 1, colony-stimulating factor 2 and interleukin 17F, without effects on interleukin 1α or interleukin 1ß, suggesting a disturbance in interleukin 1 signaling. Our results indicate a markedly disturbed immune signature in the cerebrospinal fluid of cases that is consistent with immune activation in the central nervous system, and a shift toward an allergic or T helper type-2 pattern associated with autoimmunity.


Subject(s)
Cytokines/analysis , Cytokines/immunology , Fatigue Syndrome, Chronic/immunology , Fatigue Syndrome, Chronic/metabolism , Adult , Case-Control Studies , Chemokine CCL11/immunology , Chemokine CCL11/metabolism , Cytokines/cerebrospinal fluid , Female , Humans , Interleukin-17 , Interleukin-1beta , Male , Middle Aged , Multiple Sclerosis/cerebrospinal fluid , Multiple Sclerosis/immunology , Multiple Sclerosis/metabolism
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