Structure, scale and emergence.

In this paper I consider the structures that chemists and physicists attribute at the molecular scale to substances and materials of various kinds, and how they relate to structures and processes at other scales. I argue that the structure of a substance is the set of properties and relations which are preserved across all the conditions in which it can be said to exist. In short, structure is abstraction.

The Effects of Acute Exercise on Short- and Long-Term Memory: Considerations for the Timing of Exercise and Phases of Memory.

The specific questions addressed from this research include: (1) Does high-intensity acute exercise improve memory?, (2) If so, do the mechanisms occur via encoding, consolidation, or retrieval? and (3) If acute exercise occurs in multiple phases of memory (e.g., before encoding and during consolidation), does this have an additive effect on memory? Three experimental, within-subject, counterbalanced studies were conducted among young adults.

Comprehensive Characterization of Transcriptional Activity during Influenza A Virus Infection Reveals Biases in Cap-Snatching of Host RNA Sequences.

Macrophages in the lung detect and respond to influenza A virus (IAV), determining the nature of the immune response. Using terminal-depth cap analysis of gene expression (CAGE), we quantified transcriptional activity of both host and pathogen over a 24-h time course of IAV infection in primary human monocyte-derived macrophages (MDMs). This method allowed us to observe heterogenous host sequences incorporated into IAV mRNA, "snatched" 5' RNA caps, and corresponding RNA sequences from host RNAs.

Niche partitioning of intertidal seagrasses: evidence of the influence of substrate temperature.

The influence of soil temperature on rhizome depths of four intertidal seagrass species was investigated in central Queensland, Australia. We postulated that certain intertidal seagrass species are soil temperature-sensitive and vertically stratify rhizome depths. Below-ground vertical stratification of intertidal seagrass rhizome depths was analysed based upon microclimate (soil temperature) and microhabitat (soil type).

Perineal urethrostomy to treat obstructive urolithiasis in a captive hand-raised steenbok ().

The steenbok (Raphicerus campestris) is a small antelope of the family Bovidae native to the African continent. Urolithiasis, the formation of urinary calculi in the urinary tract, can be caused by a variety of factors such as diet, dehydration, infection and anatomical predisposition. Urolithiasis, with uroliths identified as magnesium calcium phosphate carbonate in composition, was diagnosed in a hand-reared 5-month-old steenbok.

Increases in Endogenous or Exogenous Progestins Promote Virus-Target Cell Interactions within the Non-human Primate Female Reproductive Tract.

Currently, there are mounting data suggesting that HIV-1 acquisition in women can be affected by the use of certain hormonal contraceptives. However, in non-human primate models, endogenous or exogenous progestin-dominant states are shown to increase acquisition. To gain mechanistic insights into this increased acquisition, we studied how mucosal barrier function and CD4+ T-cell and CD68+ macrophage density and localization changed in the presence of natural progestins or after injection with high-dose DMPA.

Live virus vaccines based on a vesicular stomatitis virus (VSV) backbone: Standardized template with key considerations for a risk/benefit assessment.

The Brighton Collaboration Viral Vector Vaccines Safety Working Group (V3SWG) was formed to evaluate the safety of live, recombinant viral vaccines incorporating genes from heterologous viral and other microbial pathogens in their genome (so-called "chimeric virus vaccines"). Many such viral vector vaccines are now at various stages of clinical evaluation. Here, we introduce an attenuated form of recombinant vesicular stomatitis virus (rVSV) as a potential chimeric virus vaccine for HIV-1, with implications for use as a vaccine vector for other pathogens.

Growth effects of shading and sedimentation in two tropical seagrass species: Implications for port management and impact assessment.

Seagrass meadows in many parts of the globe are threatened by a range of processes including port development, dredging and land clearing in coastal catchments, which can reduce water clarity and increase sedimentation pressure. As rates of seagrass loss increase, there is an urgent need to understand the potential impacts of development on these critical species. This research compares the effects of shading and burial by fine sand on two seagrass species Zostera muelleri and Halophila ovalis in Port Curtis Bay, an industrial harbour located on the continental margin adjacent to the Great Barrier Reef Heritage Area, Australia.

Immanent philosophy of X.

In this paper I examine the relationship between historians, philosophers and sociologists of science, and indeed scientists themselves. I argue that (i) they co-habit a shared intellectual territory (science and its past); and (ii) they should be able to do so peacefully, and with mutual respect, even if they disagree radically about how to describe the methods and results of science. I then go on to explore some of the challenges to mutually respectful cohabitation between history, philosophy and sociology of science.

Coxsackievirus B3 replication and pathogenesis.

Viruses such as coxsackievirus B3 (CVB3) are entirely host cell-dependent parasites. Indeed, they must cleverly exploit various compartments of host cells to complete their life cycle, and consequently launch disease. Evolution has equipped this pico-rna-virus, CVB3, to use different strategies, including CVB3-induced direct damage to host cells followed by a host inflammatory response to CVB3 infection, and cell death to super-additively promote target organ tissue injury, and dysfunction.

Scaling silicon photonic switch fabrics for data center interconnection networks.

With the rapidly increasing aggregate bandwidth requirements of data centers there is a growing interest in the insertion of optically interconnected networks with high-radix transparent optical switch fabrics. Silicon photonics is a particularly promising and applicable technology due to its small footprint, CMOS compatibility, high bandwidth density, and the potential for nanosecond scale dynamic connectivity. In this paper we analyze the feasibility of building silicon photonic microring based switch fabrics for data center scale optical interconnection networks.

A polyvalent Clade B virus-like particle HIV vaccine combined with partially protective oral preexposure prophylaxis prevents simian-human immunodeficiency virus Infection in macaques and primes for virus-amplified immunity.

Vaccination and preexposure prophylaxis (PrEP) with antiretrovirals have shown only partial protection from HIV-1 infection in human trials. Oral Truvada (emtricitabine/tenofovir disoproxil fumarate) is FDA approved as PrEP but partial adherence reduces efficacy. If combined as biomedical preventions (CBP), an HIV vaccine could protect when PrEP adherence is low and PrEP could prevent vaccine breakthroughs.

A new transcriptional role for matrix metalloproteinase-12 in antiviral immunity.

Interferon-α (IFN-α) is essential for antiviral immunity, but in the absence of matrix metalloproteinase-12 (MMP-12) or IκBα (encoded by NFKBIA) we show that IFN-α is retained in the cytosol of virus-infected cells and is not secreted. Our findings suggest that activated IκBα mediates the export of IFN-α from virus-infected cells and that the inability of cells in Mmp12(-/-) but not wild-type mice to express IκBα and thus export IFN-α makes coxsackievirus type B3 infection lethal and renders respiratory syncytial virus more pathogenic. We show here that after macrophage secretion, MMP-12 is transported into virus-infected cells.

Pharmacokinetic and safety analyses of tenofovir and tenofovir-emtricitabine vaginal tablets in pigtailed macaques.

Vaginal rapidly disintegrating tablets (RDTs) containing tenofovir (TFV) or TFV and emtricitabine (FTC) were evaluated for safety and pharmacokinetics in pigtailed macaques. Two separate animal groups (n = 4) received TFV (10 mg) or TFV-FTC (10 mg each) RDTs, administered near the cervix. A third group (n = 4) received 1 ml TFV gel.

Targeting matrix metalloproteinase activity and expression for the treatment of viral myocarditis.

Infectious agents including viruses can infect the heart muscle, resulting in the development of heart inflammation called myocarditis. Chronic myocarditis can lead to dilated cardiomyopathy (DCM). DCM develops from the extensive extracellular matrix (ECM) remodeling caused by myocarditis and may result in heart failure.

Evaluation of pigtail macaques as a model for the effects of copper intrauterine devices on HIV infection.

Background: Long-acting, hormonal contraception may increase HIV risk. Copper intrauterine devices (IUDs) could serve as non-hormonal alternatives. We pilot a pigtail macaque model for evaluating HIV susceptibility factors during copper IUD use.

Exposure of pregnant women to cookstove-related household air pollution in urban and periurban Trujillo, Peru.

Although evidence suggests associations between maternal exposure to air pollution and adverse birth outcomes, pregnant women's exposure to household air pollution in developing countries is understudied. Personal exposures of pregnant women (N = 100) in Trujillo, Peru, to air pollutants and their indoor concentrations were measured. The effects of stove-use-related characteristics and ambient air pollution on exposure were determined using mixed-effects models.

Intravaginal ring eluting tenofovir disoproxil fumarate completely protects macaques from multiple vaginal simian-HIV challenges.

Topical preexposure prophylaxis interrupts HIV transmission at the site of mucosal exposure. Intermittently dosed vaginal gels containing the HIV-1 reverse transcriptase inhibitor tenofovir protected pigtailed macaques depending on the timing of viral challenge relative to gel application. However, modest or no protection was observed in clinical trials.

Sharing control of appointment length with patients in general practice: a qualitative study.

Background: There is little published research into the impact, on both doctor and patient, of handing over responsibility for choosing appointment length to the patient.

Aim: To investigate what impact giving patients control of their appointment length has on the patient and doctor experience.

Design And Setting: A qualitative study in a single medical practice in Inverness, Scotland.

Susceptibility to repeated, low-dose, rectal SHIVSF162P3 challenge is independent of TRIM5 genotype in rhesus macaques.

Infections following repeated, low-dose (RLD), mucal S(H)IV exposures of macaques are used to model sexual HIV exposures for biomedical prevention testing. Different susceptibilities among animals can complicate study designs. In rhesus macaques, TRIM5 alleles Q, CypA, and TFP are resistance factors for infection with some S(H)IV strains, but not for SIVmac239 due to its capsid properties.

Safety and pharmacokinetics of intravaginal rings delivering tenofovir in pig-tailed macaques.

Antiretroviral-based microbicides applied topically to the vagina may play an important role in protecting women from HIV infection. Incorporation of the nucleoside reverse transcriptase inhibitor tenofovir (TFV) into intravaginal rings (IVRs) for sustained mucosal delivery may lead to increased microbicide product adherence and efficacy compared with those of conventional vaginal formulations. Formulations of a novel "pod IVR" platform spanning a range of IVR drug loadings and daily release rates of TFV were evaluated in a pig-tailed macaque model.

Reduced inflammation and CD4 loss in acute SHIV infection during oral pre-exposure prophylaxis.

Background: The impact of pre-exposure prophylaxis (PrEP) with antiretrovirals on breakthrough HIV or SHIV infection is not fully documented. We addressed the hypothesis that SHIV(SF162P3) infection despite active PrEP results in altered early immune parameters, compared with untreated infection.

Methods: Eleven rhesus macaques were infected during repeated, rectal, low-dose SHIV(SF162P3) exposures while receiving concurrent oral PrEP (Truvada [n = 2] or GS7340 [n = 4]) or as untreated controls (n = 5).