New Techniques for Viral Detection: Potential for Meningoencephalitis Diagnosis

Currently, the majority of cases of viral meningoencephalitis go undiagnosed as to the viral agent responsible for the disease. Of the cases actually diagnosed, the majority are found in the herpes virus family, where we have several sensitive and specific PCR tests for these more common etiologies. But what of the other viral causes? How can we even be sure a virus is responsible? It would help if we could be more sure of that, since there are always causes other than viruses to think about.

The paper below describes a new generic platform for detection of viral nucleic acids that can capture the needed information. This test seems to me to have a high potential to improve and streamline viral meningitis and encephalitis testing greatly, assuming that it is commercially (for the makers) and economically (for the hospitals) feasible, and can be shown to be sensitive and specific enough for good utility when used on day-old CSF samples.

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ABSTRACT

Virome Capture Sequencing Enables Sensitive Viral Diagnosis and Comprehensive Virome Analysis

Authors: Thomas Briesea, Amit Kapoora, Nischay Mishraa, Komal Jaina, Arvind Kumara, Omar J. Jabadoa, W. Ian Lipkina,

mbio, published online 22 September 2015

Insensitivity and technical complexity have impeded the implementation of high-throughput nucleic acid sequencing in differential diagnosis of viral infections in clinical laboratories. Here, we describe the development of a virome capture sequencing platform for vertebrate viruses (VirCapSeq-VERT) that increases the sensitivity of sequence-based virus detection and characterization. The system uses ~2 million probes that cover the genomes of members of the 207 viral taxa known to infect vertebrates, including humans. A biotinylated oligonucleotide library was synthesized on the NimbleGen cleavable array platform and used for solution-based capture of viral nucleic acids present in complex samples containing variable proportions of viral and host nucleic acids. The use of VirCapSeq-VERT resulted in a 100- to 10,000-fold increase in viral reads from blood and tissue homogenates compared to conventional Illumina sequencing using established virus enrichment procedures, including filtration, nuclease treatments, and RiboZero rRNA subtraction.

VirCapSeq-VERT had a limit of detection comparable to that of agent-specific real-time PCR in serum, blood, and tissue extracts. Furthermore, the method identified novel viruses whose genomes were approximately 40% different from the known virus genomes used for designing the probe library. The VirCapSeq-VERT platform is ideally suited for analyses of virome composition and dynamics.

Importance: VirCapSeq-VERT enables detection of viral sequences in complex sample backgrounds, including those found in clinical specimens, such as serum, blood, and tissue. The highly multiplexed nature of the system allows both the simultaneous identification and the comprehensive genetic characterization of all known vertebrate viruses, their genetic variants, and novel viruses. The operational simplicity and efficiency of the VirCapSeq-VERT platform may facilitate transition of high-throughput sequencing to clinical diagnostic as well as research applications.

So, will the NSA and CIA be investing in covert air samplers and rRNA sequencers next year?

Here.

ABSTRACT

Humans differ in their personal microbial cloud

Authors: James F. Meadow​, Adam E. Altrichter, Ashley C. Bateman, Jason Stenson, GZ Brown, Jessica L. Green, Brendan J.M. Bohannan

PEERJ: Published online September 22, 2015

Dispersal of microbes between humans and the built environment can occur through direct contact with surfaces or through airborne release; the latter mechanism remains poorly understood. Humans emit upwards of 106 biological particles per hour, and have long been known to transmit pathogens to other individuals and to indoor surfaces. However it has not previously been demonstrated that humans emit a detectible microbial cloud into surrounding indoor air, nor whether such clouds are sufficiently differentiated to allow the identification of individual occupants.

We used high-throughput sequencing of 16S rRNA genes to characterize the airborne bacterial contribution of a single person sitting in a sanitized custom experimental climate chamber. We compared that to air sampled in an adjacent, identical, unoccupied chamber, as well as to supply and exhaust air sources. Additionally, we assessed microbial communities in settled particles surrounding each occupant, to investigate the potential long-term fate of airborne microbial emissions. Most occupants could be clearly detected by their airborne bacterial emissions, as well as their contribution to settled particles, within 1.5–4 h. Bacterial clouds from the occupants were statistically distinct, allowing the identification of some individual occupants.

Our results confirm that an occupied space is microbially distinct from an unoccupied one, and demonstrate for the first time that individuals release their own personalized microbial cloud.

Working long hours (> 55 hours per week) linked to an increased risk of MI and stroke.

According to this article in the Lancet this week, working long hours can increase risk of coronary artery disease events by a factor of 13% (relative risk, 1.13) and the risk of stroke by 33% (relative risk, 1.33). The researchers adjusted for exercise and hypertension in the analysis but did not adjust for sleep quantity or quality, an omission that may be significant, as any worker working days and occasional second job nights and physicians whose long hours of work are added to significantly by sleep-interrupting night call may know.

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ABSTRACT

Long working hours and risk of coronary heart disease and stroke: a systematic review and meta-analysis of published and unpublished data for 603 838 individuals

Prof Mika Kivimäki, PhDcorrespondenceemail, Markus Jokela, PhD, Solja T Nyberg, MSc, Archana Singh-Manoux, PhD, Eleonor I Fransson, PhD, Prof Lars Alfredsson, PhD, Prof Jakob B Bjorner, MD, Marianne Borritz, MD, Hermann Burr, PhD, Annalisa Casini, PhD, Els Clays, PhD, Prof Dirk De Bacquer, PhD, Prof Nico Dragano, PhD, Prof Raimund Erbel, MD, Goedele A Geuskens, PhD, Mark Hamer, PhD, Wendela E Hooftman, PhD, Irene L Houtman, PhD, Prof Karl-Heinz Jöckel, Prof France Kittel, PhD, Prof Anders Knutsson, MD, Prof Markku Koskenvuo, MD, Thorsten Lunau, MSc, Ida E H Madsen, PhD, Martin L Nielsen, MD, Maria Nordin, PhD, Tuula Oksanen, MD, Jan H Pejtersen, PhD, Jaana Pentti, MSc, Prof Reiner Rugulies, PhD, Prof Paula Salo, PhD, Martin J Shipley, MSc, Prof Johannes Siegrist, PhD, Prof Andrew Steptoe, DSc, Prof Sakari B Suominen, MD, Prof Töres Theorell, MD, Prof Jussi Vahtera, MD, Prof Peter J M Westerholm, MD, Prof Hugo Westerlund, PhD, Dermot O'Reilly, PhD, Prof Meena Kumari, PhD, G David Batty, DSc, Jane E Ferrie, PhD, Prof Marianna Virtanen, PhD for the IPD-Work Consortium

Published Online: 19 August 2015

Open AccessArticle has an altmetric score of 175

DOI: http://dx.doi.org/10.1016/S0140-6736(15)60295-1 |

Summary

Background

Long working hours might increase the risk of cardiovascular disease, but prospective evidence is scarce, imprecise, and mostly limited to coronary heart disease. We aimed to assess long working hours as a risk factor for incident coronary heart disease and stroke.

Methods

We identified published studies through a systematic review of PubMed and Embase from inception to Aug 20, 2014. We obtained unpublished data for 20 cohort studies from the Individual-Participant-Data Meta-analysis in Working Populations (IPD-Work) Consortium and open-access data archives. We used cumulative random-effects meta-analysis to combine effect estimates from published and unpublished data.

Findings

We included 25 studies from 24 cohorts in Europe, the USA, and Australia. The meta-analysis of coronary heart disease comprised data for 603 838 men and women who were free from coronary heart disease at baseline; the meta-analysis of stroke comprised data for 528 908 men and women who were free from stroke at baseline. Follow-up for coronary heart disease was 5·1 million person-years (mean 8·5 years), in which 4768 events were recorded, and for stroke was 3·8 million person-years (mean 7·2 years), in which 1722 events were recorded. In cumulative meta-analysis adjusted for age, sex, and socioeconomic status, compared with standard hours (35–40 h per week), working long hours (≥55 h per week) was associated with an increase in risk of incident coronary heart disease (relative risk [RR] 1·13, 95% CI 1·02–1·26; p=0·02) and incident stroke (1·33, 1·11–1·61; p=0·002). The excess risk of stroke remained unchanged in analyses that addressed reverse causation, multivariable adjustments for other risk factors, and different methods of stroke ascertainment (range of RR estimates 1·30–1·42). We recorded a dose–response association for stroke, with RR estimates of 1·10 (95% CI 0·94–1·28; p=0·24) for 41–48 working hours, 1·27 (1·03–1·56; p=0·03) for 49–54 working hours, and 1·33 (1·11–1·61; p=0·002) for 55 working hours or more per week compared with standard working hours (ptrend<0·0001).

Interpretation

Employees who work long hours have a higher risk of stroke than those working standard hours; the association with coronary heart disease is weaker. These findings suggest that more attention should be paid to the management of vascular risk factors in individuals who work long hours.

Image credit: ACP (acpinternist.org)

New vaccine for Ebola seems safe and effective.

Here.

For training working memory, run an obstacle course?

Prior studies have shown the benefit of walking and other moderate aerobic exercise programs on verbal memory and other cognition in the elderly. Working memory is usually intact in such subjects, so that the effects on working memory of walking programs are less well documented.

According to this article, working memory benefited from exercise requiring both locomotion and proprioception. This brings up the intriguing possibility of specific exercise programs to retrain specific cognitive deficits. On the critical side, I'd note that the results would have been more robust as specific to activities like climbing if a control group of fast walking or other aerobic program had been done, rather than just classroom and yoga control groups.

ABSTRACT

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Ross G. Alloway and Tracy Packiam Alloway (2015) THE WORKING MEMORY BENEFITS OF PROPRIOCEPTIVELY DEMANDING TRAINING: A PILOT STUDY, . Perceptual and Motor Skills: Volume 120, Issue , pp. 766-775.

doi: 10.2466/22.PMS.120v18x1

THE WORKING MEMORY BENEFITS OF PROPRIOCEPTIVELY DEMANDING TRAINING: A PILOT STUDY1, 2

Ross G. Alloway1 and Tracy Packiam Alloway1 1University of North Florida

Summary.—The aim of this study was to investigate the effect of proprioception on working memory. It was also of interest whether an acute and highly intensive period of exercise would yield working memory gains. The training group completed a series of proprioceptively demanding exercises. There were also control classroom and yoga groups. Working memory was measured using a backward digit recall test. The data indicated that active, healthy adults who undertook acute, proprioceptively demanding training improved working memory scores compared to the classroom and yoga groups. One possible reason that the training yielded significant working memory gains could be that the training was proprioceptively dynamic, requiring proprioception and at least one other factor—such as locomotion or navigation—at the same time, which may have contributed to the improvements in working memory performance.

Hawaiian Reef Photos: 'Alakuma and Humuhumunukunukuapuaʻa

I went snorkeling yesterday with ohana at Two-Step (just beyond the rocks bordering Keone'ele Cove at the north of Pu'uhonua o Honaunau, the old City of Refuge in south Kona district). This spot has some of the best coral formations easily accessible from the shorelines of the Big Island.

The 'Alakuma (Carpilius maculatus) has many common names: spotted reef crab, or the seven-eleven crab from numberings of its spotted markings. From the Hawaiian just-so story of the crab wounding the grasping fingers of a sea-god, it's also been called the bloody finger crab, with its bloodred spots as the god's fingerprints. Some of the locals here claim it can be poisonous to eat, perhaps from its diet of occasionally poisonous cone snails?

The state fish of Hawaii is the Humuhumunukunukuapuaʻa (Rhinecanthus rectangulus), a reef triggerfish with a mouthful of a name.

Sexual Identification: Genotype, Phenotype, and Sociotype

An amazing cuttlefish trick: underwater cross-dressing in body coloration. Wow.

Sexual identity is a cognitive, intentional state about ourselves. Like all intentional states, it may need to be subjected to error correction. On the other hand, the sexual classification of living things is an aspect of biology. In biology, a given organism may be identified as to its gender by genotype (determined mostly by XX versus XY chromosomal analysis in humans, with the usual border cases), or by phenotype (primary and secondary mammalian sexual characteristics in the case of humans).

In humans, the postmodernist conceit that gender is different from the biology of genotype and phenotype suggests that what we need is a sociotype of sex. A sociotype would be male and female as self identified or identified by one's society (for example, the M or F on the driver's license or birth certificate, which is one's legally defined gender).

Denying that biology is destiny here is mere foolish conceit on the part of the postmodernist. It is like saying that the cuttlefish is changing its sex by altering its color patterning. No biologist would agree that it does that.