The transcriptional landscape of polyploid wheat

The coordinated expression of highly related homoeologous genes in polyploid species underlies the phenotypes of many of the world's major crops. Here we combine extensive gene expression datasets to produce a comprehensive, genome-wide analysis of homoeolog expression patterns in hexaploid bread wheat. Bias in homoeolog expression varies between tissues, with ~30% of wheat homoeologs showing nonbalanced expression. We found expression asymmetries along wheat chromosomes, with homoeologs showing the largest inter-tissue, inter-cultivar, and coding sequence variation, most often located in high-recombination distal ends of chromosomes. These transcriptionally dynamic genes potentially represent the first steps toward neo- or subfunctionalization of wheat homoeologs. Coexpression networks reveal extensive coordination of homoeologs throughout development and, alongside a detailed expression atlas, provide a framework to target candidate genes underpinning agronomic traits in wheat.

Homeopathic Prevention and Management of Epidemic Diseases

Background Homeopathy has been used to treat epidemic diseases since the time of Hahnemann, who used Belladonna to treat scarlet fever. Since then, several approaches using homeopathy for epidemic diseases have been proposed, including individualization, combination remedies, genus epidemicus, and isopathy.

Methods The homeopathic research literature was searched to find examples of each of these approaches and to evaluate which were effective.

Results There is good experimental evidence for each of these approaches. While individualization is the gold standard, it is impractical to use on a widespread basis. Combination remedies can be effective but must be based on the symptoms of a given epidemic in a specific location. Treatment with genus epidemicus can also be successful if based on data from many practitioners. Finally, isopathy shows promise and might be more readily accepted by mainstream medicine due to its similarity to vaccination.

Conclusion Several different homeopathic methods can be used to treat epidemic diseases. The challenge for the future is to refine these approaches and to build on the knowledge base with additional rigorous trials. If and when conventional medicine runs out of options for treating epidemic diseases, homeopathy could be seen as an attractive alternative, but only if there is viable experimental evidence of its success.

Point-of-care and point-of-'can': leveraging reference-laboratory capacity for integrated diagnosis of fever syndromes in the tropics

BACKGROUND

There is an urgent need for integrated diagnosis of febrile syndromes able to account for multiple pathogens and to inform decisions for clinical care and public health.

AIMS

To reflect on the evolving roles of laboratory-based testing for non-malarial febrile illnesses (NMFIs) in low-resource settings, and to consider how advances in diagnostics, in connectivity and transport, and in implementation of quality systems may substantially enhance the capacity of reference laboratories to bridge the current gap between remote passive surveillance and clinically meaningful integrated fever diagnosis.

SOURCES

Iterative search of PubMed databases, organizational reports, and expert consultation.

CONTENT

Implementation of new technologies-such as very broad molecular panels for surveillance and mass spectrometry-may considerably diminish capability gaps in reference laboratories in low-resource settings. Although the need for clinical bacteriology diagnostics is now recognized, the lack of new simple and rapid phenotypic tests for antimicrobial resistance remains a key deficiency. Several initiatives to strengthen diagnostic preparedness for infectious disease outbreaks have highlighted the need for functional tiered laboratory networks. Recently, dramatic headway in connectivity-such as combining automated readers with the image processing and data transmission capabilities of smartphones-now allows for more complex testing and interfacing with distant laboratory information systems while reducing workload and errors. Together with connectivity to transmit and receive results, new approaches to specimen collection and transport-such as the validation of rectal swabs and the use of aerial drones to transport specimens to distant laboratories-now make remote testing feasible. The above innovations also open up the possibility of implementing quality systems through community-level diagnostic stewardship. Finally, strengthened laboratory networks actively support the feasibility of implementing quality-assured point-of-care testing where it is needed.

IMPLICATIONS

Recent advances offer the present-day possibility of innovations to re-invent the relationship between distant reference laboratories and end-users for integrated diagnosis of NMFIs.

Perceptions of risk and therapy among patients with Barrett's esophagus: a patient survey study

Nondysplastic Barrett's esophagus has a risk of progression to esophageal adenocarcinoma as low as 0.18-0.3% per person per year, and low-grade dysplasia as low as 0.5%. While adherence to guidelines and selection of management options varies, little is known about what modifies patient decision-making. This study aims to evaluate and identify factors that influence patient perceptions of risk and decisions about management. An independently developed and piloted survey was administered to patients at an academic hospital. Risk perception and desire for therapy were assessed using a standard reference gamble paradigm, and responses were stratified based on patient and disease characteristics. Data were analyzed with Student's t and chi-squared tests. A total of 42 of 50 patients with Barrett's esophagus and no prior endoscopic therapy participated (84% response; 76% nondysplastic Barrett's esophagus, 22% low-grade dysplasia, 2% indeterminate for dysplasia; mean age 61 years, 29% female). On average, patients perceived their risk of developing esophageal adenocarcinoma in the next year, 10 years and lifetime as 6, 14, and 19%, respectively. Nearly half viewed their lifetime risk of developing esophageal adenocarcinoma to be the same or higher than diabetes, heart disease, or colon cancer. Although 92% of patients felt surveillance beneficial, only 54% believed endoscopic therapy to be effective in most or all cases. As many as 83% of patients were willing to undergo endoscopic therapy with a hypothetical success rate as low as 70%, and a majority (64%) accepted complication rates up to 30%. Compared to patients with low risk perception of developing esophageal adenocarcinoma, those with high risk perception more often believed their risk for developing esophageal adenocarcinoma was greater than diabetes (p = 0.04) or colon cancer (p = 0.002). Those with lifetime low risk perception were less likely to accept modest complication rates (<10%) of therapy (P < 0.05). Age, gender, degree of dysplasia, lifetime endoscopies and duration of symptoms had no impact on perceived effectiveness of surveillance or therapy, and did not correlate with desire for treatment at varying levels of risk and effectiveness. Patients with Barrett's esophagus overestimate their risk of developing esophageal adenocarcinoma and will accept low success rates and high risk of complications to undergo endoscopic therapy. Baseline risk perception correlates with the desire for endoscopic therapy.

Alps to Apennines zircon roller coaster along the Adria microplate margin

We have traced the particle path of high-pressure metasedimentary rocks on Elba Island, Northern Apennines, with the help of a U-Pb-Hf detrital zircon study. One quarter of the analysed zircons are surprisingly young, 41-30 Ma, with a main age peak at ca. 32 Ma, indicating an unexpected early Oligocene maximum deposition age. These Oligocene ages with negative εHf indicate a volcanic source region in the central-southern Alps. Though young by geological means, these zircons record an extraordinary geodynamic history. They originated in a volcanic arc, during the convergence/collision of the the Adria microplate with Europe from ca. 65 to 30 Ma. Thereafter, the Oligocene zircons travelled ca. 400 km southward along the Adria margin and the accretionary prism to present-day Tuscany, where they were subducted to depths of at least 40 km. Shortly thereafter, they were brought to the surface again in the wake of hinge roll back of the Apennine subduction zone and the resulting rapid extensional exhumation. Such a zircon roller coaster requires a microplate that has back-to-back subduction zones with opposing polarities on two sides.

Mass media exposure and modern contraceptive use among married West African adolescents

PURPOSE

The purpose of this study was to examine whether family planning (FP) messaging is reaching married adolescent women in West Africa, and whether such messaging is associated with increased contraceptive use.

MATERIALS AND METHODS

We utilised data from the 2010 Demographic and Health Surveys (DHS) for Burkina Faso and Senegal (women 15-49; N = 17,067 and N = 15,688, respectively). We used chi-square tests to evaluate whether FP messaging exposure (via TV, radio, and/or print) differed according to socio-demographic characteristics. Subsequent analysis focussed on married adolescents (15-19; N = 961 in Burkina Faso, N = 996 in Senegal) which utilised propensity score matching and multivariable logistic regression models to test the association between self-reported FP messaging exposure and modern contraceptive use, knowledge of a modern contraceptive method, and future intention to use contraception.

RESULTS

A higher proportion of women 15-49 who reported FP messaging exposure were urban, from higher wealth quintiles, and had higher education levels, compared with unexposed women. A smaller proportion of adolescents reported exposure compared to older age groups. Among married adolescents, there was a positive but non-significant association between FP messaging exposure and use of a modern contraceptive method in Senegal (adjusted odds ratio (aOR) = 2.3; 95% CI: 0.92, 5.73). No such association was found in Burkina Faso (aOR = 0.98; 95% CI: 0.43, 2.26).

CONCLUSIONS

Mass media campaigns are not reaching the most vulnerable populations in West Africa, such as adolescents and poorer rural women. Adapting mass media campaigns to address these gaps is important for increasing exposure to FP messaging.

Preparing facilitators to use and adapt mathematics professional development materials productively

BACKGROUND

Determining whether a professional development program can be enacted with integrity in different settings and by different facilitators is critical to understanding efficacy. In this paper, we describe the two-stage preparation process of a facilitator as she prepared to use and adapt the highly specified Learning and Teaching Geometry video-based professional development materials with fidelity. The latter stage of the preparation process involved a rehearsal, during which the research team used two instruments to measure fidelity.

METHODS

Two existing instruments were used to explore fidelity through different lenses, including timing and modification of activities and learning goals.

RESULTS

Results from both fidelity instruments indicate that the facilitator used the materials as intended by the developers. However, these instruments did not capture important information regarding modifications the facilitator made, including timing and content-focused adaptations.

CONCLUSIONS

Suggestions are made with respect to measuring fidelity, preparing facilitators, and supporting productive adaptations.

Biomarkers of Tuberculosis Severity and Treatment Effect: A Directed Screen of 70 Host Markers in a Randomized Clinical Trial

More efficacious treatment regimens are needed for tuberculosis, however, drug development is impeded by a lack of reliable biomarkers of disease severity and of treatment effect. We conducted a directed screen of host biomarkers in participants enrolled in a tuberculosis clinical trial to address this need. Serum samples from 319 protocol-correct, culture-confirmed pulmonary tuberculosis patients treated under direct observation as part of an international, phase 2 trial were screened for 70 markers of infection, inflammation, and metabolism. Biomarker assays were specifically developed for this study and quantified using a novel, multiplexed electrochemiluminescence assay. We evaluated the association of biomarkers with baseline characteristics, as well as with detailed microbiologic data, using Bonferroni-adjusted, linear regression models. Across numerous analyses, seven proteins, SAA1, PCT, IL-1β, IL-6, CRP, PTX-3 and MMP-8, showed recurring strong associations with markers of baseline disease severity, smear grade and cavitation; were strongly modulated by tuberculosis treatment; and had responses that were greater for patients who culture-converted at 8weeks. With treatment, all proteins decreased, except for osteocalcin, MCP-1 and MCP-4, which significantly increased. Several previously reported putative tuberculosis-associated biomarkers (HOMX1, neopterin, and cathelicidin) were not significantly associated with treatment response. In conclusion, across a geographically diverse and large population of tuberculosis patients enrolled in a clinical trial, several previously reported putative biomarkers were not significantly associated with treatment response, however, seven proteins had recurring strong associations with baseline radiographic and microbiologic measures of disease severity, as well as with early treatment response, deserving additional study.