New Perspectives on the Hole Argument

This special issue of Foundations of Physics collects together articles representing some recent new perspectives on the hole argument in the history and philosophy of physics. Our task here is to introduce those new perspectives

Reconstructing (super)trees from data sets with missing distances: Not all is lost

The wealth of phylogenetic information accumulated over many decades of biological research, coupled with recent technological advances in molecular sequence generation, present significant opportunities for researchers to investigate relationships across and within the kingdoms of life. However, to make best use of this data wealth, several problems must first be overcome. One key problem is finding effective strategies to deal with missing data. Here, we introduce Lasso, a novel heuristic approach for reconstructing rooted phylogenetic trees from distance matrices with missing values, for datasets where a molecular clock may be assumed. Contrary to other phylogenetic methods on partial datasets, Lasso possesses desirable properties such as its reconstructed trees being both unique and edge-weighted. These properties are achieved by Lasso restricting its leaf set to a large subset of all possible taxa, which in many practical situations is the entire taxa set. Furthermore, the Lasso approach is distance-based, rendering it very fast to run and suitable for datasets of all sizes, including large datasets such as those generated by modern Next Generation Sequencing technologies. To better understand the performance of Lasso, we assessed it by means of artificial and real biological datasets, showing its effectiveness in the presence of missing data. Furthermore, by formulating the supermatrix problem as a particular case of the missing data problem, we assessed Lasso's ability to reconstruct supertrees. We demonstrate that, although not specifically designed for such a purpose, Lasso performs better than or comparably with five leading supertree algorithms on a challenging biological data set. Finally, we make freely available a software implementation of Lasso so that researchers may, for the first time, perform both rooted tree and supertree reconstruction with branch lengths on their own partial datasets

The physiological expression of inducible nitric oxide synthase (iNOS) in the human colon

Inducible nitric oxide synthase (iNOS) is expressed in the colonic epithelium in both inflammatory bowel disease and colorectal cancer. Nitric oxide (NO), the product of this enzyme, has been implicated in the pathogenesis of both conditions. However, there are conflicting data on whether iNOS is expressed in the normal, uninflamed human colon. To evaluate the expression of iNOS in histologically normal, non-inflamed human colonic mucosa. Reverse transcription polymerase chain reaction (RT-PCR), immunoblotting, and immunohistochemistry were used to investigate the expression of iNOS in 17 histologically normal specimens obtained at colectomy performed for colorectal neoplasia. In addition, 16 endoscopic mucosal biopsies, taken from normal individuals, were also evaluated. Eleven surgical specimens and 16 endoscopic biopsies from patients with refractory ulcerative colitis were used as inflammatory controls. All types of specimens expressed iNOS mRNA. Immunoblotting revealed a protein of approximately 130 kDa consistent with iNOS in mucosal extracts of 77% of normal individuals, and 85% of diseased controls. Immunolabelling localised this protein to the surface epithelium in most of the normal specimens and also to the crypt epithelium and inflammatory cells in the diseased controls. These findings provide evidence that iNOS is often expressed in the surface epithelium of non-inflamed human colon, suggesting that it is induced by local luminal factors, such as bacterial lipopolysaccharide (endotoxin). The resultant NO produced at this site might act as an oxidative barrier, reducing bacterial translocation and providing a means of defence against pathogenic microorganisms

Patient and public involvement in the design of clinical trials: An overview of systematic reviews

BACKGROUNDFunders encourage lay-volunteer inclusion in research. There are controversy and resistance, given concerns of role confusion, exploratory methods, and limited evidence about what value lay-volunteers bring to research. This overview explores these areas.METHODSEleven databases were searched without date or language restrictions for systematic reviews of public and patient involvement (PPI) in clinical trials design. This systematic overview of PPI included 27 reviews from which areas of good and bad practice were identified. Strengths, weaknesses, opportunities, and threats of PPI were explored through use of meta-narrative analysis.RESULTSInclusion criteria were met by 27 reviews ranging in quality from high (n = 7), medium (n = 14) to low (n = 6) reviews. Reviews were assessed using CERQUAL NICE, CASP for qualitative research and CASP for systematic reviews. Four reviews report risk of bias. Public involvement roles were primarily in agenda setting, steering committees, ethical review, protocol development, and piloting. Research summaries, follow-up, and dissemination contained PPI, with lesser involvement in data collection, analysis, or manuscript authoring. Trialists report difficulty in finding, retaining, and reimbursing volunteers. Respectful inclusion, role recognition, mutual flexibility, advance planning, and sound methods were reported as facilitating public involvement in research. Public involvement was reported to have increased the quantity and quality of patient relevant priorities and outcomes, enrollment, funding, design, implementation, and dissemination. Challenges identified include lack of clarity within common language, roles, and research boundaries, while logistical needs include extra time, training, and funding. Researchers report struggling to report involvement and avoid tokenism.CONCLUSIONSInvolving patients and the public in clinical trials design can be beneficial but requires resources, preparation, training, flexibility, and time. Issues to address include reporting deficits for risk of bias, study quality, and conflicts of interests. We need to address these tensions and improve dissemination strategies to increase PPI and health literacy.</p

Ribosomal DNA sequence heterogeneity reflects intraspecies phylogenies and predicts genome structure in two contrasting yeast species

The ribosomal RNA encapsulates a wealth of evolutionary information, including genetic variation that can be used to discriminate between organisms at a wide range of taxonomic levels. For example, the prokaryotic 16S rDNA sequence is very widely used both in phylogenetic studies and as a marker in metagenomic surveys and the internal transcribed spacer region, frequently used in plant phylogenetics, is now recognized as a fungal DNA barcode. However, this widespread use does not escape criticism, principally due to issues such as difficulties in classification of paralogous versus orthologous rDNA units and intragenomic variation, both of which may be significant barriers to accurate phylogenetic inference. We recently analyzed data sets from the Saccharomyces Genome Resequencing Project, characterizing rDNA sequence variation within multiple strains of the baker's yeast Saccharomyces cerevisiae and its nearest wild relative Saccharomyces paradoxus in unprecedented detail. Notably, both species possess single locus rDNA systems. Here, we use these new variation datasets to assess whether a more detailed characterization of the rDNA locus can alleviate the second of these phylogenetic issues, sequence heterogeneity, while controlling for the first. We demonstrate that a strong phylogenetic signal exists within both datasets and illustrate how they can be used, with existing methodology, to estimate intraspecies phylogenies of yeast strains consistent with those derived from whole-genome approaches. We also describe the use of partial Single Nucleotide Polymorphisms, a type of sequence variation found only in repetitive genomic regions, in identifying key evolutionary features such as genome hybridization events and show their consistency with whole-genome Structure analyses. We conclude that our approach can transform rDNA sequence heterogeneity from a problem to a useful source of evolutionary information, enabling the estimation of highly accurate phylogenies of closely related organisms, and discuss how it could be extended to future studies of multilocus rDNA systems. [concerted evolution; genome hydridisation; phylogenetic analysis; ribosomal DNA; whole genome sequencing; yeast]

Medical student wellbeing - a consensus statement from Australia and New Zealand

Abstract Background Medical student wellbeing – a consensus statement from Australia and New Zealand outlines recommendations for optimising medical student wellbeing within medical schools in our region. Worldwide, medical schools have responsibilities to respond to concerns about student psychological, social and physical wellbeing, but guidance for medical schools is limited. To address this gap, this statement clarifies key concepts and issues related to wellbeing and provides recommendations for educational program design to promote both learning and student wellbeing. The recommendations focus on student selection; learning, teaching and assessment; learning environment; and staff development. Examples of educational initiatives from the evidence-base are provided, emphasising proactive and preventive approaches to student wellbeing. Main recommendations The consensus statement provides specific recommendations for medical schools to consider at all stages of program design and implementation. These are:Design curricula that promote peer support and progressive levels of challenge to students.Employ strategies to promote positive outcomes from stress and to help others in need.Design assessment tasks to foster wellbeing as well as learning.Provide mental health promotion and suicide prevention initiatives.Provide physical health promotion initiatives.Ensure safe and health-promoting cultures for learning in on-campus and clinical settings.Train staff on student wellbeing and how to manage wellbeing concerns. Conclusion A broad integrated approach to improving student wellbeing within medical school programs is recommended. Medical schools should work cooperatively with student and trainee groups, and partner with clinical services and other training bodies to foster safe practices and cultures. Initiatives should aim to assist students to develop adaptive responses to stressful situations so that graduates are prepared for the realities of the workplace. Multi-institutional, longitudinal collaborative research in Australia and New Zealand is needed to close critical gaps in the evidence needed by medical schools in our region

Release of cell wall phenolic esters during hydrothermal pretreatment of rice husk and rice straw

Background: Rice husk and rice straw represent promising sources of biomass for production of renewable fuels and chemicals. For efficient utilisation, lignocellulosic components must first be pretreated to enable efficient enzymatic saccharification and subsequent fermentation. Existing pretreatments create breakdown products such as sugar-derived furans, and lignin-derived phenolics that inhibit enzymes and fermenting organisms. Alkali pretreatments have also been shown to release significant levels of simple, free phenolics such as ferulic acid that are normally esterified to cell wall polysaccharides in the intact plant. These phenolics have recently been found to have considerable inhibitory properties. The aim of this research has been to establish the extent to which such free phenolic acids are also released during hydrothermal pretreatment of rice straw (RS) and rice husk (RH). Results: RS and RH were subjected to hydrothermal pretreatments over a wide range of severities (1.57–5.45). FTIR analysis showed that the pretreatments hydrolysed and solubilised hemicellulosic moieties, leading to an enrichment of lignin and crystalline cellulose in the insoluble residue. The residues also lost the capacity for UV autofluorescence at pH 7 or pH 10, indicating the breakdown or release of cell wall phenolics. Saponification of raw RS and RH enabled identification and quantification of substantial levels of simple phenolics including ferulic acid (tFA), coumaric acid (pCA) and several diferulic acids (DiFAs) including 8-O-4′-DiFA, 8,5′-DiFA and 5,5′-DiFA. RH had higher levels of pCA and lower levels of tFA and DiFAs compared with RS. Assessment of the pretreatment liquors revealed that pretreatment-liberated phenolics present were not free but remained as phenolic esters (at mM concentrations) that could be readily freed by saponification. Many were lost, presumably through degradation, at the higher severities. Conclusion: Differences in lignin, tFA, DiFAs and pCA between RS and RH reflect differences in cell wall physiology, and probably contribute to the higher recalcitrance of RH compared with RS. Hydrothermal pretreatments, unlike alkali pretreatments, release cinnamic acid components as esters. The potential for pretreatment-liberated phenolic esters to be inhibitory to fermenting microorganisms is not known. However, the present study shows that they are found at concentrations that could be significantly inhibitory if released as free forms by enzyme activity

Analysis of a ten-day wave record obtained near Middleton Island in the Gulf of Alaska

Thesis (Ph.D.) University of Alaska Fairbanks, 1976A bottom mounted surface wave gauge was operated in 70 m of water near Middleton Island in the Gulf of Alaska for 10 days in October and November 1973. Standard fast-Fourier transform techniques have been applied to the data, and a second-order lowpass Butterworth filter has been designed to examine low-frequency components in the record. During the time the wave gauge was in operation, two earthquakes were reported with epicenters near the middle of the Aleutian Islands. The first had a surface wave magnitude of 6.4 on the Richter scale; the second, which occurred about 9 hours later, had a surface wave magnitude of 6.3. Spectra for data taken after the occurrence of these earthquakes have shown that generation of ocean waves by these quakes is questionable. Hourly spectra from the first part of the record reveal a peak around 0.065 Hz which moves toward higher frequencies for about 18 hours. The frequency of the peak then remains constant for about 24 hours, after which it again increases. The changes are well correlated with a large storm which remained stationary in the North Pacific, then moved rapidly into the Gulf of Alaska and subsided. Wave group velocities are used to estimate possible distances of the wave source from the gauge. The actual distances of the storm from the gauge show a close correlation with wave-derived distances. Comparison with changes in wave spectra for a storm in the North Atlantic in March 1968 indicates the same time rate of change in the spectral peak as was found in the North Pacific for time periods when the storms are subsiding