Analysis of Methods for Screening Plant Viruses

Potato virus X, belonging to the group of viruses known as the potexviruses, is an economically important virus, affecting potato crops worldwide. The detection of this and other plant viruses has, so far, mainly been dependent upon the antigen-antibody assays such as the enzyme-linked immunosorbent assay (or ELISA). By using the ELISA: 1) a large number of samples can be handled at the same time; 2) the antigen-antibody reaction is specific for the virus; 3) results can be obtained within a couple of hours using prepared trays, 4) the assay uses an immunoglobulin marker in place of a radiolabelled isotope, resulting in negligable loss of activity after extended periods of time, and 5) the assay is sensitive with small amounts of enzyme-labelled immunoglobulin, thereby dispensing with expensive detection systems. The use of the ELISA for the detection of PVX strains in crude plant sap showed a high degree of sensitivity. The assay could detect isolates of both strain-group 3 (PVX/PVX N) and strain-group 2 (PVB) to at least 10 x dilution (reaching 10 x dilution with one isolate of strain-group 3). The assay was also very sensitive in the detection of purified PVX/PVB viral particles, detecting 20 ng of viral particles or 200 pg RNA with purified RNA samples (equivalent to approximately 33 ng virus particles). However, the main disadvantage of using serological assays, even with one as sensitive as the ELISA, is that only viral antigens are detected, giving no information about the infectious RNA within. An alternative system was, therefore, developed with the aim that it would be as sensitive as the ELISA, easy to handle, and one which allowed the detection of the infectious viral RNA. The assay was a dotblot system using nitrocellulose to which the RNA was bound by baking. Aliquots of infected sap, purified viral particles or RNA were applied and bound to sheets of nitrocellulose. The filter, containing the samples, was then be hybridised with labelled complementary DNA probes, detecting the RNA. Two systems were devised for the hybridisation stage of the assay using two different probes, one radiolabelled and the other a biotinylated probe. Both 32P-labelled and biotinylated nucleotides were incorporated into cDNA probes, using PVX N RNA as template. These probes hybridised to complementary sequences, detecting the signals on the filters by autoradiography for the 32P-labelled probe and with an enzyme reaction (streptavidin conjugated to biotinylated alkaline phosphatase) for the the biotinylated probe. The alkaline peroxidase-conjugated streptavidin, in the presence of substrates, converted the substrates into visible precipitates on the filters. With the radiolabelled probe, RNA in the viral particles of crude sap could only be detected to 10-1 x dilution with both PVB and PVX isolates (reaching 10-2 x dilution maximum), compared to 10-3 to 10-6 obtained with the same sample using ELISA. For the detection of purified viral particles, the radiolabelled probe was sensitive to 20 ng and to 200 pg with purified RNA. Results for the biotinylated probe were identical, although the radiolabelled probe could be increased in sensitivity when the exposure time to X-ray film was increased. A third probe, produced by cDNA cloning a section of the PVX N RNA template and labelled by nick translation, was also used to detect complementary RNA on filters. The final clone (pPVX21 N) used for hybridisations contained an insert between 550-600 bp in length but only detected PVX RNA in the PVX (strain-Group 3, PBI) crude sap samples to 10 and purified RNA to 20 ng with a 7 day exposure, results which were much less sensitive than either of the cDNA probes by at least 2 logs. However, an increase of non-specific hybridisation was also noted with the filter. The nick-translated probe did not detect PVB (strain-Group 2, PBI) or PVX N in the crude sap isolates or purified viral particles at all, unlike the cDNA probes. In addition to the development of these assays for the detection of viral RNA, studies were undertaken to obtain structural information on the 3' terminal region of the RNA. These studies included the synthesis of complementary DNA from an RNA template in the presence and absence of various primers. Initial results conflicted with the published literature of Sonenberg (1978) which reported the absence of poly (A) sequences at it 3' terminus, but confirmed the report of a poly (A)-rich region in PVX RNA by Morozov et al. (1983). These results were checked by affinity chromatography on oligo d(T) cellulose columns which selectively bound poly (A)-rich regions in RNAs. These experiments were further backed by selectively degrading the RNA with enzymes which could then be sized on polyacrylamide gels. The position of the poly (A) sequences was determined using RNase H, an enzyme which specifically attacked and degraded these poly (A) nucleotide sequences when bound to oligo d(T), leaving the RNA in two or more fragments which could then be analysed by polyacrylamide gel electrophoresis. Lastly, the size and position of these poly (A) sequences were checked by direct RNA sequencing, a method dependent upon a series of base-specific RNases. PVX RNA was labelled, purified on a 4% polyacrylamide gel to remove excess label, digested with the enzymes and analysed on a thin gel by thin-layer, polyacrylamide gel electrophoresis and autoradiography. The size of the poly (A) region in PVX N RNA was found to be between 8 and 16 nucleotides long and positioned at the 3' terminus rather than being an internal sequence

Fourier Growth of Structured ??-Polynomials and Applications

We analyze the Fourier growth, i.e. the L? Fourier weight at level k (denoted L_{1,k}), of various well-studied classes of "structured" m F?-polynomials. This study is motivated by applications in pseudorandomness, in particular recent results and conjectures due to [Chattopadhyay et al., 2019; Chattopadhyay et al., 2019; Eshan Chattopadhyay et al., 2020] which show that upper bounds on Fourier growth (even at level k = 2) give unconditional pseudorandom generators. Our main structural results on Fourier growth are as follows: - We show that any symmetric degree-d m F?-polynomial p has L_{1,k}(p) ? Pr [p = 1] ? O(d)^k. This quadratically strengthens an earlier bound that was implicit in [Omer Reingold et al., 2013]. - We show that any read-? degree-d m F?-polynomial p has L_{1,k}(p) ? Pr [p = 1] ? (k ? d)^{O(k)}. - We establish a composition theorem which gives L_{1,k} bounds on disjoint compositions of functions that are closed under restrictions and admit L_{1,k} bounds. Finally, we apply the above structural results to obtain new unconditional pseudorandom generators and new correlation bounds for various classes of m F?-polynomials

Proof over promise: towards a more inclusive ranking of Dutch academics in Economics & Business

The Dutch Economics top-40, based on publications in ISI listed journals, is - to the best of our knowledge - the oldest ranking of individual academics in Economics and is well accepted in the Dutch academic community. However, this ranking is based on publication volume, rather than on the actual impact of the publications in question. This paper therefore uses two relatively new metrics, the citations per author per year (CAY) metric and the individual annual h-index (hIa) to provide two alternative, citation-based, rankings of Dutch academics in Economics & Business. As a data source, we use Google Scholar instead of ISI to provide a more comprehensive measure of impact, including citations to and from publications in non-ISI listed journals, books, working and conference papers. The resulting rankings are shown to be substantially different from the original ranking based on publications. Just like other research metrics, the CAY or hIa-index should never be used as the sole criterion to evaluate academics. However, we do argue that the hIa-index and the related citations per author per year metric provide an important additional perspective over and above a ranking based on publications in high impact journals alone. Citation-based rankings are also shown to inject a higher level of diversity in terms of age, gender, discipline and academic affiliation and thus appear to be more inclusive of a wider range of scholarship

Myonuclear accretion is a determinant of exercise-induced remodeling in skeletal muscle.

Skeletal muscle adapts to external stimuli such as increased work. Muscle progenitors (MPs) control muscle repair due to severe damage, but the role of MP fusion and associated myonuclear accretion during exercise are unclear. While we previously demonstrated that MP fusion is required for growth using a supra-physiological model (Goh and Millay, 2017), questions remained about the need for myonuclear accrual during muscle adaptation in a physiological setting. Here, we developed an 8 week high-intensity interval training (HIIT) protocol and assessed the importance of MP fusion. In 8 month-old mice, HIIT led to progressive myonuclear accretion throughout the protocol, and functional muscle hypertrophy. Abrogation of MP fusion at the onset of HIIT resulted in exercise intolerance and fibrosis. In contrast, ablation of MP fusion 4 weeks into HIIT, preserved exercise tolerance but attenuated hypertrophy. We conclude that myonuclear accretion is required for different facets of exercise-induced adaptive responses, impacting both muscle repair and hypertrophic growth

Symmetry energy of dense matter in holographic QCD

We study the nuclear symmetry energy of dense matter using holographic QCD. To this end, we consider two flavor branes with equal quark masses in a D4/D6/D6 model. We find that at all densities the symmetry energy monotonically increases. At small densities, it exhibits a power law behavior with the density, $E_{\rm sym} \sim \rho^{1/2}$.Comment: 9 pages, 3 figure

Learning Moore Machines from Input-Output Traces

The problem of learning automata from example traces (but no equivalence or membership queries) is fundamental in automata learning theory and practice. In this paper we study this problem for finite state machines with inputs and outputs, and in particular for Moore machines. We develop three algorithms for solving this problem: (1) the PTAP algorithm, which transforms a set of input-output traces into an incomplete Moore machine and then completes the machine with self-loops; (2) the PRPNI algorithm, which uses the well-known RPNI algorithm for automata learning to learn a product of automata encoding a Moore machine; and (3) the MooreMI algorithm, which directly learns a Moore machine using PTAP extended with state merging. We prove that MooreMI has the fundamental identification in the limit property. We also compare the algorithms experimentally in terms of the size of the learned machine and several notions of accuracy, introduced in this paper. Finally, we compare with OSTIA, an algorithm that learns a more general class of transducers, and find that OSTIA generally does not learn a Moore machine, even when fed with a characteristic sample

Normal levels of p27Xic1 are necessary for somite segmentation and determining pronephric organ size

The Xenopus laevis cyclin dependent kinase inhibitor p27Xic1 has been shown to be involved in exit from the cell cycle and differentiation of cells into a quiescent state in the nervous system, muscle tissue, heart and retina. We show that p27Xic1 is expressed in the developing kidney in the nephrostomal regions. Using over-expression and morpholino oligonucleotide (MO) knock-down approaches we show normal levels of p27Xic1 regulate pronephros organ size by regulating cell cycle exit. Knock-down of p27Xic1 expression using a MO prevented myogenesis, as previously reported; an effect that subsequently inhibits pronephrogenesis. Furthermore, we show that normal levels of p27Xic1 are required for somite segmentation also through its cell cycle control function. Finally, we provide evidence to suggest correct paraxial mesoderm segmentation is not necessary for pronephric induction in the intermediate mesoderm. These results indicate novel developmental roles for p27Xic1, and reveal its differentiation function is not universally utilised in all developing tissues

Health services research in the public healthcare system in Hong Kong: An analysis of over 1 million antihypertensive prescriptions between 2004-2007 as an example of the potential and pitfalls of using routinely collected electronic patient data

<b>Objectives</b> Increasing use is being made of routinely collected electronic patient data in health services research. The aim of the present study was to evaluate the potential usefulness of a comprehensive database used routinely in the public healthcare system in Hong Kong, using antihypertensive drug prescriptions in primary care as an example.<p></p> <b>Methods</b> Data on antihypertensive drug prescriptions were retrieved from the electronic Clinical Management System (e-CMS) of all primary care clinics run by the Health Authority (HA) in the New Territory East (NTE) cluster of Hong Kong between January 2004 and June 2007. Information was also retrieved on patients’ demographic and socioeconomic characteristics, visit type (new or follow-up), and relevant diseases (International Classification of Primary Care, ICPC codes). <p></p> <b>Results</b> 1,096,282 visit episodes were accessed, representing 93,450 patients. Patients’ demographic and socio-economic details were recorded in all cases. Prescription details for anti-hypertensive drugs were missing in only 18 patients (0.02%). However, ICPC-code was missing for 36,409 patients (39%). Significant independent predictors of whether disease codes were applied included patient age > 70 years (OR 2.18), female gender (OR 1.20), district of residence (range of ORs in more rural districts; 0.32-0.41), type of clinic (OR in Family Medicine Specialist Clinics; 1.45) and type of visit (OR follow-up visit; 2.39). <p></p> In the 57,041 patients with an ICPC-code, uncomplicated hypertension (ICPC K86) was recorded in 45,859 patients (82.1%). The characteristics of these patients were very similar to those of the non-coded group, suggesting that most non-coded patients on antihypertensive drugs are likely to have uncomplicated hypertension. <p></p> <b>Conclusion</b> The e-CMS database of the HA in Hong Kong varies in quality in terms of recorded information. Potential future health services research using demographic and prescription information is highly feasible but for disease-specific research dependant on ICPC codes some caution is warranted. In the case of uncomplicated hypertension, future research on pharmaco-epidemiology (such as prescription patterns) and clinical issues (such as side-effects of medications on metabolic parameters) seems feasible given the large size of the data set and the comparability of coded and non-coded patients

Hypofractionated radiotherapy has the potential for second cancer reduction

<p>Abstract</p> <p>Background and Purpose</p> <p>A model for carcinoma and sarcoma induction was used to study the dependence of carcinogenesis after radiotherapy on fractionation.</p> <p>Materials and methods</p> <p>A cancer induction model for radiotherapy doses including fractionation was used to model carcinoma and sarcoma induction after a radiation treatment. For different fractionation schemes the dose response relationships were obtained. Tumor induction was studied as a function of dose per fraction.</p> <p>Results</p> <p>If it is assumed that the tumor is treated up to the same biologically equivalent dose it was found that large dose fractions could decrease second cancer induction. The risk decreases approximately linear with increasing fraction size and is more pronounced for sarcoma induction. Carcinoma induction decreases by around 10% per 1 Gy increase in fraction dose. Sarcoma risk is decreased by about 15% per 1 Gy increase in fractionation. It is also found that tissue which is irradiated using large dose fractions to dose levels lower than 10% of the target dose potentially develop less sarcomas when compared to tissues irradiated to all dose levels. This is not observed for carcinoma induction.</p> <p>Conclusions</p> <p>It was found that carcinoma as well as sarcoma risk decreases with increasing fractionation dose. The reduction of sarcoma risk is even more pronounced than carcinoma risk. Hypofractionation is potentially beneficial with regard to second cancer induction.</p