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Motivation Pangenomes provide novel insights for population and quantitative genetics, genomics and breeding not available from studying a single reference genome. Instead, a species is better represented by a pangenome or collection of genomes. Unfortunately, managing and using pangenomes for genomically diverse species is computationally and practically challenging. We developed a trellis graph representation anchored to the reference genome that represents most pangenomes well and can be used to impute complete genomes from low density sequence or variant data. Results The Practical Haplotype Graph (PHG) is a pangenome pipeline, database (PostGRES & SQLite), data model (Java, Kotlin or R) and Breeding API (BrAPI) web service. The PHG has already been able to accurately represent diversity in four major crops including maize, one of the most genomically diverse species, with up to 1000-fold data compression. Using simulated data, we show that, at even 0.1× coverage, with appropriate reads and sequence alignment, imputation results in extremely accurate haplotype reconstruction. The PHG is a platform and environment for the understanding and application of genomic diversity. Availability and implementation All resources listed here are freely available. The PHG Docker used to generate the simulation results is https://hub.docker.com/ as maizegenetics/phg:0.0.27. PHG source code is at https://bitbucket.org/bucklerlab/practicalhaplotypegraph/src/master/. The code used for the analysis of simulated data is at https://bitbucket.org/bucklerlab/phg-manuscript/src/master/. The PHG database of NAM parent haplotypes is in the CyVerse data store (https://de.cyverse.org/de/) and named/iplant/home/shared/panzea/panGenome/PHG_db_maize/phg_v5Assemblies_20200608.db. Supplementary information Supplementary data are available at Bioinformatics online.

Funded by the NSF CubeSat and NASA ELaNa programs, the Dynamic Ionosphere CubeSat Experiment (DICE) mission consists of two 1.5U CubeSats which were launched into an eccentric low Earth orbit on October 28, 2011. Each identical spacecraft carries two Langmuir probes to measure ionospheric in-situ plasma densities, electric field probes to measure in-situ DC and AC electric fields, and a science grade magnetometer to measure in-situ DC and AC magnetic fields. Given the tight integration of these multiple sensors with the CubeSat platforms, each of the DICE spacecraft is effectively a “sensor-sat” capable of comprehensive ionospheric diagnostics. The use of two identical sensor-sats at slightly different orbiting velocities in nearly identical orbits permits the de-convolution of spatial and temporal ambiguities in the observations of the ionosphere from a moving platform. In addition to demonstrating nanosat-based constellation science, the DICE mission is advancing a number of groundbreaking CubeSat technologies including miniaturized mechanisms and high-speed downlink communications.

As an extension of the BSP076 study (see the article 'Collaborative Study for the Standardisation of the Histamine Sensitizing Test in Mice and the CHO Cell-based Assay for the Residual Toxicity Testing of Acellular Pertussis Vaccines (BSP076)', page 51 of this issue of Pharmeuropa BioScientific Notes), it was decided to publish the following experimental method for the temperature-based histamine-sensitisation test, validated at the SSI (Statens Serum Institut, Denmark), as a working basis for the growth of the method in individual laboratories.

Based on the energy balance equation for a crop canopy a method is explicitly described for determination of a region of predicted values of crop canopy-air temperature in relation to vapor pressure deficit as well as for estimation of the lower base line as the best fit line through that region. Theoretical lower base lines are calculated for a number of climate crop parameter combinations (net radiation 500–700 W m-2, temperature 10–30°C, vapor pressure 0–3 kPa, aerodynamic resistance 5–25 s m-1 and crop resistance 20–60 s m-1) and the results are presented in terms of values of intercept and slope of the lower base lines obtained. Within the range of parameters employed the analysis showed that net radiation has only limited influence on the slope whereas the intercept increase for increasing values of net radiation, that slope and intercept increase and decrease, respectively, for increasing values of the aerodynamic resistance whereas the slope as well as the intercept increase for increasin...

We describe a fiber-optic interferometer that employs wavelength changes to achieve maximum sensitivity. Wavelength changes are induced by adjusting the operating temperature of the laser, eliminating the need for an actuator to vary the spacing between the sensing fiber and the object to be monitored. The instrument and techniques described are suitable for cryogenic, high vacuum applications such as magnetic resonance force microscopy, where space is limited and micromanipulation can be challenging. The noise floor of 1.6×10−3 nm/Hz is adequate for monitoring subangstrom displacement of force microscope cantilevers.

Transition state analogue boronic acid inhibitors mimicking the structures and interactions of good penicillin substrates for the TEM-1 beta-lactamase of Escherchia coli were designed using graphic analyses based on the enzyme's 1.7 A crystallographic structure. The synthesis of two of these transition state analogues, (1R)-1-phenylacetamido-2-(3-carboxyphenyl)ethylboronic acid (1) and (1R)-1-acetamido-2-(3-carboxy-2-hydroxyphenyl)ethylboronic acid (2), is reported. Kinetic measurements show that, as designed, compounds 1 and 2 are highly effective deacylation transition state analogue inhibitors of TEM-1 beta-lactamase, with inhibition constants of 5.9 and 13 nM, respectively. These values identify them as among the most potent competitive inhibitors yet reported for a beta-lactamase. The best inhibitor of the current series was (1R)-1-phenylacetamido-2-(3-carboxyphenyl)ethylboronic acid (1, K(I) = 5.9 nM), which resembles most closely the best known substrate of TEM-1, benzylpenicillin (penicillin G). The high-resolution crystallographic structures of these two inhibitors covalently bound to TEM-1 are also described. In addition to verifying the design features, these two structures show interesting and unanticipated changes in the active site area, including strong hydrogen bond formation, water displacement, and rearrangement of side chains. The structures provide new insights into the further design of this potent class of beta-lactamase inhibitors.

We report theory and observations of paramagnetic resonance in a measured field gradient of 44,000 T per meter by the technique of magnetic resonance force microscopy (MRFM). Resonance was induced in a dilute solid solution of diphenylpicrylhydrazyl in polystyrene at 77 and 10 K by an amplitude-modulated microwave field. This modulated the force between resonant sample spins and a micrometer-scale SmCo magnetic tip on a force microscope cantilever. The force signals were typically of order 10 fN, and were detected above a thermal noise floor of 80 aN per root hertz at 10 K, equivalent to a magnetic moment noise of 200 μ B per root hertz of bandwidth. Resonance saturation was readily observed. Starting with the Bloch equations, we derived simple analytic expressions for the predicted cantilever signal amplitudes and T 1 -dependent phase lags, valid at low microwave power levels. For power levels below saturation, the data were in good agreement with the Bloch equation predictions, while above saturation the measured force increased more slowly with power than predicted. Several ESR mechanisms which might lead to non-Bloch dynamics in the MRFM environment are reviewed. Spin-relaxation mechanisms are also reviewed. A detailed description of the experimental apparatus is offered.

The biosynthesis of clavulanic acid and related clavam metabolites is only now being elucidated. Understanding of this pathway has resulted from a combination of both biochemical studies of purified biosynthetic enzymes, and molecular genetic studies of the genes encoding these enzymes. Clavulanic acid biosynthesis has been most thoroughly investigated in Streptomyces clavuligerus where the biosynthetic gene cluster resides immediately adjacent to the cluster of cephamycin biosynthetic genes. A minimum of eight structural genes have been implicated in clavulanic acid biosynthesis, although more are probably involved. While details of the early and late steps of the pathway remain unclear, synthesis proceeds from arginine and pyruvate, as the most likely primary metabolic precursors, through the monocyclic beta-lactam intermediate, proclavaminic acid, to the bicyclic intermediate, clavaminic acid, which is a branch point leading either to clavulanic acid or the other clavams. Conversion of clavaminic acid to clavulanic acid requires side chain modification as well as inversion of ring stereochemistry. This stereochemical change occurs coincident with acquisition of the beta-lactamase inhibitory activity which gives clavulanic acid its therapeutic and commercial importance. In contrast, the other clavam metabolites all arise from clavaminic acid with retention of configuration and lack beta-lactamase inhibitory activity.

Left ventricular diastolic dysfunction is currently recognized in patients with different heart diseases. Three abnormal filling patterns of the left ventricle detected by pulsed-Doppler echocardiography are observed in patients with heart disease. Each filling pattern is characterised by different symptoms, and by differences in function and dimension of the left atrium and filling pressures. Mitral and pulmonary venous flow velocities and durations obtained by pulsed Doppler technique can be used to evaluate left ventricular diastolic function in patients with different heart diseases. However, several factors affect the transmitral and pulmonary venous flow such as age, heart rate, positioning of the sample volume and aortic- and mitral valve insufficiency. These factors must be taken into consideration when the diastolic function is evaluated by pulsed Doppler technique.

Silent ischaemia (objective signs of myocardial ischaemia without symptoms) can be diagnosed using a conventional exercise-test or ambulatory Holter monitoring. Silent ischaemia is a frequent phenomenon in patients with ischaemic heart disease, i.e. patients with angina pectoris or previous myocardial infarction. The reason why ischaemia is symptomatic in some cases, and asymptomatic in others is unknown. Different possible mechanisms are discussed. Myocardial ischaemia, symptomatic or not is accompanied by a compromised function of the left ventricle, including reduced ejection fraction during exercise. In selected groups of patients, silent ischaemia is related to an impaired prognosis, while it does not seem to carry any prognostic information in other groups of patients. Silent ischaemia can be treated/reduced using antianginal medication or revascularization, but for the time being it is not known if treatment can improve prognosis. Studies concerning the latter are under way.

A 29-year-old woman with two previous births, suffered a non-fatal Q-wave myocardial infarction early in the second trimester of pregnancy. She gave uncomplicated birth to a healthy child 25 weeks later. Post-partum coronary arteriography revealed a 66% stenosis on the left anterior descending coronary artery. The patient was successfully treated with percutaneous transluminal coronary angioplasty

Amiodarone (Cordarone) is used in the treatment of cardiac arrhythmias. A blue-grey skin pigmentation appears after long term use or a high concentration of amiodarone. Two cases are described. Histopathological findings of skin punch biopsies from the face showed collections of yellow-brown granula pigment within histiocytes throughout the dermis. Sunlight initiates accumulation of the pigment. It is recommended to use sunprotection to avoid the pigmentation.

"This paper develops an intertemporal simulation model capable of addressing the macroeconomic and distributional effects of demographic shocks in a small open economy. Two sources of population aging are examined, viz. lower birth rates and prolonged expected lifetimes at retirement age. Due to strong expectational effects, both shocks are found to change average consumption in a downward direction, in the short run as well as in the long run. This effect is matched by a strong net acquisition of foreign assets. Furthermore, it turns out that the intergenerational distribution of the burden of adjusting to an aging population is strongly dependent on whether the benefit rate, the contribution rate, or the relative non-capital income of pensioners and workers is held fixed."

Three patients with "lone" paroxysmal atrial flutter complicated by paroxysms of 1:1 AV conduction are presented. One patient (42 years of age) had been misdiagnosed as an neurotic for 18 years. The mechanism, diagnosis and treatment of the condition are outlined. The most characteristic symptoms are dizzy spells and fainting. The recommended diagnostic procedures include long term ECG recording by telemetry or Holter, exercise-ECG and oesophageal-ECG.

In connection with an extensive screening programme for blood cholesterol, the cholesterol values in 105 participants were measured on a sample of capillary blood employing a Reflotron and, simultaneously, samples of venous blood were examined by conventional enzymatic analysis in a laboratory. Whereas the day-to-day variation and the scatter involved were quite limited in the laboratory, the variation scatter between the two methods of measurement was 0.65 mmol/l. This figure was, however, no greater than that described between different laboratories in USA. Nevertheless, it is an important problem with the Reflotron method that even slight deviations from the recommended procedure of withdrawing blood involve a systematic risk for erroneously low cholesterol results.

At present, it appears to be probable that both dietary changes and medicinal treatment can reduce the risk of development of coronary disease in middle-aged men with moderately to severely raised blood cholesterol values. Internationally, the limits for cholesterol intervention are considerably lower than in Denmark. Extensive cholesterol screening is, however, very expensive and the identified persons with high cholesterol values will frequently be found in sex and age groups where the beneficial effect of intervention is probably limited. A model for selective cholesterol screening in high risk groups in general practice is described here. In 20 general practices, all of the men aged 45-59 years belonging to the practice were invited to examination of cholesterol and blood pressure. Plasma cholesterol was measured by means of a Reflotron (results are available within three minutes) and the blood pressure and tobacco consumption were registered. After this, the patient's own general practitioner calculated with each of the persons the risk for development of myocardial infarction within the next ten years and intervention could be commenced immediately. 41% of those invited came for examination. Out of these, 29% had cholesterol values greater than or equal to 7.0 mmol/l (Danish limiting value), 44% greater than or equal to 6.5 mmol/l (limiting value in the remainder of Western Europe), and 5% greater than or equal to 9.0 mmol/l (severe hypercholesterolaemia) while only 18% had completely normal cholesterol less than 5.2 mmol/l. In every practice, two patients on an average were found with severe hypercholesterolaemia greater than or equal to 9.0 mmol/l. 28% of the participants had at least two of the three risk factors investigated. (ABSTRACT TRUNCATED AT 250 WORDS)

In connection with a screening investigation for high blood cholesterol in middle-aged men in general practice in the Municipality of Copenhagen, all participants with cholesterol values greater than or equal to 7.5 mmol/l were given brief advice by their own general practitioner and were invited to come for fasting blood lipid tests approximately ten days later. In cases with continued cholesterol greater than or equal to 6.8 mmol/l, the participants together with wives or partners were invited to formalized dietary advice in small groups. Already before the formalized dietary advice, an average decrease in serum cholesterol of 10% was observed. This was attributed to biological variation, absence of fasting, the degree of error between the measuring methods and also a genuine decrease on the basis of the brief dietary advice by the general practitioner. On control after dietary advice, a further decrease in cholesterol of 15% was observed while low density lipoprotein cholesterol fell by 20% and triglycerides by 23%. These decreases must be considered to result mainly from the dietary advice. It is concluded that a single but professional session of dietary advice in small groups and with involvement of the wives or partners is an effective method of treatment in hypercholesterolaemia. If the decrease in cholesterol obtained can be maintained, the literature suggests that the risk of development of ischaemic heart disease during the subsequent 5-7 years is reduced by 20-30%.

A case of cholelithiasis in a 5-year-old girl is presented in which the main symptom was recurrent pain of the upper abdomen. The diagnosis was made by ultrasound examination of the abdomen and confirmed at surgery. Possible etiological factors of gallstones in children are discussed and the role of abdominal ultrasound examination is emphasized.

Canopy temperatures of wheat, barley, rape and perennial rye grass crops, grown under temperate humid climatic conditions at different irrigation regimes were measured during two growing seasons, 1986 and 1987, by determining the emission of radiation in the wavelength interval 8

Magnetic resonance force microscopy (MRFM) and other emerging scanning probe microscopies entail the detection of attonewton-scale forces. Requisite force sensitivities are achieved through the use of soft force microscope cantilevers as high resonant-Q micromechanical oscillators. In practice, the dynamics of these oscillators are greatly improved by the application of force feedback control computed in real time by a digital signal processor (DSP). Improvements include increased sensitive bandwidth, reduced oscillator ring up/down time, and reduced cantilever thermal vibration amplitude. However, when the cantilever tip and the sample are in close proximity, electrostatic and Casimir tip-sample force gradients can significantly alter the cantilever resonance frequency, foiling fixed-gain narrow-band control schemes. We report an improved, adaptive control algorithm that uses a Hilbert transform technique to continuously measure the vibration frequency of the thermally-excited cantilever and seamlessly a...

The enzymatically active form of protease 1, the major exocellular protein produced by Pseudomonas aeruginosa strain 34362, has been shown to exist exclusively exocellularly with no significant cell-associated activity. However, the presence of a cell-associated, enzymatically inactive protein which is serologically cross-reactive with, and convertible to, active enzyme has been demonstrated. One method of conversion of "precursor" to active enzyme is via limited proteolysis. Two assay systems for precursor were developed, one a radioimmune assay, and the other a proteolytic activation procedure. Localization studies suggest that the cell-associated precursor resides primarily in the envelope (periplasmic) fraction, and that the association while more tenacious than classical periplasmic enzymes is still an ionic rather than a covalent one. Kinetics of production studies showed the precursor to be synthesized early in the growth cycle and to accumulate prior to the rapid release of the active enzyme. Molecular weight studies showed only slight changes produced upon activation.

A rare case of Waldenström's macroglobulinaemia is presented. In this case, the lymphoplasmacytoid cell infiltration which is characteristic of the disease was demonstrable only in the lungs.

Membrane suspensions prepared from Micrococcus luteus (sodonensis) in both the exponential and stationary phases of growth contained a transglycosidase activity capable of synthesizing linear peptidoglycan. Exponential-phase membranes also contained an N-acetylmuramyl-L-alanine amidase activity which degraded the peptidoglycan as it was formed. The product of this amidase was purified and found to be free pentapeptide. The amidase was specific for peptidoglycan and could not attack lower-molecular-weight substrates even though the susceptible bond was present. Crude cell wall preparations isolated from exponential-phase cells also contained high levels of amidase. This cell wall-bound amidase would preferentially degrade in vitro-synthesized peptidoglycan over its own cell wall. Amidase activity could be solubilized from both cell walls and membranes by Triton X-100 treatment, butanol extraction, or LiCl extraction. Both membrane- and cell wall-derived amidases, solubilized by LiCl extraction, appeared to be of high molecular weight (greater than 150,000). Once solubilized, these wall- and membrane-derived amidases could attack the cross-bridged peptidoglycan of purified native cell walls, whereas bound amidases could not.

A defined medium capable of supporting growth and exocellular protease production by clinical isolates of Pseudomonas aeruginosa has been developed. Control of protease production is effected by a mixture of three amino acids and glucose.

Exocellular protease production was examined in two separate strains of Pseudomonas aeruginosa, one a clinical isolate and the other a laboratory strain. Both strains produced two separate proteases (proteases 1 and 2) which were indistinguishable from one strain to the other. The two proteases were purified by a two-step procedure of gel filtration chromatography followed by ion-exchange chromatography. Proteases 1 and 2 were shown to be distinct serologically and unrelated by physicochemical parameters examined. Protease 1 was the major exocellular protein produced and contributed about 95% of the total protease activity of the culture. It was estimated to have a molecular weight of 34 850 and was also shown to contain 10% glucosamine by weight. Protease 2, in contrast, had an estimated molecular weight of 52750 and contained no detectable carbohydrate. Proteases 1 and 2 were both stimulated by Ca2+, and Mg2+ and inhibited by Co2+Zn2+, and 1,10-o-phenanthroline. Protease 1 was also inhibited by EDTA. In addition to protease activity, both proteases 1 and 2 demonstrated elastase activity as well as a limited collagenase activity. Specificity of the two proteases against synthetic peptides was, however, quite different. Protease 1, but not protease 2, showed a preference for peptide bonds in which the amino group was contributed by an amino acid with a hydrophobic R group.

Two enzyme activities involved in the biosynthesis of peptidoglycan in Micrococcus luteus (sodonensis), a transglycosidase and a phosphodiesterase, have been demonstrated in isolated membrane preparations. The transglycosidase activity promotes the in vitro synthesis of an uncross-bridged peptidoglycan that is completely susceptible to lysozyme. This in vitro-synthesized peptidoglycan consists of 76% "soluble" and 24% "insoluble" material. The soluble peptidoglycan is primarily a single low-molecular-weight species of approximately 20 disaccharide peptide units. "Insoluble" peptidoglycan, which likely represents newly synthesized material incorporated into an existing cell wall, was solubilized by butanol extraction, and the two were compared. The phosphodiesterase activity demonstrated in this system cleaves uridine diphosphate-N-acetylmuramyl-L-alanyl-D-isoglutamyl-L-lysyl-D-alanyl-D-alanine to yield N-acetylmuramyl-L-alanyl-D-isoglutamyl-L-lysyl-D-alanyl-D-alanine plus uridine 5'-monophosphate plus inorganic phosphate. This phosphodiesterase activity, not detected under normal transglycosidase assay conditions, is a recycling mechanism and acts indirectly through formation and subsequent cleavage of a lipid-linked intermediate.