Yield prediction in a peanut breeding program using remote sensing data and machine learning algorithms

Peanut is a critical food crop worldwide, and the development of high-throughput phenotyping techniques is essential for enhancing the crop's genetic gain rate. Given the obvious challenges of directly estimating peanut yields through remote sensing, an approach that utilizes above-ground phenotypes to estimate underground yield is necessary. To that end, this study leveraged unmanned aerial vehicles (UAVs) for high-throughput phenotyping of surface traits in peanut. Using a diverse set of peanut germplasm planted in 2021 and 2022, UAV flight missions were repeatedly conducted to capture image data that were used to construct high-resolution multitemporal sigmoidal growth curves based on apparent characteristics, such as canopy cover and canopy height. Latent phenotypes extracted from these growth curves and their first derivatives informed the development of advanced machine learning models, specifically random forest and eXtreme Gradient Boosting (XGBoost), to estimate yield in the peanut plots. The random forest model exhibited exceptional predictive accuracy (R2 = 0.93), while XGBoost was also reasonably effective (R2 = 0.88). When using confusion matrices to evaluate the classification abilities of each model, the two models proved valuable in a breeding pipeline, particularly for filtering out underperforming genotypes. In addition, the random forest model excelled in identifying top-performing material while minimizing Type I and Type II errors. Overall, these findings underscore the potential of machine learning models, especially random forests and XGBoost, in predicting peanut yield and improving the efficiency of peanut breeding programs.

<i>Staphylococcus aureus</i> antimicrobial efflux pumps and their inhibitors: recent developments

<abstract> <p>The microorganism <italic>Staphylococcus aureus</italic> is a notorious causative agent of bacterial infection. The widespread presence of this pathogen has caused significant morbidity and mortality rates in clinical healthcare settings and communities. Due to its increasingly frequent recalcitrant nature towards clinically available antimicrobial agents, the bacterium poses a considerable public health crisis. A significant bacterial mechanism of antimicrobial agent resistance includes multidrug efflux pump systems. These antimicrobial efflux determinants translate into several large superfamilies of transporters that share related amino acid sequences, similarities in three-dimensional structures, modes of energization, and solute transport catalysis across the membrane. Because of their ubiquitous nature and functional role in virulence, these multidrug transporters make good targets for inhibition. This review briefly summarizes recent key findings regarding multidrug efflux activity and modulation in the MATE, SMR, and MFS transporters.</p> </abstract>

Baseline survey on functioning of abortion services in government approved CAC centers in three pilot districts of Nepal

BACKGROUND

Abortion has been legalized in Nepal since September 2002 and under this law, Comprehensive Abortion Care (CAC) service is being provided through listed service providers and listed health facilities from 2004. Nepal Government has prioritized the national safe abortion program and is working with many government and non government partners for providing this service. Till date medical abortion services are not made available at any of the health facility. Government is now preparing to introduce this service in six selected pilot districts.

OBJECTIVE

This survey was carried out to assess the functioning of existing abortion services in 12 Government approved CAC sites of three districts.

MATERIALS AND METHODS

Direct observation of the functioning of these centers, assessment of physical facilities and service provider's skill was done. At the same time service provider's attitude and knowledge on CAC service and other abortion services were also assessed through semi structured interviews. Quality of record keeping and the feasibility of initiating the medical abortion service in these sites were also studied.

RESULT

Number of listed centers in six pilot districts was twenty nine. Study districts have 16 listed centers. Visited sites were twelve; four managed by Government and eight by non government organizations. Thirty three thousand nine hundred and twenty women have availed this service so far: only 4.76% of them received service from Government facilities. Marie Stopes International (MSI) topped the list in providing service to the maximum number of clients (75.64%) and Family planning association of Nepal (FPAN) was the second. MSI centre was also first to initiate the service. Government facilities provide 24 hours service unlike private facilities which are open only up to 5.00 pm. Cost for the service varies from rupees 900/- to rupees 1365/- and is cheaper at Government facilities. Private sectors have separate setups and Government have allocated some space within their already existing infrastructure for CAC service. Private sectors were better in providing the information to public about the availability of service. There were total 20 trained service providers for first trimester abortion service. They are more at Government facilities. They seem to be positive to CAC service and had good knowledge and skill of service delivery. Complications were not recorded at most of the sites. Pain management and infection prevention practice needs improvement at the Government sites. All the sites had identified their referral sites and had one or the other arrangement for referral.

CONCLUSION

CAC service has become accessible and affordable to Nepalese women even at peripheral level. CAC sites are functioning well. Initiation of medical abortion and second trimester abortion services at these sites are feasible and would expand the option and choices available.

Test of isospin symmetry via low-energy 1H(pi{-},pi{0})n charge exchange

We report measurements of the pi;{-}p-->pi;{0}n differential cross sections at six momenta (104-143 MeV/c) and four angles (0 degrees -40 degrees ) by detection of gamma-ray pairs from pi;{0}-->gammagamma decays using a photon-pair spectrometer at TRIUMF. This kinematic region exhibits a vanishing zero-degree cross section from destructive interference between s and p waves, thus yielding special sensitivity to pion-nucleon dynamics. Our data and previous data do not agree, with important implications for earlier claims of large isospin-violating effects.

Proteolytic cleavage of a spectrin-related protein by calcium-dependent protease in Neurospora crassa

To investigate the functional significance of a cytoskeletal spectrin-like protein, we studied its localization pattern in Neurospora crassa and sought the answer to whether it is a substrate for another apically localized protein, the calcium-dependent protease (CDP II). Immunoblots of crude extracts from exponentially growing mycelia, separated by one- and two-dimensional sodium dodecyl sulfate-polyacrylamide gel electrophoresis using antichicken alpha/beta-spectrin antibodies, revealed a single band of approximately relative mass (Mr) 100 kDa with an isoeletric point (pI) in the range of 6.5 to 7.0. Despite rigorous efforts, we could not confirm the presence of an Mr 240- to 220-kDa spectrin-like protein in N. crassa. The immunofluorescence- and immunogold-labeling Mr 100-kDa protein showed its predominance along the plasma membrane of the conidia during the swelling phase of germination. In contrast, in the germ tubes and the growing hyphae, the localization was polarized and concentrated mainly in the apical region. The in vitro proteolysis experiments showed that indeed this protein is a preferred substrate of CDP II which is, as mentioned previously, also localized in the apical regions of the hyphae. These results indicate a putative functional relationship between these two proteins (spectrin-like protein and CDP II) in the dynamics of tip growth.

DNA nucleotide sequence homologies between some zoosporic fungi

Representative species from the monoflagellate Blastocladiales and the biflagellate Saprolegniales were studied for their DNA base composition, heterogeneity, nucleotide sequence homology and divergence. Intergeneric, intrageneric and interstrain DNAs of Blastocladiales were heterogenous. The G+C values for their main component (average 64 percent) and two minor ones (average 52 and 44 percent) were found to be significantly higher than the corresponding values from the biflagellate Saprolegnia ferax (55, 46 and 36 percent respectively). In Allomyces species, the two hybrid, male and female strains were found to have closer homology with their parental types than these last between themselves. Among Blastocladiales, interspecific similarities between the epigynous A. macrogynus and the hypogynous A. arbuscula were higher (average 75 percent) than intergeneric similarities between Allomyces and Blastocladiella (average 58 percent). The biflagellate S. ferax was found to be distantly related to the uniflagellate Allomyces (average 48 percent similarity). The nucleotide sequence divergences obtained from thermal elution data correlated the hybridization values.

Distribution of intimal and medial thickening in the human right coronary artery: a study of 17 RCAs

OBJECTIVE

To quantify the distribution of intimal and medial thickening in human right coronary arteries (RCAs) obtained at autopsy.

BACKGROUND

The shear and tensile stresses created by arterial bifurcation are believed to result in eccentric fibromuscular intimal thickening that leads to atherosclerosis. Vascular curvature has been cited as a cause of atherosclerosis; however, details of the location and extent of intimal and medial thickness in the largely curved human RCA are not adequately documented.

METHODS

The right coronary arteries were obtained from 40 postmortem hearts and cut into 20-30 segments, each being 3-4 mm in length. Microscopic sections from the proximal, acute margin, and distal regions of the RCA were digitized around the circumference of the vessel. Seventeen arteries showed insignificant stenosis (<50%) and were selected for detailed examination.

RESULTS

Seventy-one percent (12/17) of proximal sections displayed eccentric intimal thickening. Normalized ensemble averaging revealed a preferential thickening on the myocardial side of the artery. At the acute margin region where curvature is most pronounced and at the distal region, 51% (8/17) of the samples showed eccentric thickening, but the ensemble average thickening in these regions showed no preferential location. In these mildly diseased arteries, the thickened intima comprised of mainly smooth muscle cells with an extracellular matrix of collagen and some elastin. A relatively uniform medial smooth muscle layer was seen at all three locations.

CONCLUSIONS

The proximal region of the RCA appears to be a site of intrinsic eccentric intimal thickening with maximum thickness on the myocardial side of the artery. Eccentric thickening does occur in the acute margin and distal regions; however, no distinct pattern or location was evident.

In vitro hemodynamic evaluation of a Simon nitinol vena cava filter: possible explanation of IVC occlusion

PURPOSE

To evaluate the local hemodynamics in the region of the Simon nitinol filter (SNF), used to prevent pulmonary emboli by capturing clot and promoting lysis.

MATERIALS AND METHODS

The hemodynamics of the Simon nitinol inferior vena cava (IVC) filter were evaluated under steady flow (Re = 600) in a 20-mm-diameter IVC model. The photochromic dye tracer technique was used to estimate the velocity and wall shear stress. These flow features were determined for the unoccluded and partially occluded (clot volume = 1,500 mm(3)) states of the SNF along its center plane.

RESULTS

A region of low velocities developed around the central axis of the filter extending from the leading edge of the central strut to the filter tip. This phenomenon was created by the strong redirection of flow toward the periphery of the filter. With the presence of the clot, these effects were enhanced, causing flow separation and recirculation. In addition, the shear stress on the hip of the clot was about 30 times that of the upstream value, and turbulence developed in the near-downstream region.

CONCLUSIONS

The extended region of almost-stagnant flow near the midsection of the umbrella region could lead to organization of thrombus and fibrin mesh network development. The presence of a simulated clot led to a significant increase in the size of the stagnant, thrombus-prone region as well as turbulence, which, overall, may contribute to caval occlusion.

Factors influencing blood flow patterns in the human right coronary artery

Evidence suggests that atherogenesis is linked to local hemodynamic factors such as wall shear stress. We investigated the velocity and wall shear stress patterns within a human right coronary artery (RCA), an important site of atherosclerotic lesion development. Emphasis was placed on evaluating the effect of flow waveform and inlet flow velocity profile on the hemodynamics in the proximal, medial, and distal arterial regions. Using the finite-element method, velocity and wall shear stress patterns in a rigid, anatomically realistic model of a human RCA were computed. Steady flow simulations (ReD=500) were performed with three different inlet velocity profiles; pulsatile flow simulations utilized two different flow waveforms (both with Womersley parameter=1.82, mean ReD=233), as well as two of the three inlet profiles. Velocity profiles showed Dean-like secondary flow features that were remarkably sensitive to the local curvature of the RCA model. Particularly noteworthy was the "rotation" of these Dean-like profiles, which produced large local variations in wall shear stress along the sidewalls of the RCA model. Changes in the inlet velocity profiles did not produce significant changes in the arterial velocity and wall shear stress patterns. Pulsatile flow simulations exhibited remarkably similar cycle-average wall shear stress distributions regardless of waveform and inlet velocity profile. The oscillatory shear index was very small and was attributed to flow reversal in the waveform, rather than separation. Cumulatively, these results illustrate that geometric effects (particularly local three-dimensional curvature) dominate RCA hemodynamics, implying that studies attempting to link hemodynamics with atherogenesis should replicate the patient-specific RCA geometry.

Histology and morphology of 59 internal thoracic artery grafts and their distal anastomoses

BACKGROUND

The left internal thoracic artery (LITA) is accepted as a superior graft for the left coronary system because of its better long-term patency rate than saphenous grafts. The postsurgical histomorphometric changes at the distal anastomosis of LITA grafts are not well documented.

METHODS

The cellular changes within the intima of 59 LITA grafts were analyzed by light microscopy.

RESULTS

Grafts implanted 1 week or less (n = 34) showed no postsurgical tissue proliferation. Of the 7 grafts implanted 1 to 8 weeks, only the suture sites exhibited intimal thickening (6 of 7 grafts, 0.08 +/- 0.07 mm). The remaining grafts (n = 18), aged 2 months to 10 years, showed significant intimal thickening at the suture sites (0.39 +/- 0.17 mm) and on the hood (0.29 +/- 0.25 mm), with variable thickening on the floor (10 of 18 left anterior descending coronary arteries, 0.11 +/- 0.12 mm). The graft body showed insignificant intimal changes (10 of 18, 0.03 +/- 0.04 mm), with mild focal atherosclerotic lesions in 2 of 18 late LITA grafts.

CONCLUSIONS

Left internal thoracic artery grafts develop fibromuscular intimal hyperplasia primarily around the anastomosis. The response on the hood appears to be a hemodynamic response, secondary to that of the suture sites.

An in vitro comparison of the hemodynamics of two inferior vena cava filters

PURPOSE

The effectiveness of an inferior vena cava (IVC) filter in preventing pulmonary embolism while preserving caval flow is significantly affected by its hemodynamic characteristics. Flow fields surrounding two types of IVC filters were compared to assess how the design of a filter may influence performance.

METHODS

The 12F Titanium Greenfield and VenaTech LGM inferior vena cava filters were studied in vitro with a noninvasive flow visualization technique, the photochromic flow visualization and measurement technique. Axial velocity profiles and wall shear stress distributions were measured. These results were compared with analytical data corresponding to the flow field in the absence of a filter to determine the relative extent of the flow disturbances.

RESULTS

The reductions in near-wall axial velocity and wall shear stress caused by the VenaTech filter were more extensive and severe than those caused by the Greenfield filter. These changes were the consequence of differences in the geometry and dimensions of the struts of the two filters. The measurements showed the flow fields to be laminar, with no evidence of turbulence in both cases.

CONCLUSION

Two factors that have been linked to thrombogenesis, near-wall velocity and wall-shear stress, were significantly affected by the larger frontal profile area of the VenaTech filter. Although a larger area may increase clot-trapping efficiency, as shown by previous studies, the reduced near-wall velocities and wall shear stresses may increase the potential for thrombogenesis and, thus, caval occlusion. In contrast to other in vitro flow visualization studies, no turbulence was observed with either filter.

Velocity and wall shear stress patterns in the human right coronary artery

Blood flow dynamics in the human right coronary artery have not been adequately quantified despite the clinical significance of coronary atherosclerosis. In this study, a technique was developed to construct a rigid flow model from a cast of a human right coronary artery. A laser photochromic method was used to characterize the velocity and wall shear stress patterns. The flow conditions include steady flow at Reynolds numbers of 500 and 1000 as well as unsteady flow with Womersley parameter and peak Reynolds number of 1.82 and 750, respectively. Characterization of the three-dimensional geometry of the artery revealed that the largest spatial variation in curvature occurred within the almost branch-free proximal region, with the greatest curvature existing along the acute margin of the heart. In the proximal segment, high shear stresses were observed on the outer wall and lower, but not negative, stresses along the inner wall. Low shear stress on the inner wall may be related to the preferential localization of atherosclerosis in the proximal segment of the right coronary artery. However, it is possible that the large difference between the outer and inner wall shear stresses may also be involved.

Comparative studies of Ca2+-dependent proteases (CDP I and CDP II) from Allomyces arbuscula

Allomyces arbuscula, an aquatic fungus, contains two Ca2+-dependent neutral cysteine proteases (CDP I and CDP II), eluting respectively, at 0.07 and 0.2 M NaCl from DEAE cellulose columns. The purified CDP I has a Mr of 39 kDa whereas CDP II appears as a doublet of 43 and 40 kDa. Both enzymes require free thiol, the same concentration of Ca2+ for half maximal activation, and are inactivated by thiol protease inhibitors. Our results show that despite these similarities the two enzymes are different because affinity-purified CDP II antibodies do not cross-react with CDP I antigen in Western blots. In contrast, there is a strong cross-reaction between the two 43 and 40 kDa CDP II peptides and their respective antibodies. Both enzymes cleave preferentially the carboxy terminus of Arg and to a limited extent Lys on the cleavage site. This primary specificity is governed by the nature of the amino acids in the P2 and P3 positions. In general either Pro or Gly in P2 is required, with preference for Pro and in P3 position, Gly over Val. CDP II has higher catalytic activity than CDP I. The sulfhydryl reagent NEM is a more potent inhibitor of CDP I than CDP II. Although the function of the phosphorylable site(s) is not clear, both CDP I and CDP II contain phosphorylable serine residue(s).

Flow waveform effects on end-to-side anastomotic flow patterns

PURPOSE

Restenosis due to distal anastomotic intimal hyperplasia, a leading cause of arterial bypass graft failure, is thought to be promoted by hemodynamic effects, specifically 'abnormal' wall shear stress patterns. The purpose of this study was to quantify the effects of flow waveform on peri-anastomotic flow and wall shear stress patterns.

METHODS

Blood flow and wall shear stress patterns were numerically computed in a representative three-dimensional anastomosis using femoral, iliac and coronary flow waveforms suitable for humans at rest. Numerical results were validated against experimental data.

RESULTS

Peri-anastomotic wall shear stress patterns were influenced by a complex interplay between secondary flow effects and unsteadiness. Peripheral flow waveforms (iliac, femoral) produced large temporal and spatial wall shear stress gradients on the host artery bed. In comparison, the coronary flow waveform produced normalized bed wall shear stress gradients that were a factor of 2-3 less than for the peripheral waveforms, even though average bed wall shear stress magnitudes were similar for the two waveforms.

CONCLUSIONS

If anastomotic intimal hyperplasia is promoted by large spatial and/or temporal gradients of wall shear stress, as has been proposed, this study predicts that there will be markedly less intimal hyperplasia on the host artery bed of coronary bypass grafts than for peripheral bypass grafts. This information, in conjunction with a comparative histopathologic study of intimal hyperplasia distribution, could help determine specific wall shear stress factors promoting intimal hyperplasia.

Histological and morphometric analyses of early and late aortocoronary vein grafts and distal anastomoses

BACKGROUND

Aortocoronary vein grafts develop fibromuscular intimal hyperplasia within the first year of implantation. Tissue remodeling may promote development of graft atherosclerosis and thrombosis. Angiographic studies show that human aortocoronary vein grafts in situ for one or more years become stenosed, preferentially at the distal anastomosis versus the body or trunk of the graft or at the proximal anastomosis. Previous studies have not reported morphological data on the nature and distribution of intimal lesions around the distal graft/artery anastomoses.

OBJECTIVE

To examine and quantify histological and morphometric changes within the intima of 27 aortocoronary vein grafts and their distal anastomoses.

METHODS

Seventy-two hearts obtained at autopsy and one at heart transplantation were examined, photographed and fixed in 10% buffered formaldehyde solution. Three to seven 3 mm long segments of grafts and their distal anastomoses were sectioned, stained and examined by light microscopy.

RESULTS

Eleven early grafts were implanted for six weeks or less, and they showed significant cellular hyperplasia mainly at the suture line. In 16 late grafts in situ 1.5 to 15 years, the degree of fibromuscular intimal thickening was greatest on the hood and at the suture line, whereas on the floor of the native artery and in the graft body the degree of thickening was approximately one-third and two-thirds, respectively, that seen on the hood.

CONCLUSIONS

Stenosis of aortocoronary vein grafts at their distal anastomosis is likely related to the preferential development of intimal thickening on the hood of the graft and at the suture line. Because fibromuscular intimal hyperplasia has been reported to play a role in the development of atherosclerosis and thrombosis in the body of vein grafts, this focal hyperplasia at the distal anastomosis may also play a role in vein graft failure.

Compliance mismatch may promote graft-artery intimal hyperplasia by altering suture-line stresses

The role of graft-artery compliance mismatch in the development of distal anastomotic intimal hyperplasia (DAIH) is not yet resolved. Although DAIH develops at all surgically created anastomoses, increased compliance mismatch does not lead to greater hyperplasia formation in end-to-end anastomoses, but in end-to-side anastomoses, it leads to a profound increase in hyperplasia. The current study was undertaken to determine whether suture-induced anastomotic stresses could explain these findings. A large strain finite element analysis of vascular wall mechanics was performed to compare the influence of compliance mismatch on intramural stresses in end-to-end versus end-to-side anastomoses. A novel modelling approach was implemented which includes suture-induced stress concentrations. End-to-end and end-to-side graft-artery simulations were executed using (1) artery (compliance = C = 0.44% kPa(-1)), (2) vein (C = 0.33% kPa(-1)), and (3) Dacron (C = 0.14% kPa(-1)) grafts. Residual stresses due to axial tension were included and the anastomoses were statically inflated to 13.3 kPa (100 mmHg). Elevated intramural stresses were found to exist at both the end-to-end and end-to-side graft-artery junctions; however, in the end-to-end anastomosis, the maximum anastomotic stress was not a function of the graft compliance, whereas in the end-to-side anastomosis, the maximum stress was a strong function of graft compliance. For the 45 degree end-to-side geometry considered in this study, the maximum anastomotic stress concentration obtained using a stiff Dacron graft was more than 40% greater than that obtained using a compliant artery graft. In the end-to-end anastomosis, the Dacron graft led to a less than 5% increase in maximum stress over the artery graft. Therefore, increased compliance mismatch increases stresses and promotes DAIH in end-to-side junctions, but, it has little influence on either stresses or DAIH in end-to-end junctions. Thus, the proliferative influence of increased compliance mismatch on suture-line hyperplasia in end-to-side anastomoses can be explained by the resulting increase in intramural stresses. In addition, since high stresses were found in both geometries, elevated suture-line intramural stresses may be an important proliferative stimulus for intimal hyperplasia formation in all vascular reconstructions.

In vitro assessment of the hemodynamic effects of a partial occlusion in a vena cava filter

PURPOSE

Flow fields surrounding a vena cava filter were studied with a noninvasive method of flow visualization to examine the underlying hemodynamic factors that contribute to its function and patency.

METHODS

The photochromic technique was used to measure axial velocity profiles and wall shear stress distributions in a 12F titanium Greenfield filter partially occluded with a simulated volume of entrapped thrombi. These results were compared with similar measurements obtained for an unoccluded filter and with a theoretic prediction of the velocity profile and wall shear stress without a vena cava filter. Shear stress distributions were obtained along the vessel wall and for the partially occluded filter along the surface of the simulated clot.

RESULTS

The unoccluded filter was observed to have little effect on the flow field. In the case of the partially occluded filter, the results of these measurements show that caval blood flow is preserved by the creation of an annular region of increased flow around the periphery of the clot. Within this region high shear stresses that develop as a result of the increased flow are observed along the vessel wall and along the surface of the simulated clot. No vortices or turbulence were observed with either the unoccluded or the partially occluded filter.

CONCLUSIONS

The elevated levels of shear stress may be a factor in the lysis of trapped clots observed in vivo. Although increased shear stress is reported to cause thrombogenesis in an in vivo study in canines, particularly under turbulent flow conditions, the levels of shear measured in this study around the simulated clot were well below such values.

Relation of the flow field distal to a moderate stenosis to the Doppler power

An experimental investigation was undertaken to establish how different flow regimes affect the Doppler signal. A rigid tube model consisting of a 70% asymmetric area stenosis was used with steady and pulsatile flow conditions. The characteristics of the flow field at various sites was determined using a photochromic flow visualization method. Continuous-wave Doppler measurements were made using a 41% suspension of human red blood cells (RBCs) in saline as well as a dilute suspension of 4% fixed RBCs. For steady flow, the photochromic results indicated that for Reynolds numbers (Re) of 545 and 1410, turbulence was generated and the length of the turbulent region was found to increase with increasing Re. Under pulsatile flow conditions, turbulence was triggered around peak systole and began to dissipate in late deceleration, and by the end of diastole the flow field almost relaminarized. During the turbulent phase of the flow cycle, the poststenotic flow field was seen to consist of four distinct flow regimes similar to those observed for steady flow. For higher Womersley parameters and Reynolds numbers the turbulent zone was found to be larger and to occupy a greater fraction of the flow cycle. These flow visualization results were compared with the Doppler power measurements made at the same locations and under similar flow conditions. At physiological hematocrits (41%) the onset of turbulence for both steady and pulsatile flow increased the backscattered Doppler power. The location of the peak Doppler power coincided with the region of maximum turbulence observed using the photochromic technique.

Defining the limitations of measurements from Doppler spectral recordings

PURPOSE

The purpose of this study was to determine whether Doppler measurements of peak velocity and four other quantitative measures of spectral shape are affected significantly by the site of the Doppler recording in relation to the location of the maximum stenosis.

METHOD

Continuous-wave and pulsed Doppler recordings were made distal to a 70% (area reduction or 45% diameter reduction) asymmetric stenosis in an in vitro flow model under steady and pulsatile flow conditions. Recordings were taken at six different locations proximal and distal to the stenosis. A photochromic dye technique was used to visualize the actual flow field in the model.

RESULTS

Distal to the stenosis, the flow visualization results demonstrated a strong radial and axial variation of the velocity field and thus explained why the Doppler measurements of peak frequency and spectral broadening were strongly dependent on the recording site. The peak frequency was maximum within the throat of the stenosis and returned to the prestenotic value five tube diameters distal to the stenosis. Other measurements of spectral broadening and spectral shape varied greatly depending on the location of the recording site in the poststenotic region. Higher order spectral moments such as the coefficient of kurtosis were found to exhibit large temporal variability, which makes them inappropriate as diagnostic indicators.

CONCLUSIONS

Because of the complex nature of the poststenotic flow field, these results clearly demonstrate that no single Doppler measurement can accurately quantify the severity of a stenosis. Of the Doppler measurements only peak velocity is related to the severity of stenosis. Reproducible peak velocity measurements are obtained only if the Doppler sample volume is positioned at or very near the throat of the stenosis and at an appropriate radial site that may not necessarily be at the center of the vessel.

Purification, properties and developmental regulation of a Ca(2+)-independent serine-cysteine protease from Allomyces arbuscula

Reproductive differentiation in Allomyces takes place against the background of substrate limitation, a sharp increase in intracellular proteolysine and the induction of at least one specific protease. The aim of this report is to describe the purification, properties and developmental regulation of this enzyme. The enzyme has been partially purified by a combination of ion exchange chromatography, ultrogel filtration and affinity chromatography. The purified enzyme in SDS-PAGE appeared as a doublet of M(r) 40-43 kDa. Two bands corresponding to a relative molecular mass of 40-43 kDa were also apparent in activity gels. The protein has an apparent molecular mass in the region of 43 kDa as estimated by gel filtration. The enzyme therefore, seems to be a monomer of 43 kDa. The second band in SDS-PAGE and activity gels is probably the proteolyzed form of the enzyme. The protease recognized alanine and to a lesser extent phenylalanine in the P1 position when assayed with a range of synthetic peptides. The active site of the enzyme contains a reactive serine residue, as shown by its inhibition with PMSF and soya bean trypsin inhibitor. There is probably a reactive cysteine residue as well since the enzyme activity is strongly inhibited by HgCl2, a thiol group binding reagent. The enzyme is present in zoospores but disappears progressively during germination and hyphal growth. It reappears when actively growing cultures are transferred to dilute salt solution. In conclusion, we have purified a serine-cysteine protease of M(r) 43 kDa. This enzyme has a very restricted substrate specificity and appears to be developmentally regulated.

Ca(2+)-dependent protease I from Allomyces arbuscula

A monomeric Ca(2+)-dependent protease (CDP I) of 39 kDa active at neutral pH has been purified from the aquatic fungus Allomyces arbuscula. The enzyme elutes at NaCl molarity of 0.07 M from the DEAE (DE52)-cellulose columns in contrast to the second Ca(2+)-dependent protease (CDP II) characterized earlier which elutes at 0.18 M NaCl. The enzyme has no basal activity in the absence of Ca2+ and requires 1.7 mM Ca2+ for half maximum activation of the in vitro enzyme activity. The enzyme prefers substrates with Arg in P1 position but this specificity also depends strongly on the nature of the subsite residues, for example Pro in P2 position. The enzyme is glycosylated and contains essential cysteine residues in the active site. It appears to be an atypical cysteine protease as it is inactivated to varying degree with some serine protease inhibitors.

Influence of angle on wall shear stress distribution for an end-to-side anastomosis

PURPOSE

The purpose of this article was to study the effects of anastomotic angle on the wall shear stress distribution for end-to-side anastomosis models under pulsatile flow conditions.

METHOD

The photochromic tracer technique was used to visualize the flow field and to determine the instantaneous wall shear stress at multiple locations simultaneously. Models with angles of 20, 30, 45, and 60 degrees were examined.

RESULTS

For all angles, low shear stress was present at the heel and on the bed opposite the heel of the anastomosis apparently as a result of the complete occlusion of the proximal end of the host vessel. Near the toe, increased flow separation occurred with increasing angle. On the bed across from the toe, increasing the angle led to increased shear stress. In addition, in this region the anastomotic angle significantly altered other properties of the shear stress field such as the mean and peak-to-peak magnitudes and cycle-to-cycle fluctuations.

CONCLUSIONS

This study provides quantitative data on the wall shear stress distribution within an end-to-side anastomosis and its relation to the anastomotic angle. The results are discussed in terms of possible roles of shear-induced intimal hyperplasia.

Wall shear stress temporal gradient and anastomotic intimal hyperplasia

Unusual wall shear stress patterns on the bed of end-to-side arterial anastomoses appear to be the primary factor in the development of intimal hyperplasia that often leads to arterial bypass graft failure. In this in vitro study using the photochromic tracer technique, the shear stress variation on the bed of a 30 degrees anastomosis was examined before and after the development of hyperplasia. With the disease-free model, a rapid downstream shift in the stagnation point was seen on the bed during the systolic phase of the flow cycle, which led to sharp temporal changes in the shear stress from positive to negative values, ie, rapid changes in the direction of the shearing force. The resulting negative temporal gradients were roughly eight times larger than those seen in a straight tube, and it is suggested that this may lead to endothelial deformation or injury and eventually to intimal thickening. With the diseased model, the simulated tissue overgrowth on the bed appeared to act as a flow divider that restricted the motion of the stagnation point, and this drastically reduced the rapid changes in the direction of the shearing forces. Thus, it seems that the development of bed anastomotic intimal hyperplasia may be a response designed to reduce shear-induced endothelial deformation or injury.

Immunocytochemical localization of Ca(2+)-dependent protease from Allomyces arbuscula

The Ca(2+)-dependent protease antisera and the purified specific antibodies from Allomyces arbuscula have shown very specific recognition when blotted against the total protein extract or the purified 43-40 kDa Ca(2+)-dependent protease from this aquatic fungus. By immunoblotting and immunofluorescence techniques using specific antibodies, we have shown that the enzyme activity is developmentally regulated and is related to the presence of antigen and not to any specific inhibitor. The immunofluorescence was absent in zoospores but appeared in polarized forms in germinating spores. In elongating hyphae the protease was mainly localized along the cytoplasmic membrane and in the cytoplasm, with predominance at the apex.

Simulation of three-dimensional pulsatile flow through an asymmetric stenosis

The main objective of this work was to use desktop workstations to evaluate the computer code HEMO as a tool for predicting coronary blood flows. The flows are usually characterised by complex vortical structures and transitional effects, and as such present challenging computational problems. As the results of the computations shown in the paper demonstrate, we can predict realistic pulsatile flows in constricted tubes using the Sun Sparcstation 1+ in a matter of hours. The results shown in the paper have also demonstrated that the computer simulations can be very useful as a complementary tool for experimental investigations.

Spatial and temporal variations of wall shear stress within an end-to-side arterial anastomosis model

Wall shear stress has been strongly implicated in the initiation of fibrous intimal hyperplasia that leads to arterial bypass graft failure. In this study, the photochromic tracer technique was used to determine the instantaneous value of the wall shear stress in order to provide a detailed description of its spatial and temporal variations within a 45 degrees end-to-side anastomosis model. At the heel and on the bed across from the heel, the shear stress was close to zero throughout the sinusoidal flow cycle. Flow separation was produced just beyond the toe where the peak phase-averaged shear stress was 6 dyn cm-2, whilst on the bed across from the toe it was 27 dyn cm-2. The stagnation point was seen to fluctuate quite sharply on the bed over a distance of about one tube radius upstream from the site across from the toe. This led to large spatial gradients of the wall shear stress with a peak value of 580 dyn cm-3. In addition, the sudden motion of the stagnation point around peak flow produced sharp temporal gradients of the wall shear stress with a peak absolute value of 3400 dyn cm-2 s-1. When compared to the sites where intimal hyperplasia tends to occur, a strong correlation is seen with low wall shear stress at the heel and toe, and with the sharp temporal variations of the magnitude and spatial gradient of the wall shear stress on the bed across from the junction.

Evidence that turbulence is not the cause of poststenotic dilatation in rabbit carotid arteries

The purpose of this study was to relate local blood flow conditions to the development of poststenotic dilatation (PSD) in the common carotid arteries of rabbits. We investigated the effects of the geometry of the stenoses on PSD formation to gain insight into the mechanisms of this phenomenon. With short stenoses, the maximum diameter of the PSD after 3 weeks increased from about 25% to 50% above the proximal diameter by increasing the severity of the stenoses from 50% to 60% diameter reduction. By contrast, increasing the length of the constricted region of 60% stenoses did not affect the PSD, and in all cases, the site of maximum dilatation occurred within 3 tube diameters from the stenoses. In vitro studies were conducted with the photochromic tracer technique. The most striking observation was that the transition to turbulence did not occur with a 55% short stenosis. By increasing the severity of this short stenosis to 70%, the transition to very localized turbulence was triggered approximately 6 to 8 tube diameters from the stenosis during the early deceleration phase of the flow cycle. The transition point moved farther downstream by increasing the length of this moderate stenosis. This study demonstrated that PSD can occur under turbulence-free conditions, and even when turbulence was generated, the site of the PSD was remote from that of the localized turbulence zone. The wall shear stress pattern was determined for the long 60% stenosis.(ABSTRACT TRUNCATED AT 250 WORDS)

Hemodynamics of a side-to-end proximal arterial anastomosis model

PURPOSE

The purpose of this article was to analyze the fluid mechanical effects of a side-to-end proximal anastomosis and to compare the results with those from our earlier study on the end-to-side distal anastomosis.

METHODS

The photochromic tracer technique was used to determine the instantaneous wall shear stress and to visualize the overall flow field under pulsatile flow conditions. The flow consisted of a sinusoid plus a steady component with mean and modulation Reynolds numbers of 355 and 565, respectively, and a Womersley number of 7.9.

RESULTS

At the toe and heel of the junction, very high and positive wall shear stresses were seen together with substantial nonperiodic fluctuations. The peak wall shear stress was about four times higher at the toe and about seven times higher at the heel than the maximum values observed at about four tube diameters upstream from the junction. On the bed of the host vessel, nonperiodic fluctuations were also observed, but the shear stresses were mainly negative with magnitudes comparable to those seen upstream. With leakages of 11% and 28% of the mean flow through the blocked end of the host vessel, the shear stress pattern seemed to be significantly affected only at the toe for the higher leakage. Further, when the mean Reynolds number was reduced to 320, the magnitudes of the variations in the wall shear stress were reduced proportionately, except at the heel, where the reduction was much larger than expected.

CONCLUSIONS

It appears that the preferential development of intimal hyperplasia at the distal end-to-side anastomosis may be promoted by low wall shear stress at the toe and heel, and probably by high shear stresses or shear stress gradients on the bed.

A numerical simulation of flow in a two-dimensional end-to-side anastomosis model

In order to understand the possible role that hemodynamic factors may play in the pathogenesis of distal anastomotic intimal hyperplasia, we carried out numerical simulations of the flow field within a two-dimensional 45 degree rigid-walled end-to-side model anastomosis. The numerical code was tested and compared with experimental (photochromic dye tracer) studies using steady and near-sinusoidal waveforms, and agreement was generally very good. Using a normal human superficial femoral artery waveform, numerical simulations indicated elevated instantaneous wall shear stress magnitudes at the toe and heel of the graft-host junction and along the host artery bed. These sites also experienced highly variable wall shear stress behavior over the cardiac cycle, as well as elevated spatial gradients of wall shear stress. These observations provide additional evidence that intimal hyperplasia may be correlated to wall shear stresses over the cardiac cycle, high wall shear stress gradients, or a combination of the three. The limitations of the present work (especially in regard to the two-dimensional nature of the flow simulations) are discussed, and results are compared to previous observations about distal anastomotic intimal hyperplasia.

Purification and properties of a casein kinase II-like enzyme from Neurospora crassa

A serine/threonine protein kinase was partially purified from Neurospora crassa. Its physical and catalytic properties were typical of casein kinase II. In vitro, the kinase phosphorylated a calpain like protease from Allomyces arbuscula with higher affinity than a mixture of caseins.

Steady and pulsatile flow fields in an end-to-side arterial anastomosis model

We investigated the flow field within a rigid-walled in vitro model of an end-to-side 45 degree anastomosis in an attempt to identify possible hemodynamic factors that may contribute to the pathogenesis of distal anastomotic intimal hyperplasia. A high-resolution photochromic tracer technique was used to visualize the flow in orthogonal planes and to determine the axial wall shear stress profiles for both steady and pulsatile flows over a range of physiologically relevant conditions. The flow field showed qualitative similarities to those seen in curved vessel: rapidly moving fluid from the graft section affects the bed of the host vessel, that is, the wall opposite the anastomosis, eventually advancing down the host vessel in a spiraling motion. A small mobile separation zone was noted at the toe of the anastomosis. Comparison of wall shear stress profiles with previously reported preferential sites for the development of intimal hyperplasia supported a low wall shear stress and/or flow separation pathogenesis hypothesis. One notable exception was the bed of the host artery that appeared to be subjected to a complex hemodynamic environment.

Detailed visualization of pulsatile flow fields produced by modelled arterial stenoses

A multiple trace photochromic method was used to visualize the pulsatile flow field created by modelled arterial stenoses of 38% and 65% area reductions. Using flow parameters similar to those of a medium sized artery in man, the flow patterns at seven axial locations in relation to the stenosis were simultaneously photographed at various times throughout the flow cycle. With the 65% stenosis, the wall shear stress in the vicinity of the reattachment point was found to fluctuate quite strongly during the turbulent phase of the flow cycle, giving rise to instantaneous shear stresses that were at least eight times larger than those measured upstream. For the 38% stenosis, much smaller shear stresses were observed. These and other results are described in detail.

Evidence of a possible link between poststenotic dilation and wall shear stress

The effects of an axisymmetric 65% area reduction stenosis on a pulsatile flow were investigated by use of an in vitro model that permits simultaneous visualization of the flow velocity profiles at seven sites. By use of seven lenses to focus the ultraviolet light from a nitrogen laser, seven thin blue lines were produced in the photochromic solution flowing through the tube. The displacement profiles of the dye traces were photographed, resulting in the acquisition of the velocity profiles. From these traces, the flow pattern was determined, and the wall shear stresses were measured. Turbulence was generated 3.3 to 6.5 tube diameters downstream from the edge of the stenosis, depending on the time in the pulsatile flow cycle. Maximum wall shear stress fluctuations between positive and negative values appeared to lie within 1.6 to 3.3 tube diameters downstream of the stenosis. In several illustrative clinical cases of thoracic outlet arterial compression, the poststenotic dilation was maximum at 2.0 +/- 0.3 vessel diameters downstream. Based on these observations, it is postulated that wall shear stress fluctuations may be important in the development of poststenotic dilation.

Potential limitations of center-line pulsed Doppler recordings: an in vitro flow visualization study

In this study an in vitro model that permits visualization of the flow velocity profile has been used to determine if duplex pulsed Doppler recordings made with a small sample volume in the center line of the vessel can determine the severity of a stenosis in the 38% to 75% range of cross-sectional area reduction. Because most Doppler instruments measure the maximum peak frequency and the extent of spectral broadening, observations in the flow model included changes in the center-line maximum velocity and the location and intensity of flow disturbances. The results showed that center-line measurements of maximum velocity (equivalent to peak Doppler frequency) were directly related to the severity of the stenosis as long as the recordings were made from within the throat to about 1.5 to 3 tube diameters downstream, depending on the shape of the stenosis. However, flow disturbances (equivalent to spectral broadening) did not always occur in the center line of the vessel. Stenoses greater than 50% area reduction produced turbulence across the entire vessel in the region 4.5 to 7.5 diameters downstream. The turbulent period started just before peak systole and extended to just less than half the pulse cycle. In the more proximal zone a forward flow jet was present in the central part of the vessel, and reverse flow was present in the outer region. The interfacial layer between these two regions is subjected to high shear rates that resulted in the formation of waves and vortices.(ABSTRACT TRUNCATED AT 250 WORDS)

Novel Ca2+-activated neutral protease from an aquatic fungus, Allomyces arbuscula

A Ca2+-activated neutral protease was purified to homogeneity from an aquatic Phycomycete fungus, Allomyces arbuscula. It requires millimolar concentrations of Ca2+ for activation (1.8 to 2 mM for 50% activation). Sr2+ can replace Ca2+ but at higher concentrations (4 mM for 50% activation). The enzyme is a dimer of 40-kilodalton subunits and contains six cysteine residues, three of which are revealed only after the addition of micromolar concentrations of Ca2+; the other three are free. Enzyme activity is strongly inhibited by SH-group inhibitors and some trypsin inhibitors (leupeptin and alpha-N-tosyl-L-lysine chloromethyl ketone). The enzyme lacks general trypsinlike specificity, since substrates containing tryptic cleavage sites are not cleaved nor is enzyme activity inhibited by other trypsin inhibitors. The enzyme has many functional similarities to the extensively characterized mammalian and avian Ca2+-activated neutral proteases but differs in its substrate specificity, inhibition by alpha-N-tosyl-L-phenylalanine chloromethyl ketone, and subunit structure. It is, nevertheless, presumed that this enzyme has a similar high order of specificity and is involved in the regulation of a specific growth function.

Ribosomal RNA genes in Kluyveromyces marxianus

DNA from the yeast Kluyveromyces marxianus was studied for its heterogeneity and the multiplicity of rRNA cistrons. These cistrons banded at a slightly different density from the bulk DNA in preparative CsCl or Hg2+-Cs2SO4 equilibrium density gradients. The reassociation kinetics of the bulk DNA showed that the repetitive fraction represented a small amount of the total cellular DNA (10%) and that the single copy fraction had a complexity of 6.3 X 10(9) daltons. Approximately 2.2% of the DNA hybridized to 3H-labelled rRNA at saturation. On the basis of the above genome size, the multiplicity of the rRNA cistrons was calculated to be about 70 per haploid nucleus.

Loss of rRNA genes during a phenotypic, masculinizing mutation in Allomyces arbuscla

Saturation hybridization of 3H rRNA from Allomyces arbuscula Bali wild-type to homologous DNA and to DNA preparations from Allomyces arbuscula Bali X-ray induced male mutant and an interspecific male hybrid (Allomyces arbuscula X Allomyces macrogynus Emerson and Wilson) has shown approximately 50--60% reduction in the cistrons coding for rRNA in the masculinized strains.

Presence of RNA in the nucleoprotein complex spontaneously released by human lymphocytes and frog auricles in culture

Cell systems as different as normal human blood lymphocytes and frog auricles release spontaneously a nucleoprotein complex in their culture medium. This release seems to be an active mechanism that is unrelated to cell death. The presence of RNA in this complex is demonstrated. The amount of extracellular RNA is regulated by the same homeostatic mechanism that has previously been shown to govern DNA release in the same cell systems. This extracellular RNA is linked by hydrogen bonds to the extracellular DNA and cannot be extracted by a usual phenol procedure, due perhaps to the presence of a glycoprotein. Further purifications by chloroform, sodium perchlorate, and hydroxyapatite are necessary to obtain an RNA molecule that is acid precipitable, RNase and KOH sensitive, and orcinol positive. The extracellular RNA sediments between 2.5 and 4S and is not a transfer RNA. It is more highly methylated than the 28S, 18S, and 4 to 5S cellular RNA. It activates DNA synthesis in vitro.

Characterization of Allomyces genome

Allomyces arbuscula DNA isolated from whole cells (bulk DNA) is composed of a major (alpha) and two minor components (beta & gamma) with buoyant densities in neutral CsCl corresponding to 1.721, 1.710 and 1.702 g/cm3, respectively. The DNA obtained from purified nuclei contains alpha component only. The beta component corresponds to mitochondrial DNA. The gamma component is also extra-nuclear but has not been characterized. The reassociation kinetics of sheared, bulk and nuclear DNA show that (i) 25 % bulk and 10% of nuclear DNA reanneal very rapidly and contain highly repeated sequences; (ii) moderately repeated sequences, accounting for 15% of both bulk and nuclear DNA, have a sequence complexity of approximately 7.2-10(6) daltons and are repeated about 320 times; (iii) the slow reannealing fraction accounts for about 60% of the genome and has kinetic properties similar to single copy sequences. The sequence complexity of this fraction was determined in relation to that of Escherichia coli. After a correction for the size of the repeated sequences the genome size of A. arbuscula was calculated to be 1.7-10(10) daltons.

Ribosomal RNA cistrons in Allomyces arbuscula

Bulk and nuclear DNA have been fractionated by preparative neutral CsCl equilibrium density gradient centrifugation and each fraction hybridized to labeled rRNA (25 + 18 S). The cistrons coding for rRNA appeared on the light side of the main peak. Hybridization of the nuclear DNA fractionated by preparative Ag+-Cs2SO4 gradients at different pHs showed that the banding profile did not change as compared to the CsCl pattern. In Hg2+-Cs2SO4 gradients, however, the peak of the fRNA-DNA hybrids shifted on the heavier side of the profile. This indicates that the ribosomal RNA cistrons in Allomyces are A-T-rich. Hybridization with homologous rRNA showed that, at saturation, 3.25% of the DNA is complementary to rRNA. With the genome size of 1.7-10(10) daltons, the multiplicity of rRNA cistrons has been found to be close to 270.