Earbox, an open tool for high-throughput measurement of the spatial organization of maize ears and inference of novel traits.

BACKGROUND: Characterizing plant genetic resources and their response to the environment through accurate measurement of relevant traits is crucial to genetics and breeding. Spatial organization of the maize ear provides insights into the response of grain yield to environmental conditions. Current automated methods for phenotyping the maize ear do not capture these spatial features. RESULTS: We developed EARBOX, a low-cost, open-source system for automated phenotyping of maize ears. EARBOX integrates open-source technologies for both software and hardware that facilitate its deployment and improvement for specific research questions. The imaging platform consists of a customized box in which ears are repeatedly imaged as they rotate via motorized rollers. With deep learning based on convolutional neural networks, the image analysis algorithm uses a two-step procedure: ear-specific grain masks are first created and subsequently used to extract a range of trait data per ear, including ear shape and dimensions, the number of grains and their spatial organisation, and the distribution of grain dimensions along the ear. The reliability of each trait was validated against ground-truth data from manual measurements. Moreover, EARBOX derives novel traits, inaccessible through conventional methods, especially the distribution of grain dimensions along grain cohorts, relevant for ear morphogenesis, and the distribution of abortion frequency along the ear, relevant for plant response to stress, especially soil water deficit. CONCLUSIONS: The proposed system provides robust and accurate measurements of maize ear traits including spatial features. Future developments include grain type and colour categorisation. This method opens avenues for high-throughput genetic or functional studies in the context of plant adaptation to a changing environment.

The Effect of Inadequate Presample Blood Volume Withdrawal from Intravenous Catheter and Extension Sets on Measured Circulating L-Blood Lactate Concentration in Horses Receiving Lactated Ringer's Solution.

BACKGROUND: Circulating l-lactate concentration is commonly measured in hospitalized horses by sampling from indwelling intravenous (IV) catheters. However, there are no published evidence-based recommendations to prevent contamination by lactated Ringer's solution (LRS). HYPOTHESIS: Withdrawing 10 mL of blood from the LRS-containing extension set connected to the IV catheter before obtaining the sample for analysis should be adequate to obtain accurate measurement of blood lactate concentration (BLC). ANIMALS: Thirty-three adult hospitalized horses receiving constant rate infusion of LRS. METHODS: Immediately after disconnecting the LRS, 5 sequential 5 mL blood samples were obtained by aspiration from an extension set connected to an indwelling IV catheter, followed by 3 samples collected by direct venipuncture of the contralateral jugular vein. Samples were analyzed with 1 portable blood lactate analyzer. A linear mixed model was used to examine differences in lactate concentrations among samples collected from the catheter and by direct venipuncture. RESULTS: After considering differences in age, breed, sex, and reason for hospitalization, BLCs were higher (P < .001) in the first and second 5 mL samples collected through the extension set/catheter than in all other extension set/catheter samples or the direct venipuncture samples. The largest difference observed between the third and subsequent catheter or venipuncture samples was 0.34 mmol/L with an upper 95% CI of 1.12 mmol/L. CONCLUSIONS AND CLINICAL IMPORTANCE: Withdrawing 15 mL of blood from a LRS-containing extension set connected to an IV catheter (5.9 mL total volume capacity) before obtaining the sample for blood lactate analysis is suggested to optimize accuracy of BLC measurements.

A new method to characterize hydraulic short-circuits in defective borehole seals.

A new approach has been developed to detect, characterize, and quantify hydraulic short-circuits in boreholes with faulty seals. The methodology, applicable to an aquifer-aquitard-aquifer system, involves a series of successive, constant-rate pumping tests in the lower aquifer while determining the leakage rate with a simultaneous nonreactive tracer test. During each pumping step, the tracer is injected under constant concentration and constant hydraulic head from a piezometer in the upper aquifer. If a seal defect exists, the tracer will follow the leak and will be recovered from the pumped water. The theoretical equations relate the leakage rate, the pumping rate, the concentration of the injected tracer, and the recovered concentration. Leakage rates can be determined for any pumping rate. The theory is tested using numerical analysis and a full-scale field test.

An analytical solution for ground water transit time through unconfined aquifers.

An exact, closed-form analytical solution is developed for calculating ground water transit times within Dupuit-type flow systems. The solution applies to steady-state, saturated flow through an unconfined, horizontal aquifer recharged by surface infiltration and discharging to a downgradient fixed-head boundary. The upgradient boundary can represent, using the same equation, a no-flow boundary or a fixed head. The approach is unique for calculating travel times because it makes no a priori assumptions regarding the limit of the water table rise with respect to the minimum saturated aquifer thickness. The computed travel times are verified against a numerical model, and examples are provided, which show that the predicted travel times can be on the order of nine times longer relative to existing analytical solutions.

The demographic evolution of rural France (1968-1982).

"After more than a century of decline, noticeable increases in the rural population of France became apparent in the 1982 census. The spatial patterns of these changes are interpreted by comparing a set of demographic variables in the 1968-1975 and 1975-1982 intercensal periods. Migration to rural areas near many of the major cities (rurbanization) and to the southern part of France is the main demographic explanation. Using factor analysis and a hierarchical classification system the underlying demographic associations are established and the nation is differentiated into seven types. A method for estimating the probabilities of any one type occurring is also demonstrated. The timing of the demographic changes and the fundamental societal forces which have influenced them suggest that government policy has played a minor part in the evolution."

Structural and functional studies in C1q deficiency.

The sera of two brothers were found totally lacking hemolytic C activity. One of them, a 16-yr-old male, presented a severe lupus-like syndrome, whereas the other was apparently healthy. Immunochemical quantitation of C components in both sera showed depressed levels of C1q, whereas the levels of C1r, C1s, and C1 inhibitor were elevated. C4, C3, C5, factor B, and beta 1H levels were in the normal range. Hemolytic C1 activity was totally lacking. C4 titers were elevated (150% of normal). C2 hemolytic activity was about one-third of normal, and the titers of the terminal components C3-C9 were also reduced in the two siblings. Double immunodiffusion against anti-C1q antiserum showed a partial loss of C1q antigenic determinants in the two siblings. Furthermore, the C1q of both siblings was unable to interact with immunoglobulins or to associate with C1r and C1s. Addition of purified human C1q to the sera restored their total C and C1 hemolytic activity. The dose response to the C1q addition was linear, indicating that the functional deficiency was not due to the presence of a serum inhibitor. Although antigenically deficient in comparison with normal C1q, the abnormal C1q appeared to have a larger m.w., as determined by gel chromatography. Investigation of other members of this family suggests a genetically linked disorder, because four out of six siblings had the same dysfunctional C1q in their serum.

The first component of complement. I. Purification and properties of native C1.

The first component of complement has been purified by using affinity chromatography on Sepharose-bound IgG. Unlike earlier procedures that yield the activated form of C1, in this method C1 is maintained in the native form by the protease inhibitor p-nitrophenyl, p'-guanidinobenzoate (NPGB). The procedure requires only two steps and yields pure C1 as judged both by SDS-PAGE analysis and by effective molecule calculations. The yields have varied from 30 to 50% in over 50 preparations. The functional properties of the purified native C1 correspond to those of C1 in serum. The dose-response activity profile is nonlinear, but becomes linear when C1 IS ALLOWED TO SELF-ACTIVATE. From SDS-PAGE analysis of the self-activated C1, all the C1r and C1s subcomponents are converted to the activated split products, indicating that all C1 molecules are biologically active. The recovery of C1 activity is dependent on the use of a heterologous source for the IgG on the affinity absorbant. The conditions of binding and elution from the Sepharose-IgG column are critical, indicating that immunoglobulin-bound C1 is rapidly inactivated under physiologic conditions by serum inactivators. The activation of the purified C1 in fluid phase has been explored both in the presence and absence of C1-inhibitor.

Selective proteolysis of the J chain component in human polymeric immunoglobulin.

To clarify the losses that have been observed in the J chain portion of human IgM and IgA, were carried out studies on the enzymatic susceptibility of the J polypeptide. When Waldenström macroglobulins and myeloma IgA polymers were subjected to limited proteolysis with various endopeptidases, only subtilisin was found to attack the J chain component. The pattern of cleavage was a function of the polymer species. The J chain in IgM was highly susceptible to digestion, quantitative cleavage being achieved at very low enzyme to IgM ratios and without significant changes in the remaining pentamer structure. Analyses of the digestion products showed that the initial cleavage occurred at an exposed region midway in the J sequence and was followed by extensive degradation of the carboxy-terminal segment. These findings indicated that the observed loss of the IgM J component can be explained by the inadvertent introduction of subtilisin in vitro or by the attack of in vivo enzymes with a specificity similar to subtilisin. In contrast, the IgA J chain was found to be much more resistant to subtilisin proteolysis; its cleavage required higher enzyme concentrations and was accompanied by significant degradation of the alpha-chains. Thus, it appears unlikely that the IgA J polypeptide is degraded by either in vitro or in vivo enzymes unless its accessibility is first enhanced by changes in the IgA Fc structure.

Linkage and assembly of polymeric IgA immunoglobulins.

The intersubunit linkage of polymeric IgA immunoglobulins was determined from studies of the products of reductive and cyanogen bromide cleavage. Under conditions of limited dithioerythritol reduction tetramer IgA molecules were cleaved to yield two monomers and a J chain containing dimer. The stability of the dimer and the conservation of the J chain disulfides indicated that the J chain joins two monomer subunits. Evidence confirming the J chain dimer clasp was obtained from the depolymerization of tetramer and dimer IgA by cyanogen bromide treatment. The cleavage studies also showed that (a) the S-S bonds directly joining the other subunits are located at the same penultimate alpha chain half-cystines that constitute the site of J chain attachment and (b) during limited reduction the monomer-monomer bonds undergo interchange to release subunits without a concomitant generation of alpha chain thiols. These linkage data provide strong support for the assembly of IgA and IgM polymers by sequential disulfide exchanges beginning with the formation of a J chain containing dimer.

Mechanism of IgM polymerization.

The stoichiometry of J chain in pentamer IgM has been determined by measuring the radiolabeled thiols in the constituent chains after complete reduction and alkylation of the polymer. One mole of J was found to be disulfide bonded to 1 mol of pentamer. The linkage of J chain in IgM has been determined by correlating the J disulfides cleaved with the subunits released after limited reduction and alkylation of the polymer. The analyses showed that: (a) Significant amounts of monomers, as well as small quantities of dimers, trimers, and tetramers, were generated by the reducing conditions employed. (b) The number of J disulfide bonds broken did not correspond to the extent of depolymerization. (c) No J disulfides were cleaved in the J-containing dimer products of the limited reduction. These data demonstrated that the J chain is located as a disulfide clasp between two of the IgM monomer subunits. From the observed linkage, the assembly of IgM is postulated to proceed by a series of sequential disulfide exchanges beginning with the formation of the J-containing dimer.