A biomedical open knowledge network harnesses the power of AI to understand deep human biology.

Knowledge representation and reasoning (KR&R) has been successfully implemented in many fields to enable computers to solve complex problems with AI methods. However, its application to biomedicine has been lagging in part due to the daunting complexity of molecular and cellular pathways that govern human physiology and pathology. In this article we describe concrete uses of SPOKE, an open knowledge network that connects curated information from 37 specialized and human-curated databases into a single property graph, with 3 million nodes and 15 million edges to date. Applications discussed in this article include drug discovery, COVID-19 research and chronic disease diagnosis and management.

COMPARATIVE RENAL DISPOSITION OF CREATINE, AND TECHNETIUM DIAGNOSTIC CONTRAST AGENTS IN THE PIGEON (COLUMBA LIVIA).

Clinical assessment of renal function in avian species often involves the measurement of plasma uric acid and blood urea nitrogen, relatively insensitive markers of renal dysfunction and dehydration. In mammals, endogenous creatinine is widely used as an indicator of renal glomerular dysfunction. However, avian species produce primarily creatine. Here, renal creatine, 99mTc99-DTPA (diethylenepentaacetic acid, DTPA) and 99mTc-MAG3 (mercaptoacetyl triglycine, MAG3) renal clearances are characterized in the pigeon avian model by infusing DTPA with inulin and creatine with each tracer and examining the slope of their blood disappearance curves. Clearance curves for inulin and DTPA were parallel, suggesting DTPA is cleared by renal filtration. MAG3 clearance (slope: -2.74 × 105, r2 = 0.97) had a slope almost 10-fold steeper than for DTPA (slope: -6.29 × 104, r2 = 0.90), and orders of magnitude steeper than for creatine (slope: -1.4, r2 = 1.0). These results suggest that DTPA is cleared by glomerular filtration like inulin, while MAG3 is filtered and actively excreted in a manner similar to mammals. In contrast, creatine is filtered and resorbed, has a larger volume of distribution (Vd), or exhibits a greater blood protein binding, making it more complex as a renal marker, when compared with creatinine handling in mammals. The two radiotracers can be readily adapted for use in birds, inviting both qualitative and semiquantitative functional evaluation of avian renal function for research and clinical purposes. The elimination of creatine appears to be more complex requiring further study.

An Image Analysis Solution For Quantification and Determination of Immunohistochemistry Staining Reproducibility.

With immunohistochemical (IHC) staining increasingly being used to guide clinical decisions, variability in staining quality and reproducibility are becoming essential factors in generating diagnoses using IHC tissue preparations. The current study tested a method to track and quantify the interrun, intrarun, and intersite variability of IHC staining intensity. Our hypothesis was that staining precision between laboratory sites, staining runs, and individual slides may be verified quantitatively, efficiently and effectively utilizing algorithm-based, automated image analysis. To investigate this premise, we tested the consistency of IHC staining in 40 routinely processed (formalin-fixed, paraffin-embedded) human tissues using 10 common antibiomarker antibodies on 2 Dako Omnis instruments at 2 locations (Carpinteria, CA: 30 m above sea level and Longmont, CO: 1500 m above sea level) programmed with identical, default settings and sample pretreatments. Digital images of IHC-labeled sections produced by a whole slide scanner were analyzed by a simple commercially available algorithm and compared with a board-certified veterinary pathologist's semiquantitative scoring of staining intensity. The image analysis output correlated well with pathology scores but had increased sensitivity for discriminating subtle variations and providing reproducible digital quantification across sites as well as within and among staining runs at the same site. Taken together, our data indicate that digital image analysis offers an objective and quantifiable means of verifying IHC staining parameters as a part of laboratory quality assurance systems.

Assessment of novel avian renal disease markers for the detection of experimental nephrotoxicosis in pigeons (Columba livia).

Renal disease is a major cause of illness in captive and wild avian species. Current renal disease markers (e.g., uric acid, blood urea nitrogen, and creatinine) are insensitive. Two endogenous markers, creatine and N-acetyl-beta-D-glucosaminidase (NAG), were selected for study in the pigeon (Columba livia). Representative organs from four pigeons were surveyed to determine those exhibiting the highest level of each marker. In a separate study, NAG and creatine from plasma and urine were assayed before and after gentamicin (50 mg/kg twice daily), administration for up to 9 days. Observer-blinded pathologic scoring (five saline solution controls, 17 treated birds) was used to verify the presence of renal disease that corresponded to marker increases. The first study revealed that kidney tissue had the highest NAG activity (by approximately six times), and pectoral muscle had the most creatine (>900 times). In response to gentamicin, plasma creatine (>five times) and NAG increased (approximately six times), which paralleled uric acid (>10 times). Urine creatine (approximately 60 times) and NAG increased dramatically (approximately 50 times) in response to gentamicin. In conclusion, NAG, especially in the urine, may be of value to noninvasively detect renal toxin exposures and to monitor potentially nephrotoxic drugs, and might be of value to screen free-ranging birds in large exhibits or in the wild by assaying fresh urate samples at feeding stations.

Sucrose helps regulate cold acclimation of Arabidopsis thaliana.

A test was carried out to see if sucrose could regulate cold-acclimation-associated gene expression in Arabidopsis. In plants and excised leaves, sucrose caused an increase in GUS activity, as a reporter for the activity of the cold-responsive COR78 promoter. This increase was transient at 21 degrees C but lasted for at least 4 d at 4 degrees C in continuous darkness. However, at 4 degrees C with a 16 h photoperiod, GUS activity was similarly high with solutions lacking sucrose or with different concentrations of sucrose. In peeled lower epidermis in the cold dark environment, 40 mM sucrose increased COR78 transcript abundance to substantially above that in the controls, but sorbitol had no effect. Similarly to the cold and dark conditions, sucrose increased COR78 transcript abundance in the epidermis in the warm light and warm dark environments, but not in a cold light environment. Sucrose had much less effect on COR78 transcript abundance in leaves without the lower epidermis. Thus sucrose regulates expression of COR78, possibly mainly in the epidermis, at the level of transcription. Furthermore, 40 mM sucrose at 4 degrees C for 24 h in constant darkness was sufficient to give the same GUS activity as in fully acclimated plants of the same age in a 16 h photoperiod, although by 48 h, GUS activity had become intermediate between control and fully cold-acclimated plants. Thus sucrose has a regulatory role in the acclimation of whole plants to cold and this may be important during diurnal dark periods.

Lack of association between ectoparasite intensities and rabies virus neutralizing antibody seroprevalence in wild big brown bats (Eptesicus fuscus), Fort Collins, Colorado.

Recently, bat ectoparasites have been demonstrated to harbor pathogens of potential importance to humans. We evaluated antirabies antibody seroprevalence and the presence of ectoparasites in big brown bats (Eptesicus fuscus) sampled in 2002 and 2003 in Colorado to investigate if an association existed between ectoparasite intensity and exposure to rabies virus (RV). We used logistic regression and Akaike's Information Criteria adjusted for sample size (AICc) in a post-hoc analysis to investigate the relative importance of three ectoparasite species, as well as bat colony size, year sampled, age class, colony size, and year interaction on the presence of rabies virus neutralizing antibodies (VNA) in serum of wild E. fuscus. We obtained serum samples and ectoparasite counts from big brown bats simultaneously in 2002 and 2003. Although the presence of ectoparasites (Steatonyssus occidentalis and Spinturnix bakeri) were important in elucidating VNA seroprevalence, their intensities were higher in seronegative bats than in seropositive bats, and the presence of a third ectoparasite (Cimex pilosellus) was inconsequential. Colony size and year sampled were the most important variables in these AICc models. These findings suggest that these ectoparasites do not enhance exposure of big brown bats to RV.

Ectoparasites in an urban population of big brown bats (Eptesicus fuscus) in Colorado.

Ectoparasites of an urban population of big brown bats (Eptesicus fuscus) in Fort Collins, Colorado, were investigated during summers 2002, 2003, and 2004. Eleven species of ectoparasites were found (the macronyssid mite Steatonyssus occidentalis, the wing mite Spinturnix bakeri, the myobiid mites Acanthophthirius caudata and Pteracarus aculeus, the chirodiscid mite Alabidocarpus eptesicus, the demodicid mite Demodex sp., the chigger Leptotrombidium myotis, the soft tick Carios kelleyi, the batfly Basilia forcipata, the batbug Cimex pilosellus, and the flea Myodopsylla borealis). Five species were analyzed by prevalence and intensity (C. pilosellus, M. borealis, L. myotis, S. bakeri, and S. occidentalis) based on 2161 counts of 1702 marked individual bats over the 3 summer study periods. We investigated 4 factors potentially influencing prevalence and intensity: age class of the host, reproductive status of adult female hosts, roosts in which the hosts were found, and abiotic conditions during the year sampled. The macronyssid mite, S. occidentalis, was the most prevalent and abundant ectoparasite. Adult big brown bats had more ectoparasites than volant juveniles for most of the species analyzed. In a sample of known age bats at 1 large colony, bats of 4 yr of age or greater had higher ectoparasite loads of S. occidentalis and S. bakeri when compared with younger bats. Lactating female bats had the highest prevalence and intensities of most ectoparasites. Annual differences in ectoparasite prevalence and intensity were related to temperature and humidity, which can affect the nidicolous species of ectoparasites. Residents of 2 buildings sprayed insecticides in response to Cimex sp., and this appeared to reduce ectoparasitism of S. occidentalis and C. pilosellus present at these buildings. Intensity of S. occidentalis had no influence on annual survival of big brown bats.

Sampling blood from big brown bats (Eptesicus fuscus) in the field with and without anesthesia: impacts on survival.

Blood was collected from wild big brown bats (Eptesicus fuscus) with and without anesthesia in Fort Collins, Colorado in 2004 to assess the impacts of these procedures on short-term survival and 1-yr return rates. Short-term survival and 1-yr return rates after release were passively monitored using PIT tag detection hoops placed at selected buildings. Comparison of 14-day maximum likelihood survival estimates from bats not bled (142 adult females, 62 volant juveniles), and bats sampled for blood with anesthesia (96 adult females, 23 volant juveniles) and without anesthesia (112 adult females, 22 volant juveniles) indicated no adverse effects of either treatment (juveniles: chi(2) = 53.38, df = 41, P = 0.09; adults: chi(2) = 39.09, df = 44, P = 0.68). Return rates of bats one year after sampling were similar among adult female controls (75.4%, n = 142, 95% CI = 67.4-82.2%), females sampled for blood with anesthesia (83.0%, n = 112, 95% CI = 74.8-89.5%), and females sampled without anesthesia (87.5%, n = 96, 95% CI = 79.2-93.4%). Lack of an effect was also noted in 1-yr return rates of juvenile females. These data suggest that the use of anesthesia during sampling of blood has no advantages in terms of enhancement of survival in big brown bats.

Anesthesia and blood sampling of wild big brown bats (eptesicus fuscus) with an assessment of impacts on survival.

We anesthetized and blood sampled wild big brown bats (Eptesicus fuscus) in Fort Collins, Colorado (USA) in 2001 and 2002 and assessed effects on survival. Inhalant anesthesia was delivered into a specially designed restraint and inhalation capsule that minimized handling and bite exposures. Bats were immobilized an average of 9.1+/-5.1 (SD) min (range 1-71, n=876); blood sample volumes averaged 58+/-12 microl (range 13-126, n=718). We randomly selected control (subject to multiple procedures before release) and treatment (control procedures plus inhalant anesthesia and 1% of body weight blood sampling) groups in 2002 to assess treatment effects on daily survival over a 14-day period for adult female and volant juvenile bats captured at maternity roosts in buildings. We monitored survival after release using passive integrated transponder tag detection hoops placed at openings to selected roosts. Annual return rates of bats sampled in 2001 were used to assess long-term outcomes. Comparison of 14-day maximum-likelihood daily survival estimates from control (86 adult females, 92 volant juveniles) and treated bats (187 adult females, 87 volant juveniles) indicated no adverse effect from anesthesia and blood sampling (juveniles: chi2=22.22, df=27, P>0.05; adults: chi2=9.72, df=18, P>0.05). One-year return rates were similar among adult female controls (81%, n=72, 95% confidence interval [CI]=70-91%), females treated once (82%, n=276, 95% CI=81-84%), and females treated twice (84%, n=50, 95% CI=74-94%). Lack of an effect was also noted in 1-yr return rates of juvenile female controls (55%, n=29, 95% CI=37-73%), juveniles treated once (66%, n=113, 95% CI=58-75%), and juveniles treated twice (71%, n=17, 95% CI=49-92%). These data suggest that anesthesia and blood sampling for health monitoring did not measurably affect survival of adult female and volant juvenile big brown bats.

Sugars regulate cold-induced gene expression and freezing-tolerance in barley cell cultures.

The hypothesis that the extracellular concentration of sugars helps regulate the acclimation of plant cells to cold was tested in this work. Suspension cultures were used to control the concentration of sugars in the medium supplied to barley cell cultures (Hordeum vulgare L. cv. Igri), replacing the medium daily to help maintain the concentration. Freezing tolerance and the levels of mRNA expression of the stress-response genes blt4.9 (coding for a non- specific lipid transfer protein) and dhn1 (coding for a dehydrin) were measured. Similar levels of freezing-tolerance and gene expression were obtained in the experiments as occur during cold-acclimation in the crown of the whole plant. In the cell cultures, cold (6/2 degrees C) did not induce an increase in freezing tolerance or in the expression of detectable levels of blt4.9 or dhn1 mRNAs when only 1 g l-1 sucrose was supplied. However, the cells in this low sucrose medium in the cold were not sugar-starved, indicating that this did not explain the failure of the cells to acclimate when grown in the cold environment. Ten g l-1 sucrose supplied to cells grown in the warm (25 degrees C) induced acclimation to freezing and up-regulation of expression of blt4.9 and dhn1 mRNAs. Osmolality of the medium did not explain this. Thirty g l-1 sucrose induced yet higher levels of freezing tolerance and of blt4.9 and dhn1 mRNAs in cultures grown in either the cold or the warm environment. The results implicate sugars in the regulation of cold acclimation

Extracellular freezing in leaves of freezing-sensitive species.

Low-temperature scanning-electron microscopy was used to study the freezing of leaves of five species that have no resistance to freezing: bean (Phaseolus vulgaris L.), tobacco (Nicotiana tabacum L.), tomato (Lycopersicon esculentum L.), cucumber (Cucumis sativus L.), and corn (Zea mays L.). In the leaves of the four dicotyledonous species, ice was extracellular and the cells of all tissues were collapsed. In contrast, in maize leaves ice was extracellular in the mesophyll, and these cells were collapsed, but the epidermal and bundle-sheath cells apparently retained their original shapes and volume. It is concluded that the leaves of the freezing-sensitive dicotyledonous species tested were killed by cellular dehydration induced by extracellular freezing, and not by intracellular freezing. Freezing injury in maize leaves apparently resulted from a combination of freezing-induced cellular dehydration of some cells and intracellular ice formation in epidermal and bundle-sheath cells.