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Viruses of microbes are ubiquitous biological entities that reprogram their hosts' metabolisms during infection in order to produce viral progeny, impacting the ecology and evolution of microbiomes with broad implications for human and environmental health. Advances in genome sequencing have led to the discovery of millions of novel viruses and an appreciation for the great diversity of viruses on Earth. Yet, with knowledge of only "who is there?" we fall short in our ability to infer the impacts of viruses on microbes at population, community, and ecosystem-scales. To do this, we need a more explicit understanding "who do they infect?" Here, we developed a novel machine learning model (ML), Virus-Host Interaction Predictor (VHIP), to predict virus-host interactions (infection/non-infection) from input virus and host genomes. This ML model was trained and tested on a high-value manually curated set of 8849 virus-host pairs and their corresponding sequence data. The resulting dataset, 'Virus Host Range network' (VHRnet), is core to VHIP functionality. Each data point that underlies the VHIP training and testing represents a lab-tested virus-host pair in VHRnet, from which meaningful signals of viral adaptation to host were computed from genomic sequences. VHIP departs from existing virus-host prediction models in its ability to predict multiple interactions rather than predicting a single most likely host or host clade. As a result, VHIP is able to infer the complexity of virus-host networks in natural systems. VHIP has an 87.8% accuracy rate at predicting interactions between virus-host pairs at the species level and can be applied to novel viral and host population genomes reconstructed from metagenomic datasets., Competing Interests: The authors have declared that no competing interests exist., (Copyright: © 2024 Bastien et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)

Oxygen (O2) concentrations often fluctuate over diel timescales within wetlands, driven by temperature, sunlight, photosynthesis and respiration. These daily fluxes have been shown to impact biogeochemical transformations (e.g. denitrification), which are mediated by the residing microbial community. However, little is known about how resident microbial communities respond to diel physical and chemical fluxes in freshwater wetland ecosystems. In this study, total microbial (bacterial and archaeal) community structure was significantly related to diel time points in just one out of four distinct freshwater wetlands sampled. This suggests that daily environmental shifts may influence wetlands differentially based upon the resident microbial community and specific physical and chemical conditions of a freshwater wetland. When exploring the microbial communities within each wetland at finer resolutions, subcommunities of taxa within two wetlands were found to correspond to fluctuating O2 levels. Microbial taxa that were found to be susceptible to fluctuating O2 levels within these subnetworks may have intimate ties to metabolism and/or diel redox cycles. This study highlights that freshwater wetland microbial communities are often stable in community structure when confronted with short-term O2 fluxes; however, specialist taxa may be sensitive to these same fluxes.

Aims: To identify maternal, obstetric and neonatal characteristics of opioid-dependent Indigenous Australians in rural and metropolitan settings., Methods: Retrospective cohort study of 232 metropolitan and 67 rural infants born to mothers maintained on methadone throughout pregnancy for the treatment of opiate dependency, between January 2000 and December 2006. Medical records of identified mother/infant dyads were reviewed by evaluating 20 different maternal, obstetric and neonatal parameters., Results: The number of infants of opiate-dependent mothers (IODMs) identified to be of Aboriginal ethnicity was 47 in the rural and 50 in the metropolitan setting. This reflected a significantly higher proportion in the rural versus metropolitan areas (70.1% vs 21.6%, P < 0.05). The effect of rurality was independent of ethnicity with significantly lower rates of neonatal withdrawal requiring treatment (P < 0.001), antenatal consultations (P < 0.01), department of community services (DoCS) involvement (P < 0.001) and shorter infant lengths of stay (P < 0.001). There was a non-significant trend towards more intrauterine growth restriction in Aboriginal infants. There were no significant differences in parameters in rural Indigenous versus rural non-Indigenous infants., Conclusions: Significant differences exist between rural and metropolitan IODMs in terms of less attendance at antenatal consultations, less neonatal withdrawal requiring treatment, shorter average length of hospital stay for the infant and less documented DoCS involvement. These differences maybe a reflection of a different diagnostic and management approach. Ethnicity had no major clinical impact in either the rural or the metropolitan settings. Future research comparing the long-term outcomes would be of interest.

The physician who is entrusted with a large quantity of resources for the treatment of ARF/MOSF has a social responsibility for optimizing the treatment, auditing the outcome, and where possible, preventing the illness. Best treatment includes not only modern techniques but also efficient organization and leadership of the ICU team. Audit is an individual responsibility, may be fruitfully pursued on a multicenter basis, and is a cost-containment discipline. Audit of the St. Thomas' Hospital ARF program has resulted in a predictive scoring formula. This is used to illustrate a cost-effective analysis related to disease severity. Prevention of ARF/MOSF is a challenge to emergency services. There may also be a considerable opportunity to prevent ARF in high-risk surgical patients. A randomized study carried out at St. George's Hospital illustrates the health gains which could result.

The European Dialysis and Transplantation Association-European Renal Association (EDTA-ERA) Registry conducted a special study on anaemia in dialysis patients because it seemed important to elucidate the various factors that influence the degree of anaemia and the use of regular transfusions in dialysis patients before the introduction of recombinant human erythropoietin (rHuEpo) for larger groups of patients. In a 20% sample of all patients recorded to have been dialysed throughout 1987, statistically significant associations could be found by multifactorial analysis between haemoglobin (Hb) concentration and age, sex, primary renal disease, type of treatment, hours of dialysis per week, and number of years on renal replacement therapy. The type of dialyser membrane did not seem to play a role (although there was weak evidence of an effect of the dialyser). Mean Hb concentration for dialysis patients differed between countries as did the transfusion policy. In view of the high costs of the rHuEpo treatment and potential side-effects, factors such as method of dialysis and hours of haemodialysis per week should be taken into consideration in the treatment of anaemia in dialysis patients.

Peritonitis rates were compared in patients receiving continuous ambulatory peritoneal dialysis (CAPD) via either a Y-set dialysate delivery system or a standard system. Forty patients in each arm of the trial were matched for age (range 20-67 years, mean 49 years), and remained in the study for similar periods (range 3-36 months, mean 14.1 months). The observation time was 564 patient-months for each arm of the trial. There were 22 episodes of peritonitis in nine out of 40 patients using the Y-set and 57 episodes in 21 out of 40 patients using the standard system (P = 0.005 Wilcoxon signed rank test for episodes, P = 0.02 McNemar's chi 2 test for patients). Peritonitis rates were one episode per 25 patient-months in the Y-set group, and one episode per 9.7 patient-months in the standard group. In the Y-set group there were significantly fewer episodes caused by coagulase-negative staphylococci and Acinetobacter spp. There was no difference in the rate of episodes caused by Staphylococcus aureus, streptococci, enterococci, corynebacteria, enterobacteria or pseudomonads. There was no difference in the incidence of catheter exit wound infections. The Y-set dialysis delivery system is effective in reducing peritonitis rates in CAPD patients caused by organisms derived from the commensal skin flora, principally coagulase-negative staphylococci, but does not reduce peritonitis caused by other organisms.

The educational status, employment rate and social situation were studied in 617 patients between 21 and 35 years of age who started renal replacement therapy (RRT) as children. The data were derived from a special questionnaire concerning disability and rehabilitation sent to dialysis and transplant centres reporting to the EDTA Registry. Fifty-six percent of patients completed secondary school and one in three went on to vocational training. Eleven percent of patients attended university, and 16% were reported to have gone to a special school for the handicapped. Up to one-third of patients who attended different school types failed to complete their education. There were notable geographical differences in schooling and in employment. Fifty-six percent of all patients were employed. Lack of schooling was considered to be a major reason for unemployment. Sixty-one percent of patients with disabilities and 34% without disabilities were receiving invalidity payments. The place of residence of these patients aged 21-35 was usually the parental home. Compared to the general population of similar age, only a few patients were married (13.5% of the total study group) and 8% had children. In summary, the present report shows that the major factors influencing rehabilitation on RRT are the presence of disabilities, the method of treatment, geographical factors, duration of RRT, and the underlying primary renal disease.

The aim of this study was to analyse rehabilitation during RRT in 617 young adults from different European countries who started dialysis or transplantation before the age of 15 years. The data were derived from the EDTA Registry patient data files and a special questionnaire that was sent to centres reporting to the EDTA Registry. The duration of RRT was more than 10 years in 63% of patients. Fifty-four percent were living with a functioning graft and 46% were on dialysis. The prevalence and severity of motor, hearing, sight, and mental disabilities were analysed retrospectively. They were found to vary according to primary renal disease and method of treatment. One-third of patients had one or more disabilities at the start of RRT. Although disability status had changed in many patients by 31 December 1986, some disability remained in one-third of the patients available for study. Disabilities were recorded as mild in the majority of patients. Both improvement and worsening of motor and mental disability occurred more often than changes of hearing capacity and sight. It is concluded that prevention and treatment of disabilities need special attention in children and young adults on RRT in order to improve rehabilitation.

This study reports the geographical incidence of successful pregnancies in women on renal replacement therapy (RRT) and related information on gestation and clinical status of newborns. The impact of successful pregnancy on graft function was assessed by means of a retrospective case-control study. Since 1977 special questionnaires have been sent to each dialysis and transplant centre which reported babies born to mothers on RRT on the yearly centre questionnaire. After 10 years of data collection, a total of 490 pregnancies and 500 babies were available for analysis. A percentage of 88.4 of the babies were born to mothers with a functioning graft, 11.2% to mothers on chronic haemodialysis, and the remaining 0.4% to mothers on CAPD. Almost 50% of all successful pregnancies were reported from the UK. The number of successful pregnancies increased steadily and in parallel with the increasing number of females of childbearing age with a functioning renal transplant. The majority of mothers delivered at age 24-32. For transplanted mothers delivery occurred most commonly during the 3rd and 4th year after successful transplantation. In approximately 85% of cases the duration of pregnancy was shorter than the lower 10th percentile of normal. Birthweight was reduced in accordance with gestational age. Newborn mortality was 1.8%. Fifty-three mothers with a successful pregnancy in 1984-1987 were computer matched with controls according to a number of criteria. The serum creatinine concentration recorded in coded form at the end of each year on the individual EDTA patient questionnaire was used to assess changes in graft function.(ABSTRACT TRUNCATED AT 250 WORDS)

The major complication of central venous catheterization for immediate access for haemodialysis is infection. The Quinton Permcath is a tunnelled, double lumen, flexible silastic catheter with a Dacron cuff, and is claimed to be associated with a low rate of infection. In a two-year study we have monitored all complications including catheter-associated infection related to this device in haemodialysis patients while following a simple aseptic programme for the care of the catheter exit wound. Thirty four Permcaths were inserted in 30 patients for a mean duration of 6.2 months (SD +/- 5.7; range 2 days to 23 months). Catheter use amounted to a total of 197 months. Of twenty-seven catheter wound infections, 6 (22%) were caused by Staphylococcus aureus, and 15 (56%) by coagulase-negative staphylococci or corynebacteria. These occurred in 19 patients, giving an exit site infection rate of one episode per 7.4 catheter months. Catheter-associated septicaemia occurred in three patients (two S. aureus, one S. epidermidis), at a rate of one episode per 66 months. It was possible to correlate three episodes of infection with breakdown in aseptic care. This study confirms the low rate of infection associated with the use of the Permcath, and we conclude that the design of the device and aseptic care of the catheter and its wound contribute to this.

Ciprofloxacin at a dose of 25 mg/L of dialysate was administered intraperitoneally for five days as a single agent for the empirical treatment of CAPD peritonitis. One hundred and seventeen consecutive episodes of peritonitis occurred in 65 patients during the study period, and 100 episodes were entered in the study. This therapy was successful in 79% of episodes. Resistant organisms (MIC greater than 4 mg/L) all of them coagulase-negative staphylococci, were isolated in nine (7.8%) of the 117 episodes. Mean ciprofloxacin concentrations in dialysate and serum on the last day of treatment were 6.1 mg/L (range 0.3-15.7) and 0.3 mg/L (range 0-0.9) respectively. No adverse effects were reported.

In a large pedigree of Caribbean origin with adult polycystic kidney disease, linkage has been established to the 3'HVR probe on chromosome 16. Although there are five different fathers in this pedigree, only one of whom was available for DNA analysis, the polymorphic nature of 3'HVR has enabled gene tracking to be carried out. The same allele cosegregates with the disease in every affected family member.

This report summarises the outcome of 90 combined kidney/pancreatic grafts performed in Europe in 1986. Data for the combined kidney/pancreas grafts were obtained by a special questionnaire. The one-year patient and kidney graft survival is compared to the results of a group of 389 patients with diabetic nephropathy on the EDTA Registry data file who received kidney grafts alone. The recipients of combined kidney-pancreas grafts were younger, whereas a greater proportion of males received kidney graft alone. Patient survival at one year after transplantation was similar: 89% in recipients of combined transplants compared to 90% in recipients of kidney grafts alone. Kidney graft survival was 78% at one year for recipients of combined grafts versus 76%. It is concluded that pancreas transplantation has little effect on the fate of concomitant kidney grafts. The procedure should-in experienced hands and in selected patients-be almost as safe as kidney grafting alone.

In 1987 a preventive programme was initiated to address the problem of high hospital and community-acquired CAPD infection. It concentrated on reducing Staphylococcus aureus carriage, improving aseptic operative technique, intensive training for nursing staff and patients in stringent aseptic care of the exit site, and avoidance of contact of the exit site with unsterile water. This programme was associated with an overall 10-fold reduction in exit site infection, a 2-fold reduction in peritonitis, and a 4.5-fold reduction in catheter loss from infection. These reductions have been sustained. Preventing infection in CAPD patients requires persistence and commitment but improves the patient's quality of life and reduces the cost of treatment.

In a retrospective case control study the prevalence of signs and symptoms of dialysis osteoarthropathy was analysed. Cases and controls had received over 9 years of maintenance haemodialysis uninterrupted by peritoneal dialysis or transplantation. The cases comprised 55 patients treated predominantly with polyacrylonitrile (AN69) dialysers. They were compared to a matched group dialysed exclusively with cellulosic membranes. Over 60% of all patients, cases and controls, showed one or more signs of disabling osteoarthropathy, with joint pains occurring more frequently in the older age groups. Twenty-seven of the 55 cases who had received less than 2 years of cellulosic membrane dialysis followed by 7-12 years of AN69 dialysis tended to have a lower prevalence of joint pains, carpal-tunnel syndrome and bone cysts. However, no statistically significant differences were obtained compared to the matched control group dialysed exclusively on cellulosic membranes (mostly cuprophane). The remaining 28 cases, who had been treated for more than 2 years with cellulosic membranes preceding the longer treatment period with polyacrylonitrile dialysers, showed a prevalence similar to that of their cellulosic controls. This study thus shows little, if any, influence of the two types of membranes on the prevalence of signs and symptoms of beta 2-microglobulin amyloidosis.

This report contains EDTA Registry data concerning transplant co-ordination services. It is a summary of the results of a special questionnaire mailed in 1989 to all renal transplant centres known to the EDTA Registry in Europe and Mediterranean countries. The response rate to the questionnaire was 86%. A transplant co-ordination service was available in more than 70% of the centres. The larger the transplant activity of a centre, the greater was the likelihood of a co-ordinator service being available. The educational background of the transplant co-ordinator was most commonly that of nurse. More than 70% of the centres had one or two transplant co-ordinators. A service shared by several centres was fairly common in the United Kingdom and France. The most important duties and activities appeared to be the organisation of transportation of donor teams and organs, giving feedback to the donor hospital's staff, and providing information to the public regarding organ donation.

The history of the Registry of the European Dialysis and Transplant Association-European Renal Association (EDTA-ERA) is outlined. The development of this Registry, which is run by physicians for physicians, the progress from analyses by hand to computerization, the generation of financial support, and the contribution to the annual congresses of the EDTA-ERA are described. In view of the many smaller countries in Europe, the importance of multicenter research that is organized by a registry serving a large population base is stressed.

One hundred and fifty out of 944 European dialysis centers reported experience with patients suffering from psoriasis. Ninety-three centers returned special questionnaires on 97 patients with end stage renal failure (ESRF patients) and on 49 patients dialyzed for psoriasis but who had normal renal function (NRF patients). Improvement of skin disease was reported in 17 out of 27 NRF patients according to both "objective criteria" and the patients' personal opinions. However, most of these patients had been on dialysis for less than one year (9.9 +/- 11.1 months) which is too short to allow for the spontaneous recurrence of psoriasis. In contrast, 60% of ESRF patients had been on dialysis for 45 +/- 3.1 months. Skin disease definitely improved in 20% of these patients after commencement of dialysis. This proportion is greater than the expected spontaneous long-term remission of psoriasis.

Cardiovascular and acid-base changes were studied in 18 adult haemodialysis patients during a single dialysis against acetate or bicarbonate dialysate. Tachycardia was significantly greater with acetate but, otherwise, blood pressure and peripheral resistance fell and cardiac output increased to a similar degree with the two types of dialysate. Arterial PCO2 increased with bicarbonate and fell slightly with acetate, while hypoxaemia was significantly worse during acetate dialysis. Arterial acetate concentrations increased in 2 of 12 patients during bicarbonate dialysis. No differences in patient symptomatology or hypotensive episodes were noted with acetate or bicarbonate. Any beneficial effects of bicarbonate dialysis are more likely to be related to preservation of arterial PO2 than to the absence of adverse cardiovascular effects of acetate.

Statistical surveys of dialysis and transplantation activities, conducted every year since 1965, and in greater detail since 1971, by the European Dialysis and Transplant Association and, according to its example, also by certain institutions in other countries, are very valuable and serve as a basis for a further development of these activities and for their management in the different countries. Also the firms manufacturing dialysis equipment make use of this information for the planning of their production. The dialysis and transplant therapy in the national range in the rich industrial countries was on the increase at the turn of sixties and seventies. This expansion was enabled by the sophisticated dialysis technique, produced in the factories and by the fact that the governments were taking on all expenses of the therapy. The development of dialysis and transplant activity in the European socialist countries was slower than in the western rich industrial states. It was due to the lack of currency for the import of dialysis technique. As the dialysis technique has been produced in some of these countries from the beginning of the eighties, one can expect the same expansion of the dialysis and transplant therapy in this decade as it was in the western countries ten years ago. The dialysis and transplant programme in the developing countries is negligible because their gross national product per capita is too low. Success of the dialysis therapy depends on the quality of the dialysis technique. It is hardly understandable why less expensive modes of therapy such as home dialysis and transplantation are less frequently used than centre dialysis in the majority of countries.

The problems inherent in using actuarial survival calculations in order to compare different methods for treating end-stage renal failure (ESRF) are emphasized. Assumptions must be made concerning the date for commencement of follow-up observation, the method for handling patients who change therapy, and the impact of antecedent therapies on the one under consideration. It is stressed that patients involved in different treatment methods do not comprise comparable groups since they are not randomly assigned but are selected by the availability and applicability of treatment modes as well as physician and patient preferences. We have proposed that interval mortality and treatment change rates are descriptions of clinical events that have happened to any defined group of patients and may be easily understood by the physician who must advise and make decisions.

We used impedance cardiography to monitor changes in cardiac output in 22 adult patients with terminal renal failure during hemodialysis against a dialyzate containing acetate. In 7 patients arterial acetate levels rose progressively during dialysis while in the remainder they remained low and steady. Patients who developed hyperacetatemia were able to maintain an elevated cardiac output during dialysis in contrast to the patients with stable acetate levels in whom cardiac output fell. These results strengthen our previous conclusion that acetate as used in conventional regular hemodialysis does not have a cardiodepressant action. The reported benefits of bicarbonate dialysis therefore involve other factors.

Extensive survival data are presented from the EDTA Registry's files for patients who started renal replacement therapy in 1970-1974 compared to 1980-1984. The contribution of the different treatment modalities (haemodialysis, continuous peritoneal dialysis, and transplantation) to the survival of patients according to geographical region is also shown. Survival on renal replacement therapy, irrespective of treatment modality and of primary renal disease, was best in the 10-14-year-old patients, with 58% at 10 years and 52% at 15 years, and decreased with rising age to 28% at 10 years and 16% at 15 years in patients aged 45-54 when they commenced therapy in 1970-1974. When comparing the 0-4-year-old with the 10-14-year-old cohort of the paediatric patients, 5-year survival rates for patients starting renal replacement therapy in the early eighties declined from 85% to 70% with decreasing age. Treatment policy, as reflected by the proportion of patients on different modes of therapy, varied markedly between European regions but affected survival to a small extent only. The large population with diabetic nephropathy incurred annual mortality rates 2-3 times greater than those observed in patients with 'standard' primary renal diseases. Haemodialysis and continuous peritoneal dialysis, although not comparable because of important differences in selection policy, yielded similar survival rates. Patients and graft survival rates have improved markedly when comparing patients starting renal replacement therapy in the early seventies with the eighties; particularly for cadaveric transplantation. Patient survival after second grafting was similar to that after first grafting, with 83% at 5 years after second cadaveric grafting in the 15-44-year-old cohort, vs 85% after first cadaver transplantation in 1980-1984. Second cadaveric graft survival was superior to average first-graft survival for those recipients whose first graft had been functioning for more than 1 year. However, second-graft survival in rapid rejectors of a first graft as well as third cadaveric graft survival were curtailed by the large number of early losses, with only 52% of third grafts functioning at 1 year. For living related donor transplantation, parents were mostly used in children whilst identical siblings predominated in adults older than 45. In the early eighties, patient survival was 92% at 5 years for recipients younger than 15, 87% for the 15-45 year old cohort and 72% for those aged 45 or older.(ABSTRACT TRUNCATED AT 400 WORDS)