Computational Efficiency and Precision for Replicated-Count and Batch-Marked Hidden Population Models.

We address two computational issues common to open-population N-mixture models, hidden integer-valued autoregressive models, and some hidden Markov models. The first issue is computation time, which can be dramatically improved through the use of a fast Fourier transform. The second issue is tractability of the model likelihood function for large numbers of hidden states, which can be solved by improving numerical stability of calculations. As an illustrative example, we detail the application of these methods to the open-population N-mixture models. We compare computational efficiency and precision between these methods and standard methods employed by state-of-the-art ecological software. We show faster computing times (a ∼ 6 to ∼ 30 times speed improvement for population size upper bounds of 500 and 1000, respectively) over state-of-the-art ecological software for N-mixture models. We also apply our methods to compute the size of a large elk population using an N-mixture model and show that while our methods converge, previous software cannot produce estimates due to numerical issues. These solutions can be applied to many ecological models to improve precision when logs of sums exist in the likelihood function and to improve computational efficiency when convolutions are present in the likelihood function. Supplementary materials accompanying this paper appear online. Supplementary materials for this article are available at 10.1007/s13253-022-00509-y.

Under-reporting of COVID-19 in the Northern Health Authority region of British Columbia.

Asymptomatic and pauci-symptomatic presentations of COVID-19 along with restrictive testing protocols result in undetected COVID-19 cases. Estimating undetected cases is crucial to understanding the true severity of the outbreak. We introduce a new hierarchical disease dynamics model based on the N-mixtures hidden population framework. The new models make use of three sets of disease count data per region: reported cases, recoveries and deaths. Treating the first two as under-counted through binomial thinning, we model the true population state at each time point by partitioning the diseased population into the active, recovered and died categories. Both domestic spread and imported cases are considered. These models are applied to estimate the level of under-reporting of COVID-19 in the Northern Health Authority region of British Columbia, Canada, during 30 weeks of the provincial recovery plan. Parameter covariates are easily implemented and used to improve model estimates. We compare two distinct methods of model-fitting for this case study: (1) maximum likelihood estimation, and (2) Bayesian Markov chain Monte Carlo. The two methods agreed exactly in their estimates of under-reporting rate. When accounting for changes in weekly testing volumes, we found under-reporting rates varying from 60.2% to 84.2%.

Le recours à des protocoles de tests restrictifs et l'existence de formes asymptomatiques et paucisymptomatiques de la COVID­19 contribuent à la non détection de cas COVID­19. Pour comprendre la véritable gravité de l'épidémie, il est primordial d'estimer correctement le nombre de cas non détectés. A cette fin, les auteurs de ce travail proposent un nouveau modèle hiérarchique des dynamiques de la maladie basé sur l'approche de N­mélanges de population cachée. Ces modèles utilisent trois types de données régionales, à savoir, les nombres de cas déclarés, guéris et décédés. En faisant appel à l'amincissement binomial (binomial thinning) et en traitant les nombres de cas déclarés et guéris comme étant sous­évalués, les auteurs proposent une modélisation de l'état réel de l'épidémie basée sur une partition de la population malade en trois catégories : cas actifs, cas guéris et cas décédés. Cette partition tient compte des cas de propagation intérieure et des cas importés. Les auteurs ont utilisé les données recueillies durant les trente semaines du plan de rétablissement provincial de la région de l'Autorité sanitaire du Nord de la Colombie­Britannique, Canada pour illustrer leur approche et estimer le niveau de sous­déclaration COVID­19 associé. Des covariables peuvent être facilement incorporées au modèle proposé et améliorer la qualité des estimations. Deux méthodes d'ajustement sont retenues: (1) l'estimation par maximum de vraisemblance, et (2) la méthode de Monte Carlo par chaînes de Markov. Les estimations du taux de sous­déclaration obtenues par ces deux méthodes concordent exactement et varient entre 60,2% et 84,2% après ajustement des variations des volumes de tests hebdomadaires.

Impact of the early coronavirus disease 2019 pandemic on blood utilization in the United States: A time-series analysis of data reported to the National Healthcare Safety Network Hemovigilance Module.

INTRODUCTION: The coronavirus disease 2019 (COVID-19) pandemic has disrupted healthcare services worldwide. However, little has been reported regarding the impact on blood utilization. We quantified the impact of COVID-19 on blood utilization and discards among facilities reporting to the National Healthcare Safety Network Hemovigilance Module. METHODS: Facilities continuously reporting data, during January 2016-June 2020, on transfused and discarded blood components, stratified by component type (red blood cells [RBC], platelets, and plasma), were included. Interrupted time-series analysis with generalized estimating equations, adjusting for facility surgical volume and seasonality, was used to quantify changes in blood utilization and discards relative to a Centers for Medicare & Medicaid Services notification delaying nonessential medical procedures (March 2020). RESULTS: Seventy-two facilities included in the analyses, on average, transfused 44,548 and discarded 2,202 blood components monthly. Following the March 2020 notification and after multivariable adjustment, RBC and platelet utilization declined, -9.9% (p < .001) and -13.6% (p = .014), respectively. Discards increased for RBCs (30.2%, p = .047) and platelets (60.4%, p = .002). No statistically significant change in plasma was found. Following these abrupt changes, blood utilization and discards rebounded toward baseline with RBC utilization increasing by 5.7% (p < .001), and platelet and RBC discards decreasing -16.4% (<0.001) and -12.7 (p = .001), respectively. CONCLUSION: Following notification delaying elective surgical procedures, blood utilization declined substantially while blood discards increased, resulting in substantial wastage of blood products. Ongoing and future pandemic response efforts should consider the impact of interventions on blood supply and demand to ensure blood availability.

Dialysis and driving: an anonymous survey of patients receiving dialysis for end-stage kidney disease.

BACKGROUND: Driving is a complex task requiring multiple cognitive domains and the musculoskeletal system. Cognitive dysfunction is associated with driving impairment. Dialysis patients are known to have a high prevalence of cognitive impairment and other comorbidities, and may be at risk of driving impairment. No Australian guidelines address driving safety in dialysis patients. AIMS: To estimate the proportion of dialysis patients who were driving and those at risk of driving impairment, and to investigate the agreement between objective and subjective markers of risk. METHODS: This single-centre study involved dialysis patients voluntarily completing two questionnaires relating to risk of driving impairment; the first questionnaire focussed on objective markers, and the second questionnaire focussed on subjective markers. Risk of driving impairment was established using pre-determined criteria, and the agreement between objective and subjective markers was estimated using Cohen kappa. RESULTS: A total of 44.8% (99/221) of patients participated; 76.8% (76/99) of participants were driving, and 76.3% (58/76) of drivers were at risk of driving impairment. Factors associated with at-risk driving included post dialysis dizziness, leg weakness or numbness, falling asleep while driving and hypoglycaemia. Sixteen patients reported collisions since commencing dialysis. The questionnaires displayed slight agreement (Cohen kappa = 0.20) between objective and subjective markers. CONCLUSIONS: Dialysis patients are at risk of driving impairment based on self-reported questionnaire responses. Discrepancies between patients' perceptions and objective markers were apparent. Further research into appropriate risk assessments, as well as development of guidelines to aid in determining driving safety in dialysis patients, is needed.

Serologic Testing of US Blood Donations to Identify Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2)-Reactive Antibodies: December 2019-January 2020.

BACKGROUND: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the virus that causes coronavirus disease 2019 (COVID-19), was first identified in Wuhan, China, in December 2019, with subsequent worldwide spread. The first US cases were identified in January 2020. METHODS: To determine if SARS-CoV-2-reactive antibodies were present in sera prior to the first identified case in the United States on 19 January 2020, residual archived samples from 7389 routine blood donations collected by the American Red Cross from 13 December 2019 to 17 January 2020 from donors resident in 9 states (California, Connecticut, Iowa, Massachusetts, Michigan, Oregon, Rhode Island, Washington, and Wisconsin) were tested at the Centers for Disease Control and Prevention for anti-SARS-CoV-2 antibodies. Specimens reactive by pan-immunoglobulin (pan-Ig) enzyme-linked immunosorbent assay (ELISA) against the full spike protein were tested by IgG and IgM ELISAs, microneutralization test, Ortho total Ig S1 ELISA, and receptor-binding domain/ACE2 blocking activity assay. RESULTS: Of the 7389 samples, 106 were reactive by pan-Ig. Of these 106 specimens, 90 were available for further testing. Eighty-four of 90 had neutralizing activity, 1 had S1 binding activity, and 1 had receptor-binding domain/ACE2 blocking activity >50%, suggesting the presence of anti-SARS-CoV-2-reactive antibodies. Donations with reactivity occurred in all 9 states. CONCLUSIONS: These findings suggest that SARS-CoV-2 may have been introduced into the United States prior to 19 January 2020.

Relationship between residual kidney function and symptom burden in haemodialysis patients.

BACKGROUND: Residual kidney function (RKF) has been associated with improved solute clearance and survival in haemodialysis (HD) patients. However, whether RKF impacts symptom burden in HD patients is unknown. AIMS: To determine the prevalence of RKF in HD patients and to explore associations between higher levels of RKF with symptom burden, as well as clinical and biochemical parameters. METHODS: This is a single-centre, retrospective, observational study. RKF was assessed as urea clearance (KRU) by interdialytic urine collection. Symptom burden was measured using the palliative care outcome scale renal questionnaire. RESULTS: A total of 90 maintenance HD patients was recruited; 31.9% had KRU ≥1 mL/min/1.73 m2 . Patients with KRU ≥1 mL/min/1.73 m2 reported fewer symptoms (5.3 ± 3.5 vs 7.7 ± 3.8) (P = 0.011), including less shortness of breath (15% vs 55%) (P = 0.0013) and vomiting (0% vs 30%) (P = 0.0016). Higher RKF was associated with lower ß2 -microglobilin (P < 0.0001), and lower serum potassium (P = 0.02), but no difference in phosphate, haemoglobin, C-reactive protein or serum albumin. CONCLUSION: Higher RKF was significantly associated with fewer symptoms, and lower serum ß2 -microglobulin and potassium, suggesting that strategies to preserve RKF may be beneficial.

Outcomes of patients commencing peritoneal dialysis with and without back-up arteriovenous fistulas.

BACKGROUND: Transitions from peritoneal dialysis (PD) to haemodialysis (HD) are often unpredictable and central venous catheters (CVCs) are frequently required. Early studies found few back-up arteriovenous fistulas (bAVFs) were ever used. The PD population's characteristics have changed over time which may have altered the likelihood of bAVFs being used. This study aimed to report use of, and outcomes associated with, bAVFs in a contemporary cohort of peritoneal dialysis patients. METHOD: A single-centre, retrospective study of PD patients commencing dialysis between 2006-2016, stratified according to presence/absence of bAVF. RESULTS: One hundred seventy-six patients were included-82 with bAVF, 94 without bAVF-of whom 156 transitioned off PD. Transitions were to HD (49%), transplantation (23%), death (15%) and renal-recovery (1%). 51% of bAVFs were successfully used and 82% of bAVFs were patent when required. Median time from creation to bAVF use was 2.5 years. More patients with a bAVF transitioned to HD (62 vs 38%, p < 0.005). However, CVC requirement at the time of transition to HD was much less common in the bAVF group (18 vs 83%, p < 0.0001), such that the overall risk of requiring a CVC was significantly lower in the bAVF group (11 vs 31%, p < 0.005). Rates of returning to PD amongst patients who transitioned to HD with a CVC or an AVF were similar (19 vs 26%, p = 0.16). CONCLUSIONS: In this cohort of PD patients, utilisation of back-up arteriovenous fistulas was higher than previously reported, and presence of a back-up arteriovenous fistula was associated with a lower rate of future CVC use.

Changes in Symptom Burden in Dialysis Patients Assessed Using a Symptom-Reporting Questionnaire in Clinic.

INTRODUCTION: To determine the prevalence, severity, and change in symptoms experienced by dialysis patients following the introduction of use of a symptom-reporting questionnaire in nephrology clinic. METHODS: This is an observational study of 160 prevalent dialysis patients. Palliative care Outcome Scale symptom (POS-renal) questionnaires modified for patients with end-stage kidney disease were completed at baseline and follow-up (median 3 months), with results available to nephrologists at clinic appointments. FINDINGS: The baseline prevalence of individual symptoms ranged from 15% to 66%. The most common symptoms were lack of energy (66%) and poor mobility (58%). The median number of symptoms was 7/17 (interquartile range [IQR]: 4-10). Forty-nine percent of patients rated at least 1 symptom as severe or overwhelming. At follow-up, the median number of symptoms experienced was unchanged at 7/17 (IQR: 3-10). However, there was considerable flux in symptom severity. On average, individual symptoms that were present at baseline improved in 56% of patients and worsened in 18%; only 26% had stable symptom severity. Individual symptoms newly occurred in 8% to 20% of patients between time points, with 77% of patients experiencing at least 1 new symptom. The percent of patients rating at least 1 symptom as severe or overwhelming was reduced from 49% to 39% (P = .040). CONCLUSIONS: Use of the POS-renal questionnaire identified a high symptom burden. The presence and severity of symptoms changed dramatically over a short follow-up period, highlighting the need for regular surveillance of symptoms in the dialysis population. Routine use of a symptom questionnaire in clinic may be useful for the identification and management of symptoms in dialysis patients.

IMU Sensor Fusion Algorithm for Monitoring Knee Kinematics in ACL Reconstructed Patients.

In this paper we propose a sensor embedded knee brace to monitor knee flexion and extension and other lower limb joint kinematics after anterior cruciate ligament (ACL) injury. The system can be easily attached to a standard post-surgical brace and uses a novel sensor fusion algorithm that does not require calibration. The wearable system and the sensor fusion algorithm were validated for various physical therapy exercises against a validated motion capture system. The proposed sensor fusion algorithm demonstrated significantly lower root-mean-square error (RMSE) than the benchmark Kalman filtering algorithm and excellent correlation coefficients (CCC and ICC). The demonstrated error for most exercises was lower than other devices in the literature. The quantitative measures obtained by this system can be used to obtain longitudinal range-of-motion and functional biomarkers. These biomarkers can be used to improve patient outcomes through the early detection of at-risk patients, tracking patient function outside of the clinic, and the identification of relationships between patient presentation, intervention, and outcomes.

Phosphate nephropathy: an avoidable complication of bowel preparation for colonoscopy.

It is known that oral sodium phosphate, used as bowel preparation for colonoscopy, can cause acute phosphate nephropathy, a potentially severe and irreversible form of acute kidney injury. Due to these safety concerns, guidelines have advised against the routine use of this agent for a decade. We present a case report and biopsy series that demonstrate that oral sodium phosphate is still being used and that cases of APN are still occurring, in Australia.

The Thiazide-Sensitive Co-Transporter Promotes the Development of Sodium Retention in Mice with Diet-Induced Obesity.

BACKGROUND/AIMS: Intravascular volume expansion due to sodium retention is involved in the pathogenesis of obesity-related hypertension. Institution of high fat diet (HFD) feeding leads to an initial state of positive sodium balance due to enhanced tubular reabsorption of sodium, but which tubular sodium transporters are responsible for this remains undefined. METHODS: C57/Bl6 mice were fed control or HFD for 3 weeks. Blood pressures were recorded by tail cuff method. Sodium transporter expression and phosphorylation were determined by Western blotting. In vivo activity of NCC was determined using natriuretic responses to hydrochlorothiazide. Expression of NCC mRNA was determined using qPCR. RESULTS: At 3 weeks HFD mice had significant weight gains compared to control mice, but blood pressures were not yet elevated. There were no changes in expression or phosphorylation of the bumetanide-sensitive cotransporter, NKCC2, or in expression of subunits of the amiloride-sensitive ion channel, ENaC. However, there were significant increases in mRNA and protein expression of the thiazide-sensitive co-transporter, NCC, in kidneys from HFD mice. Consistent with this, HFD mice had increased in vivo activity of NCC. CONCLUSIONS: Increased expression of NCC promotes the sodium loading response to institution of HFD feeding before onset of hypertension.

AMPK couples plasma renin to cellular metabolism by phosphorylation of ACC1.

Salt reabsorption is the major energy-requiring process in the kidney, and AMP-activated protein kinase (AMPK) is an important regulator of cellular metabolism. Mice with targeted deletion of the ß1-subunit of AMPK (AMPK-ß1(-/-) mice) had significantly increased urinary Na(+) excretion on a normal salt diet. This was associated with reduced expression of the ß-subunit of the epithelial Na(+) channel (ENaC) and increased subapical tubular expression of kidney-specific Na(+)-K(+)-2Cl(-) cotransporter 2 (NKCC2) in the medullary thick ascending limb of Henle. AMPK-ß1(-/-) mice fed a salt-deficient diet were able to conserve Na(+), but renin secretion increased 180% compared with control mice. Cyclooxygenase-2 mRNA also increased in the kidney cortex, indicating greater signaling through the macula densa tubular salt-sensing pathway. To determine whether the increase in renin secretion was due to a change in regulation of fatty acid metabolism by AMPK, mice with a mutation of the inhibitory AMPK phosphosite in acetyl-CoA carboxylase 1 [ACC1-knockin (KI)(S79A) mice] were examined. ACC1-KI(S79A) mice on a normal salt diet had no increase in salt loss or renin secretion, and expression of NKCC2, Na(+)-Cl(-) cotransporter, and ENaC-ß were similar to those in control mice. When mice were placed on a salt-deficient diet, however, renin secretion and cortical expression of cyclooxygenase-2 mRNA increased significantly in ACC1-KI(S79A) mice compared with control mice. In summary, our data suggest that renin synthesis and secretion are regulated by AMPK and coupled to metabolism by phosphorylation of ACC1.