Causal inference with recurrent and competing events.

Many research questions concern treatment effects on outcomes that can recur several times in the same individual. For example, medical researchers are interested in treatment effects on hospitalizations in heart failure patients and sports injuries in athletes. Competing events, such as death, complicate causal inference in studies of recurrent events because once a competing event occurs, an individual cannot have more recurrent events. Several statistical estimands have been studied in recurrent event settings, with and without competing events. However, the causal interpretations of these estimands, and the conditions that are required to identify these estimands from observed data, have yet to be formalized. Here we use a formal framework for causal inference to formulate several causal estimands in recurrent event settings, with and without competing events. When competing events exist, we clarify when commonly used classical statistical estimands can be interpreted as causal quantities from the causal mediation literature, such as (controlled) direct effects and total effects. Furthermore, we show that recent results on interventionist mediation estimands allow us to define new causal estimands with recurrent and competing events that may be of particular clinical relevance in many subject matter settings. We use causal directed acyclic graphs and single world intervention graphs to illustrate how to reason about identification conditions for the various causal estimands based on subject matter knowledge. Furthermore, using results on counting processes, we show that our causal estimands and their identification conditions, which are articulated in discrete time, converge to classical continuous time counterparts in the limit of fine discretizations of time. We propose estimators and establish their consistency for the various identifying functionals. Finally, we use the proposed estimators to compute the effect of blood pressure lowering treatment on the recurrence of acute kidney injury using data from the Systolic Blood Pressure Intervention Trial.

Radiological features of brain hemorrhage through automated segmentation from computed tomography in stroke and traumatic brain injury.

Introduction: Radiological assessment is necessary to diagnose spontaneous intracerebral hemorrhage (ICH) and traumatic brain injury intracranial hemorrhage (TBI-bleed). Artificial intelligence (AI) deep learning tools provide a means for decision support. This study evaluates the hemorrhage segmentations produced from three-dimensional deep learning AI model that was developed using non-contrast computed tomography (CT) imaging data external to the current study. Methods: Non-contrast CT imaging data from 1263 patients were accessed across seven data sources (referred to as sites) in Norway and Sweden. Patients were included based on ICH, TBI-bleed, or mild TBI diagnosis. Initial non-contrast CT images were available for all participants. Hemorrhage location frequency maps were generated. The number of estimated haematoma clusters was correlated with the total haematoma volume. Ground truth expert annotations were available for one ICH site; hence, a comparison was made with the estimated haematoma volumes. Segmentation volume estimates were used in a receiver operator characteristics (ROC) analysis for all samples (i.e., bleed detected) and then specifically for one site with few TBI-bleed cases. Results: The hemorrhage frequency maps showed spatial patterns of estimated lesions consistent with ICH or TBI-bleed presentations. There was a positive correlation between the estimated number of clusters and total haematoma volume for each site (correlation range: 0.45-0.74; each p-value < 0.01) and evidence of ICH between-site differences. Relative to hand-drawn annotations for one ICH site, the VIOLA-AI segmentation mask achieved a median Dice Similarity Coefficient of 0.82 (interquartile range: 0.78 and 0.83), resulting in a small overestimate in the haematoma volume by a median of 0.47 mL (interquartile range: 0.04 and 1.75 mL). The bleed detection ROC analysis for the whole sample gave a high area-under-the-curve (AUC) of 0.92 (with sensitivity and specificity of 83.28% and 95.41%); however, when considering only the mild head injury site, the TBI-bleed detection gave an AUC of 0.70. Discussion: An open-source segmentation tool was used to visualize hemorrhage locations across multiple data sources and revealed quantitative hemorrhage site differences. The automated total hemorrhage volume estimate correlated with a per-participant hemorrhage cluster count. ROC results were moderate-to-high. The VIOLA-AI tool had promising results and might be useful for various types of intracranial hemorrhage.

Prognosis of cancer survivors: estimation based on differential equations.

We present a method for estimating several prognosis parameters for cancer survivors. The method utilizes the fact that these parameters solve differential equations driven by cumulative hazards. By expressing the parameters as solutions to differential equations, we develop generic estimators that are easy to implement with standard statistical software. We explicitly describe the estimators for prognosis parameters that are often employed in practice, but also for parameters that, to our knowledge, have not been used to evaluate prognosis. We then apply these parameters to assess the prognosis of five common cancers in Norway.

Intensive Care Unit-Acquired Weakness in Patients With Acute Kidney Injury: A Contemporary Review.

Acute kidney injury (AKI) and intensive care unit-acquired weakness (ICU-AW) are 2 frequent complications of critical illness that, until recently, have been considered unrelated processes. The adverse impact of AKI on ICU mortality is clear, but its relationship with muscle weakness-a major source of ICU morbidity-has not been fully elucidated. Furthermore, improving ICU survival rates have refocused the field of intensive care toward improving long-term functional outcomes of ICU survivors. We begin our review with the epidemiology of AKI in the ICU and of ICU-AW, highlighting emerging data suggesting that AKI and AKI treated with kidney replacement therapy (AKI-KRT) may independently contribute to the development of ICU-AW. We then delve into human and animal data exploring the pathophysiologic mechanisms linking AKI and acute KRT to muscle wasting, including altered amino acid and protein metabolism, inflammatory signaling, and deleterious removal of micronutrients by KRT. We next discuss the currently available interventions that may mitigate the risk of ICU-AW in patients with AKI and AKI-KRT. We conclude that additional studies are needed to better characterize the epidemiologic and pathophysiologic relationship between AKI, AKI-KRT, and ICU-AW and to prospectively test interventions to improve the long-term functional status and quality of life of AKI survivors.

A genetic framework for regulation and seasonal adaptation of shoot architecture in hybrid aspen.

Shoot architecture is critical for optimizing plant adaptation and productivity. In contrast with annuals, branching in perennials native to temperate and boreal regions must be coordinated with seasonal growth cycles. How branching is coordinated with seasonal growth is poorly understood. We identified key components of the genetic network that controls branching and its regulation by seasonal cues in the model tree hybrid aspen. Our results demonstrate that branching and its control by seasonal cues is mediated by mutually antagonistic action of aspen orthologs of the flowering regulators TERMINAL FLOWER 1 (TFL1) and APETALA1 (LIKE APETALA 1/LAP1). LAP1 promotes branching through local action in axillary buds. LAP1 acts in a cytokinin-dependent manner, stimulating expression of the cell-cycle regulator AIL1 and suppressing BRANCHED1 expression to promote branching. Short photoperiod and low temperature, the major seasonal cues heralding winter, suppress branching by simultaneous activation of TFL1 and repression of the LAP1 pathway. Our results thus reveal the genetic network mediating control of branching and its regulation by environmental cues facilitating integration of branching with seasonal growth control in perennial trees.

Branching Regulator BRC1 Mediates Photoperiodic Control of Seasonal Growth in Hybrid Aspen.

Cessation of growth as winter approaches is a key adaptive trait for survival of perennial plants, such as long-lived trees native to boreal and temperate regions [1, 2]. The timing of growth cessation in these plants is controlled by photoperiodic cues. As shown recently, perception of growth-repressive short photoperiod (SP) mediated via components of circadian clock results in downregulation of the tree ortholog of Arabidopsis flowering regulator FLOWERING LOCUS T (FT), FT2 [3, 4]. Downregulation of FT2 results in suppression of downstream components LAP1 (orthologous to the Arabidopsis floral meristem identity gene APETALA1) and AIL1 (orthologous to AINTEGUMENTA in Arabidopsis), culminating in induction of growth cessation and bud set [5-7]. Results presented here reveal that, in addition to the CO/FT pathway, a photoperiodically controlled negative feedback loop involving a tree ortholog of Arabidopsis BRANCHED1 (BRC1) (a member of TEOSINTE BRANCHED 1, CYCLOIDEA, PCF family), LAP1, and FT2 participates in regulation of seasonal growth in the model tree hybrid aspen. In growth-promotive long photoperiod, LAP1 suppresses expression of BRC1, but upon perception of growth-repressive SP, downregulation of LAP1 de-represses expression of its downstream target BRC1. BRC1 physically interacts with FT2, and BRC1-FT interaction further reinforces the effect of SP and triggers growth cessation by antagonizing FT action. Accordingly, BRC1 gain and loss of function result in early and retarded growth cessation responses to SP, respectively. Thus, these results reveal a regulatory feedback loop that reinforces responses to SP and induction of seasonal growth cessation.

On null hypotheses in survival analysis.

The conventional nonparametric tests in survival analysis, such as the log-rank test, assess the null hypothesis that the hazards are equal at all times. However, hazards are hard to interpret causally, and other null hypotheses are more relevant in many scenarios with survival outcomes. To allow for a wider range of null hypotheses, we present a generic approach to define test statistics. This approach utilizes the fact that a wide range of common parameters in survival analysis can be expressed as solutions of differential equations. Thereby, we can test hypotheses based on survival parameters that solve differential equations driven by cumulative hazards, and it is easy to implement the tests on a computer. We present simulations, suggesting that our tests perform well for several hypotheses in a range of scenarios. As an illustration, we apply our tests to evaluate the effect of adjuvant chemotherapies in patients with colon cancer, using data from a randomized controlled trial.

Abscisic acid signalling mediates biomass trade-off and allocation in poplar.

Abscisic acid (ABA) is a well known stress hormone regulating drought adaptation of plants. Here, we hypothesised that genetic engineering of genes involved in ABA stress signalling and photoperiodic regulation affected drought resistance by trade-off with biomass production in perennial poplar trees. We grew Populus tremula × tremuloides wild-type (T89) and various transgenic lines (two transformation events of 35S::abi1-1, 35S::RCAR, RCAR:RNAi, 35S::ABI3, 35S::AREB3, 35S::FDL1, FDL1:RNAi, 35S::FDL2 and FDL2:RNAi) outdoors and exposed them to drought in the second growth period. After the winter, the surviving lines showed a huge variation in stomatal conductance, leaf size, whole-plant leaf area, tree height, stem diameter, and biomass. Whole-plant leaf area was a strong predictor for woody biomass production. The 35S::AREB3 lines were compromised in biomass production under well irrigated conditions compared with wild-type poplars but were resilient to drought. ABA signalling regulated FDL1 and FDL2 expression under stress. Poplar lines overexpressing FDL1 or FDL2 were drought-sensitive; they shed leaves and lost root biomass, whereas the FDL RNAi lines showed higher biomass allocation to roots under drought. These results assign a new function in drought acclimation to FDL genes aside from photoperiodic regulation. Our results imply a critical role for ABA-mediated processes in balancing biomass production and climate adaptation.

The additive hazard estimator is consistent for continuous-time marginal structural models.

Marginal structural models (MSMs) allow for causal analysis of longitudinal data. The standard MSM is based on discrete time models, but the continuous-time MSM is a conceptually appealing alternative for survival analysis. In applied analyses, it is often assumed that the theoretical treatment weights are known, but these weights are usually unknown and must be estimated from the data. Here we provide a sufficient condition for continuous-time MSM to be consistent even when the weights are estimated, and we show how additive hazard models can be used to estimate such weights. Our results suggest that continuous-time weights perform better than IPTW when the underlying process is continuous. Furthermore, we may wish to transform effect estimates of hazards to other scales that are easier to interpret causally. We show that a general transformation strategy can be used on weighted cumulative hazard estimates to obtain a range of other parameters in survival analysis, and explain how this strategy can be applied on data using our R packages ahw and transform.hazards.

Prevalence of vitamin D deficiency in orthopaedic patients - A single centre study.

PURPOSE: Many recent reports demonstrated high rates of vitamin D deficiency in numerous segments of Indian population but no study has been reported so far from India, which focuses specifically on vitamin D status in orthopaedic patients. This study finds out the prevalence of vitamin D deficiency in orthopaedic patients in India. METHODS: Vitamin D levels of 1132 patients were measured from OPD and Emergency Department of S.N. Medical College, Agra from 1 November 2011 to 31 October 2013. Serum 25(OH) vitamin D, calcium, phosphorus, alkaline phosphatase and routine blood investigations were done. BMI and daily sun exposure were measured. RESULTS: Out of 1132 patients included in our study, 732 (64.7%) were males and 400 (36.3%) females. Vitamin D deficiency (<30 ng/ml) was present in 1034 patients (91.3%); among them, 693 patients (61.2%) had vitamin D level <20 ng/ml and only 98 patients (8.7%) had sufficient levels of vitamin D. Vitamin D deficiency was more in elderly patients (61-80) than in younger patients. Among 1132 patients, 670 males (91.5%) and 364 females (91.0%) were found to have serum 25(OH) vitamin D levels <30 ng/dl cut-off for vitamin D sufficiency (p-value = 0.75). Vitamin D levels were lower in patients with less mean sun exposure time. BMI level was more in deficient group than the sufficient group relatively. CONCLUSION: High incidence of vitamin D insufficiency and deficiency likely exists across all age groups among orthopaedic patients. Screening and treating hypovitaminosis D appears to be important in this patient population.

Synthesis and in vitro Screening of 29, 30-Dibromo-28-oxoallobetulin against Parasitic Protozoans, Leishmania donovani and Leishmania Major.

A simple synthesis and in vitro antileishmanial activity of 29,30-dibromo-28-oxoallobetulin against the parasitic protozoans, Leishmania donovani and Leishmania major is described. The structure of the compound is established on the basis of spectral data (IR, NMR, MS). Both the antiproliferative effect and the cell cycle progression were studied.

Octaoctyl-substituted lutetium bisphthalocyanine for NADH biosensing.

Cyclic voltammetric and Raman and UV-vis spectroscopic measurements were performed on thin films of nonperipherally substituted bis[1,4,8,11,15,18,22,25-octakis(octyl)phthalocyaninato] lutetium(III) (R16LuPc2). Voltammograms exhibit one-electron quasi-reversible redox processes in 1.5 M LiClO4 aqueous solutions. The red-shift of the Q-band of R16LuPc2 in the UV-visible absorption spectra upon oxidation is attributed to the shortening of the inter-ring distance between the two phthalocyanine moieties. This observation is also consistent with the shift in the redox-sensitive vibrational modes in the Raman spectra due to the localization of the positive charge on phthalocyanine moieties. Neutralization of the oxidized R16LuPc2(+) film by dihydronicotinamide adenine dinucleotide (NADH) using different concentrations varying from 0.05 to 1 mM has been studied by UV-vis absorption and Raman spectroscopies. The reduction processes for a three month old film were found to be slower than those for freshly prepared films and showed a dependence upon NADH concentration. The data provide a basis for application of R16LuPc2 as a sensor for NADH.

In situ chemichromic studies of interactions between a lutetium bis-octaalkyl-substituted phthalocyanine and selected biological cofactors.

Spin-coated films, approximately 100 nm thick, of a newly synthesized bis[octakis(octyl)phthalocyaninato] lutetium(III) complex on ultrasonically cleaned glass substrates exhibit pronounced chemichromic behaviour with potential application in healthcare. In situ kinetic optical absorption spectroscopic measurements show that the phthalocyanine Q-band is red shifted by 60 nm upon oxidation arising from exposure to bromine vapour. Recovery to the original state is achieved by the treatment of the oxidized films with nicotinamide adenine dinucleotide and l-ascorbic acid (vitamin C) in an aqueous solution containing 1.5 M lithium perchlorate. The neutralization process is found to be governed by first-order kinetics. The linear increase of the reduction rate with increasing concentration of cofactors provides a basis for calibration of analyte concentrations ranging from 3.5 mM down to 0.03 mM.

Characterizing components of the Saw Palmetto Berry Extract (SPBE) on prostate cancer cell growth and traction.

Saw Palmetto Berry Extract (SPBE) is applied for prostate health and treatment of urinary tract infections, nonbacterial prostitis and Benign Prostatic Hyperplasia (BPH) in man. An assumption is that SPBE affects tumor cell progression and migration in breast and prostate tissue. In this work, DU-145 cells were used to demonstrate that SPBE and its sterol components, beta-sitosterol and stigmasterol, inhibit prostate cancer growth by increasing p53 protein expression and also inhibit carcinoma development by decreasing p21 and p27 protein expression. In the presence of cholesterol, these features are not only reversed but increased significantly. The results show for the first time the potential of SPBE, beta-sitosterol and stigmasterol as potential anti-tumor agents. Since the protein p53 is also regarded as nuclear matrix protein facilitating actin cytoskeletal binding, 2D tractions were measured. The cell adhesion strength in the presence of SPBE, beta-sitosterol and cholesterol and the observation was that the increase in p53 expression triggered an increase in the intracellular force generation. The results suggest a dual function of p53 in cells.

Is there a positive effect of participation on a clinical trial for patients with advanced non-small cell lung cancer?

BACKGROUND: There is general belief that patients who enrolled on a clinical trial have better outcomes compared to those who are treated outside of a trial. We analyzed if there was a 'trial effect' for patients with advanced non-small cell lung cancer (NSCLC) treated with chemotherapy. MATERIALS AND METHODS: A retrospective analysis of cohorts of patients with advanced NSCLC who received chemotherapy inside and outside of a clinical trial were analyzed for response rates (RR), progression free survival (PFS), overall survival (OS), 1 and 2 year survival. RESULTS: There were 194 patients who received chemotherapy of which, 54 were on a clinical trial and 140 outside of it. For the whole group, the RR, median PFS, OS, one and two-year survivals were 35.4%, six months (range, 2-70), seven months (range, 2-72), 29.8% and 9.7% respectively. The differences in RR and PFS of patients who were treated inside and outside of a clinical trial were not significant (P=0.6164, 0.0881). The differences in median OS and one-year survivals between the groups were significant (P=0.0052, 0.022). For the whole group, patients who received II line chemotherapy had better OS (P< or = 0.0001). More patients in the trial group received II line chemotherapy (P=0.0004).The difference in the median OS between the groups continued to be significant even after patients who received II line chemotherapy were censored (P=0.0437). CONCLUSION: Patients with advanced NSCLC who were treated inside of a clinical trial had better OS compared to those who were treated outside of it.

Thermodynamic evidence of non-muscle myosin II-lipid-membrane interaction.

A unique feature of protein networks in living cells is that they can generate their own force. Proteins such as non-muscle myosin II are an integral part of the cytoskeleton and have the capacity to convert the energy of ATP hydrolysis into directional movement. Non-muscle myosin II can move actin filaments against each other, and depending on the orientation of the filaments and the way in which they are linked together, it can produce contraction, bending, extension, and stiffening. Our measurements with differential scanning calorimetry showed that non-muscle myosin II inserts into negatively charged phospholipid membranes. Using lipid vesicles made of DMPG/DMPC at a molar ratio of 1:1 at 10mg/ml in the presence of different non-muscle myosin II concentrations showed a variation of the main phase transition of the lipid vesicle at around 23 degrees C. With increasing concentrations of non-muscle myosin II the thermotropic properties of the lipid vesicle changed, which is indicative of protein-lipid interaction/insertion. We hypothesize that myosin tail binds to acidic phospholipids through an electrostatic interaction using the basic side groups of positive residues; the flexible, amphipathic helix then may partially penetrate into the bilayer to form an anchor. Using the stopped-flow method, we determined the binding affinity of non-muscle myosin II when anchored to lipid vesicles with actin, which was similar to a pure actin-non-muscle myosin II system. Insertion of myosin tail into the hydrophobic region of lipid membranes, a model known as the lever arm mechanism, might explain how its interaction with actin generates cellular movement.

N-acetyl-D-glucosamine specific hemagglutinin receptor of Vibrio cholerae O1 in chicken erythrocyte membranes.

N-Acetyl-D-glucosamine specific cell-associated hemagglutinin (HA)/lectin, previously purified from a strain of Vibrio cholerae O1, had been established as an adhesin molecule of V. cholerae O1 cells. This communication records the isolation and purification of the glycoprotein receptor of the N-acetyl-D-glucosamine specific HA of the V. cholerae O1 strain from chicken erythrocyte membranes. The most salient feature of this study is that the pretreatment of partially purified glycoprotein with purified HA could completely inhibit the hemagglutinating activity of the V. cholerae O1 strain with chicken erythrocytes.