Alex F Bokov

• Ph.D.
• Faculty, Clinical Informatics Research Division at The University of Texas Health Science Center at San Antonio

Research Objective To predict occurrence of preventable patient safety events using only data elements that are almost universally supported in EHR systems. Study Design We drew a random sample was drawn from the EHR records of adult patients not restricted to any particular age range or diagnosis and therefore representative of a real-world healt...

IMPACT: Laying the groundwork for better predictive algorithms to inform clinical decisions and planning. OBJECTIVES/GOALS: Frailty scores predict poor patient outcomes. Validated against highly relevant outcomes, such scores can be used to inform clinical and resource utilization decisions. We generated and validated an electronic Frailty Index (E...

Introduction: Despite overall decrease in incidence of cancers in U.S., kidney cancer is one out of the only seven cancers with increasing incidence. Limited research has been conducted using national, state-wide, and regional data, especially comparing racial and ethnic disparities in incidence and outcomes for kidney cancer. Methods: Kidney cance...

Introduction: Despite overall decrease in incidence of cancers in U.S., kidney cancer is one out of the only seven cancers with increasing incidence. Limited research has been conducted using national, state-wide, and regional data, especially comparing racial and ethnic disparities in incidence and outcomes for kidney cancer. Methods: Kidney cance...

Efficiently producing transparent analyses may be difficult for beginners or tedious for the experienced. This implies a need for computing systems and environments that can efficiently satisfy reproducibility and accountability standards. To this end, we have developed a system, R package, and R Shiny application called adapr (Accountable Data Ana...

BACKGROUND Electronic health records (EHRs) are ubiquitous. Yet little is known about the use of EHRs for prospective research purposes, and even less is known about patient perspectives regarding the use of their EHR for research. OBJECTIVE This paper reports results from the initial obesity project from the Greater Plains Collaborative that is p...

Background Electronic health records (EHRs) are ubiquitous. Yet little is known about the use of EHRs for prospective research purposes, and even less is known about patient perspectives regarding the use of their EHR for research. Objective This paper reports results from the initial obesity project from the Greater Plains Collaborative that is p...

We present a method for rapidly ranking all distinct facts in an electronic medical record (EMR) system by howover-represented or under-represented they are in a patient cohort of interest relative to some larger referencepopulation of patients in the same EMR. We have implemented this method as a plugin for i2b2, the open sourcedata warehouse plat...

The hazard ratio (HR) is a measure of instantaneous relative risk of an increase in one unit of the covariate of interest, which is widely reported in clinical researches involving time-to-event data. However, the measure fails to capture absolute risk reduction. Other measures such as number needed to treat (NNT) and risk difference (RD) provide a...

Mitochondrial dysfunction underlies numerous age-related pathologies. In an effort to uncover how the detrimental effects of mitochondrial dysfunction might be alleviated, we examined how the nematode C. elegans not only adapts to disruption of the mitochondrial electron transport chain, but in many instances responds with extended lifespan. Studie...

There are many legitimate reasons why standards for formatting of biomedical research data are lengthy and complex (Souza, Kush, & Evans, 2007). However, the common scenario of a biostatistician simply needing to import a given dataset into their statistical software is at best under-served by these standards. Statisticians are forced to act as ama...

Mitochondrial dysfunction underlies numerous age-related pathologies. In an effort to uncover how the detrimental effects of mitochondrial dysfunction might be alleviated, we examined how the nematode C. elegans not only adapts to disruption of the mitochondrial electron transport chain, but in many instances responds with extended lifespan. Studie...

Quantification of Ptbb-6::GFP reporter protein induction following RNAi-mediated knockdown of mitochondrial ETC targets. All ETC subunits targeted by feeding RNAi in the current analysis—subunits are organized by complex (see S2 Table for a list of all known ETC subunits in C. elegans). Graphed data shows change in GFP fluorescence (mean +/-SD) fol...

Quantification of Pgst-4::GFP reporter protein induction following RNAi-mediated knockdown of mitochondrial ETC targets. All ETC subunits targeted by feeding RNAi in the current analysis—subunits are organized by complex (see S2 Table for a list of all known ETC subunits in C. elegans). Graphed data shows change in GFP fluorescence (mean +/-SD) fol...

Quantification of Phsp-6::GFP reporter protein induction following RNAi-mediated knockdown of mitochondrial ETC targets. All ETC subunits targeted by feeding RNAi in the current analysis—subunits are organized by complex (see S2 Table for a list of all known ETC subunits in C. elegans). Graphed data shows change in GFP fluorescence (mean +/-SD) fol...

Presence of paralogs does not account for the heterogeneous expression of GFP reporter constructs following RNAi-mediated knockdown of subunits within each ETC complex. Data presented in Fig 2B of main text is reproduced on left. All ETC subunits with paralogs (marked with red daggers in S1–S3 Figs) were removed from the initial analysis and then G...

RNAi-mediated disruption of non-ETC mitochondrial targets induce Ptbb-6::GFP reporter protein expression and long-life. RNAi clones targeting non-ETC mitochondrial targets and which have previously have been reported to increase lifespan also induce Ptbb-6::GFP expression. Targets include the mitochondrial ribosome machinery (B0261.4/mrpl-47 [12] a...

Quantification of Ptbb-6::GFP, Pgst-4::GFP and Phsp-6::GFP reporter expression in wild-type, isp-1(qm150), nuo-6(qm200), ctb-1(qm189) and isp-1(qm150); ctb-1(qm189) mutant backgrounds. (A) Constitutive GFP fluorescence in wild-type, isp-1(qm150), nuo-6(qm200), ctb-1(qm189) and isp-1(qm150); ctb-1(qm189) mutants carrying the listed reporter construc...

Ptbb-6::GFP retrograde pathway activation is under pmk-3 MAPK control. (A) Induction of Ptbb-6::GFP expression in isp-1(qm150);ctb-1(qm189) worms is blocked by pmk-3, sek-3 and dlk-1 RNAi. Both atfs-1 and vhp-1 RNAi result in increased reporter fluorescence. Data is presented as mean (+/- SD) normalized to vector-control treated animals. Asterisks...

(A) nuo-6(qm200); Ptbb-6GFP worms arrest growth when cultured on vhp-1 RNAi (top row). Larval arrest is by-passed following the genetic removal of pmk-3 in pmk-3(ok169); nuo-6(qm200);Ptbb-6::GFP worms (bottom row). (B) Knockdown of pmk-3 by bacterial feeding RNAi uniquely rescued both the larval arrest and blocked Ptbb-6::GFP reporter expression of...

Raw survival data. Raw survival data for the lifespan analyses used to generate S4 Table. (XLSX)

Effect of mitochondrial disruption on reporter gene expression in wild-type animals. Ptbb-6::GFP, Pgst-4::GFP and Phsp-6::GFP transcriptional reporter expression in wild-type worms following RNAi-mediated disruption of nuclear-encoded mitochondrial proteins. (XLSX)

Lifespan statistics and Cox hazard analyses. Survival analyses (Excel sheet #1), and Genotype:RNAi interaction terms (Excel sheet #2). (XLSX)

Supplemental experimental procedures. Detailed list of experimental protocols. (DOCX)

Effect of MAPK RNAi, and vhp-1:MAPK combination RNAi (50:50), on wild-type worms containing the Ptbb-6::GFP reporter. (A) RNAi-mediated knockdown of vhp-1 in Ptbb-6::GFP worms results in weak hypodermal GFP fluorescence and smaller adult worms. The decrease in adult size is proportional to vhp-1 RNAi dose. (B-D) RNAi-mediated knockdown of none of t...

Ptbb-6::GFP reporter expression defines a UPRmt independent pathway. (A) isp-1(qm150) worms carrying Ptbb-6::GFP, Pgst-4::GFP or Phsp-6::GFP reporter genes were exposed to atfs-1 or skn-1 feeding RNAi then GFP fluorescence was quantified in day one adults. Data is presented as mean (+/- SD) normalized to vector-control treated animals. Asterisks in...

Quantification of GFP reporter protein expression in isp-1(qm150) worms following RNAi-mediated knockdown of genes that function epistatically to atfs-1 in the UPRmt. isp-1(qm150) worms containing Ptbb-6::GFP, Pgst-4::GFP or Phsp-6::GFP were cultured on feeding RNAi targeting components of the cellular surveillance pathway known to function upstrea...

Genes upregulated independent of atfs-1 upon spg-7 RNAi. List of C. elegans genes up-regulated independently of atfs-1 following exposure to spg-7 RNAi. Shown are gene descriptions and fold induction in the presence and absence of atfs-1 relative to vector control. (XLSX)

Effect of mitochondrial disruption on reporter gene expression and development in isp-1(qm150) Mit mutants. Ptbb-6::GFP, Pgst-4::GFP and Phsp-6::GFP transcriptional reporter expression and development in isp-1(qm150) worms following RNAi-mediated disruption of nuclear-encoded mitochondrial proteins. (XLSX)

Worm strains. List of strains employed in current study, along with a description of relevant strain constructions. (XLSX)

Table S3 Metabolites known to competitively inhibit α‐ketoglutarate dependent hydroxylases. See also Table 7 in (Rose et al., 2011).

Table S2 Proton NMR data corresponding to Fig. 3A.

Table S1 Survival data for all lifespan studies.

Table S4 Proton NMR data corresponding to Fig. S9.

Fig. S1 Proton NMR spectrum of 2‐oxobutyrate before and after a 72 h incubation in the presence of growth‐limited ‘fresh’ (2‐day‐old) or ‘old’ (37 day‐old) OP50 bacteria. Peaks of unknown identity in the +72 h samples are marked with a question mark. Fig. S2 Proton NMR spectrum of 3‐methyl‐2‐oxobutyrate before and after a 72 h incubation in the pr...

Data S1 Materials and methods.

Genetic ablation of CuZn-superoxide dismutase (Sod1) in mice (Sod1−/− mice) leads to shortened lifespan with a dramatic increase in hepatocellular carcinoma and accelerated aging phenotypes, including early onset sarcopenia. To study the tissue specific effects of oxidative stress in the Sod1−/− mice, we generated mice that only express the human S...

Disruption of mitochondrial respiration in the nematode Caenorhabditis elegans can extend lifespan. We previously showed that long-lived respiratory mutants generate elevated amounts of α-ketoacids. These compounds are structurally related to α-ketoglutarate, suggesting they may be biologically relevant. Here, we show that provision of several such...

We examined the effect of rapamycin on the life span of a mouse model of type 2 diabetes, db/db mice. At 4 months of age, male and female C57BLKSJ-lepr db/db mice (db/db) were placed on either a control diet, lacking rapamycin or a diet containing rapamycin and maintained on these diets over their life span. Rapamycin was found to reduce the life s...

Synucleinopathy is any of a group of age-related neurodegenerative disorders including Parkinson's disease, multiple system atrophy, and dementia with Lewy Bodies, which is characterized by α-synuclein inclusions and parkinsonian motor deficits affecting millions of patients worldwide. But there is no cure at present for synucleinopathy. Rapamycin...

Helicobacter pylori (H. pylori) infection is a common risk factor (RF) for gastric adenocarcinoma. Although the infection is highly prevalent worldwide, US rates vary. Recent analysis of 286 Hispanic and non-Hispanic white men in a prospective cohort found significant associations between H. pylori-positive (+) serology and Hispanic ethnicity. This...

Rapamycin, a drug that has been shown to increase lifespan in mice, inhibits the target of rapamycin (TOR) pathway, a major pathway that regulates cell growth and energy status. It has been hypothesized that rapamycin and dietary restriction (DR) extend lifespan through similar mechanisms/pathways. Using microarray analysis, we compared the transcr...

Negative elongation factor (NELF) is known to enforce promoter-proximal pausing of RNA polymerase II (Pol II), a pervasive phenomenon observed across multicellular genomes. However, the physiological impact of NELF on tissue homeostasis remains unclear. Here, we show that whole-body conditional deletion of the B subunit of NELF (NELF-B) in adult mi...

Rapamycin was found to increase (11% to 16%) the lifespan of male and female C57BL/6J mice most likely by reducing the increase in the hazard for mortality (i.e., the rate of aging) term in the Gompertz mortality analysis. To identify the pathways that could be responsible for rapamycin's longevity effect, we analyzed the transcriptome of liver fro...

Rapamycin (Rapa) and dietary restriction (DR) have consistently been shown to increase lifespan. To investigate whether Rapa and DR affect similar pathways in mice, we compared the effects of feeding mice ad libitum (AL), Rapa, DR, or a combination of Rapa and DR (Rapa + DR) on the transcriptome and metabolome of the liver. The principal component...

Data S1 Methods.

Fig. S1 mTOR signaling pathways have similar decrease in all three groups. Fig. S2 Rapamycin levels in livers of Rapa and Rapa + DR mice. Fig. S3 qRT-PCR of genes in the livers of female mice fed multiple doses of rapamycin. Table S1 Both linear discrimination predictor and quadratic discriminant analysis show differences between Rapa and DR. Table...

Recent studies have challenged the prevailing view that reduced mitochondrial function and increased oxidative stress are correlated with reduced longevity. Mice carrying a homozygous knockout (KO) of the Surf1 gene showed a significant decrease in mitochondrial electron transport chain Complex IV activity, yet displayed increased lifespan and redu...

Target of rapamycin inhibition by rapamycin feeding has previously been shown to extend life in genetically heterogeneous mice. To examine whether it similarly affected mouse health, we fed encapsulated rapamycin or a control diet to C57BL/6Nia mice of both sexes starting at 19 months of age. We performed a range of health assessments 6 and 12 mont...

Dietary restriction is a powerful aging intervention that extends the life span of diverse biological species ranging from yeast to invertebrates to mammals, and it has been argued that the anti-aging action of dietary restriction occurs through reduced oxidative stress/damage. Using Sod1-/- mice, which have previously been shown to have increased...

Chronic treatment of mice with an enterically released formulation of rapamycin (eRapa) extends median and maximum life span, partly by attenuating cancer. The mechanistic basis of this response is not known. To gain a better understanding of thesein vivo effects, we used a defined preclinical model of neuroendocrine cancer, Rb1+/- mice. Previous r...

Interference in insulin and/or insulin-like growth factor 1 (IGF-1) signaling can extend invertebrate life span, and interference in IGF-1 signaling can extend murine life span. Whether interference with murine insulin signaling, which can be diabetogenic and pathological, is also life-extending is controversial. We therefore measured life span in...

The nematode Caenorhabditis elegans is a model organism that has seen extensive use over the last four decades in multiple areas of investigation. In this study we explore the response of the nematode Caenorhabditis elegans to acute anoxia using gas-chromatography mass-spectrometry (GC-MS). We focus on the readily-accessible worm exometabolome to s...

Response curves for GC-MS analysis of selected metabolites. Four-point GC-MS response curves for alanine, isoleucine, leucine, succinate, and valine were established by integrating the peak at each analyte's established retention time in an extracted ion chromatogram corresponding to a characteristic fragment for that compound (usually [M-57]+). Th...

Raw data and statistical analyses. (XLS)

Rea Lab mass spectral library. (MSP)

Effect of sucrose wash step on exometabolome composition. 250,000 one day old adult N2 and MQ1333 [nuo-6(qm200)] worms were prepared for exometabolome collection exactly as described under Materials & Methods. Each worm sample was split into two equal fractions and processed identically, except only one fraction from each pair was subjected to sucr...

The study was undertaken to explore the effect of rapamycin, an anti-inflammatory agent, on the metabolic profile of type 2 diabetic mice. Seven-month-old diabetic db/db mice and their lean littermate non-diabetic controls (db/m) were randomized to receive control chow or chow mixed with rapamycin (2.24 mg/kg/day) (each group n =20, males and femal...

Synaptic dysfunction is considered the primary substrate for the functional declines observed within the nervous system during age-related neurodegenerative disease. Dietary restriction (DR), which extends lifespan in numerous species, has been shown to have beneficial effects on many neurodegenerative disease models. Existing data sets suggest tha...

Amyotrophic lateral sclerosis (ALS) is a devastating neurodegenerative disease. We sought to determine whether peroxisome proliferator-activated receptor γ coactivator 1α (PGC-1α) would have a beneficial effect on this disease. PGC-1α transgenic mice were crossed with SOD1 mutant G93A DL mice. We observed a moderate but non-significant increase in...

Igf1r Expression. The mRNA levels of Igf1r were measured in the indicated tissues from male and female mice at 6 and 25 months of age. The mean and SEM columns are for ΔΔCT values of Igf1r mRNA normalized to the median expression level of the male WT group in each respective tissue. The Student's t-test was used for the comparisons. The p-values ar...

Males and Females, Disease Burden. Disease burden is defined as the number of distinct lesions observed in an animal (either total lesions or only neoplastic ones) as described in Materials and Methods. In calculating neoplastic burden, lesions were counted separately for each organ in which they were observed with the exception of lymphoma, which...

Lifespan of Female WT and Igf1r+/− Mice on a C57BL/6X129Sv F1 Background. Male C57Bl/6 Igf1r+/− mice were crossed to female 129 mice to generate female WT and Igf1r+/− mice on a C57BL/6x129Sv F1 background. Of the 66 WT mice, 47 mice died from natural causes, 5 mice were censored, and 14 mice were alive at the time of data analysis. Of 24 Igf1r+/−...

Males and Females, Severity. Organ-specific lesions (glomerulonephritis, gonadal degeneration, nephrocalcinosis, pituitary adenoma, and subscapular hyperplasia) were assigned a severity grade as described in Methods by Ikeno et. al. [20]–[22]. For lymphoma and lymphocytic infiltration, the number of organs where those lesions were observed was used...

Incidence of Lesions in Females. See legend for table S3. (PDF)

Circulating Levels of IGF-1. Serum from three mice from each group was assayed for IGF-1 as described in Materials and Methods, and the IGF-1 levels (expressed in ng/ml) are shown. (PDF)

Incidence of Lesions in Males. The presence or absence of each lesion or category of lesions shown was coded as 0 or 1, respectively, for each animal. Where a lesion was judged to have caused the death of an animal, the total incidence and the incidence of just the fatal instance of that lesion are shown on separate lines indented below the name of...

Mutations in insulin/IGF-1 signaling pathway have been shown to lead to increased longevity in various invertebrate models. Therefore, the effect of the haplo-insufficiency of the IGF-1 receptor (Igf1r(+/-)) on longevity/aging was evaluated in C57Bl/6 mice using rigorous criteria where lifespan and end-of-life pathology were measured under optimal...

We examined the effects of increased levels of thioredoxin 1 (Trx1) on resistance to oxidative stress and aging in transgenic mice overexpressing Trx1 [Tg(TRX1)(+/0)]. The Tg(TRX1)(+/0) mice showed significantly higher Trx1 protein levels in all the tissues examined compared with the wild-type littermates. Oxidative damage to proteins and levels of...

Dietary restriction (DR) and rapamycin (Rapa) have been shown to increase the lifespan of a variety of organisms leading to the speculation that these interventions increase lifespan through related mechanisms. However, both these interventions have a detrimental effect in the G93A mutant mouse model of amyotrophic lateral sclerosis (ALS). Our prev...

Multiple stress resistance pathways were evaluated in the liver of Ames dwarf mice before and after exposure to the oxidative toxin diquat, seeking clues to the exceptional longevity conferred by this mutation. Before diquat treatment, Ames dwarf mice, compared with nonmutant littermate controls, had 2- to 6-fold higher levels of expression of mRNA...

While most of the amino acids in proteins are potential targets for oxidation, the thiol group in cysteine is one of the most reactive amino acid side chains. The thiol group can be oxidized to several states, including the disulfide bond. Despite the known sensitivity of cysteine to oxidation and the physiological importance of the thiol group to...

Cognitive dysfunction and memory loss are common features of Alzheimer's disease (AD). Abnormalities in the expression profile of immediate early genes that play a critical role in memory formation, such as the cAMP-response element binding protein (CREB), have been reported in the brains of AD patients. Here we show that amyloid-β (Aβ) accumulatio...

Many rodent experiments have assessed effects of diets, drugs, genes, and other factors on life span. A challenge with such experiments is their long duration, typically over 3.5 years given rodent life spans, thus requiring significant time costs until answers are obtained. We collected longevity data from 15 rodent studies and artificially trunca...

Hypothalamic tuberoinfundibular dopaminergic (TIDA) neurons secrete dopamine, which inhibits pituitary prolactin (PRL) secretion. PRL has demonstrated neurotrophic effects on TIDA neuron development in PRL-, GH-, and TSH-deficient Ames (df/df) and Snell (dw/dw) dwarf mice. However, both PRL and PRL receptor knockout mice exhibit normal-sized TIDA n...

While most of the amino acids in proteins are potential targets for oxidation, the thiol group in cysteine is one of the most reactive amino acid side chains. The thiol group can be oxidized to several states, including the disulfide bond. Despite the known sensitivity of cysteine to oxidation and the physiological importance of the thiol group to...

Currently, the oxidative stress (or free radical) theory of aging is the most popular explanation of how aging occurs at the molecular level. While data from studies in invertebrates (e.g., C. elegans and Drosophila) and rodents show a correlation between increased lifespan and resistance to oxidative stress (and in some cases reduced oxidative dam...

To test the impact of increased mitochondrial oxidative stress as a mechanism underlying aging and age-related pathologies, we generated mice with a combined deficiency in two mitochondrial-localized antioxidant enzymes, Mn superoxide dismutase (MnSOD) and glutathione peroxidase-1 (Gpx-1). We compared life span, pathology, and oxidative damage in G...

Methionine sulfoxide reductase A (MsrA) repairs oxidized methionine residues within proteins and may also function as a general antioxidant. Previous reports have suggested that modulation of MsrA in mice and mammalian cell culture can affect the accumulation of oxidized proteins and may regulate resistance to oxidative stress. Thus, under the oxid...

To probe the connection between longevity and stress resistance, we compared the sensitivity of Ames long-lived dwarf mice and control littermates with paraquat, diquat, and dobutamine. In young adult animals, 95% of male and 39% of female controls died after paraquat administration, but no dwarf animals died. When the experiment was repeated at an...

We evaluated the effect of overexpressing antioxidant enzymes on the lifespans of transgenic mice that overexpress copper zinc superoxide dismutase (CuZnSOD), catalase, or combinations of either CuZnSOD and catalase or CuZnSOD and manganese superoxide dismutase (MnSOD). Our results show that the overexpression of these major antioxidant enzymes, wh...

The sexual dimorphism of life span and caloric restriction effects in numerous species suggest that estradiol (E2) is protective against oxidative damage. The only direct test of E2's protective effect in mice against in vivo oxidative stress to date may have been confounded by E2's direct chemical action as an antioxidant because it was administer...

The Free Radical/Oxidative Stress Theory of Aging, which was first proposed in 1956, is currently one of the most popular explanations for how aging occurs at the biochemical/molecular level. However, most of the evidence in support of this theory is correlative, e.g., oxidative damage to various biomolecules increases with age, and caloric restric...