• Improved spectral comparisons of paleoclimate models and observations via proxy system modeling: Implications for multi-decadal variability

      Dee, S. G.; Parsons, L. A.; Loope, G. R.; Overpeck, J. T.; Ault, T. R.; Emile-Geay, J.; Univ Arizona, Dept Geosci (ELSEVIER SCIENCE BV, 2017-10-15)
      The spectral characteristics of paleoclimate observations spanning the last millennium suggest the presence of significant low-frequency (multi-decadal to centennial scale) variability in the climate system. Since this low-frequency climate variability is critical for climate predictions on societally-relevant scales, it is essential to establish whether General Circulation models (GCMs) are able to simulate it faithfully. Recent studies find large discrepancies between models and paleoclimate data at low frequencies, prompting concerns surrounding the ability of GCMs to predict long-term, high-magnitude variability under greenhouse forcing (Laepple and Huybers, 2014a, 2014b). However, efforts to ground climate model simulations directly in paleoclimate observations are impeded by fundamental differences between models and the proxy data: proxy systems often record a multivariate and/or nonlinear response to climate, precluding a direct comparison to GCM output. In this paper we bridge this gap via a forward proxy modeling approach, coupled to an isotope-enabled GCM. This allows us to disentangle the various contributions to signals embedded in ice cores, speleothem calcite, coral aragonite, tree-ring width, and tree-ring cellulose. The paper addresses the following questions: (1) do forward-modeled “pseudoproxies” exhibit variability comparable to proxy data? (2) if not, which processes alter the shape of the spectrum of simulated climate variability, and are these processes broadly distinguishable from climate? We apply our method to representative case studies, and broaden these insights with an analysis of the PAGES2k database (PAGES2K Consortium, 2013). We find that current proxy system models (PSMs) can help resolve model-data discrepancies on interannual to decadal timescales, but cannot account for the mismatch in variance on multi-decadal to centennial timescales. We conclude that, specific to this set of PSMs and isotope-enabled model, the paleoclimate record may exhibit larger low-frequency variability than GCMs currently simulate, indicative of incomplete physics and/or forcings.
    • Diagnosing Abnormal Electrocardiogram (ECG) via Deep Learning

      Gao, Xin; Univ Arizona, Dept Elect & Comp Engn (INTECHOPEN, 2019-04-03)
      In this chapter, we investigate the most recent automatic detecting algorithms on abnormal electrocardiogram (ECG) in a variety of cardiac arrhythmias. We present typical examples of a medical case study and technical applications related to diagnosing ECG, which include (i) a recently patented data classifier on the basis of deep learning model, (ii) a deep neural network scheme to diagnose variable types of arrhythmia through wearable ECG monitoring devices, and (iii) implementation of the health cloud platform, which consists of automatic detection, data mining, and classifying via the Android terminal module. Our work establishes a cross-area study, which relates artificial intelligence (AI), deep learning, cloud computing on huge amount of data to minishape ECG monitoring devices, and portable interaction platforms. Experimental results display the technical advantages such as saving cost, better reliability, and higher accuracy of deep learning-based models in contrast to conventional schemes on cardiac diagnosis.
    • Dental evidence for wild tuber processing among Titicaca Basin foragers 7000 ybp

      Watson, James T.; Haas, Randall; Univ Arizona, Arizona State Museum; Univ Arizona, Sch Anthropol (Wiley, 2017-09)
      Objectives: The objective of this work is to characterize dental wear in a skeletal sample dating to the Middle/Late Archaic period transition (8,000-6,700 cal. B.P.) from the Lake Titicaca Basin, Peru to better define subsistence behaviors of foragers prior to incipient sedentism and food production. Materials and Methods: The dental sample consists of 251 teeth from 11 individuals recovered from the site of Soro Mik'aya Patjxa (SMP), the earliest securely dated burial assemblage in the Lake Titicaca Basin and the only burial assemblage in the region from an unequivocal forager context. Occlusal surface wear was quantified according to Smith (1984) and Scott (1979a) to characterize diversity within the site and to facilitate comparison with other foraging groups worldwide. General linear modeling was used to assess observation error and principal axis analysis was used to compare molar wear rates and angles. Teeth were also examined for caries and specialized wear. Results: Occlusal surface attrition is generally heavy across the dental arcade and tends to be flat among posterior teeth. Only one carious lesion was observed. Five of the 11 individuals exhibit lingual surface attrition of the maxillary anterior teeth (LSAMAT). Discussion: Tooth wear rates, molar wear plane, and caries rates are consistent with terrestrial foraging and a diverse diet. The presence of LSAMAT indicates tuber processing. The results therefore contribute critical new data toward our understanding of forager diet in the Altiplano prior to plant and animal domestication in the south-central Andes.
    • Assessing the national trends in colon cancer among Native Americans: A 12 year SEER database study

      Thuraisingam, R.; Jandova, J.; Pandit, V.; Michailidou, M.; Nfonsam, V. N.; Univ Arizona, UA Dept Surg, Div Surg Oncol (EXCERPTA MEDICA INC-ELSEVIER SCIENCE INC, 2017-08-01)
      Introduction: Native Americans (NA) form a unique cohort of colon cancer (CC) patients among whom the variability in demographics and cancer characteristics remains unclear. Methods: We abstracted the national estimates for NA with CC using the Surveillance, Epidemiology, and End Result (SEER) database. Trend analysis of incidence, variation in location and patient demographic analysis were performed. Results: A total number of 26,674 NA with CC were reported during the 12-year study period. While the overall incidence of CC decreased by 12% during the study period, incidence increased by 38% in NA. Incidence of CC was more prevalent and higher increase (42%) seen in NA females than males (p = 0.02; 34%). Stage III tumors represented 29% of all CC, sigmoid colon the most common site location (38%) with 72% of all tumors being moderately differentiated. 55% tumors were localized in left, 36% in right and 9% in transverse colon. 92% of the NA were insured. Conclusion: Incidence of CC continues to rise in NA with majority of CC presented at higher stage and moderate differentiation. Published by Elsevier Inc.
    • Differential susceptibility of human peripheral blood T cells to suppression by environmental levels of sodium arsenite and monomethylarsonous acid

      Burchiel, Scott W; Lauer, Fredine T; Beswick, Ellen J; Gandolfi, A Jay; Parvez, Faruque; Liu, Ke Jian; Hudson, Laurie G; Univ Arizona, Dept Pharmacol & Toxicol (PUBLIC LIBRARY SCIENCE, 2014-10-01)
      Human exposure to arsenic in drinking water is known to contribute to many different health outcomes such as cancer, diabetes, and cardiopulmonary disease. Several epidemiological studies suggest that T cell function is also altered by drinking water arsenic exposure. However, it is unclear how individual responses differ to various levels of exposure to arsenic. Our laboratory has recently identified differential responses of human peripheral blood mononuclear cell (HPMBC) T cells as measured by polyclonal T cell activation by mitogens during sodium arsenite exposure. T cells from certain healthy individuals exposed to various concentrations (1–100 nM) of arsenite in vitro showed a dose-dependent suppression at these extremely low concentrations (∼0.1–10 ppb) of arsenite, whereas other individuals were not suppressed at low concentrations. In a series of more than 30 normal donors, two individuals were found to be sensitive to low concentration (10 nM equivalent ∼1 ppb drinking water exposure) to sodium arsenite-induced inhibition of T cell proliferation produced by phytohemagglutinin (PHA) and anti-CD3/anti-CD28. In an arsenite-susceptible individual, arsenite suppressed the activation of Th1 (Tbet) cells, and decreased the percentage of cells in the double positive Th17 (RORγt) and Treg (FoxP3) population. While the majority of normal blood donors tested were not susceptible to inhibition of proliferation at the 1–100 nM concentrations of As+3, it was found that all donors were sensitive to suppression by 100 nM monomethylarsonous acid (MMA+3), a key metabolite of arsenite. Thus, our studies demonstrate for the first time that low ppb-equivalent concentrations of As+3 are immunosuppressive to HPBMC T cells in some individuals, but that most donor HPBMC are sensitive to suppression by MMA+3 at environmentally relevant exposure levels.
    • kMEn: Analyzing noisy and bidirectional transcriptional pathway responses in single subjects

      Li, Qike; Schissler, A. Grant; Gardeux, Vincent; Berghout, Joanne; Achour, Ikbel; Kenost, Colleen; Li, Haiquan; Zhang, Hao Helen; Lussier, Yves A.; Univ Arizona, Ctr Biomed Informat & Biostat; Univ Arizona, Inst Bio5; Univ Arizona, Dept Med; Univ Arizona, Grad Interdisciplinary Program Stat; Univ Arizona, Dept Math; Univ Arizona, Canc Ctr (ACADEMIC PRESS INC ELSEVIER SCIENCE, 2017-01-01)
      Motivation: Understanding dynamic, patient-level transcriptomic response to therapy is an important step forward for precision medicine. However, conventional transcriptome analysis aims to discover cohort-level change, lacking the capacity to unveil patient-specific response to therapy. To address this gap, we previously developed two N-of-l-pathways methods, Wilcoxon and Mahalanobis distance, to detect unidirectionally responsive transcripts within a pathway using a pair of samples from a single subject. Yet, these methods cannot recognize bidirectionally (up and down) responsive pathways. Further, our previous approaches have not been assessed in presence of background noise and are not designed to identify differentially expressed mRNAs between two samples of a patient taken in different contexts (e.g. cancer vs non cancer), which we termed responsive transcripts (RTs). Methods: We propose a new N-of-l-pathways method, k-Means Enrichment (kMEn), that detects bidirectionally responsive pathways, despite background noise, using a pair of transcriptomes from a single patient. kMEn identifies transcripts responsive to the stimulus through k-means clustering and then tests for an over-representation of the responsive genes within each pathway. The pathways identified by kMEn are mechanistically interpretable pathways significantly responding to a stimulus. Results: In similar to 9000 simulations varying six parameters, superior performance of kMEn over previous single-subject methods is evident by: (i) improved precision-recall at various levels of bidirectional response and (ii) lower rates of false positives (1-specificity) when more than 10% of genes in the genome are differentially expressed (background noise). In a clinical proof-of-concept, personal treatment specific pathways identified by kMEn correlate with therapeutic response (p-value < 0.01). Conclusion: Through improved single-subject transcriptome dynamics of bidirectionally-regulated signals, kMEn provides a novel approach to identify mechanism-level biomarkers. (C) 2016 Published by Elsevier Inc.
    • Association between YAP expression in neoplastic and non-neoplastic breast tissue with arsenic urinary levels

      Gladis, Michel-Ramirez; Recio-Vega, Rogelio; Ocampo-Gomez, Guadalupe; Palacios-Sanchez, Eduardo; Delgado-Macias, Manuel; Delgado-Gaona, Manuel; Clark Lantz, Robert; Gandolfi, Jay; Gonzalez-Cortes, Tania; University of Coahuila, Torreon, Coahuila, Mexico; University of Arizona, Tucson, AZ, USA; Univ Arizona, Southwest Environm Hlth Sci Ctr; Univ Arizona, Dept Cellular & Mol Med; Univ Arizona, Dept Pharmacol & Toxicol (WILEY, 2017-10-01)
      The Hippo pathway regulates cell proliferation and apoptosis and it has been noted that loss of critical components of this pathway can lead to uncontrolled cell growth. Yes-associated protein (YAP) is an important component of this Hippo pathway because YAP is the nuclear effector of the Hippo tumor suppressor pathway and it is crucial for the response to oxidative stress induced by cellular process and by different xenobiotics, including arsenic. It has been proposed that YAP dysregulation can contribute to a malignant cellular phenotype acting as both a tumor suppressor and an oncogene. The aim of the study was to assess and compare the expression of YAP in neoplastic and non-neoplastic breast tissue of women chronically exposed to arsenic through drinking water. YAP expression was assessed by immunohistochemistry in 120 breast biopsies from women with breast cancer and from women with other non-neoplastic breast pathologies. Arsenic concentration was quantified in urine. The results disclosed a significant lower percentage of cytoplasm YAP expression in cases and that YAP high-intensity staining in the cytoplasm but not in the nucleus decreases the risk for breast cancer. In conclusion, our overall data suggest that YAP may act as a tumor suppressor protein because their reduced expression in cases, which can induce an environment favorable for inhibition of apoptosis and promoting cellular proliferation by increasing genetic instability of cells, which might contribute to the pathogenesis of cancer.
    • Development and evaluation of the See Me Smoke-Free multi-behavioral mHealth app for women smokers

      Gordon, Judith; Armin, Julie; Hingle, Melanie D.; Giacobbi, Peter, Jr.; Cunningham, James K.; Johnson, Thienne; Abbate, Kristopher; Howe, Carol L.; Roe, Denise J.; University of Arizona; Univ Arizona, Coll Med, Dept Family & Community Med; Univ Arizona, Coll Agr & Life Sci, Dept Nutr Sci; Univ West Virginia, Coll Phys Act & Sports Sci; Univ Arizona, Dept Comp Sci; Univ Arizona, Dept Elect & Comp Engn; Univ Arizona, Coll Med; Univ Arizona, Dept Epidemiol & Biostat, Mel & Enid Zuckerman Coll Publ Hlth (Oxford Academic, 2017-06)
      Background: Women face particular challenges when quitting smoking, especially those with weight concerns. A multi-behavioral smoking cessation intervention addressing these concerns and incorporating guided imagery may assist women to engage in healthy lifestyle behaviors. An mHealth app can easily disseminate such an intervention. Purpose: The goals of this pilot study were to develop and test the feasibility and potential of the See Me Smoke-Free™ mHealth app to address smoking, diet and physical activity among women smokers. Methods: We used pragmatic, direct-to-consumer methods to develop and test program content, functionality, and the user interface, and conduct a pre-/post-test, 90-day pilot study. Results: We enrolled 151 participants. Attrition was 52%, leaving 73 participants. At 90 days, 47% of participants reported 7-day abstinence, and significant increases in physical activity and fruit consumption. Conclusions: Recruitment methods worked well, but similar to other mHealth studies, we experienced high attrition. This study suggests that a guided imagery mHealth app has the potential to address multiple behaviors. Future research should consider different methods to improve retention and assess efficacy.
    • Majority Logic Decoding Under Data-Dependent Logic Gate Failures

      Brkic, Srdan; Ivanis, Predrag; Vasic, Bane; Univ Arizona, Dept Elect & Comp Engn (IEEE-INST ELECTRICAL ELECTRONICS ENGINEERS INC, 2017-10)
      A majority logic decoder made of unreliable logic gates, whose failures are transient and data-dependent, is analyzed. Based on a combinatorial representation of fault configurations a closed-form expression for the average bit error rate for a one-step majority logic decoder is derived, for a regular low-density parity-check (LDPC) code ensemble and the proposed failure model. The presented analysis framework is then used to establish bounds on the one-step majority logic decoder performance under the simplified probabilistic gateoutput switching model. Based on the expander property of Tanner graphs of LDPC codes, it is proven that a version of the faulty parallel bit-flipping decoder can correct a fixed fraction of channel errors in the presence of data-dependent gate failures. The results are illustrated with numerical examples of finite geometry codes.
    • A scaffolding approach to coreference resolution integrating statistical and rule-based models

      We describe a scaffolding approach to the task of coreference resolution that incrementally combines statistical classifiers, each designed for a particular mention type, with rule-based models (for sub-tasks well-matched to determinism). We motivate our design by an oracle-based analysis of errors in a rule-based coreference resolution system, showing that rule-based approaches are poorly suited to tasks that require a large lexical feature space, such as resolving pronominal and common-noun mentions. Our approach combines many advantages: it incrementally builds clusters integrating joint information about entities, uses rules for deterministic phenomena, and integrates rich lexical, syntactic, and semantic features with random forest classifiers well-suited to modeling the complex feature interactions that are known to characterize the coreference task. We demonstrate that all these decisions are important. The resulting system achieves 63.2 F1 on the CoNLL-2012 shared task dataset, outperforming the rule-based starting point by over seven F1 points. Similarly, our system outperforms an equivalent sieve-based approach that relies on logistic regression classifiers instead of random forests by over four F1 points. Lastly, we show that by changing the coreference resolution system from relying on constituent-based syntax to using dependency syntax, which can be generated in linear time, we achieve a runtime speedup of 550 per cent without considerable loss of accuracy.+
    • Stuck in the spin cycle: Avoidance and intrusions following breast cancer diagnosis

      Bauer, Margaret R; Wiley, Joshua F; Weihs, Karen L; Stanton, Annette L; Univ Arizona, Dept Psychiat (WILEY, 2017-09-01)
      Objectives. Theories and research regarding cognitive and emotional processing during the experience of profound stressors suggest that the presence of intrusive thoughts and feelings predicts greater use of avoidance and that the use of avoidance paradoxically predicts more intrusions. However, empirical investigations of their purported bidirectional relationship are limited. Design. This study presents a longitudinal investigation of the reciprocal relationship between intrusions and avoidance coping over a 6-month period in the year following breast cancer diagnosis. Methods. Breast cancer patients (N = 460) completed measures of cancer-related intrusions and avoidance at study entry, 3 months, and 6 months later (i.e., an average of 2, 5, and 8 months after diagnosis, respectively). Results. Cross-lagged panel analyses revealed that intrusive thoughts, feelings, and images at study entry predicted greater avoidance 3 months later, and avoidance coping at study entry predicted intrusions 3 months later, controlling for the stability of intrusions and avoidance as well as time since diagnosis. Findings were not statistically significant for avoidance predicting intrusions, or vice versa, between the 3-month and the 6-month assessment period, during which they declined. Conclusions. These findings provide empirical support for the theoretical contention that avoidance and intrusive thoughts and emotions reciprocally influence one another following stressful events. Additionally, in the months shortly after breast cancer diagnosis, intrusions and avoidance are positively related. However, the relationships attenuate over time, which could indicate resolved cognitive and emotional processing of the cancer experience.
    • The Integration of Common Core and Response to Intervention: Supporting Vulnerable Readers in a Time of Sophisticated Standards

      Jaeger, Elizabeth L.; Pearson, P. David; Univ Arizona, Coll Educ (ROUTLEDGE JOURNALS, TAYLOR & FRANCIS LTD, 2017)
      The Common Core State Standards and Response to Intervention are significant contemporary educational initiatives that have emerged largely in isolation from one another. We argue that an integration of these initiatives is beneficial. We trace the independent development of these two initiatives and offer suggestions for how they might fruitfully transact, fully supporting vulnerable readers in their efforts to master sophisticated standards. Results from a school implementing these initiatives as an integrated whole are discussed.
    • Evolutionary trends in host physiology outweigh dietary niche in structuring primate gut microbiomes

      Amato, Katherine R; G Sanders, Jon; Song, Se Jin; Nute, Michael; Metcalf, Jessica L; Thompson, Luke R; Morton, James T; Amir, Amnon; J McKenzie, Valerie; Humphrey, Gregory; Gogul, Grant; Gaffney, James; L Baden, Andrea; A O Britton, Gillian; P Cuozzo, Frank; Di Fiore, Anthony; J Dominy, Nathaniel; L Goldberg, Tony; Gomez, Andres; Kowalewski, Martin M; J Lewis, Rebecca; Link, Andres; L Sauther, Michelle; Tecot, Stacey; A White, Bryan; E Nelson, Karen; M Stumpf, Rebecca; Knight, Rob; R Leigh, Steven; Univ Arizona, Sch Anthropol (NATURE PUBLISHING GROUP, 2019-03-01)
      Over the past decade several studies have reported that the gut microbiomes of mammals with similar dietary niches exhibit similar compositional and functional traits. However, these studies rely heavily on samples from captive individuals and often confound host phylogeny, gut morphology, and diet. To more explicitly test the influence of host dietary niche on the mammalian gut microbiome we use 16S rRNA gene amplicon sequencing and shotgun metagenomics to compare the gut microbiota of 18 species of wild non-human primates classified as either folivores or closely related non-folivores, evenly distributed throughout the primate order and representing a range of gut morphological specializations. While folivory results in some convergent microbial traits, collectively we show that the influence of host phylogeny on both gut microbial composition and function is much stronger than that of host dietary niche. This pattern does not result from differences in host geographic location or actual dietary intake at the time of sampling, but instead appears to result from differences in host physiology. These findings indicate that mammalian gut microbiome plasticity in response to dietary shifts over both the lifespan of an individual host and the evolutionary history of a given host species is constrained by host physiological evolution. Therefore, the gut microbiome cannot be considered separately from host physiology when describing host nutritional strategies and the emergence of host dietary niches.
    • The Amplifying Role of Need in Giving Decisions

      Danvers, Alexander Francois; Hackman, Joseph V.; Hruschka, Daniel; Univ Arizona (ELSEVIER SCIENCE INC, 2019-03)
      Hamilton's rule predicts that altruism should depend on costs incurred and benefits provided, but these depend on the relative needs of the donor and recipient. Rewriting Hamilton's rule to account for relative need suggests an amplifying effect of need on relatedness, but not necessarily other relationship qualities. In a reanalysis of three studies of social discounting and a new replication, we find that relative need amplifies the effects of relatedness on giving in two samples of U.S. adults recruited online, but not U.S. undergraduates or Indian adults recruited online. Among U.S. online participants, the effect of genetic kinship was greater when the partner was perceived to be in higher need than when in lower need. In the other samples, relatedness and greater partner need were associated with greater giving, but the effect of relatedness on giving was not significantly amplified by need. Need never amplified the effect of social closeness on giving, although it did diminish the effect of closeness in U.S. undergraduates, likely reflecting a ceiling effect. These results confirm predictions from a modification of Hamilton's rule in a sample of U.S. adults, but raise important questions about why they hold in some samples but not others. They also illustrate the importance of understanding how contextual factors, such as relative need, can moderate the importance of common variables used in evolutionary cost-benefit analyses.
    • Aggression and hormones are associated with heterogeneity in parasitism and parasite dynamics in the brown mouse lemur

      Zohdy, Sarah; Bisanzio, Donal; Tecot, Stacey; Wright, Patricia C.; Jernvall, Jukka; Univ Arizona, Sch Anthropol (ACADEMIC PRESS LTD- ELSEVIER SCIENCE LTD, 2017-10)
      Animal behaviours, like aggression, can directly affect host health by influencing exposure to parasites. Aggressive individuals may experience an increase in agonistic interactions and contact rates with conspecifics, which might increase their probability of acquiring parasites. However, aggression is not the only factor that shapes parasitism; proximate mechanisms like hormone-modulated immunosuppression can also have broad impacts. Here, we hypothesized that high levels of aggression, cortisol and testosterone would be positively associated with parasitism and that aggressive individuals would play a larger role spreading parasites to conspecifics than would docile individuals. We measured aggression using the level of aggressive response to human handling during capture. Our aim was to examine associations between aggression and hormones (cortisol and testosterone) on variation in endo-and ectoparasitism in a population of wild mouse lemurs (Microcebus rufus) over a 3-year period. By tracking the movement of lice (directly transmitted parasites) in the population, we also examined the effect of host aggression on population-wide parasite dynamics. We show that animals with high testosterone and cortisol were more likely to exhibit aggressive behaviours, and cortisol was associated with significantly higher ectoparasite infestations. Aggressive individuals were significantly more infested by lice, and also donated significantly more lice to conspecifics in the population. Taken together, our results offer insight into the individual and population health costs of aggression, and empirical support of a trade-off between aggression and ectoparasitism, which may have driven the evolution of aggression and interactions with conspecifics. (C) 2017 The Association for the Study of Animal Behaviour. Published by Elsevier Ltd. All rights reserved.
    • A fresh CP look at mixed-binary QPs: new formulations and relaxations

      Bomze, Immanuel M.; Cheng, Jianqiang; Dickinson, Peter J. C.; Lisser, Abdel; Univ Arizona, Dept Syst & Ind Engn (SPRINGER HEIDELBERG, 2017-11)
      Triggered by Burer's seminal characterization from 2009, many copositive reformulations of mixed-binary QPs have been discussed by now. Most of them can be used as proper relaxations, if the intractable co(mpletely)positive cones are replaced by tractable approximations. While the widely used approximation hierarchies have the disadvantage to use positive-semidefinite (psd) matrices of orders which rapidly increase with the level of approximation, alternatives focus on the problem of keeping psd matrix orders small, with the aim to avoid memory problems in the interior point algorithms. This work continues this approach, proposing new reformulations and relaxations. Moreover, we provide a thorough comparison of the respective duals and establish a monotonicity relation among their duality gaps. We also identify sufficient conditions for strong duality/zero duality gap in some of these formulations and generalize some of our observations to general conic problems.
    • Cytomegalovirus (CMV) research in immune senescence comes of age: overview of the 6th International Workshop on CMV and Immunosenescence

      Nikolich-Žugich, Janko; van Lier, René A W; Univ Arizona, Coll Med, Dept Immunobiol; Univ Arizona, Coll Med, Arizona Ctr Aging; Univ Arizona, Inst BIO5 (SPRINGER, 2017-06-01)
      Cytomegalovirus (CMV) is one of the most complex and most ubiquitous latent persistent viruses, with a considerable ability to evade and manipulate the immune system. Following an early-life infection, most immunocompetent humans spend several decades living with CMV, and, because the virus in these hosts does not cause manifest disease, CMV can be considered part of normal aging for more than half of humanity. However, there is accumulating evidence that CMV carriage is not a null event and that both potentially harmful and potentially beneficial outcomes emanate from the interaction of CMV with its mammalian hosts. This article provides an overview of the 6th International Workshop on CMV and Immunosenescence, highlighting the advances in the field made in the past two years, as related to CMV epidemiology/geroscience, CMV virology with an accent on latency, and CMV immune evasion and immune recognition of the virus and its antigens.
    • The telescope conjecture for algebraic stacks

      Hall, Jack; Rydh, David; Univ Arizona, Dept Math (WILEY, 2017-09)
      Using Balmer-Favi's generalized idempotents, we establish the telescope conjecture for many algebraic stacks. Along the way, we classify the thick tensor ideals of perfect complexes of stacks.
    • Seasonality and clinical impact of human parainfluenza viruses

      Maykowski, Philip; Smithgall, Marie; Zachariah, Philip; Oberhardt, Matthew; Vargas, Celibell; Reed, Carrie; Demmer, Ryan T.; Stockwell, Melissa S.; Saiman, Lisa; Univ Arizona, Coll Med Phoenix (WILEY, 2018-11)
      Background Widespread availability of rapid diagnostic testing for respiratory viruses allows more in-depth studies of human parainfluenza viruses (HPIV). Objectives This study aimed to assess seasonality of HPIV types 1-4, clinical outcomes by HPIV type, and risk factors for illness severity. Patients/Methods This retrospective study was performed from January 2013 to December 2015 in children and adults with HPIV, detected by multiplex reverse transcription polymerase chain reaction, participating in a community surveillance study of acute respiratory infections (ARIs) in New York City and patients admitted to a tertiary care center in the same neighborhood. Seasonality trends by HPIV type were compared between the community and hospital groups. The associations between HPIV type, demographics, clinical characteristics, and illness severity were assessed. Results HPIV was detected in 69 (4%) of 1753 community surveillance participants (median age 9.2years) and 680 hospitalized patients (median age 6.8years). Seasonality for HPIV types 1-3 agreed with previously described patterns; HPIV-4 occurred annually in late summer and fall. In the community cohort, 22 (32%) participants sought medical care, 9 (13%) reported antibiotic use, and 20 (29%) reported 1day of missed work or school. Among hospitalized patients, 24% had 4 chronic conditions. Multivariable ordinal logistic regression demonstrated that increased severity of illness was significantly associated with HPIV-4 and chronic cardiovascular and respiratory conditions in children and with age 65years and chronic respiratory conditions in adults. Conclusions HPIV-4 presented late summer and early fall annually and was associated with increased severity of illness in hospitalized children.
    • The smallest 'true chameleon' from Madagascar: a new, distinctly colored species of the Calumma boettgeri complex (Squamata, Chamaeleonidae)

      Prötzel, David; Lambert, Shea M.; Andrianasolo, Ginah Tsiorisoa; Hutter, Carl R.; Cobb, Kerry A.; Scherz, Mark D.; Glaw, Frank; Univ Arizona, Dept Ecol & Evolut Biol (PENSOFT PUBL, 2018-10-19)
      On a recent expedition to eastern Madagascar, we discovered a distinct new species of the genus Calumma that we describe here using an integrative approach combining morphology, coloration, osteology and molecular genetics. Calumma roaloko sp. n. has a dermal rostral appendage and occipital lobes, and belongs to the C. boettgeri complex, within the Madagascar-endemic phenetic C. nasutum species group. It is readily distinguished from other species of the C. boettgeri complex by a characteristic two-toned body coloration and small body size with a snout-vent length of 45.6 mm in an adult male. The osteology of the skull, with a prominent maxilla and broad parietal, is similar to the closest related species, C. uetzi. Analysis of uncorrected genetic distances within the C. nasutum group using the mitochondrial gene ND2 shows a minimum pairwise distance of 11.98% to C. uetzi from the Sorata massif and Marojejy National Park >500 km north of the type locality of C. roaloko sp. n.. Given an apparently small range (potentially <300 km(2)), located entirely outside of any nationally-protected areas, we recommend this new species be classified as Endangered under criterion B1ab(iii) of the IUCN Red List. The discovery of clearly distinct species like C. roaloko sp. n. in an area of Madagascar that is comparatively thoroughly surveyed highlights the critical role of continued field surveys for understanding the true extent of Madagascar's spectacular biodiversity.