• Calibration of activity-related energy expenditure in the Hispanic Community Health Study/Study of Latinos (HCHS/SOL)

      Shaw, PA; McMurray, R; Butte, N; Sotres-Alvarez, D; Sun, H; Stoutenberg, M; Evenson, KR; Wong, WW; Moncrieft, AE; Sanchez-Johnsen, LAP; Carnethon, MR; Arredondo, E; Kaplan, RC; Matthews, CE; Mossavar-Rahmani, Y; Stoutenberg, Mark|0000-0001-5206-7627 (2019-03-01)
      © 2018 Sports Medicine Australia Objectives: Usual physical activity (PA) is a complex exposure and typical instruments to measure aspects of PA are subject to measurement error, from systematic biases and biological variability. This error can lead to biased estimates of associations between PA and health outcomes. We developed a calibrated physical activity measure that adjusts for measurement error in both self-reported and accelerometry measures of PA in adults from the US Hispanic Community Health Study/Study of Latinos (HCHS/SOL), a community-based cohort study. Design: Total energy expenditure (TEE) from doubly labeled water and resting energy expenditure (REE) from indirect calorimetry were measured in 445 men and women aged 18–74 years in 2010–2012, as part of the HCHS/SOL Study of Latinos: Nutrition & Physical Activity Assessment Study (SOLNAS). Measurements were repeated in a subset (N = 98) 6 months later. Method: Calibration equations for usual activity-related energy expenditure (AEE = 0.90 × TEE-REE) were developed by regressing this objective biomarker on self-reported PA and sedentary behavior, Actical accelerometer PA, and other subject characteristics. Results: Age, weight and height explained a significant amount of variation in AEE. Actical PA and wear-time were important predictors of AEE; whereas, self-reported PA was not independently associated with AEE. The final calibration equation explained fifty percent of variation in AEE. Conclusions: The developed calibration equations can be used to obtain error-corrected associations between PA and health outcomes in HCHS/SOL. Our study represents a unique opportunity to understand the measurement characteristics of PA instruments in an under-studied Hispanic/Latino cohort.
    • CALIS - A CALibration Insertion System for the DarkSide-50 dark matter search experiment

      Agnes, P; Albuquerque, IFM; Alexander, T; Alton, AK; Asner, DM; Back, HO; Baldin, B; Biery, K; Bocci, V; Bonfini, G; Bonivento, W; Bossa, M; Bottino, B; Brigatti, A; Brodsky, J; Budano, F; Bussino, S; Cadeddu, M; Cadonati, L; Cadoni, M; Calaprice, F; Canci, N; Candela, A; Caravati, M; Cariello, M; Carlini, M; Catalanotti, S; Cavalcante, P; Chepurnov, A; Cicalò, C; Cocco, AG; Covone, G; D'Angelo, D; D'Incecco, M; Davini, S; De Cecco, S; De Deo, M; De Vincenzi, M; Derbin, A; Devoto, A; Di Eusanio, F; Di Pietro, G; Dionisi, C; Edkins, E; Empl, A; Fan, A; Fiorillo, G; Fomenko, K; Forster, G; Franco, D; Gabriele, F; Galbiati, C; Giagu, S; Giganti, C; Giovanetti, GK; Goretti, AM; Granato, F; Grandi, L; Gromov, M; Guan, M; Guardincerri, Y; Hackett, BR; Herner, K; Hughes, D; Humble, P; Hungerford, EV; Ianni, A; Ianni, A; James, I; Johnson, TN; Jollet, C; Keeter, K; Kendziora, CL; Koh, G; Korablev, D; Korga, G; Kubankin, A; Li, X; Lissia, M; Loer, B; Lombardi, P; Longo, G; Ma, Y; Machado, AA; Machulin, IN; Mandarano, A; Mari, SM; Maricic, J; Marini, L; Martoff, CJ; Meregaglia, A; Meyers, PD; Milincic, R; Miller, JD; Montanari, D; Monte, A; Mount, BJ; Muratova, VN; Musico, P; Napolitano, J (2017-12-18)
      © 2017 The Author(s). This paper describes the design, fabrication, commissioning and use of a CALibration source Insertion System (CALIS) in the DarkSide-50 direct dark matter search experiment. CALIS deploys radioactive sources into the liquid scintillator veto to characterize the detector response and detection efficiency of the DarkSide-50 Liquid Argon Time Projection Chamber, and the surrounding 30 t organic liquid scintillator neutron veto. It was commissioned in September 2014 and has been used successfully in several gamma and neutron source campaigns since then. A description of the hardware and an excerpt of calibration analysis results are given below.
    • Can the microRNA expression profile help to identify novel targets for zoledronic acid in breast cancer?

      Fanale, D; Amodeo, V; Bazan, V; Insalaco, L; Incorvaia, L; Barraco, N; Castiglia, M; Rizzo, S; Santini, D; Giordano, A; Castorina, S; Russo, A; Giordano, Antonio|0000-0002-5959-016X (2016-05-17)
      Zoledronic acid (ZOL), belonging to third generation bisphosphonate family, is a potent inhibitor of osteoclast-mediated bone resorption, widely used to effectively prevent osteolysis in breast cancer patients who develop bone metastases. Low doses of ZOL have been shown to exhibit a direct anticancer role, by inhibiting cell adhesion, invasion, cytoskeleton remodelling and proliferation in MCF-7 breast cancer cells. In order to identify the molecular mechanisms and signaling pathways underlying the anticancer activity exerted by ZOL, we analyzed for the first time the microRNA expression profile in breast cancer cells. A large-scale microarray analysis of 377 miRNAs was performed on MCF7 cells treated with 10 μM ZOL for 24 h compared to untreated cells. Furthermore, the expression of specific ZOL-induced miRNAs was analyzed in MCF-7 and SkBr3 cells through Real-time PCR. Low-dose treatment with ZOL significantly altered expression of 54 miRNAs. Nine upregulated and twelve downregulated miRNAs have been identified after 24 h of treatment. Also, ZOL induced expression of 11 specific miRNAs and silenced expression of 22 miRNAs. MiRNA data analysis revealed the involvement of differentially expressed miRNAs in PI3K/Akt, MAPK, Wnt, TGF-Β, Jak-STAT and mTOR signaling pathways, and regulation of actin cytoskeleton. Our results have been shown to be perfectly coherent with the recent findings reported in literature concerning changes in expression of some miRNAs involved in bone metastasis formation, progression, therapy resistance in breast cancer. In conclusion, this data supports the hypothesis that ZOL-induced modification of the miRNA expression profile contributes to the anticancer efficacy of this agent.
    • Cancer survival disparities by health insurance status

      Niu, Xiaoling; Roche, Lisa M; Pawlish, Karen S; Henry, Kevin A (2013-06)
      Previous studies found that uninsured and Medicaid insured cancer patients have poorer outcomes than cancer patients with private insurance. We examined the association between health insurance status and survival of New Jersey patients 18-64 diagnosed with seven common cancers during 1999-2004. Hazard ratios (HRs) with 95% confidence intervals for 5-year cause-specific survival were calculated from Cox proportional hazards regression models; health insurance status was the primary predictor with adjustment for other significant factors in univariate chi-square or Kaplan-Meier survival log-rank tests. Two diagnosis periods by health insurance status were compared using Kaplan-Meier survival log-rank tests. For breast, colorectal, lung, non-Hodgkin lymphoma (NHL), and prostate cancer, uninsured and Medicaid insured patients had significantly higher risks of death than privately insured patients. For bladder cancer, uninsured patients had a significantly higher risk of death than privately insured patients. Survival improved between the two diagnosis periods for privately insured patients with breast, colorectal, or lung cancer and NHL, for Medicaid insured patients with NHL, and not at all for uninsured patients. Survival from cancer appears to be related to a complex set of demographic and clinical factors of which insurance status is a part. While ensuring that everyone has adequate health insurance is an important step, additional measures must be taken to address cancer survival disparities.
    • Canine CNGA3 gene mutations provide novel insights into human achromatopsia-associated channelopathies and treatment

      Tanaka, N; Dutrow, EV; Miyadera, K; Delemotte, L; MacDermaid, CM; Reinstein, SL; Crumley, WR; Dixon, CJ; Casal, ML; Klein, ML; Aguirre, GD; Tanaka, JC; Guziewicz, KE (2015-09-25)
      © 2015 Tanaka et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Cyclic nucleotide-gated (CNG) ion channels are key mediators underlying signal transduction in retinal and olfactory receptors. Genetic defects in CNGA3 and CNGB3, encoding two structurally related subunits of cone CNG channels, lead to achromatopsia (ACHM). ACHM is a congenital, autosomal recessive retinal disorder that manifests by cone photoreceptor dysfunction, severely reduced visual acuity, impaired or complete color blindness and photophobia. Here, we report the first canine models for CNGA3-associated channelopathy caused by R424W or V644del mutations in the canine CNGA3 ortholog that accurately mimic the clinical and molecular features of human CNGA3-associated ACHM. These two spontaneous mutations exposed CNGA3 residues essential for the preservation of channel function and biogenesis. The CNGA3-R424W results in complete loss of cone function in vivo and channel activity confirmed by in vitro electrophysiology. Structural modeling and molecular dynamics (MD) simulations revealed R424-E306 salt bridge formation and its disruption with the R424Wmutant. Reversal of charges in a CNGA3- R424E-E306R double mutant channel rescued cGMP-activated currents uncovering new insights into channel gating. The CNGA3-V644del affects the C-terminal leucine zipper (CLZ) domain destabilizing intersubunit interactions of the coiled-coil complex in the MD simulations; the in vitro experiments showed incompetent trimeric CNGA3 subunit assembly consistent with abnormal biogenesis of in vivo channels. These newly characterized large animal models not only provide a valuable system for studying cone-specific CNG channel function in health and disease, but also represent prime candidates for proof-ofconcept studies of CNGA3 gene replacement therapy for ACHM patients.
    • Canvass: A Crowd-Sourced, Natural-Product Screening Library for Exploring Biological Space

      Kearney, SE; Zahoránszky-Kohalmi, G; Brimacombe, KR; Henderson, MJ; Lynch, C; Zhao, T; Wan, KK; Itkin, Z; Dillon, C; Shen, M; Cheff, DM; Lee, TD; Bougie, D; Cheng, K; Coussens, NP; Dorjsuren, D; Eastman, RT; Huang, R; Iannotti, MJ; Karavadhi, S; Klumpp-Thomas, C; Roth, JS; Sakamuru, S; Sun, W; Titus, SA; Yasgar, A; Zhang, YQ; Zhao, J; Andrade, RB; Brown, MK; Burns, NZ; Cha, JK; Mevers, EE; Clardy, J; Clement, JA; Crooks, PA; Cuny, GD; Ganor, J; Moreno, J; Morrill, LA; Picazo, E; Susick, RB; Garg, NK; Goess, BC; Grossman, RB; Hughes, CC; Johnston, JN; Joullie, MM; Kinghorn, AD; Kingston, DGI; Krische, MJ; Kwon, O; Maimone, TJ; Majumdar, S; Maloney, KN; Mohamed, E; Murphy, BT; Nagorny, P; Olson, DE; Overman, LE; Brown, LE; Snyder, JK; Porco, JA; Rivas, F; Ross, SA; Sarpong, R; Sharma, I; Shaw, JT; Xu, Z; Shen, B; Shi, W; Stephenson, CRJ; Verano, AL; Tan, DS; Tang, Y; Taylor, RE; Thomson, RJ; Vosburg, DA; Wu, J; Wuest, WM; Zakarian, A; Zhang, Y; Ren, T; Zuo, Z; Inglese, J; Michael, S; Simeonov, A; Zheng, W; Shinn, P; Jadhav, A; Boxer, MB; Hall, MD; Xia, M; Guha, R; Rohde, JM (2018-12-26)
      © 2018 American Chemical Society. Natural products and their derivatives continue to be wellsprings of nascent therapeutic potential. However, many laboratories have limited resources for biological evaluation, leaving their previously isolated or synthesized compounds largely or completely untested. To address this issue, the Canvass library of natural products was assembled, in collaboration with academic and industry researchers, for quantitative high-throughput screening (qHTS) across a diverse set of cell-based and biochemical assays. Characterization of the library in terms of physicochemical properties, structural diversity, and similarity to compounds in publicly available libraries indicates that the Canvass library contains many structural elements in common with approved drugs. The assay data generated were analyzed using a variety of quality control metrics, and the resultant assay profiles were explored using statistical methods, such as clustering and compound promiscuity analyses. Individual compounds were then sorted by structural class and activity profiles. Differential behavior based on these classifications, as well as noteworthy activities, are outlined herein. One such highlight is the activity of (-)-2(S)-cathafoline, which was found to stabilize calcium levels in the endoplasmic reticulum. The workflow described here illustrates a pilot effort to broadly survey the biological potential of natural products by utilizing the power of automation and high-throughput screening.
    • Capture, movement, trade, and consumption of mammals in Madagascar

      Reuter, KE; Randell, H; Wills, AR; Janvier, TE; Belalahy, TR; Sewall, BJ (2016-02-01)
      © 2016 Reuter et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Wild meat trade constitutes a threat to many animal species. Understanding the commodity chain of wild animals (hunting, transportation, trade, consumption) can help target conservation initiatives. Wild meat commodity chain research has focused on the formal trade and less on informal enterprises, although informal enterprises contribute to a large portion of the wild meat trade in sub-Saharan Africa. We aimed to provide a more comprehensive understanding of the formal and informal components of these commodity chains by focusing on the mammalian wild meat trade in Madagascar. Our objectives were to: (1) identify hunting strategies used to capture different wild mammals; (2) analyze patterns of movement of wild meat from the capture location to the final consumer; (3) examine wild meat prices, volumes, and venues of sale; and (4) estimate the volume of wild meat consumption. Data were collected in May-August 2013 using semi-structured interviews with consumers (n = 1343 households, 21 towns), meat-sellers (n = 520 restaurants, open-air markets stalls, and supermarkets, 9 towns), and drivers of inter-city transit vehicles (n = 61, 5 towns). We found that: (1) a wide range of hunting methods were used, though prevalence of use differed by animal group; (2) wild meat was transported distances of up to 166 km to consumers, though some animal groups were hunted locally (<10 km) in rural areas; (3) most wild meat was procured from free sources (hunting, gifts), though urban respondents who consumed bats and wild pigs were more likely to purchase those meats; and (4) wild meat was consumed at lower rates than domestic meat, though urban respondents consumed wild meat twice as much per year compared to rural respondents. Apart from the hunting stage, the consumption and trade of wild meat in Madagascar is also likely more formalized than previously thought.
    • Caracterización de la degradación de los pantanos de palmeras turbosos desde el espacio y sobre el terreno: Un estudio exploratorio en la Amazonia peruana

      Center for International Forestry Research (CIFOR) (2017)
      El Perú tiene la cuarta mayor área de turberas de los trópicos. Su cobertura terrestre de turba más representativa es el pantano de palmeras (denominado a partir de ahora PP denso) dominado por la especie Mauritia flexuosa, que ha estado sometido a presión humana durante décadas debido a la alta demanda del fruto de M. flexuosa, que a menudo se recolecta cortando toda la palmera. La degradación de estos bosques densos en carbono puede afectar de manera sustancial las emisiones de gases de efecto invernadero y contribuir al cambio climático. El primer objetivo de esta investigación fue evaluar el impacto de la degradación de los PP densos sobre la estructura forestal y las reservas de carbono de la biomasa. El segundo fue explorar el potencial de mapear la distribución de los PP densos con diferentes niveles de degradación utilizando datos y métodos de teledetección. Las reservas de biomasa se midieron en parcelas de 0,25 ha establecidas en áreas de PP densos con degradación baja (n = 2 parcelas), media (n = 2) y alta (n = 4). Se combinaron datos de campo y de teledetección de los satélites Landsat TM y ALOS/PALSAR para diferenciar entre áreas que tipifican PP densos con degradación baja, media y alta y bosques de tierra firme, restinga y PP mixtos (no dominados por M. flexuosa). Para ello, se utilizó un algoritmo de clasificación de aprendizaje automático Random Forest. Los resultados sugieren un cambio en la composición forestal, de bosques dominados por palmeras a bosques dominados por árboles leñosos después de la degradación. También se encontró que la intervención humana en los PP densos se traduce en reducciones significativas en las reservas de carbono de los árboles, con disminuciones de las reservas de biomasa iniciales (aérea y subterránea) (135,4 ± 4,8 Mg C ha-1) de 11% y 17% luego de una degradación media y alta, respectivamente. El análisis de teledetección indica una alta separabilidad entre PP densos con degradación baja y todas las demás categorías. Los PP densos con degradación media y alta fueron altamente separables de la mayoría de las categorías con excepción de los bosques de restinga y los PP mixtos. Los resultados también mostraron que los datos de sensores de teledetección tanto activos como pasivos son importantes para el mapeo de la degradación de PP densos. La precisión general de la clasificación de la cobertura terrestre fue alta (91%). Los resultados de este análisis piloto son alentadores para seguir explorando el uso de datos y métodos de teledetección para el monitoreo de la degradación de PP densos a escalas más amplias en la Amazonia peruana. Brindar estimados precisos sobre la extensión espacial de la degradación de los PP densos y sobre las emisiones derivadas de la biomasa y la turba es necesario para evaluar las emisiones nacionales derivadas de la degradación forestal en el Perú y es esencial para apoyar iniciativas dirigidas a reducir las actividades de degradación.
    • Cardioprotective effect of Ulmus wallichiana planchon in β-Adrenergic agonist induced cardiac hypertrophy

      Syed, AA; Lahiri, S; Mohan, D; Valicherla, GR; Gupta, AP; Kumar, S; Maurya, R; Bora, HK; Hanif, K; Gayen, JR; Kumar, Sudhir|0000-0002-9918-8212 (2016-01-01)
      © 2016 Syed, Lahiri, Mohan, Valicherla, Gupta, Kumar, Maurya, Bora, Hanif and Gayen. Ulmus wallichiana Planchon (Family: Ulmaceae), a traditional medicinal plant, was used in fracture healing in the folk tradition of Uttarakhand, Himalaya, India. The present study investigated the cardioprotective effect of ethanolic extract (EE) and butanolic fraction (BF) of U. wallichiana in isoprenaline (ISO) induced cardiac hypertrophy in Wistar rats. Cardiac hypertrophy was induced by ISO (5 mg/kg/day, subcutaneously) in rats. Treatment was performed by oral administration of EE and BF of U. wallichiana (500 and 50 mg/kg/day). The blood pressure (BP) and heart rate (HR) were measured by non-invasive blood pressure measurement technique. Plasma renin, Ang II, NO, and cGMP level were estimated using an ELISA kit. Angiotensin converting enzyme activity was estimated. BP and HR were significantly increased in ISO group (130.33 ± 1.67 mmHg vs. 111.78 ± 1.62 mmHg, p < 0.001 and 450.51 ± 4.90 beats/min vs. 347.82 ± 6.91 beats/min, respectively, p < 0.001). The BP and HR were significantly reduced (EE: 117.53 ± 2.27 mmHg vs. 130.33 ± 1.67 mmHg, p < 0.001, BF: 119.74 ± 3.32 mmHg vs. 130.33 ± 1.67 mmHg, p < 0.001); HR: (EE: 390.22 ± 8.24 beats/min vs. 450.51 ± 4.90 beats/min, p < 0.001, BF: 345.38 ± 6.79 beats/min vs. 450.51 ± 4.90 beats/min, p < 0.001) after the treatment of EE and BF of U. wallichiana, respectively. Plasma renin, Ang II, ACE activity was decreased and NO, cGMP level were increased. The EE and BF of U. wallichiana down regulated the expression of ANP, BNP, TNF-a, IL-6, MMP9, ß1-AR, TGFß1 and up regulated NOS3, ACE2 and Mas expression level, respectively. Thus, this study demonstrated that U. wallichiana has cardioprotective effect against ISO induced cardiac hypertrophy.
    • Caregiver Influences on Eating Behaviors in Young Children: A Scientific Statement From the American Heart Association

      Wood, AC; Blissett, JM; Brunstrom, JM; Carnell, S; Faith, MS; Fisher, JO; Hayman, LL; Khalsa, AS; Hughes, SO; Miller, AL; Momin, SR; Welsh, JA; Woo, JG; Haycraft, E (2020-05-18)
      A substantial body of research suggests that efforts to prevent pediatric obesity may benefit from targeting not just what a child eats, but how they eat. Specifically, child obesity prevention should include a component that addresses reasons why children have differing abilities to start and stop eating in response to internal cues of hunger and satiety, a construct known as eating self-regulation. This review summarizes current knowledge regarding how caregivers can be an important influence on children's eating self-regulation during early childhood. First, we discuss the evidence supporting an association between caregiver feeding and child eating self-regulation. Second, we discuss what implications the current evidence has for actions caregivers may be able to take to support children's eating self-regulation. Finally, we consider the broader social, economic, and cultural context around the feeding environment relationship and how this intersects with the implementation of any actions. As far as we are aware, this is the first American Heart Association (AHA) scientific statement to focus on a psychobehavioral approach to reducing obesity risk in young children. It is anticipated that the timely information provided in this review can be used not only by caregivers within the immediate and extended family but also by a broad range of community-based care providers.
    • Caregiving, intellectual disability, and dementia: Report of the Summit Workgroup on Caregiving and Intellectual and Developmental Disabilities

      Heller, T; Scott, HM; Janicki, MP; Esbensen, A; Fazio, S; Yoshizaki-Gibbons, H; Hartley, DH; Jokinen, N; Kallmyer, B; Keller, S; Magana, S; Marsack, C; McCallion, P; Perkins, E; Putnam, M; Qualls, S; Rader, R; Roberto, K; Wheeler, B; Mccallion, Philip|0000-0001-5129-6399 (2018-01-01)
      © 2018 Introduction: A specially commissioned working group produced a report on caregiving, intellectual and developmental disabilities (IDDs), and dementia for the National Institutes of Health–located National Research Summit on Care, Services, and Supports for Persons with Dementia and Their Caregivers. Methods: Experts in caregiving, dementia, and IDDs examined the current state of research, policy, and practice related to caregiving and supports; identified the similarities and dissimilarities between IDD-related care and services and the general population affected by dementia; and considered how these findings might contribute to the conversation on developing a dementia care research and services development agenda. Results: Five major areas related to programs and caregiving were assessed: (1) challenges of dementia; (2) family caregiving interventions; (3) supportive care settings; (4) effects of diversity; and (5) bridging service networks of aging and disability. Discussion: Recommendations included increasing supports for caregivers of adults with IDDs and dementia; increasing research on community living settings and including caregivers of persons with IDDs in dementia research; acknowledging cultural values and practice diversity in caregiving; increasing screening for dementia and raising awareness; and leveraging integration of aging and disability networks.
    • Casting a wider net: Differentiating between inner nuclear envelope and outer nuclear envelope transmembrane proteins

      Tingey, M; Mudumbi, KC; Schirmer, EC; Yang, W; Yang, Weidong|0000-0002-3554-3035 (2019-11-01)
      © 2019 by the authors. Licensee MDPI, Basel, Switzerland. The nuclear envelope (NE) surrounds the nucleus with a double membrane in eukaryotic cells. The double membranes are embedded with proteins that are synthesized on the endoplasmic reticulum and often destined specifically for either the outer nuclear membrane (ONM) or the inner nuclear membrane (INM). These nuclear envelope transmembrane proteins (NETs) play important roles in cellular function and participate in transcription, epigenetics, splicing, DNA replication, genome architecture, nuclear structure, nuclear stability, nuclear organization, and nuclear positioning. These vital functions are dependent upon both the correct localization and relative concentrations of NETs on the appropriate membrane of the NE. It is, therefore, important to understand the distribution and abundance of NETs on the NE. This review will evaluate the current tools and methodologies available to address this important topic.
    • Catalytic mechanism of Escherichia coli ribonuclease III: Kinetic and inhibitor evidence for the involvement of two magnesium ions in RNA phosphodiester hydrolysis

      Sun, W; Pertzev, A; Nicholson, AW (2005-10-18)
      Escherichia coli ribonuclease III (RNase III; EC 3.1.24) is a double-stranded(ds)-RNA-specific endonuclease with key roles in diverse RNA maturation and decay pathways. E.coli RNase III is a member of a structurally distinct superfamily that includes Dicer, a central enzyme in the mechanism of RNA interference. E.coli RNase III requires a divalent metal ion for activity, with Mg2+ as the preferred species. However, neither the function(s) nor the number of metal ions involved in catalysis is known. To gain information on metal ion involvement in catalysis, the rate of cleavage of the model substrate R1.1 RNA was determined as a function of Mg2+ concentration. Single-turnover conditions were applied, wherein phosphodiester cleavage was the rate-limiting event. The measured Hill coefficient (nH) is 2.0 ± 0.1, indicative of the involvement of two Mg2+ ions in phosphodiester hydrolysis. It is also shown that 2-hydroxy-4H-isoquinoline-1,3-dione - an inhibitor of ribonucleases that employ two divalent metal ions in their catalytic sites-inhibits E.coli RNase III cleavage of R1.1 RNA. The IC50 for the compound is 14 μM for the Mg2+-supported reaction, and 8 μM for the Mn2+-supported reaction. The compound exhibits noncompetitive inhibitory kinetics, indicating that it does not perturb substrate binding. Neither the O-methylated version of the compound nor the unsubstituted imide inhibit substrate cleavage, which is consistent with a specific interaction of the N-hydroxyimide with two closely positioned divalent metal ions. A preliminary model is presented for functional roles of two divalent metal ions in the RNase III catalytic mechanism. © The Author 2005. Published by Oxford University Press. All rights reserved.
    • Catalytic prior distributions with application to generalized linear models

      Huang, D; Stein, N; Rubin, DB; Kou, SC; Rubin, Donald B.|0000-0001-7127-9262 (2020-06-02)
      © 2020 National Academy of Sciences. All rights reserved. A catalytic prior distribution is designed to stabilize a high-dimensional “working model” by shrinking it toward a “simplified model.” The shrinkage is achieved by supplementing the observed data with a small amount of “synthetic data” generated from a predictive distribution under the simpler model. We apply this framework to generalized linear models, where we propose various strategies for the specification of a tuning parameter governing the degree of shrinkage and study resultant theoretical properties. In simulations, the resulting posterior estimation using such a catalytic prior outperforms maximum likelihood estimation from the working model and is generally comparable with or superior to existing competitive methods in terms of frequentist prediction accuracy of point estimation and coverage accuracy of interval estimation. The catalytic priors have simple interpretations and are easy to formulate.
    • Causal Pathways from Enteropathogens to Environmental Enteropathy: Findings from the MAL-ED Birth Cohort Study

      Kosek, MN; Ahmed, T; Bhutta, ZA; Caulfield, L; Guerrant, RL; Houpt, E; Kang, G; Lee, G; Lima, AAM; McCormick, BJJ; Platts-Mills, J; Seidman, JC; Blank, RR; Gottlieb, M; Knobler, SL; Lang, DR; Miller, MA; Tountas, KH; Checkley, W; Mason, CJ; Murray-Kolb, LE; Petri, WA; Bessong, P; Haque, R; John, S; Mduma, ER; Oriá, RB; Shrestha, PS; Shrestha, SK; Svensen, E; Zaidi, AKM; Abreu, CB; Acosta, AM; Ahmed, I; Shamsir Ahmed, AM; Ali, A; Ambikapathi, R; Barrett, L; Bauck, A; Bayyo, E; Bodhidatta, L; Bose, A; Daniel Carreon, J; Chandyo, RK; Charu, V; Costa, H; Dillingham, R; Di Moura, A; Doan, V; Filho, JQ; Graham, J; Hoest, C; Hossain, I; Islam, M; Steffi Jennifer, M; Kaki, S; Koshy, B; Leite, ÁM; Lima, NL; Maciel, BLL; Mahfuz, M; Mahopo, C; Maphula, A; McGrath, M; Mohale, A; Moraes, M; Mota, FS; Muliyil, J; Mvungi, R; Nayyar, G; Nyathi, E; Olortegui, MP; Oria, R; Vasquez, AO; Pan, WK; Pascal, J; Patil, CL; Pendergast, L; Pinedo, SR; Psaki, S; Raghava, MV; Ramanujam, K; Rasheed, M; Rasmussen, ZA; Richard, SA; Rose, A; Roshan, R; Schaefer, B; Scharf, R; Sharma, SL; Shrestha, B; Shrestha, R; Simons, S; Soares, AM; Mota, RMS; Soofi, S; Strand, T; Tofail, F; Thomas, RJ; Turab, A (2017-04-01)
      © 2017 The Authors Background Environmental enteropathy (EE), the adverse impact of frequent and numerous enteric infections on the gut resulting in a state of persistent immune activation and altered permeability, has been proposed as a key determinant of growth failure in children in low- and middle-income populations. A theory-driven systems model to critically evaluate pathways through which enteropathogens, gut permeability, and intestinal and systemic inflammation affect child growth was conducted within the framework of the Etiology, Risk Factors and Interactions of Enteric Infections and Malnutrition and the Consequences for Child Health and Development (MAL-ED) birth cohort study that included children from eight countries. Methods Non-diarrheal stool samples (N = 22,846) from 1253 children from multiple sites were evaluated for a panel of 40 enteropathogens and fecal concentrations of myeloperoxidase, alpha-1-antitrypsin, and neopterin. Among these same children, urinary lactulose:mannitol (L:M) (N = 6363) and plasma alpha-1-acid glycoprotein (AGP) (N = 2797) were also measured. The temporal sampling design was used to create a directed acyclic graph of proposed mechanistic pathways between enteropathogen detection in non-diarrheal stools, biomarkers of intestinal permeability and inflammation, systemic inflammation and change in length- and weight- for age in children 0–2 years of age. Findings Children in these populations had frequent enteric infections and high levels of both intestinal and systemic inflammation. Higher burdens of enteropathogens, especially those categorized as being enteroinvasive or causing mucosal disruption, were associated with elevated biomarker concentrations of gut and systemic inflammation and, via these associations, indirectly associated with both reduced linear and ponderal growth. Evidence for the association with reduced linear growth was stronger for systemic inflammation than for gut inflammation; the opposite was true of reduced ponderal growth. Although Giardia was associated with reduced growth, the association was not mediated by any of the biomarkers evaluated. Interpretation The large quantity of empirical evidence contributing to this analysis supports the conceptual model of EE. The effects of EE on growth faltering in young children were small, but multiple mechanistic pathways underlying the attribution of growth failure to asymptomatic enteric infections had statistical support in the analysis. The strongest evidence for EE was the association between enteropathogens and linear growth mediated through systemic inflammation. Funding Bill & Melinda Gates Foundation.
    • CDK9 inhibitors in acute myeloid leukemia

      Boffo, S; Damato, A; Alfano, L; Giordano, A; Boffo, Silvia|0000-0002-6352-160X; Giordano, Antonio|0000-0002-5959-016X (2018-02-23)
      © 2018 The Author(s). Current treatment for acute myeloid leukemia (AML) is less than optimal, but increased understanding of disease pathobiology and genomics has led to clinical investigation of novel targeted therapies and rational combinations. Targeting the cyclin-dependent kinase 9 (CDK9) pathway, which is dysregulated in AML, is an attractive approach. Inhibition of CDK9 leads to downregulation of cell survival genes regulated by super enhancers such as MCL-1, MYC, and cyclin D1. As CDK9 inhibitors are nonselective, predictive biomarkers that may help identify patients most likely to respond to CDK9 inhibitors are now being utilized, with the goal of improving efficacy and safety.
    • Challenges in microbial ecology: Building predictive understanding of community function and dynamics

      Widder, S; Allen, RJ; Pfeiffer, T; Curtis, TP; Wiuf, C; Sloan, WT; Cordero, OX; Brown, SP; Momeni, B; Shou, W; Kettle, H; Flint, HJ; Haas, AF; Laroche, B; Kreft, JU; Rainey, PB; Freilich, S; Schuster, S; Milferstedt, K; Van Der Meer, JR; Grobkopf, T; Huisman, J; Free, A; Picioreanu, C; Quince, C; Klapper, I; Labarthe, S; Smets, BF; Wang, H; Soyer, OS; Allison, SD; Chong, J; Lagomarsino, MC; Croze, OA; Hamelin, J; Harmand, J; Hoyle, R; Hwa, TT; Jin, Q; Johnson, DR; de Lorenzo, V; Mobilia, M; Murphy, B; Peaudecerf, F; Prosser, JI; Quinn, RA; Ralser, M; Smith, AG; Steyer, JP; Swainston, N; Tarnita, CE; Trably, E; Warren, PB; Wilmes, P (2016-11-01)
      © 2016 International Society for Microbial Ecology All rights reserved. The importance of microbial communities (MCs) cannot be overstated. MCs underpin the biogeochemical cycles of the earth's soil, oceans and the atmosphere, and perform ecosystem functions that impact plants, animals and humans. Yet our ability to predict and manage the function of these highly complex, dynamically changing communities is limited. Building predictive models that link MC composition to function is a key emerging challenge in microbial ecology. Here, we argue that addressing this challenge requires close coordination of experimental data collection and method development with mathematical model building. We discuss specific examples where model-experiment integration has already resulted in important insights into MC function and structure. We also highlight key research questions that still demand better integration of experiments and models. We argue that such integration is needed to achieve significant progress in our understanding of MC dynamics and function, and we make specific practical suggestions as to how this could be achieved.
    • Changes in the frequencies of Plasmodium falciparum dhps and dhfr drug-resistant mutations in children from Western Kenya from 2005 to 2018: the rise of Pfdhps S436H

      Pacheco, MA; Schneider, KA; Cheng, Q; Munde, EO; Ndege, C; Onyango, C; Raballah, E; Anyona, SB; Ouma, C; Perkins, DJ; Escalante, AA (2020-12-01)
      © 2020, The Author(s). Background: Sulfadoxine-pyrimethamine (SP) is the only anti-malarial drug formulation approved for intermittent preventive treatment in pregnancy (IPTp). However, mutations in the Plasmodium falciparum dhfr (Pfdhfr) and dhps (Pfdhps) genes confer resistance to pyrimethamine and sulfadoxine, respectively. Here, the frequencies of SP resistance-associated mutations from 2005 to 2018 were compared in samples from Kenyan children with malaria residing in a holoendemic transmission region. Methods: Partial sequences of the Pfdhfr and Pfdhps genes were amplified and sequenced from samples collected in 2005 (n = 81), 2010 (n = 95), 2017 (n = 43), and 2018 (n = 55). The frequency of known mutations conferring resistance to pyrimethamine and sulfadoxine were estimated and compared. Since artemisinin-based combination therapy (ACT) is the current first-line treatment for malaria, the presence of mutations in the propeller domain of P. falciparum kelch13 gene (Pfk13) linked to ACT-delayed parasite clearance was studied in the 2017/18 samples. Results: Among other changes, the point mutation of Pfdhps S436H increased in frequency from undetectable in 2005 to 28% in 2017/18. Triple Pfdhfr mutant allele (CIRNI) increased in frequency from 84% in 2005 to 95% in 2017/18, while the frequency of Pfdhfr double mutant alleles declined (allele CICNI from 29% in 2005 to 6% in 2017/18, and CNRNI from 9% in 2005 to undetectable in 2010 and 2017/18). Thus, a multilocus Pfdhfr/Pfdhps genotype with six mutations (HGEAA/CIRNI), including Pfdhps S436H, increased in frequency from 2010 to 2017/18. Although none of the mutations associated with ACT-delayed parasite clearance was observed, the Pfk13 mutation A578S, the most widespread Pfk13 SNP found in Africa, was detected in low frequency (2.04%). Conclusions: There were changes in SP resistance mutant allele frequencies, including an increase in the Pfdhps S436H. Although these patterns seem consistent with directional selection due to drug pressure, there is a lack of information to determine the actual cause of such changes. These results suggest incorporating molecular surveillance of Pfdhfr/Pfdhps mutations in the context of SP efficacy studies for intermittent preventive treatment in pregnancy (IPTp).
    • Characterization of Aquifex aeolicus ribonuclease III and the reactivity epitopes of its pre-ribosomal RNA substrates

      Shi, Z; Nicholson, RH; Jaggi, R; Nicholson, AW (2011-04-01)
      Ribonuclease III cleaves double-stranded (ds) structures in bacterial RNAs and participates in diverse RNA maturation and decay pathways. Essential insight on the RNase III mechanism of dsRNA cleavage has been provided by crystallographic studies of the enzyme from the hyperthermophilic bacterium, Aquifex aeolicus. However, the biochemical properties of A. aeolicus (Aa)-RNase III and the reactivity epitopes of its substrates are not known. The catalytic activity of purified recombinant Aa-RNase III exhibits a temperature optimum of ∼70-85°C, with either Mg2+ or Mn2+ supporting efficient catalysis. Small hairpins based on the stem structures associated with the Aquifex 16S and 23S rRNA precursors are cleaved at sites that are consistent with production of the immediate precursors to the mature rRNAs. Substrate reactivity is independent of the distal box sequence, but is strongly dependent on the proximal box sequence. Structural studies have shown that a conserved glutamine (Q157) in the Aa-RNase III dsRNA-binding domain (dsRBD) directly interacts with a proximal box base pair. Aa-RNase III cleavage of the pre-16S substrate is blocked by the Q157A mutation, which reflects a loss of substrate binding affinity. Thus, a highly conserved dsRBD-substrate interaction plays an important role in substrate recognition by bacterial RNase III. © 2011 The Author(s).
    • Characterization of face-selective patches in orbitofrontal cortex

      Troiani, V; Dougherty, CC; Michael, AM; Olson, IR (2016-06-14)
      © 2016 Troiani, Dougherty, Michael and Olson. Face processing involves a complex, multimodal brain network. While visual-perceptual face patches in posterior parts of the brain have been studied for over a decade, the existence and properties of face-selective regions in orbitofrontal cortex (OFC) is a relatively new area of research. While regions of OFC are implicated in the emotional processing of faces, this is typically interpreted as a domain-general response to affective value rather than a face- or socially-specific response. However, electrophysiology studies in monkeys have identified neurons in OFC that respond more to faces than any other stimuli. Here, we characterize the prevalence and location of OFC face-selective regions in 20 healthy college students. We did this by including another biologically motivating category (appetizing foods) in a variant of the standard face localizer. Results show that face-selective patches can be identified at the individual level. Furthermore, in both a region of interest (ROI) and a whole brain analysis, medial regions of the OFC were face-selective, while lateral regions were responsive to faces and foods, indicating a domain-general response in lateral OFC. Medial OFC (mOFC) response to faces scales in relationship to a measure of social motivation that is distinct from face processing abilities associated with fusiform cortex.