Browsing by Subject "Statistics, Nonparametric"
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Item Open Access An estimate of the number of tropical tree species.(Proc Natl Acad Sci U S A, 2015-06-16) Slik, JW Ferry; Arroyo-Rodríguez, Víctor; Aiba, Shin-Ichiro; Alvarez-Loayza, Patricia; Alves, Luciana F; Ashton, Peter; Balvanera, Patricia; Bastian, Meredith L; Bellingham, Peter J; van den Berg, Eduardo; Bernacci, Luis; da Conceição Bispo, Polyanna; Blanc, Lilian; Böhning-Gaese, Katrin; Boeckx, Pascal; Bongers, Frans; Boyle, Brad; Bradford, Matt; Brearley, Francis Q; Breuer-Ndoundou Hockemba, Mireille; Bunyavejchewin, Sarayudh; Calderado Leal Matos, Darley; Castillo-Santiago, Miguel; Catharino, Eduardo LM; Chai, Shauna-Lee; Chen, Yukai; Colwell, Robert K; Chazdon, Robin L; Clark, Connie; Clark, David B; Clark, Deborah A; Culmsee, Heike; Damas, Kipiro; Dattaraja, Handanakere S; Dauby, Gilles; Davidar, Priya; DeWalt, Saara J; Doucet, Jean-Louis; Duque, Alvaro; Durigan, Giselda; Eichhorn, Karl AO; Eisenlohr, Pedro V; Eler, Eduardo; Ewango, Corneille; Farwig, Nina; Feeley, Kenneth J; Ferreira, Leandro; Field, Richard; de Oliveira Filho, Ary T; Fletcher, Christine; Forshed, Olle; Franco, Geraldo; Fredriksson, Gabriella; Gillespie, Thomas; Gillet, Jean-François; Amarnath, Giriraj; Griffith, Daniel M; Grogan, James; Gunatilleke, Nimal; Harris, David; Harrison, Rhett; Hector, Andy; Homeier, Jürgen; Imai, Nobuo; Itoh, Akira; Jansen, Patrick A; Joly, Carlos A; de Jong, Bernardus HJ; Kartawinata, Kuswata; Kearsley, Elizabeth; Kelly, Daniel L; Kenfack, David; Kessler, Michael; Kitayama, Kanehiro; Kooyman, Robert; Larney, Eileen; Laumonier, Yves; Laurance, Susan; Laurance, William F; Lawes, Michael J; Amaral, Ieda Leao do; Letcher, Susan G; Lindsell, Jeremy; Lu, Xinghui; Mansor, Asyraf; Marjokorpi, Antti; Martin, Emanuel H; Meilby, Henrik; Melo, Felipe PL; Metcalfe, Daniel J; Medjibe, Vincent P; Metzger, Jean Paul; Millet, Jerome; Mohandass, D; Montero, Juan C; de Morisson Valeriano, Márcio; Mugerwa, Badru; Nagamasu, Hidetoshi; Nilus, Reuben; Ochoa-Gaona, Susana; Onrizal; Page, Navendu; Parolin, Pia; Parren, Marc; Parthasarathy, Narayanaswamy; Paudel, Ekananda; Permana, Andrea; Piedade, Maria TF; Pitman, Nigel CA; Poorter, Lourens; Poulsen, Axel D; Poulsen, John; Powers, Jennifer; Prasad, Rama C; Puyravaud, Jean-Philippe; Razafimahaimodison, Jean-Claude; Reitsma, Jan; Dos Santos, João Roberto; Roberto Spironello, Wilson; Romero-Saltos, Hugo; Rovero, Francesco; Rozak, Andes Hamuraby; Ruokolainen, Kalle; Rutishauser, Ervan; Saiter, Felipe; Saner, Philippe; Santos, Braulio A; Santos, Fernanda; Sarker, Swapan K; Satdichanh, Manichanh; Schmitt, Christine B; Schöngart, Jochen; Schulze, Mark; Suganuma, Marcio S; Sheil, Douglas; da Silva Pinheiro, Eduardo; Sist, Plinio; Stevart, Tariq; Sukumar, Raman; Sun, I-Fang; Sunderland, Terry; Suresh, HS; Suzuki, Eizi; Tabarelli, Marcelo; Tang, Jangwei; Targhetta, Natália; Theilade, Ida; Thomas, Duncan W; Tchouto, Peguy; Hurtado, Johanna; Valencia, Renato; van Valkenburg, Johan LCH; Van Do, Tran; Vasquez, Rodolfo; Verbeeck, Hans; Adekunle, Victor; Vieira, Simone A; Webb, Campbell O; Whitfeld, Timothy; Wich, Serge A; Williams, John; Wittmann, Florian; Wöll, Hannsjoerg; Yang, Xiaobo; Adou Yao, C Yves; Yap, Sandra L; Yoneda, Tsuyoshi; Zahawi, Rakan A; Zakaria, Rahmad; Zang, Runguo; de Assis, Rafael L; Garcia Luize, Bruno; Venticinque, Eduardo MThe high species richness of tropical forests has long been recognized, yet there remains substantial uncertainty regarding the actual number of tropical tree species. Using a pantropical tree inventory database from closed canopy forests, consisting of 657,630 trees belonging to 11,371 species, we use a fitted value of Fisher's alpha and an approximate pantropical stem total to estimate the minimum number of tropical forest tree species to fall between ∼ 40,000 and ∼ 53,000, i.e., at the high end of previous estimates. Contrary to common assumption, the Indo-Pacific region was found to be as species-rich as the Neotropics, with both regions having a minimum of ∼ 19,000-25,000 tree species. Continental Africa is relatively depauperate with a minimum of ∼ 4,500-6,000 tree species. Very few species are shared among the African, American, and the Indo-Pacific regions. We provide a methodological framework for estimating species richness in trees that may help refine species richness estimates of tree-dependent taxa.Item Open Access Communication practices in physician decision-making for an unstable critically ill patient with end-stage cancer.(J Palliat Med, 2010-08) Mohan, Deepika; Alexander, Stewart C; Garrigues, Sarah K; Arnold, Robert M; Barnato, Amber EBACKGROUND: Shared decision-making has become the standard of care for most medical treatments. However, little is known about physician communication practices in the decision making for unstable critically ill patients with known end-stage disease. OBJECTIVE: To describe communication practices of physicians making treatment decisions for unstable critically ill patients with end-stage cancer, using the framework of shared decision-making. DESIGN: Analysis of audiotaped encounters between physicians and a standardized patient, in a high-fidelity simulation scenario, to identify best practice communication behaviors. The simulation depicted a 78-year-old man with metastatic gastric cancer, life-threatening hypoxia, and stable preferences to avoid intensive care unit (ICU) admission and intubation. Blinded coders assessed the encounters for verbal communication behaviors associated with handling emotions and discussion of end-of-life goals. We calculated a score for skill at handling emotions (0-6) and at discussing end of life goals (0-16). SUBJECTS: Twenty-seven hospital-based physicians. RESULTS: Independent variables included physician demographics and communication behaviors. We used treatment decisions (ICU admission and initiation of palliation) as a proxy for accurate identification of patient preferences. Eight physicians admitted the patient to the ICU, and 16 initiated palliation. Physicians varied, but on average demonstrated low skill at handling emotions (mean, 0.7) and moderate skill at discussing end-of-life goals (mean, 7.4). We found that skill at discussing end-of-life goals was associated with initiation of palliation (p = 0.04). CONCLUSIONS: It is possible to analyze the decision making of physicians managing unstable critically ill patients with end-stage cancer using the framework of shared decision-making.Item Open Access Comparison of Structural Disease Burden to Health-related Quality of Life Scores in 264 Adult Spinal Deformity Patients With 2-Year Follow-up: Novel Insights into Drivers of Disability.(Clinical spine surgery, 2017-03) Bakhsheshian, Joshua; Scheer, Justin K; Gum, Jeffrey L; Horner, Lance; Hostin, Richard; Lafage, Virginie; Bess, Shay; Protopsaltis, Themistocles S; Burton, Douglas C; Keefe, Malla; Hart, Robert A; Mundis, Gregory M; Shaffrey, Christopher I; Schwab, Frank; Smith, Justin S; Ames, Christopher P; International Spine Study Group (ISSG)Study design
This is a review of a prospective multicenter database.Objective
To investigate the relationship between preoperative disability and sagittal deformity in patients with high Oswestry Disability Index (ODI) and no sagittal malalignment, or low ODI and high sagittal malalignment.Summary of background data
The relationship between ODI and sagittal malalignment varies between each adult spinal deformity (ASD) patient.Methods
A prospective multicenter database of 365 patients with ASD undergoing surgical reconstruction was analyzed. Inclusion criteria entailed: age 18 years or above and the presence of spinal deformity as defined by a coronal Cobb angle≥20 degrees, sagittal vertical axis (SVA)≥5 cm, pelvic tilt (PT) angle≥25 degrees, or thoracic kyphosis≥60 degrees. Radiographic and health-related quality of life (HRQOL) variables were examined and compared, preoperatively and at 2-year postoperative follow-up. Group 1 (low disability high sagittal-LDHS) consisted of ODI<40 and SVA≥5 cm or PT≥25 degrees or pelvic incidence-lumbar lordosis≥11 degrees and group 2 (high disability low sagittal-HDLS) consisted of ODI>40 and SVA<5 cm and PT<25 degrees and pelvic incidence-lumbar lordosis<11 degrees.Results
Of 264 patients with follow-up, 58 (22.0%) patients were included in LDHS and 30 (11.4%) were included in HDLS. Both groups had similar demographics and preoperative coronal angles. HDLS had worse baseline HRQOL for all measures (P<0.05) except leg and back pain. HDLS had a higher rate of self-reported leg weakness, arthritis, depression and neurological disorder. Both groups had similar 2-year improvements in HRQOL (P>0.05), except only HDLS had a significant Scoliosis Research Society Mental improvement and a significantly higher rate of reaching minimal clinically important differences in Scoliosis Research Society Mental scores (P<0.05).Conclusions
There is an association of worse baseline HRQOL measures, weakness, arthritis, and mental disease in HDLS. Furthermore, HDLS patients demonstrated similar improvements to LDHS. However, HDLS had greater improvements in the mental domains, perhaps indicating the responsiveness of the mental disability to surgical treatment.Level of evidence
Level III.Item Open Access Developmental exposure to a complex PAH mixture causes persistent behavioral effects in naive Fundulus heteroclitus (killifish) but not in a population of PAH-adapted killifish.(Neurotoxicol Teratol, 2016-01) Brown, DR; Bailey, JM; Oliveri, AN; Levin, ED; Di Giulio, RTAcute exposures to some individual polycyclic aromatic hydrocarbons (PAHs) and complex PAH mixtures are known to cause cardiac malformations and edema in the developing fish embryo. However, the heart is not the only organ impacted by developmental PAH exposure. The developing brain is also affected, resulting in lasting behavioral dysfunction. While acute exposures to some PAHs are teratogenically lethal in fish, little is known about the later life consequences of early life, lower dose subteratogenic PAH exposures. We sought to determine and characterize the long-term behavioral consequences of subteratogenic developmental PAH mixture exposure in both naive killifish and PAH-adapted killifish using sediment pore water derived from the Atlantic Wood Industries Superfund Site. Killifish offspring were embryonically treated with two low-level PAH mixture dilutions of Elizabeth River sediment extract (ERSE) (TPAH 5.04 μg/L and 50.4 μg/L) at 24h post fertilization. Following exposure, killifish were raised to larval, juvenile, and adult life stages and subjected to a series of behavioral tests including: a locomotor activity test (4 days post-hatch), a sensorimotor response tap/habituation test (3 months post hatch), and a novel tank diving and exploration test (3months post hatch). Killifish were also monitored for survival at 1, 2, and 5 months over 5-month rearing period. Developmental PAH exposure caused short-term as well as persistent behavioral impairments in naive killifish. In contrast, the PAH-adapted killifish did not show behavioral alterations following PAH exposure. PAH mixture exposure caused increased mortality in reference killifish over time; yet, the PAH-adapted killifish, while demonstrating long-term rearing mortality, had no significant changes in mortality associated with ERSE exposure. This study demonstrated that early embryonic exposure to PAH-contaminated sediment pore water caused long-term locomotor and behavioral alterations in killifish, and that locomotor alterations could be observed in early larval stages. Additionally, our study highlights the resistance to behavioral alterations caused by low-level PAH mixture exposure in the adapted killifish population. Furthermore, this is the first longitudinal behavioral study to use killifish, an environmentally important estuarine teleost fish, and this testing framework can be used for future contaminant assessment.Item Open Access Differential expression of systemic inflammatory mediators in amputees with chronic residual limb pain.(Pain, 2017-01) Chamessian, Alexander; Van de Ven, Thomas; Buchheit, Thomas; Hsia, Hung-Lun; McDuffie, Mary; Gamazon, Eric R; Walsh, Colin; Bruehl, Stephen; Buckenmaier, Chester 'Trip'; Shaw, AndrewChronic postsurgical pain impacts most amputees, with more than half experiencing neuralgic residual limb pain. The transition from normal acute postamputation pain to chronic residual limb pain likely involves both peripheral and central inflammatory mechanisms. As part of the Veterans Integrated Pain Evaluation Research study, we investigated links between systemic inflammatory mediator levels and chronic residual limb pain. Subjects included 36 recent active duty military traumatic amputees with chronic residual limb pain and 40 without clinically significant pain. Blood samples were obtained and plasma concentrations of an array of inflammatory mediators were analyzed. Residual limb pain intensity and pain catastrophizing were assessed to examine associations with inflammatory mediators. Pro-inflammatory mediators including tumor necrosis factor (TNF)-α, TNF-β, interleukin (IL)-8, ICAM-1, Tie2, CRP, and SAA were elevated in patients with chronic residual limb pain. Across all patients, residual limb pain intensity was associated positively with levels of several proinflammatory mediators (IL-8, TNF-α, IL-12, TNF-β, PIGF, Tie2, SAA, and ICAM-1), and inversely with concentrations of the anti-inflammatory mediator IL-13, as well as IL-2 and Eotaxin-3. Pain catastrophizing correlated positively with IL-8, IL-12, TNF-β, PIGF, and ICAM-1, and inversely with IL-13. Significant associations between catastrophizing and residual limb pain intensity were partially mediated by TNF-α, TNF- β, SAA, and ICAM-1 levels. Results suggest that chronic postamputation residual limb pain is associated with excessive inflammatory response to injury or to inadequate resolution of the postinjury inflammatory state. Impact of pain catastrophizing on residual limb pain may be because of part to common underlying inflammatory mechanisms.Item Open Access G protein signaling and vein graft intimal hyperplasia: reduction of intimal hyperplasia in vein grafts by a Gbetagamma inhibitor suggests a major role of G protein signaling in lesion development.(Arterioscler Thromb Vasc Biol, 1998-08) Davies, MG; Fulton, Gregory J; Hagen, Per-Otto Frode; Huynh, Tam; Koch, Walter J; Lefkowitz, Robert J; Svendsen, EVein grafting results in the development of intimal hyperplasia with accompanying changes in guanine nucleotide-binding (G) protein expression and function. Several serum mitogens that act through G protein-coupled receptors, such as lysophosphatidic acid, stimulate proliferative pathways that are dependent on the G protein betagamma subunit (Gbetagamma)-mediated activation of p21ras. This study examines the role of Gbetagamma signaling in intimal hyperplasia by targeting a gene encoding a specific Gbetagamma inhibitor in an experimental rabbit vein graft model. This inhibitor, the carboxyl terminus of the beta-adrenergic receptor kinase (betaARK(CT)), contains a Gbetagamma-binding domain. Vein graft intimal hyperplasia was significantly reduced by 37% (P<0.01), and physiological studies demonstrated that the normal alterations in G protein coupling phenotypically seen in this model were blocked by betaARK(CT) treatment. Thus, it appears that Gbetagamma-mediated pathways play a major role in intimal hyperplasia and that targeting inhibitors of Gbetagamma signaling offers novel intraoperative therapeutic modalities to inhibit the development of vein graft intimal hyperplasia and subsequent vein graft failure.Item Open Access Loss of cartilage structure, stiffness, and frictional properties in mice lacking PRG4.(Arthritis Rheum, 2010-06) Coles, Jeffrey M; Zhang, Ling; Blum, Jason J; Warman, Matthew L; Jay, Gregory D; Guilak, Farshid; Zauscher, StefanOBJECTIVE: To assess the role of the glycoprotein PRG4 in joint lubrication and chondroprotection by measuring friction, stiffness, surface topography, and subsurface histology of the hip joints of Prg4(-/-) and wild-type (WT) mice. METHODS: Friction and elastic modulus were measured in cartilage from the femoral heads of Prg4(-/-) and WT mice ages 2, 4, 10, and 16 weeks using atomic force microscopy, and the surface microstructure was imaged. Histologic sections of each femoral head were stained and graded. RESULTS: Histologic analysis of the joints of Prg4(-/-) mice showed an enlarged, fragmented surface layer of variable thickness with Safranin O-positive formations sometimes present, a roughened underlying articular cartilage surface, and a progressive loss of pericellular proteoglycans. Friction was significantly higher on cartilage of Prg4(-/-) mice at age 16 weeks, but statistically significant differences in friction were not detected at younger ages. The elastic modulus of the cartilage was similar between cartilage surfaces of Prg4(-/-) and WT mice at young ages, but cartilage of WT mice showed increasing stiffness with age, with significantly higher moduli than cartilage of Prg4(-/-) mice at older ages. CONCLUSION: Deletion of the gene Prg4 results in significant structural and biomechanical changes in the articular cartilage with age, some of which are consistent with osteoarthritic degeneration. These findings suggest that PRG4 plays a significant role in preserving normal joint structure and function.Item Open Access Nurse-led behavioral management of diabetes and hypertension in community practices: a randomized trial.(J Gen Intern Med, 2015-05) Edelman, David; Dolor, Rowena J; Coffman, Cynthia J; Pereira, Katherine C; Granger, Bradi B; Lindquist, Jennifer H; Neary, Alice M; Harris, Amy J; Bosworth, Hayden BBACKGROUND: Several trials have demonstrated the efficacy of nurse telephone case management for diabetes (DM) and hypertension (HTN) in academic or vertically integrated systems. Little is known about the real-world potency of these interventions. OBJECTIVE: To assess the effectiveness of nurse behavioral management of DM and HTN in community practices among patients with both diseases. DESIGN: The study was designed as a patient-level randomized controlled trial. PARTICIPANTS: Participants included adult patients with both type 2 DM and HTN who were receiving care at one of nine community fee-for-service practices. Subjects were required to have inadequately controlled DM (hemoglobin A1c [A1c] ≥ 7.5%) but could have well-controlled HTN. INTERVENTIONS: All patients received a call from a nurse experienced in DM and HTN management once every two months over a period of two years, for a total of 12 calls. Intervention patients received tailored DM- and HTN- focused behavioral content; control patients received non-tailored, non-interactive information regarding health issues unrelated to DM and HTN (e.g., skin cancer prevention). MAIN OUTCOMES AND MEASURES: Systolic blood pressure (SBP) and A1c were co-primary outcomes, measured at 6, 12, and 24 months; 24 months was the primary time point. RESULTS: Three hundred seventy-seven subjects were enrolled; 193 were randomized to intervention, 184 to control. Subjects were 55% female and 50% white; the mean baseline A1c was 9.1% (SD = 1%) and mean SBP was 142 mmHg (SD = 20). Eighty-two percent of scheduled interviews were conducted; 69% of intervention patients and 70% of control patients reached the 24-month time point. Expressing model estimated differences as (intervention--control), at 24 months, intervention patients had similar A1c [diff = 0.1 %, 95 % CI (-0.3, 0.5), p = 0.51] and SBP [diff = -0.9 mmHg, 95% CI (-5.4, 3.5), p = 0.68] values compared to control patients. Likewise, DBP (diff = 0.4 mmHg, p = 0.76), weight (diff = 0.3 kg, p = 0.80), and physical activity levels (diff = 153 MET-min/week, p = 0.41) were similar between control and intervention patients. Results were also similar at the 6- and 12-month time points. CONCLUSIONS: In nine community fee-for-service practices, telephonic nurse case management did not lead to improvement in A1c or SBP. Gains seen in telephonic behavioral self-management interventions in optimal settings may not translate to the wider range of primary care settings.Item Open Access Power and sample size calculations for the Wilcoxon-Mann-Whitney test in the presence of death-censored observations.(Stat Med, 2015-02-10) Matsouaka, Roland A; Betensky, Rebecca AWe consider a clinical trial of a potentially lethal disease in which patients are randomly assigned to two treatment groups and are followed for a fixed period of time; a continuous endpoint is measured at the end of follow-up. For some patients; however, death (or severe disease progression) may preclude measurement of the endpoint. A statistical analysis that includes only patients with endpoint measurements may be biased. An alternative analysis includes all randomized patients, with rank scores assigned to the patients who are available for the endpoint measurement on the basis of the magnitude of their responses and with 'worst-rank' scores assigned to those patients whose death precluded the measurement of the continuous endpoint. The worst-rank scores are worse than all observed rank scores. The treatment effect is then evaluated using the Wilcoxon-Mann-Whitney test. In this paper, we derive closed-form formulae for the power and sample size of the Wilcoxon-Mann-Whitney test when missing measurements of the continuous endpoints because of death are replaced by worst-rank scores. We distinguish two approaches for assigning the worst-rank scores. In the tied worst-rank approach, all deaths are weighted equally, and the worst-rank scores are set to a single value that is worse than all measured responses. In the untied worst-rank approach, the worst-rank scores further rank patients according to their time of death, so that an earlier death is considered worse than a later death, which in turn is worse than all measured responses. In addition, we propose four methods for the implementation of the sample size formulae for a trial with expected early death. We conduct Monte Carlo simulation studies to evaluate the accuracy of our power and sample size formulae and to compare the four sample size estimation methods.Item Open Access Signal transformations from cerebral cortex to superior colliculus for the generation of saccades.(Vision Res, 2001) Wurtz, RH; Sommer, MA; Paré, M; Ferraina, SThe ability of primates to make rapid and accurate saccadic eye movements for exploring the natural world is based on a neuronal system in the brain that has been studied extensively and is known to include multiple brain regions extending throughout the neuraxis. We examined the characteristics of signal flow in this system by recording from identified output neurons of two cortical regions, the lateral intraparietal area (LIP) and the frontal eye field (FEF), and from neurons in a brainstem structure targeted by these output neurons, the superior colliculus (SC). We compared the activity of neurons in these three populations while monkeys performed a delayed saccade task that allowed us to quantify visual responses, motor activity, and intervening delay activity. We examined whether delay activity was related to visual stimulation by comparing the activity during interleaved trials when a target was either present or absent during the delay period. We examined whether delay activity was related to movement by using a Go/Nogo task and comparing the activity during interleaved trials in which a saccade was either made (Go) or not (Nogo). We found that LIP output neurons, FEF output neurons, and SC neurons can all have visual responses, delay activity, and presaccadic bursts; hence in this way they are all quite similar. However, the delay activity tended to be more related to visual stimulation in the cortical output neurons than in the SC neurons. Complementing this, the delay activity tended to be more related to movement in the SC neurons than in the cortical output neurons. We conclude, first, that the signal flow leaving the cortex represents activity at nearly every stage of visuomotor transformation, and second, that there is a gradual evolution of signal processing as one proceeds from cortex to colliculus.