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arXiv 2023年

作者： Jeon, Hyeongseon Xie, Juan Jeon, Yeseul Jung, Kyeong Joo Gupta, Arkobrato Chang, Won Chung, Dongjun Department of Biomedical Informatics The Ohio State University ColumbusOH United States Pelotonia Institute for Immuno-Oncology The James Comprehensive Cancer Center The Ohio State University ColumbusOH43210 United States The Interdisciplinary PhD program in Biostatistics The Ohio State University ColumbusOH United States Department of Statistics and Data Science Yonsei University Seoul Korea Republic of Department of Applied Statistics Yonsei University Seoul Korea Republic of Department of Computer Science and Engineering The Ohio State University ColumbusOH United States Division of Statistics and Data Science University of Cincinnati CincinnatiOH United States

Gene expression profiling technologies have been used in various applications such as cancer biology. The development of gene expression profiling has expanded the scope of target discovery in transcriptomic studies, and each technology produces data with distinct characteristics. In order to guarantee biologically meaningful findings using transcriptomic experiments, it is important to consider various experimental factors in a systematic way through statistical power analysis. In this paper, we review and discuss the power analysis for three types of gene expression profiling technologies from a practical standpoint, including bulk RNA-seq, single-cell RNA-seq, and high-throughput spatial transcriptomics. Specifically, we describe the existing power analysis tools for each research objective for each of the bulk RNA-seq and scRNA-seq experiments, along with recommendations. On the other hand, since there are no power analysis tools for high-throughput spatial transcriptomics at this point, we instead investigate the factors that can influence power analysis. © 2023, CC BY-NC-ND.

关键词： RNA

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Going beyond Activity and Participation: Development of the DIF-CHUM-A patient-reported outcome measure for individuals with Dupuytren's contracture

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JOURNAL OF HAND THERAPY 2020年第3期33卷 305-313页

作者： Forget, Nancy J. Higgins, Johanne Rivard, Michele Harris, Patrick G. Univ Montreal Sch Publ Hlth Publ Hlth PhD Program Montreal PQ Canada Univ Montreal Sch Rehabil Montreal PQ Canada Ctr Interdisciplinary Res Rehabil Greater Montrea Montreal PQ Canada Univ Montreal Sch Publ Hlth Dept Social & Prevent Med Montreal PQ Canada Univ Montreal Publ Hlth Res Inst Montreal PQ Canada Univ Montreal Hosp Ctr CHUM Dept Surg Plast Surg Serv Montreal PQ Canada

Study Design: This is a cross-sectional clinical measurement. Introduction: There are currently no Dupuytren's contracture (DC)-specific, patient-reported outcomes (PROs) that can provide a thorough clinical portrait of the patients' perceptions with regard to the execution of regular activities. Purpose of the Study: The purpose of this study was to present the development of the Dupuytren's contracture Impact on Function-Centre Hospitalier de l'Universite de Montreal (DIF-CHUM), a DC-specific PRO. Methods: The development process involved consultation of 45 individuals with DC and 7 health professionals, existing literature, and DC-specific PRO. Results: The DIF-CHUM is composed of 2 sections: section 1, Activity and Participation includes 8 items per hand, scored on Difficulty and Change scales;section 2, General Impact includes up to 18 items, scored on Difficulty, Importance, Change and Satisfaction scales. Preliminary evidence suggests that the DIF-CHUM demonstrates good content validity. Discussion: The DIF-CHUM is designed to be a patient-centered measure of Activity and Participation and Functional Competence for individuals with DC that will provide hand therapists with a unique perspective of the impact of DC on patients' lives. Conclusion: Further validation of the DIF-CHUM, including its scoring, is under way. (C) 2019 Hanley & Belfus, an imprint of Elsevier Inc. All rights reserved.

关键词： Dupuytren's contracture Patient-reported outcomes Validity Activity and participation

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Income Inequality in the Great Recession did not Harm Subjective Health in Europe, 2003-2012

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APPLIED RESEARCH IN QUALITY OF LIFE 2020年第5期15卷 1451-1473页

作者： Evans, M. D. R. Kelley, Jonathan Kelley, C. G. E. Kelley, S. M. C. Univ Nevada Dept Sociol Ms 300 Reno NV 89557 USA Univ Nevada Interdisciplinary PhD Program Social Psychol Ms 300 Reno NV 89557 USA Univ Nevada Dept Survey Design & Analyt Int Survey Ctr Ms 300 Reno NV 89557 USA Child Trends 7315 Wisconsin AveSuite 1200W Bethesda MD 20814 USA

A rich tradition of research has addressed income inequality and health, but the issue has achieved a fresh currency with the reversals of economic fortunes wrought by the Great Recession. This paper analyses the degree to which changing inequality induced by the Great Recession impacted Europeans' subjective health (self-rated health and satisfaction with health). To address this question, we analyse the multilevel European Quality of Life Survey conducted mainly in 2003, 2008, and 2012 which provides representative samples from 24 European countries at all three time points, as well as national-level data on inequality (Gini coefficient) and appropriate national-level and individual-level controls. We find that, net of GDP, inequality has no statistically significant impact before, during or after the Great Recession. Turning to determinants, our variance-components multi-level models controlling for known individual-level predictors show that inequality remains insignificant at all time points, while individual family income is strongly related to subjective health GDP per capita has little effect except indirectly through income. We also assessed impacts specifically for vulnerable, at-risk groups. Including GDP per capita, Gini coefficient, and individual level controls, our model explains about one quarter of the variance in health status (R-squared >.23). All in all, our results support a rational choice, materialist hypothesis: that absolute prosperity of the individual matters to subjective health, but income inequality does not, in Europe in this period. This supports a policy emphasis on increasing levels of pay, and on poverty relief, rather than on reducing inequality.

关键词： Health Subjective health Wellbeing Great Recession Inequality Europe Income GDP Quality of life Recession

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Swing and a miss: Reflections on the "voluntariness" of pleas in juvenile court

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CHILDREN AND YOUTH SERVICES REVIEW 2020年 117卷

作者： Cabell, Jean J. Marsh, Shawn C. Univ Nevada Interdisciplinary Social Psychol PhD Program Mailstop 13001664 N Virginia St Reno NV 89557 USA Univ Nevada Judicial Studies Commun Studies & Social Psychol Reno NV 89557 USA

Plea bargaining is a common tool in the U.S. justice system. When used appropriately and with defendant protections ensured, it can help keep an overloaded system operating smoothly and improve timely administration of justice. Adolescent defendants, however, present a unique population who often face plea bargain decisions before they are considered an adult in most other relevant contexts (e.g., voting). Because of developmental and social dynamics, adolescents could be more susceptible to influence from others, thereby accepting a plea bargain they do not actually fully endorse. This susceptibility introduces interesting considerations about how adolescents participate in plea bargain decisions - particularly regarding the degree to which they make the decision voluntarily and independently. This article employs a social psychological perspective to review some of the primary dynamics that judges and other legal actors should be aware of in assessing plea bargains made by juveniles, with a particular focus on the issue of "voluntariness". We conclude with nine recommendations for improving practice in adolescent plea bargain cases, as well as suggestions for future research on this relatively unexplored topic.

关键词： Juvenile Adolescent Plea bargain Voluntariness Social influence

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Can reduced tillage sustain sugarcane yield and soil carbon if straw is removed?

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BIOENERGY RESEARCH 2019年第4期12卷 764-777页

作者： Tenelli, Sarah de Oliveira Bordonal, Ricardo Barbosa, Leandro Carneiro Nunes Carvalho, Joao Luis Brazilian Ctr Energy & Mat Res CNPEM Brazilian Biorenewables Natl Lab LNBR Giuseppe Maximo Scolfaro St 10000 BR-13083100 Campinas SP Brazil Univ Campinas UNICAMP Interdisciplinary PhD Program Bioenergy Rua Monteiro Lobato 80Cidade Univ BR-13083862 Campinas SP Brazil

Straw removal for bioelectricity, cellulosic ethanol, or other bio-products has become a common practice in Brazilian sugarcane areas, but long-term effects on soil organic carbon (SOC) and yield are unknown. Our objective was to quantify tillage intensity and removal levels on SOC stocks and sugarcane yield on contrasting edaphoclimatic conditions in Brazil. Conventional tillage-CT and reduced tillage-RT coupled with three straw removal levels (none-NR;moderate-MR;total-TR) were combined to create six treatment combinations: CTNR, CTMR, CTTR, RTNR, RTMR, and RTTR, respectively. Sugarcane yield was measured annually and soil samples to a depth of 40 cm were collected and analyzed before and after 5 years of treatments. Neither tillage practices nor straw removal significantly affected sugarcane yield on sandy loam soil, but CTMR, CTTR, and RTTR showed substantial yield reductions on clayey soil. SOC stocks for RTNR increased by as much as 1.64 Mg ha(-1) year(-1) on clayey soil, while CTMR and CTTR favored depletion of SOC stocks on both soils. Overall, each Mg of straw returned to the soil increased SOC stock by 95 kg ha(-1) for clayey soil under both tillage practices and 55 kg ha(-1) for sandy loam under the CT system. Furthermore, straw removal decreased microbial biomass C and b-glucosidase activity. These findings suggest that the adoption of RT attenuates the adverse impacts of straw removal on SOC stocks while ensuring sugarcane yields for a more sustainable bioenergy production in Brazil.

关键词： Tillage systems Saccharum spp Soil enzymatic activity Microbial biomass carbon Soil organic matter Crop residues

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A diffusion-based microfluidic device for single-cell RNA-seq

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LAB ON A CHIP 2019年第7期19卷 1247-1256页

作者： Sarma, Mimosa Lee, Jiyoung Ma, Sai Li, Song Lu, Chang Virginia Tech Dept Chem Engn Blacksburg VA 24061 USA Virginia Tech Interdisciplinary PhD Program Genet Bioinformat & Blacksburg VA USA Virginia Tech Dept Biomed Engn & Mech Blacksburg VA USA Virginia Tech Dept Crop & Soil Environm Sci Blacksburg VA 24061 USA

Microfluidic devices provide a low-input and efficient platform for single-cell RNA-seq (scRNA-seq). Existing microfluidic devices have a complicated multi-chambered structure for handling the multi-step process involved in RNA-seq and dilution between steps is used to negate the inhibitory effects among reagents. This makes the device difficult to fabricate and operate. Here we present microfluidic diffusion-based RNA-seq (MID-RNA-seq) for conducting scRNA-seq with a diffusion-based reagent swapping scheme. This device incorporates cell trapping, lysis, reverse transcription and PCR amplification all in one simple microfluidic device. MID-RNA-seq provides high data quality that is comparable to existing scRNA-seq methods while implementing a simple device design that permits multiplexing. The robustness and scalability of the MID-RNA-seq device will be important for transcriptomic studies of scarce cell samples.

关键词： RNA

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Comprehensive geriatric assessment in older people: an umbrella review of health outcomes

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AGE AND AGEING 2022年第5期51卷 afac104页

作者： Veronese, Nicola Custodero, Carlo Demurtas, Jacopo Smith, Lee Barbagallo, Mario Maggi, Stefania Cella, Alberto Vanacore, Nicola Aprile, Pierangelo Lora Ferrucci, Luigi Pilotto, Alberto Univ Palermo Dept Internal Med Geriatr Sect Palermo Italy Univ Bari Aldo Moro Dept Interdisciplinary Med Bari Italy Univ Modena & Reggio Emilia Clin & Expt Med PhD Program Modena Italy Anglia Ruskin Univ Cambridge Ctr Sport & Exercise Sci Cambridge England CNR Aging Branch Inst Neurosci Padua Italy EO Osped Galliera Dept Geriatr Care Orthogeriatr & Rehabil Genoa Italy Italian Natl Inst Hlth Natl Ctr Dis Prevent & Hlth Promot Rome Italy Italian Coll Gen Practitioners & Primary Care Florence Italy NIA Intramural Res Program Bethesda MD 20892 USA

Background Comprehensive geriatric assessment (CGA) has been in use for the last three decades. However, some doubts remain regarding its clinical use. Therefore, we aimed to capture the breadth of outcomes reported and assess the strength of evidence of the use of comprehensive geriatric assessment (CGA) for health outcomes in older persons. Methods Umbrella review of systematic reviews of the use of CGA in older adults searching in Pubmed, Embase, Scopus, Cochrane library and CINHAL until 05 November 2021. All possible health outcomes were eligible. Two independent reviewers extracted key data. The grading of evidence was carried out using the GRADE for intervention studies, whilst data regarding systematic reviews were reported as narrative findings. Results Among 1,683 papers, 31 systematic reviews (19 with meta-analysis) were considered, including 279,744 subjects. Overall, 13/53 outcomes were statistically significant (P < 0.05). There was high certainty of evidence that CGA reduces nursing home admission (risk ratio [RR] = 0.86;95% confidence interval [CI]: 0.75-0.89), risk of falls (RR = 0.51;95%CI: 0.29-0.89), and pressure sores (RR = 0.46;95%CI: 0.24-0.89) in hospital medical setting;decreases the risk of delirium (OR = 0.71;95%CI: 0.54-0.92) in hip fracture;decreases the risk of physical frailty in community-dwelling older adults (RR = 0.77;95%CI: 0.64-0.93). Systematic reviews without meta-analysis indicate that CGA improves clinical outcomes in oncology, haematology, and in emergency department. Conclusions CGA seems to be beneficial in the hospital medical setting for multiple health outcomes, with a high certainty of evidence. The evidence of benefits is less strong for the use of CGA in other settings.

关键词： comprehensive geriatric assessment older people umbrella review systematic review

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Implications of regional N₂O-N emission factors on sugarcane ethanol emissions and granted decarbonization certificates

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RENEWABLE & SUSTAINABLE ENERGY REVIEWS 2021年 149卷 111423-111423页

作者： Carvalho, Joao Luis Nunes Oliveira, Bruna Goncalves Cantarella, Heitor Chagas, Matheus Ferreira Gonzaga, Leandro Carolino Lourenco, Kesia Silva Bordonal, Ricardo Oliveira Bonomi, Antonio Brazilian Ctr Res Energy & Mat CNPEM Brazilian Biorenewables Natl Lab LNBR Rua Giuseppe Maximo Scolfaro 10000 BR-13083100 Campinas SP Brazil Agron Inst Campinas IAC Soils & Environm Resources Ctr Barao Itapura 1481 BR-13001970 Campinas SP Brazil Univ Campinas UNICAMP Interdisciplinary PhD Program Bioenergy Rua Monteiro Lobato 80Cidade Univ BR-13083862 Campinas SP Brazil

Reducing greenhouse gas (GHG) emissions by substituting fossil fuels depends on how biofuels are produced and how emissions are calculated. Nitrous oxide (N2O) emissions from synthetic and organic N fertilizers are important sources of GHG from sugarcane ethanol. This study aimed to synthesize the literature information and derive regional N2O emissions factors (EFs) for N fertilizers according to Tier 2 approach. This study also evaluated how the use of Tier 2 affects emissions compared with those obtained by the IPCC Tier 1. Moreover, this study examined how N fertilizers can affect GHG emissions and the earning of decarbonization certificates (CBIOs) by ethanol producers. For an ethanol distillery producing 339 million liters annually, the use of Tier 1 and Tier 2 resulted in emissions of 176.5 and 145.2 Gg CO2eq, whereas for the same amount of energy, gasoline would emit 661.8 Gg CO2eq. The addition of nitrification inhibitors (NIs) to N fertilizers and improvements in vinasse/fertilizer management further reduced emissions compared with Tier 2. In Tier 1, the GHG emission savings would result 485,270 CBIOs, worth 4.85 million US$ at US$10 per CBIO. But if the IPCC Tier 2 is considered, the annual CBIOs would be worth 5.17 million US$. Using NIs and improving vinasse/fertilizer management may bring an additional US$ 31,700 and US$ 48,000 revenue above that of Tier 2. Public and sectorial policies behind decarbonization certificates can encourage farmers and decision-makers to pursue more efficient and economical solutions to further decrease GHG emissions and improve the sustainability of ethanol.

关键词： Tier 2 IPCC methodology Nitrogen fertilizers Ethanol biorefinery Life cycle assessment CBIOs RenovaBio policy

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Prevalence of multidimensional frailty and pre-frailty in older people in different settings: A systematic review and meta-analysis

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AGEING RESEARCH REVIEWS 2021年 72卷 101498-101498页

作者： Veronese, Nicola Custodero, Carlo Cella, Alberto Demurtas, Jacopo Zora, Sabrina Maggi, Stefania Barbagallo, Mario Sabba, Carlo Ferrucci, Luigi Pilotto, Alberto Univ Palermo Dept Internal Med & Geriatr Geriatr Unit Via Vespro 141 I-90127 Palermo Italy Univ Bari Aldo Moro Dept Interdisciplinary Med Bari Italy EO Ospedali Galliera Dept Geriatr Care Orthogeriatr & Rehabil Genoa Italy Univ Modena & Reggio Emilia Clin & Expt Med PhD Program Modena Italy Neurosci Inst Natl Res Council Padua Italy NIA Intramural Res Program NIH Bethesda MD USA

Frailty is a common condition in older people. The epidemiological data available, however, are mainly based on the physical frailty phenotype. An extensive literature has suggested that frailty should be identified using a multidimensional approach. Based on these recommendations, we estimated the prevalence of frailty and prefrailty in the older population, using the multidimensional prognostic index (MPI), a common tool for defining multidimensional frailty. We searched several databases until 10th May 2021 for studies reporting the prevalence of frailty according to MPI values. MPI was categorized, where possible, in 0.33 (robustness), 0.33-0.66 (pre-frailty) and 0.66 (frailty) or using a RECursive Partition and AMalgamation approach. A metaanalysis of the prevalence, with the correspondent 95% confidence intervals (CIs) of pre-frailty and frailty was performed stratified by setting (population-based, ambulatory, nursing home, and hospital). Among 177 papers initially screened, we included 57 studies for a total of 56,407 older people. The mean age was 78.6 years, with a slight prevalence of women (58%). The overall prevalence of multidimensional frailty (MPI-3) was 26.8% (95% CI: 22.1-31.5), being higher in nursing home setting (51.5%) and lower in population-based studies (13.3%). The prevalence of pre-frailty (MPI-2) was 36.4% (95%CI: 33.1-39.7), being higher in hospital setting (39.3%) and lower in nursing home (20%). In conclusion, frailty and pre-frailty, according to a multidimensional definition, are common in older people affecting, respectively, one person over four and one over three. Our work further strengths the importance of screening frailty in older people using a multidimensional approach.

关键词： Multidimensional prognostic index Frailty Epidemiology Prevalence Comprehensive geriatric assessment

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Association between dietary antioxidant index and risk of Helicobacter pylori infection among adults: a case-control study

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BMC GASTROENTEROLOGY 2022年第1期22卷 413-413页

作者： Ebrahimi, Zohreh Masoodi, Mohsen Aslani, Zahra Naghshi, Sina Sikaroudi, Masoumeh Khalighi Shidfar, Farzad Iran Univ Med Sci Sch Publ Hlth Dept Nutr Tehran Iran Iran Univ Med Sci Rasoul E Akram Hosp Colorectal Res Ctr Tehran Iran Ohio State Univ Interdisciplinary PhD Program Nutr OSUN Columbus OH 43210 USA Univ Tehran Med Sci Students Sci Res Ctr Tehran Iran Univ Tehran Med Sci Sch Nutr Sci & Dietet Dept Clin Nutr Tehran Iran Ohio State Univ Comprehens Canc Ctr Columbus OH 43210 USA

Backgrounds and aims One of the most important risk factors for Helicobacter pylori (H. pylori) infection is nutrition. Balanced diets with high antioxidant properties may have protective effects against the consequences of this infection. In the current study, we aimed to investigate the association between the dietary antioxidant index and the risk of H. pylori infection among adults. Methods In a case-control study the dietary intake of patients with H. pylori infection was compared with healthy subjects. The dietary antioxidant index (DAI) was calculated using dietary intakes derived from a validated food frequency questionnaire (FFQ). Demographic information was obtained by a related questionnaire and Physical Activity was measured by International Physical Activity Questionnaire (IPAQ) were used to obtain information. Using logistic regression models, we evaluated the association between the DAI and H. pylori infection risk. The significance level was determined as P < 0.05. Results Finally, dietary data of 148 cases and 302 controls (mean age: 38.72 +/- 10.61 (were analyzed. The mean of total DAI was significantly higher in controls (7.67) when compared with H. pylori cases (3.57) (P < 0.001). After adjustment for covariates, participants with less than median DAI values had an increased risk of H. pylori onset (adjusted OR 1.08, 95% CI: 1.02-1.12, P < 0.001). Conclusions Appropriate intake of nutrient antioxidants may have a role in decreasing the likelihood of H. pylori infection risk.

关键词： Helicobacter pylori Dietary antioxidant index Antioxidants

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