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Reproducibility

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https://www.readbyqxmd.com/read/28938718/looking-back-forward-looking
#1
Scott C Edmunds, Nicole A Nogoy, Hans Zauner, Peter Li, Christopher I Hunter, Xiao Si Zhe, Laurie Goodman
GigaScience is now 5 years old, having been launched at the 2012 Intelligent Systems for Molecular Biology conference. Anyone who has attended what is the largest computational biology conference since then has had the opportunity to join us for each birthday celebration-and receive 1 of our fun T-shirts as a party prize. Since launching, we have pushed our agenda of openness, transparency, reproducibility, and reusability. Here, we look back at our first 5 years and what we have done to forward our open science goals in scientific publishing...
September 1, 2017: GigaScience
https://www.readbyqxmd.com/read/28938715/the-harm-done-to-reproducibility-by-the-culture-of-null-hypothesis-significance-testing
#2
Timothy L Lash
In the last few years, stakeholders in the scientific community have raised alarms about a perceived lack of reproducibility of scientific results. In reaction, guidelines for journals have been promulgated and grant applicants have been asked to address the rigor and reproducibility of their proposed projects. Neither solution addresses a primary culprit, which is the culture of null hypothesis significance testing that dominates statistical analysis and inference. In an innovative research enterprise, selection of results for further evaluation based on null hypothesis significance testing is doomed to yield a low proportion of reproducible results and a high proportion of effects that are initially overestimated...
September 15, 2017: American Journal of Epidemiology
https://www.readbyqxmd.com/read/28938714/lash-responds-to-is-reproducibility-thwarted-by-hypothesis-testing-and-the-need-for-cognitive-science-in-methodology
#3
Timothy L Lash
No abstract text is available yet for this article.
September 15, 2017: American Journal of Epidemiology
https://www.readbyqxmd.com/read/28938713/invited-commentary-can-issues-with-reproducibility-in-science-be-blamed-on-hypothesis-testing
#4
Clarice R Weinberg
In the accompanying article (Am J Epidemiol. 2017;186(6):646-647), Dr. Timothy Lash makes a forceful case that the problems with reproducibility in science stem from our "culture" of null hypothesis significance testing. He notes that when attention is selectively given to statistically significant findings, the estimated effects will be systematically biased away from the null. Here I revisit the recent history of genetic epidemiology and argue for retaining statistical testing as an important part of the tool kit...
September 15, 2017: American Journal of Epidemiology
https://www.readbyqxmd.com/read/28938712/invited-commentary-the-need-for-cognitive-science-in-methodology
#5
Sander Greenland
There is no complete solution for the problem of abuse of statistics, but methodological training needs to cover cognitive biases and other psychosocial factors affecting inferences. The present paper discusses 3 common cognitive distortions: 1) dichotomania, the compulsion to perceive quantities as dichotomous even when dichotomization is unnecessary and misleading, as in inferences based on whether a P value is "statistically significant"; 2) nullism, the tendency to privilege the hypothesis of no difference or no effect when there is no scientific basis for doing so, as when testing only the null hypothesis; and 3) statistical reification, treating hypothetical data distributions and statistical models as if they reflect known physical laws rather than speculative assumptions for thought experiments...
September 15, 2017: American Journal of Epidemiology
https://www.readbyqxmd.com/read/28938553/homocysteine-induced-peripheral-microcirculation-dysfunction-in-zebrafish-and-its-attenuation-by-l-arginine
#6
Sang Joon Lee, Sung Ho Park, Jinhyuk Fred Chung, Woorak Choi, Hyung Kyu Huh
Elevated blood homocysteine (Hcy) level is frequently observed in aged individuals and those with age-related vascular diseases. However, its effect on peripheral microcirculation is still not fully understood. Using in vivo zebrafish model, the degree of Hcy-induced peripheral microcirculation dysfunction is assessed in this study with a proposed dimensionless velocity parameter [Formula: see text], where [Formula: see text] and [Formula: see text] represent the peripheral microcirculation perfusion and the systemic perfusion levels, respectively...
August 29, 2017: Oncotarget
https://www.readbyqxmd.com/read/28938513/increased-anterior-default-mode-network-homogeneity-in-first-episode-drug-naive-major-depressive-disorder-a-replication-study
#7
Wenbin Guo, Xilong Cui, Feng Liu, Jindong Chen, Guangrong Xie, Renrong Wu, Zhikun Zhang, Huafu Chen, Jingping Zhao
BACKGROUND: Abnormal default-mode network (DMN) homogeneity has been involved in the neurophysiology of major depressive disorder (MDD) with inconsistent findings. The inconsistency may be due to clinical and methodological variability, and the reproducibility of the findings is limited. The present study aimed to examine alterations of the DMN homogeneity in two independent samples of patients with first-episode, drug-naive MDD. METHODS: The samples included 59 patients with MDD and 31 comparison subjects from Sample 1 and 29 patients with MDD and 24 comparison subjects from Sample 2...
September 12, 2017: Journal of Affective Disorders
https://www.readbyqxmd.com/read/28938435/the-role-of-sequential-bmp-signaling-in-directing-human-embryonic-stem-cells-to-bipotential-gonadal-cells
#8
Kirsi Sepponen, Karolina Lundin, Katri Knuus, Pia Väyrynen, Taneli Raivio, Juha S Tapanainen, Timo Tuuri
Context: Human gonads arise as a pair of epithelial ridges on the surface of intermediate mesoderm (IM)-derived mesonephros. Toxic environmental factors and mutations in various genes are known to disturb normal gonadal development, but due to a lack of suitable in vitro models, detailed studies characterizing the molecular basis of the observed defects have not been performed. Objective: Our objective was to establish an in vitro method for studying differentiation of bipotential gonadal progenitors using human embryonic stem cells (hESCs), and to investigate the role of bone morphogenetic protein (BMP) in gonadal differentiation...
August 29, 2017: Journal of Clinical Endocrinology and Metabolism
https://www.readbyqxmd.com/read/28938154/massively-parallel-sequencing-of-forensic-strs-and-snps-using-the-illumina-%C3%A2-forenseq%C3%A2-dna-signature-prep-kit-on-the-miseq-fgx%C3%A2-forensic-genomics-system
#9
Fei Guo, Jiao Yu, Lu Zhang, Jun Li
The ForenSeq™ DNA Signature Prep Kit (ForenSeq Kit) is designed to detect more than 200 forensically relevant markers in a single reaction on the MiSeq FGx™ Forensic Genomics System (MiSeq FGx System), including Amelogenin, 27 autosomal short tandem repeats (A-STRs), 7 X chromosomal STRs (X-STRs), 24 Y chromosomal STRs (Y-STRs) and 94 identity-informative single nucleotide polymorphisms (iSNPs) with the option to contain 22 phenotypic-informative SNPs (pSNPs) and 56 ancestry-informative SNPs (aSNPs). In this study, we evaluated the MiSeq FGx System on three major parts: methodological optimization (DNA extraction, sample quantification, library normalization, diluted libraries concentration, and sample-to-cell arrangement), massively parallel sequencing (MPS) performance (depth of coverage, sequence coverage ratio, and allele coverage ratio), and ForenSeq Kit characteristics (repeatability and concordance, sensitivity, mixture, stability and case-type samples)...
September 8, 2017: Forensic Science International. Genetics
https://www.readbyqxmd.com/read/28938153/massively-parallel-sequencing-of-32-forensic-markers-using-the-precision-id-globalfiler%C3%A2-ngs-str-panel-and-the-ion-pgm%C3%A2-system
#10
Zheng Wang, Di Zhou, Hui Wang, Zhenjun Jia, Jing Liu, Xiaoqin Qian, Chengtao Li, Yiping Hou
Massively parallel sequencing (MPS) technologies have proved capable of sequencing the majority of the key forensic STR markers. By MPS, not only the repeat-length size but also sequence variations could be detected. Recently, Thermo Fisher Scientific has designed an advanced MPS 32-plex panel, named the Precision ID GlobalFiler™ NGS STR Panel, where the primer set has been designed specifically for the purpose of MPS technologies and the data analysis are supported by a new version HID STR Genotyper Plugin (V4...
September 8, 2017: Forensic Science International. Genetics
https://www.readbyqxmd.com/read/28938147/development-of-an-experimental-model-of-burst-fracture-with-damage-characterization-of-the-vertebral-bodies-under-dynamic-conditions
#11
A Germaneau, T Vendeuvre, M Saget, P Doumalin, J C Dupré, F Brémand, F Hesser, C Brèque, P Maxy, M Roulaud, O Monlezun, P Rigoard
BACKGROUND: Burst fractures represent a significant proportion of fractures of the thoracolumbar junction. The recent advent of minimally invasive techniques has revolutionized the surgical treatment of this type of fracture. However mechanical behaviour and primary stability offered by these solutions have to be proved from experimental validation tests on cadaveric specimens. Therefore, the aim of this study was to develop an original and reproducible model of burst fracture under dynamic impact...
September 13, 2017: Clinical Biomechanics
https://www.readbyqxmd.com/read/28938066/systematic-optimization-of-battery-materials-key-parameter-optimization-for-the-scalable-synthesis-of-uniform-high-energy-and-high-stability-lini0-6mn0-2co0-2o2-cathode-material-for-lithium-ion-batteries
#12
Dong Ren, Yun Shen, Yao Yang, Luxi Shen, Barnaby D A Levin, Yingchao Yu, David A Muller, Héctor D Abruña
Ni-rich LiNixMnyCo1-x-yO2 (x>0.5) (NMC) materials have attracted a great deal of interest as promising cathode candidates for Li-ion batteries (LIBs) due to their low cost and high energy density. However, several issues, including sensitivity to moisture, difficulty in reproducibly preparing well-controlled morphology particles and, poor cyclability, have hindered their large scale deployment; especially for electric vehicle (EV) applications. In this work, we have developed a uniform, highly stable, high-energy density, Ni-rich LiNi0...
September 22, 2017: ACS Applied Materials & Interfaces
https://www.readbyqxmd.com/read/28938022/advising-caution-in-studying-seasonal-oscillations-in-crime-rates
#13
Kun Dong, Yunbai Cao, Beatrice Siercke, Matthew Wilber, Scott G McCalla
Most types of crime are known to exhibit seasonal oscillations, yet the annual variations in the amplitude of this seasonality and their causes are still uncertain. Using a large collection of data from the Houston and Los Angeles Metropolitan areas, we extract and study the seasonal variations in aggravated assault, break in and theft from vehicles, burglary, grand theft auto, rape, robbery, theft, and vandalism for many years from the raw daily data. Our approach allows us to see various long term and seasonal trends and aberrations in crime rates that have not been reported before...
2017: PloS One
https://www.readbyqxmd.com/read/28937495/noninvasive-computed-tomography-derived-fractional-flow-reserve-based-on-structural-and-fluid-analysis-reproducibility-of-on-site-determination-by-unexperienced-observers
#14
Keiken Ri, Kanako K Kumamaru, Shinichiro Fujimoto, Yuko Kawaguchi, Tomotaka Dohi, Sou Yamada, Kazuhisa Takamura, Yosuke Kogure, Norikazu Yamada, Etsuro Kato, Ryusuke Irie, Tomohiro Takamura, Michimasa Suzuki, Masaaki Hori, Shigeki Aoki, Hiroyuki Daida
OBJECTIVE: The aim of this study was to evaluate the reproducibility of computed tomography (CT)-derived fractional flow reserve (FFR) determined on site by inexperienced observers using a postprocessing software based on structural and fluid analysis. METHODS: Using 21 coronary vessels in 7 patients who underwent 320-row coronary CT angiography and catheter-FFR, 2 independent inexperienced observers (A: a student radiation technologist; B: a nonmedical staff) determined the CT-FFR using a postprocessing software...
September 20, 2017: Journal of Computer Assisted Tomography
https://www.readbyqxmd.com/read/28937337/ethical-and-legal-implications-of-the-methodological-crisis-in-neuroimaging
#15
Philipp Kellmeyer
Currently, many scientific fields such as psychology or biomedicine face a methodological crisis concerning the reproducibility, replicability, and validity of their research. In neuroimaging, similar methodological concerns have taken hold of the field, and researchers are working frantically toward finding solutions for the methodological problems specific to neuroimaging. This article examines some ethical and legal implications of this methodological crisis in neuroimaging. With respect to ethical challenges, the article discusses the impact of flawed methods in neuroimaging research in cognitive and clinical neuroscience, particularly with respect to faulty brain-based models of human cognition, behavior, and personality...
October 2017: Cambridge Quarterly of Healthcare Ethics: CQ: the International Journal of Healthcare Ethics Committees
https://www.readbyqxmd.com/read/28937285/assessment-of-automatic-segmentation%C3%A2-of-teeth-using%C3%A2-a-watershed-based-method
#16
Antoine Galibourg, Jean Dumoncel, Norbert Telmon, Adèle Calvet, Jérôme Michetti, Delphine Maret
OBJECTIVES: Tooth 3D automatic segmentation (AS) is being actively developed in research and clinical fields. Here, we assess the effect of automatic segmentation using a watershed-based method on the accuracy and reproducibility of 3D reconstructions in volumetric measurements by comparing it with a semi-automatic (SAS) method that has already been validated. METHODS: The study sample comprised 52 teeth, scanned with micro computed tomography (micro CT) (41µm voxel size) and cone beam computed tomography (CBCT) (76 ; 200 and 300 µm voxel size)...
September 21, 2017: Dento Maxillo Facial Radiology
https://www.readbyqxmd.com/read/28937204/j-resolved-1h-nmr-1d-projections-for-large-scale-metabolic-phenotyping-studies-application-to-blood-plasma-analysis
#17
Andrea Rodriguez-Martinez, Joram M Posma, Rafael Ayala, Nikita Harvey, Beatriz Jimenez, Ana L Neves, John C Lindon, Kazuhiro Sonomura, Taka-Aki Sato, Fumihiko Matsuda, Pierre Zalloua, Dominique Gauguier, Jeremy Kirk Nicholson, Marc-Emmanuel Dumas
1H nuclear magnetic resonance (NMR) spectroscopy-based metabolic phenotyping is now widely used for large-scale epidemiological applications. In order to minimize signal overlap present in 1D 1H NMR spectra, we have investigated the use of 2D J-resolved (JRES) 1H NMR spectroscopy for large-scale phenotyping studies. In particular, we have evaluated the use of the 1D projections of the 2D JRES spectra (pJRES), which provide single peaks for each of the J-coupled multiplets, using 706 human plasma samples from the FGENTCARD cohort...
September 22, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28937176/mesenchymal-stem-cell-mediated-endochondral-ossification-utilising-micropellets-and-brief-chondrogenic-priming
#18
C A Knuth, J Witte-Bouma, Y Ridwan, E B Wolvius, E Farrell
With limited autologous and donor bone graft availability, there is an increasing need for alternative graft substitutes. We have previously shown that chondrogenically priming mesenchymal stem cell (MSC) pellets for 28 d in vitro will reproducibly result in endochondral bone formation after in vivo implantation. However, pellet priming time for clinical applications is quite extensive. A micropellet (μpellet)-fibrin construct was developed and coupled, with a shorter priming period, determined by an in vitro time course experiment...
September 22, 2017: European Cells & Materials
https://www.readbyqxmd.com/read/28937165/a-facile-solvent-mediated-self-assembly-silver-nanoparticle-mirror-substrate-for-quantitatively-improved-surface-enhanced-raman-scattering
#19
Yanqi Qu, Chen Tan, Zhiyun Zhang, Lili He
Herein, a facile solvent mediated silver nanoparticle (AgNP) mirror was introduced as a reproducible and sensitive surface-enhanced Raman scattering (SERS) substrate. The AgNP mirror was fabricated based on commercially available citrate coated AgNPs via a facile and unique water-solvent interface assembly method without using any electrical equipment. By adding 0.2 mg ml(-1) citrate coated AgNPs dropwise into a mediating solvent, self-assembled AgNP mirrors were formed instantly and gradually settled down at the bottom...
September 22, 2017: Analyst
https://www.readbyqxmd.com/read/28937022/yield-of-p53-expression-in-esophageal-squamous-cell-cancer-and-its-relationship-with-survival
#20
Tushar H Sankalecha, Sudhir J Gupta, Nitin R Gaikwad, Nikhil U Shirole, Harit G Kothari
BACKGROUND/AIMS: Esophageal squamous cell carcinoma (ESCC) is the most aggressive type of cancer. Mutation of tumor suppressor gene p53 is observed in many gastrointestinal malignancies including ESCC. The immunohistochemical protein expression of mutant p53 has been proposed as a potential tool to evaluate the biological behavior of ESCC. Predictive value of p53 for survival is debatable, hence this study was formulated to know the survival of patients with p53 expression in ESCC. PATIENTS AND METHODS: We prospectively included 91 consecutive patients of ESCC from August 2014 to August 2016...
September 2017: Saudi Journal of Gastroenterology: Official Journal of the Saudi Gastroenterology Association
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