63 research outputs found
Towards accurate and unbiased imaging-based differentiation of Parkinson’s disease, progressive supranuclear palsy and corticobasal syndrome
No full textThe early and accurate differential diagnosis of parkinsonian disorders is still a significant challenge for clinicians. In recent years, a number of studies have used MRI data combined with machine learning and statistical classifiers to successfully differentiate between different forms of Parkinsonism. However, several questions and methodological issues remain, to minimise bias and artefact-driven classification. In this study we compared different approaches for feature selection, as well as different MRI modalities, with well matched patient groups and tightly controlling for data quality issues related to patient motion. Our sample was drawn from a cohort of 69 healthy controls, and patients with idiopathic Parkinson’s disease (n=35), Progressive Supranuclear Palsy Richardson’s syndrome (n=52) and corticobasal syndrome (n=36). Participants underwent standardised T1-weighted and diffusion-weighted MRI. Strict data quality control and group matching reduced the control and patient numbers to 43, 32, 33 and 26, respectively. We compared two different methods for feature selection and dimensionality reduction: whole-brain principal components analysis, and an anatomical region-of-interest based approach. In both cases, support vector machines were used to construct a statistical model for pairwise classification of healthy controls and patients. The accuracy of each model was estimated using a leave-two-out cross-validation approach, as well as an independent validation using a different set of subjects. Our cross-validation results suggest that using principal components analysis for feature extraction provides higher classification accuracies when compared to a region-of-interest based approach. However, the differences between the two feature extraction methods were significantly reduced when an independent sample was used for validation, suggesting that the principal components analysis approach may be more vulnerable to overfitting with cross-validation. Both T1-weighted and diffusion MRI data could be used to successfully differentiate between subject groups, with neither modality outperforming the other across all pairwise comparisons in the crossvalidation analysis. However, features obtained from diffusion MRI data resulted in significantly higher classification accuracies when an independent validation cohort was used. Overall, our results support the use of statistical classification approaches for differential diagnosis of parkinsonian disorders. However, classification accuracy can be affected by group size, age, sex and movement artifacts. With appropriate controls and out-of-sample cross validation, diagnostic biomarker evaluation including MRI based classifiers may be an important adjunct to clinical evaluation
PREreview of "A Quantitative Study of Inappropriate Image Duplication in the JournalToxicology Reports"
No full text<p><strong>This Zenodo record is a permanently preserved version of a PREreview. You can view the complete PREreview at <a href="https://prereview.org/reviews/8402209">https://prereview.org/reviews/8402209</a>.</strong></p>
<p>This review reflects comments and contributions from Martyn Rittman and Allie Tatarian. Review synthesized by Stephen Gabrielson.</p>
<p>In this study, both a human reviewer and an AI tool screened papers from the journal <em>Toxicology Reports</em> for inappropriate image duplication.</p>
<p>Major comments:</p>
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<p>Having a single human reviewer at both steps (the initial review for duplicated images, and the review of AI-flagged duplications) is a potential source of bias. The safest thing to do is to have three image reviewers - two that conduct an initial review and review the AI-flagged hits, plus a third on hand to act as a tiebreaker in case the two reviewers disagree. Or since this could be a substantial amount of work, having at least an extra reviewer to check the positive hits would be advisable.</p>
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<p>Minor comments:</p>
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<p>Would like to see more discussion of potential false positives, and what "appropriate" image duplication might look like (especially since the term "inappropriate image duplication" is used throughout).</p>
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<p>I would like to know why all papers are taken from a single journal rather than, say, a spread of journals on a similar topic. It leaves the author open to accusations of prejudice against the journal and its editors. A conflict-of-interest statement on whether the author has had previous interactions with the journal would be a useful clarification.</p>
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<p>It would be great if the author shares the example of false positive (where the images are mistakenly identified as duplicates). This would give a holistic overview of how good the manual screening was in identifying the duplicate images.</p>
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<p>On line 41: "Data duplication between papers, including charts as well as images, has been quantified as high as ~25%" -- is this equivalent to republication without appropriate citation?</p>
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<p>On line 66, the author describes that there were cases when images were also compared between other papers by the same research group or author. What prompted this more detailed investigation and why/how were some papers given more scrutiny?</p>
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<p>Comments on reporting:</p>
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<p>The venn diagram showing how the images were detected is a great idea. Adding the total numbers of papers selected to the study in the venn diagram would be nice, too.</p>
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<p>Competing interests</p>
<p>The author declares that they have no competing interests.</p>
Brief Note: Eleocharis parvula (R. & S.) Link., a New Species Record for the Flora of Ohio
No full textAuthor Institution: Department of Environmental and Plant Biology, Ohio UniversityEleocharis parvula (R. & S.) Link. (Cyperaceae) is reported from a saline site in Wayne County, OH. It was growing on the border of a saline pond on the property of the Morton Salt Company, Rittman, OH
Growth and Survival of the Halophyte Salicornia Europaera L. Under Saline Field Conditions
No full textAuthor Institution: Department of Botany, Ohio UniversityField investigations were carried out to determine growth and survival rates of Salicornia europaea L. in a saline environment at Rittman, Ohio. Collected data indicated that from 62% to 100% of the seedlings within the 'A saline zones investigated did not survive to maturity. Seedling mortality was statistically correlated at P<0.01 to rising soil salinity stress during late spring and summer. Plant growth was minimal between April and June, increasing sharply during late summer and fall
The Vegetative Composition of a Beech-Maple Climax Forest in the Glaciated Plateau of Northeastern Ohio
No full textAuthor Institution: Department of Biological Sciences, University School, Shaker Heights, OhioSurvey was made of a beech-maple forest by the quarter point method during August, 1968. The forest is located on a mesic, level upland of the glaciated Allegheny Plateau in eastern Cuyahoga County, Ohio, in the Chagrin River drainage basin. Geologically the upland is underlain by Mississippian formations capped by a thin cover of till, in which soils of the Ellsworth soil catenathe Rittman and Wadsworth silt loamsare developed.
The dominant plant species in this forest are American beech and sugar maple, which together comprise 68% of the trees recorded and have a total combined importance value of 62%. Red oak, red maple, and cucumbertree are important secondary dominants, but white ash and tuliptree are of little significance in the woodland composition. A greater overall abundance of secondary-associate mixed-mesophytic species than is normally found in such forests occurs. This composition supports the concept of a poly climax beechmaple association and is suggested to be a result of past selective lumbering and a variation in topography and soils.
Although there is some evidence of past selective lumbering, the forest appears to be in an essentially undisturbed, virgin state. It has been partially destroyed as the forest is now part of a tract of land developed as a new secondary school campus
PREreview of "Controlled experiment finds no detectable citation bump from Twitter promotion"
No full text<p><strong>This Zenodo record is a permanently preserved version of a PREreview. You can view the complete PREreview at <a href="https://prereview.org/reviews/10044712">https://prereview.org/reviews/10044712</a>.</strong></p>
<p>This review reflects comments and contributions from Melissa Chim, Allie Tatarian, Martyn Rittman, Pen-Yuan Hsing. Review synthesized by Stephen Gabrielson. </p><p>Selected journal articles were tweeted from one of several Twitter accounts with a large number of followers. The altmetrics and citations of these papers were compared with a set of control papers for a study period of three years. While altmetrics saw an increase immediately after tweeting, there was no statistically significant increase in citations for the study papers versus the controls by the end of the study period.</p><p>Major comments:</p><ul><li><p>I would like to see a more explicit acknowledgement that this experiment was conducted with only ecological papers - the results are written as if the conclusions apply to scientific research broadly and not one specific discipline. For example, disciplinary differences in citation politics and mechanisms may have a big impact on the effects of social media dissemination. Would social media affect citations of monographs in the humanities the same as ecology papers? If the authors believe their findings can be generalised to other domains, I'm happy for them to make that argument, too.</p></li><li><p>I like the authors' methodical approach to the study. It's well-designed and takes into account weaknesses of previous similar studies. I appreciate how thoroughly the authors explained their criteria for choosing articles. It's a shame that it is statistically under-powered to detect citation changes in WoS/Scopus, but that is an interesting result in itself and sets parameters for future studies. </p></li><li><p>From my perspective, the current discussion section of this paper (1) summarises the key learnings from the experiment, (2) acknowledges that social media engagement is useful beyond paper citation counts, and (3) a "wistful" commentary on the value of social media dissemination of research. These points are worthwhile. However, I'd like to see a deeper, constructive dissection into the limitations of this experiment in the discussion section. In addition to mostly ecologist accounts tweeting ecology papers, there are various potential minor issues which could be tackled in future studies. I'd love to see a discussion of them.</p></li><li><p>While the authors state that the dataset collected from this experiment is shared in the Supplementary Materials, I was not able to find it from reading the paper. Where is the dataset, and can the authors directly cite it in the text? Similarly, the current Acknowledgements section states that the publisher of these journals (John Wiley & Sons) wrote the scripts to collect much of the raw social media data. Where are these scripts published? And what about the statistical analyses? Did the authors also write scripts to do that, or were they done in some other way? There is currently very little reporting in this paper on the data and implementation details (e.g. source code). I suggest a dedicated data and code availability section that discusses which aspects of that have been published (with full citation and open source license metadata), and a discussion of limitations and reproducibility. This is not a box-ticking exercise. For example, this paper describes using classical frequentist statistics, but it may be interesting to apply a different analytical approach (e.g. Bayesian modeling). Any code that has been written should also be published in commented form for others to study, peer review, and build upon. For components which the authors could not publish for any reason, and discussion of these limitations could inform future efforts.</p></li><li><p>Not everyone is familiar with English-language social media platforms and how they work. I think this paper would be informative and useful to a wider international audience if the authors could briefly discuss how Twitter works, and how it compares to other popular platforms. This information would allow a more critical analysis into how much of the effects seen in this experiment can be attributed to Twitter versus social media in general. And because the authors are social media experts, the Discussion section could also discuss if the way Twitter and journal publishers make (nor not make) it easy to access data for this experiment. This would be a useful methodology discussion to inform future studies.</p></li></ul><p>Minor comments:</p><ul><li><p>I would have liked to see a bit more detail about the authors' backgrounds since their expertise played such a large role in the study overall.</p><ul><li><p>I agree - also it seemed to me that all of the authors and the journals they targeted were in the ecology/conservation field, but I don't think there was an explicit acknowledgement of it in the text.</p></li></ul></li><li><p>Did the authors check if any of their control articles were tweeted by other scientists during the time of their study? If this happened, it could weaken the effect and the authors could be drawing false negative conclusions.</p></li><li><p>This study was explicitly designed as a hypothesis-based experiment. In line with that, I suggest the authors explicitly state what their hypotheses is/are (and the null hypotheses, etc.) in the Materials and Methods section.</p></li><li><p>The authors acknowledge that in at least one prior study, "Twitter promotion was also associated with 24 hours of free access to the articles." For the current reported experiment, did the authors track and account for the ease of access to the 110 articles in the study? If so, how?</p></li><li><p>The authors "obtained daily download counts for articles in five of the journals" - Did the publishers of the other journals simply refuse to provide that data? Also, how is "download" defined? Is it literally someone clicking to download the PDF file? If so, did the authors account for the possibility that some of the articles studied can be read online in addition to being downloadable as a PDF file? What are the potential limitations here?</p></li><li><p>I appreciate the reporting on the growth of followers for all 11 Twitter accounts used in this experiment. Is it possible that an article tweeted later in the 3-year study period would receive higher Altmetrics or citations because the account tweeting it had more followers at that time? I suspect the randomisation tests would account for this, but I'd like to double check.</p></li><li><p>Figure(s) with color (e.g. Figure 2) should be checked and edited (if necessary) for color-blind and black-and-white printing accessibility.</p></li><li><p>Important point on inclusive terminology: The current text describes the authors as "scientists" who use social media to communicate with a diverse audience, including those in the "general public". There is a growing body of research that critiques this dichotomy. For example, are authors not also members of the "public"? And for those in the "public", can they not be called "scientists" even if they happen to perform science in some capacity? Etc. Without having to cite the relevant body of peer-reviewed literature, I suggest a few ways to make the text more inclusive of the diverse ways in which people perform science. For example, the authors could state in the Introduction that they are those who "are professionally employed to conduct scientific research at universities/research institutions, which we will shorten as 'scientists' for the practical purposes of this article. The 'general public' in this text refers to those whose primary vocation is not conducting scientific research." </p></li><li><p>Under Experimental design, the authors report that "other non-standard article types" were excluded. That is fine, but I suggest removing "non-standard" as it unnecessarily devalues those "other" articles for the purposes of this experiment or paper.</p></li><li><p>Can the authors please include a statement on contributor roles, such as expressed through the CRediT contributor roles taxonomy? (<a href="https://credit.niso.org/">https://credit.niso.org/</a>) This can be located in the Acknowledgements section, or elsewhere depending on their preference.</p></li><li><p>In the first paragraph of the introduction, it would be good to spell out "AP" to "Associated Press" for a diverse international audience.</p></li></ul><p>Comments on reporting:</p><ul><li><p>(see comment on data and code availability under major comments)</p></li></ul><p>Suggestions for future studies:</p><ul><li><p>The authors acknowledged that their study focused on articles only from John Wiley & Sons. I can see further studies being done with a focus on other journals and/or other disciplines. </p><ul><li><p>+1, and would also like to see if you see the same effect with journals that have a more broad focus or higher impact factors.</p></li></ul></li><li><p>It would be interesting to see if there is an effect based on tweeting multiple times from the same or different accounts. Previous studies took more of a marketing campaign approach, it would be interesting to see where the boundary lies in how much effort is needed to increase citations (if indeed there is a boundary!)</p></li><li><p>An interesting future meta study would be to investigate how the mechanics of different social media platforms and the makeup of their users (e.g. Twitter vs Mastodon vs Threads, etc.) relate to if and how they impact the citational metrics and citation politics of academic research across different fields of study (including non-STEM!).</p></li></ul>
<h2>Competing interests</h2>
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The author declares that they have no competing interests.
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The Relationship of Stroke Patients' Functional and Cognitive Status And Caregivers' Resilience to Caregiver Burden
No full textThe Relationship of Stroke Patients' Functional and Cognitive StatusAnd Caregivers' Resilience to Caregiver BurdenMargaret D. Nolan, Ph.D.Director: Jean Toth, Ph.D. Currently it is estimated that 795,000 persons experience a stroke every year. Of that number up to one-third of survivors will be permanently disabled. It is neither financially feasible nor desirable to place these disabled stroke survivors in long-term care facilities to provide them with the needed assistance if they can be cared for at home. Frequently, the care of these patients is assumed by family members or friends. However, providing care has been shown to be burdensome for some caregivers of stroke patients (Johnson, 1998; Scholte op Reimer, deHaan, Pijnenborg, Limburg, & van den Bos, 1998a; Van Puymbroeck, Hinojosa, & Rittman, 2008). The factors that contribute to development of caregiver burden have been studied by numerous researchers, but findings are inconclusive (Jeng-Ru, Hills, Kaplan, & Johnson, 1998; McCullagh, Brigstocke, Donaldson, & Kalra, 2005; Nelson, Smith, Martinson, Kind, & Luepker, 2008; Vincent, Desrosiers, Landreville, & Demers, 2009). The contribution of the stroke patients' functional and/or cognitive disabilities to the caregiver's burden level is not clear as a result of contradictory findings in the published research. Further, resilience has not been measured in stroke caregivers and evaluated as a possible mediating factor in burden's development. This study sought to clarify those interrelationships. A descriptive correlational design was used in this study. Fifty-six stroke patient and caregiver dyads were evaluated at least two weeks after the stroke patient returned to the home setting after experiencing an acute stroke. All of the participants were adults who spoke English. Stroke patients were evaluated functionally with the Barthel Index, and cognitively with the Mini-Mental State Exam by the investigator. Caregivers self-administered the Resilience Scale, the modified Zarit Burden Interview, and a demographic data collection tool. Demographic data was evaluated with descriptive statistics and the hypotheses were tested using multiple regression. Regression analysis indicated that the functional status and cognitive status of the stroke patients were not significantly related to the burden level of their caregivers. However, the caregivers' personal resilience level was significantly related to caregiver burden [F (4, 50) = 4.10, p = 0.048]. Demographic data analysis revealed that there was also a significant relationship between the caregivers' perception that their own physical condition made it difficult to provide care and their burden level. This study's findings contribute to the existing body of knowledge regarding caregiver burden in stroke patients. Identification of factors that contribute to or mediate the development of caregiver burden may aid nurses and other health care providers in identifying caregivers who are at risk for developing burden, and ultimately assist in maintaining stroke patients in their home setting long-term.Degree awarded: Ph.D. Nursing. The Catholic University of Americ
Hierarchical spectral clustering reveals brain size and shape changes in asymptomatic carriers of C9orf72
No full textSupplementary data: fcac182_Supplementary_Data - https://oup.silverchair-cdn.com/oup/backfile/Content_public/Journal/braincomms/4/4/10.1093_braincomms_fcac182/1/fcac182_supplementary_data.pdf?Expires=1665138780&Signature=oJFozMlNZiAmxd4~XZaq7YKd7waxislas45NEOp9AiZv-fUYr7X~LhZxFgvYXpCVINyQUQrXe0pgrm9L5kv7xdb0LltVuoEOjwb5uVveMyHMfuqTdCBsEzTVZidx9GuuOB79JsHNYHkUZPsXLiU8-lrosrTb3tasr8Mpv31u7ZVZT~4uGdUf06UsIRu7AEn4bfKf64iwudmFr1QyrLJkXMZm0uJ4e5kh8f7k6Xm~rZGqkaiphsQ~Oat4JHssfuCe5Wibgc4m~rMjQeOmutR3R7KicfH4j3xuab1mzCbf-H~~Ed5Yt8mtlMTsyDB3t-8z3dNVaS2aBrwCABvfa3G2yg__&Key-Pair-Id=APKAIE5G5CRDK6RD3PGA (pdf file).GENFI consortium authors
Sónia Afonso, Maria Rosario Almeida, Sarah Anderl-Straub, Christin Andersson, Anna Antonell, Silvana Archetti, Andrea Arighi, Mircea Balasa, Myriam Barandiaran, Nuria Bargalló, Robart Bartha, Benjamin Bender, Alberto Benussi, Sandra Black, Martina Bocchetta, Sergi Borrego-Ecija, Jose Bras, Marta Canada, Valentina Cantoni, Paola Caroppo, David Cash, Miguel Castelo-Branco, Rhian Convery, Thomas Cope, Giuseppe Di Fede, Alina Díez, Diana Duro, Chiara Fenoglio, Catarina B. Ferreira, Nick Fox, Morris Freedman, Giorgio Fumagalli, Alazne Gabilondo, Roberto Gasparotti, Serge Gauthier, Stefano Gazzina, Giorgio Giaccone, Ana Gorostidi, Caroline Greaves, Rita Guerreiro, Carolin Heller, Tobias Hoegen, Begoña Indakoetxea, Vesna Jelic, Lize Jiskoot, Hans-Otto Karnath, Ron Keren, Tobias Langheinrich, Maria João Leitão, Albert Lladó, Sandra Loosli, Carolina Maruta, Simon Mead, Lieke Meeter, Gabriel Miltenberger, Rick van Minkelen, Sara Mitchell, Katrina Moore, Jennifer Nicholas, Linn Öijerstedt, Jaume Olives, Sebastien Ourselin, Alessandro Padovani, Jessica Panman, Janne M. Papma, Georgia Peakman, Yolande Pijnenburg, Enrico Premi, Sara Prioni, Catharina Prix, Rosa Rademakers, Veronica Redaelli, Tim Rittman, Ekaterina Rogaeva, Pedro Rosa-Neto, Giacomina Rossi, Mar tin Rossor, Beatriz Santiago, Elio Scarpini, Sonja Schönecker, Elisa Semler, Rachelle Shafei, Christen Shoesmith, Miguel Tábuas-Pereira, Mikel Tainta, Ricardo Taipa, David Tang-Wai, David L Thomas, Paul Thompson, Hakan Thonberg, Carolyn Timberlake, Pietro Tiraboschi, Emily Todd, Michele Veldsman, Ana Verdelho, Jorge Villanua, Jason Warren, Carlo Wilke, Ione Woollacott, Elisabeth Wlasich, Henrik Zetterberg, Miren ZulaicaCopyright © The Author(s) 2022. Traditional methods for detecting asymptomatic brain changes in neurodegenerative diseases such as Alzheimer’s disease or frontotemporal degeneration typically evaluate changes in volume at a predefined level of granularity, e.g. voxel-wise or in a priori defined cortical volumes of interest. Here, we apply a method based on hierarchical spectral clustering, a graph-based partitioning technique. Our method uses multiple levels of segmentation for detecting changes in a data-driven, unbiased, comprehensive manner within a standard statistical framework. Furthermore, spectral clustering allows for detection of changes in shape along with changes in size. We performed tensor-based morphometry to detect changes in the Genetic Frontotemporal dementia Initiative asymptomatic and symptomatic frontotemporal degeneration mutation carriers using hierarchical spectral clustering and compared the outcome to that obtained with a more conventional voxel-wise tensor- and voxel-based morphometric analysis. In the symptomatic groups, the hierarchical spectral clustering-based method yielded results that were largely in line with those obtained with the voxel-wise approach. In asymptomatic C9orf72 expansion carriers, spectral clustering detected changes in size in medial temporal cortex that voxel-wise methods could only detect in the symptomatic phase. Furthermore, in the asymptomatic and the symptomatic phases, the spectral clustering approach detected changes in shape in the premotor cortex in C9orf72. In summary, the present study shows the merit of hierarchical spectral clustering for data-driven segmentation and detection of structural changes in the symptomatic and asymptomatic stages of monogenic frontotemporal degeneration.KU Leuven’s ‘Mady Browaeys Fonds voor Onderzoek naar Frontotemporale Degeneratie’
Studies on the influence of folic acid and riboflavin on nitric oxide production in cultured murine macrophage cells
No full textMethylenetetrahydrofolate reductase (MTHFR) is a flavin adenine dinucleotide (FAD) - dependent, folate-metabolizing enzyme. The main product of MTHFR is methylenetetrahydrofolate, an important substrate for homocysteine metabolism and synthesis of methionine and the universal methyl donor, S-adenosylmethionine. MTHFR also catalyzes the reduction of dihydrobiopterin to tetrahydrobiopterin (BH4). BH4 is an essential cofactor for nitric oxide synthase (NOS) that produces nitric oxide (NO) for multiple functions including vasodilation and blood pressure (BP) regulation. Genome-wide association studies have linked a common polymorphism, C677T, in MTHFR with BP, and riboflavin supplements have been shown to reduce BP in individuals homozygous for the 677TT variant form of the enzyme. We hypothesize that this relationship between MTHFR, riboflavin, and BP is mediated through nitric oxide synthesis and that deficiency in either folic acid or riboflavin will result in decreased NO output. We investigated this hypothesis in vitro in stimulated murine macrophage RAW cells, which express the inducible form of NOS (iNOS). The cells were exposed to standard and reduced levels of folic acid and riboflavin. They were then stimulated with LPS. The cells were grown in medium with 0.4 mg/L riboflavin and 4.0 mg/L folic acid (control), 0.04 mg/L riboflavin (LowB2), or 0.4 mg/L folic acid (LowFA) for 48 hours, and then exposed to 100 ng/ml or 1000 ng/ml lipopolysaccharide (LPS) for 24 hours. Media was then analyzed for nitric oxide production by chemiluminescence assay using a Nitric Oxide Analyzer. Quantitative PCR was used to analyze gene expression of iNOS and arginase. In all three media conditions, no differences in RAW cell proliferation rates were observed over 48 hours. After LPS exposure, nitric oxide production in the LowB2 and LowFA cells was 30-35% and 35-40% of the control cells, respectively (p ≤ 0.001). Expression of iNOS after LPS induction increased in all three media conditions. Based on the findings above we further hypothesized that the decreased NO output from the B vitamin-deficient cells was due to insufficient BH4 availability to the cells. To test this hypothesis, a precursor of BH4, sepiapterin, was provided to the LowFA and LowB2 cells before stimulating NO production with LPS. Cells were treated with the same level of deficiency in folic acid and riboflavin as above, but were supplemented with 10 umol/L of sepiapterin at 0 hour and at the time of stimulation with 100 ng/mL LPS. Cells receiving sepiapterin before and during LPS exposure did not increase NO output when compared to those exposed only to LPS (p>0.8). LPS-induced nitric oxide production is reduced in RAW cells grown in either riboflavin or folic acid deficient media independent of iNOS expression. These results demonstrate the importance of the folate cycle in maintaining NOS function, and indicate a potential mechanism for the effects of MTHFR polymorphisms on BP. They also show that providing substrate for BH4 production is not sufficient to overcome the decreased NO output caused by deficiency.M.S.Includes bibliographical referencesby Marijke Rittman
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