Postdoctoral Research Articles

Comparative analysis of forestry systems in the United States and Turkey: Practices, technologies, and challenges

The current study provides a comprehensive comparative analysis of forestry systems in the United States (US) and Turkey, covering various aspects such as forest ownership, natural resources planning, fire management, technological applications, silviculture, forestry education and challenges faced by each country. The findings mainly stems from the author’s first-hand investigations, field observations, and experiences during a postdoctoral research period in the US from 2022 to 2024. Additionally, a variety of information sources, including US forest plans, publications from the US Department of Agriculture Forest Service, relevant peer-reviewed literature, and open-source data, was used in the work employing the verbal analysis method. While certain similarities emerge, particularly in technology utilization and the historical development of forestry education, significant disparities are evident in fire management strategies, land ownership structure, silvicultural practices, and forest planning approaches between the countries. These differences can be attributed to unique environmental and historical conditions, varying economic development levels, and distinct regulatory legislations. The outcomes of this study suggest that there are valuable forestry practices that each country can learn or adopt from the other, emphasizing the potential for mutual exchange and improvement in natural resources management practices.

Food Insecurity Among Graduate Students and Postdoctoral Trainees

Food insecurity on college campuses has emerged as an urgent public health priority; however, there has been a lack of studies focused on graduate students or postdoctoral trainees, particularly those enrolled at private academic institutions. To estimate the prevalence of and factors associated with food insecurity among graduate students and postdoctoral trainees at a private academic university in Boston, Massachusetts. In this cross-sectional survey study, a survey on food insecurity was sent to graduate students and postdoctoral trainees at 3 health-focused graduate schools at Harvard University during the end of the spring 2023 academic term (April to June). Participants were studying medicine, dental medicine, or public health. Data analysis was performed from July to September 2023. Sociodemographic characteristics of graduate students and postdoctoral trainees. The primary outcome was food insecurity as assessed using the US Household Food Security Survey Module. Food insecurity also encompassed low and very low food security. Bidirectional stepwise logistic regression models were conducted to estimate the factors associated with food insecurity for graduate students and postdoctoral trainees. The analytic sample included 1745 participants (response rate, 55%): 1287 were graduate students and 458 were postdoctoral trainees. The median age of respondents was 29.0 (IQR, 7.0) years, and more than half (1073 [61.5%]) identified as female. A total of 694 respondents (39.8%) identified as Asian, 625 (35.8%) as White, and 426 (24.4%) as being of other race or ethnicity. The prevalence of food insecurity was 17.4% (224 of 1287) among graduate students and 12.7% (58 of 458) among postdoctoral trainees. Among graduate students, factors associated with food insecurity included being Asian (OR, 1.06 [95% CI, 1.01-1.11]) or of other race or ethnicity (OR, 1.07 [95% CI, 1.02-1.13]), receiving financial aid (OR, 1.09 [95% CI, 1.05-1.13]), and having housing instability (OR, 1.53 [95% CI, 1.45-1.61]). Among postdoctoral trainees, factors associated with food insecurity included receiving Supplemental Nutrition Assistance Program benefits (OR, 1.59 [95% CI, 1.28-1.97]), having housing instability (OR, 1.33 [95% CI, 1.22-1.45]), and not owning a car (OR, 1.11 [95% CI, 1.04-1.18]). In this study, a substantial proportion of graduate students and postdoctoral trainees at a private academic institution experienced food insecurity during the academic year. These findings underscore the need for national and institutional interventions to address the complex, structural factors related to food insecurity in these distinct populations.

Stationary Points of a Shallow Neural Network with Quadratic Activations and the Global Optimality of the Gradient Descent Algorithm

We consider the problem of training a shallow neural network with quadratic activation functions and the generalization power of such trained networks. Assuming that the samples are generated by a full rank matrix [Formula: see text] of the hidden network node weights, we obtain the following results. We establish that all full-rank approximately stationary solutions of the risk minimization problem are also approximate global optimums of the risk (in-sample and population). As a consequence, we establish that, when trained on polynomially many samples, the gradient descent algorithm converges to the global optimum of the risk minimization problem regardless of the width of the network when it is initialized at some value [Formula: see text], which we compute. Furthermore, the network produced by the gradient descent has a near zero generalization error. Next, we establish that initializing the gradient descent algorithm below [Formula: see text] is easily achieved when the weights of the ground truth matrix [Formula: see text] are randomly generated and the matrix is sufficiently overparameterized. Finally, we identify a simple necessary and sufficient geometric condition on the size of the training set under which any global minimizer of the empirical risk has necessarily zero generalization error. Funding: The research of E. C. Kizildag is supported by Columbia University, with the Distinguished Postdoctoral Fellowship in Statistics. Support from the National Science Foundation [Grant DMS-2015517] is gratefully acknowledged.

First person – Harini Iyer

ABSTRACT First Person is a series of interviews with the first authors of a selection of papers published in Journal of Cell Science, helping researchers promote themselves alongside their papers. Harini Iyer is first author on ‘ The Cl− transporter ClC-7 is essential for phagocytic clearance by microglia’, published in JCS. Harini conducted the research described in this article while a Postdoctoral Scholar in William Talbot's lab at Beckman Center, Stanford, USA. She is now an Assistant Professor at Rice University, Houston, USA investigating lysosomal signaling in the neuroimmune system.

Cell scientist to watch – Dan Dickinson

ABSTRACT Dan Dickinson is an Assistant Professor in Molecular Biosciences at the University of Texas at Austin (UT Austin), USA. He completed his doctoral studies at Stanford University in California, co-mentored by Prof. Bill Weis and Prof. James Nelson, where he became fascinated with cell polarity in the amoeba Dictyostelium discoideum. He next moved to Prof. Bob Goldstein's lab at the University of North Carolina at Chapel Hill for his postdoctoral research, where he developed a single-cell method to probe protein interactions in Caenorhabditis elegans zygotes. In 2017, he started his own lab at UT Austin. Intrigued by capacity of proteins to generate complex patterns across scales, his group aims to close the gap between biochemistry and cell biology using single-cell methods to investigate cell polarity in diverse contexts. For our Special Issue on Cell and Tissue Polarity, we spoke with Dan over Zoom about his goals as a researcher and educator and his dedication to teaching students the joy of scientific inquiry.

First person – Alex van Vliet

ABSTRACT First Person is a series of interviews with the first authors of a selection of papers published in Journal of Cell Science, helping researchers promote themselves alongside their papers. Alex van Vliet is first author on ‘ Exploring the ATG9A interactome uncovers interaction with VPS13A’, published in JCS. Alex conducted the research described in this article while a Postdoctoral Training Fellow in Sharon Tooze's lab at The Francis Crick Institute, London, UK. He is now an MRC Postdoc in the lab of Sean Munro at MRC Laboratory of Molecular Biology, Cambridge, UK, investigating the mechanisms of membrane trafficking.

ECR Spotlight – Allison Litmer

ECR Spotlight is a series of interviews with early-career authors from a selection of papers published in Journal of Experimental Biology and aims to promote not only the diversity of early-career researchers (ECRs) working in experimental biology but also the huge variety of animals and physiological systems that are essential for the ‘comparative’ approach. Allison Litmer is an author on ‘ Cycling temperature treatments affect estimates of digestive performance in prairie lizards (Sceloporus consobrinus)’, published in JEB. Allison conducted the research described in this article while a Doctoral Academy Fellow in Steven J. Beaupre's lab at the University of Arkansas, USA. She is now a Postdoctoral Research Scientist in the lab of Eric Gangloff at Ohio Wesleyan University, USA, investigating how environmental attributes, in particular temperature, influence ectotherm persistence with a specific emphasis on bioenergetics and life history.

ECR Spotlight – Abhilasha Joshi

ECR Spotlight is a series of interviews with early-career authors from a selection of papers published in Journal of Experimental Biology and aims to promote not only the diversity of early-career researchers (ECRs) working in experimental biology but also the huge variety of animals and physiological systems that are essential for the ‘comparative’ approach. Abhilasha Joshi is an author on ‘ Fantastic beasts and how to study them: rethinking experimental animal behavior’, published in JEB. Abhilasha conducted postdoctoral research in Dr Loren Frank's lab at the University of California San Francisco, USA, and is now a Visiting Scientist at Champalimaud Center for the Unknown, Portugal, investigating the interactions between internal cognitive computations and ongoing actions.

Per Andersen. 12 January 1930—17 February 2020

Per Andersen was one of the leading neuroscientists of the second half of the twentieth century. He spent his entire career at the University of Oslo, apart from an exceptionally productive postdoctoral period with Sir John Eccles FRS at the Australian National University in Canberra between 1961 and 1963. As a PhD student he laid the foundation of field potential analysis, which allowed synaptic function in laminated cortical structures such as the hippocampus to be followed for long periods in intact animals, an essential technical prerequisite for the study of the synaptic basis of memory. In Canberra he identified the neurons responsible for feed-back inhibition in the hippocampus and feed-forward inhibition in the cerebellum, the first inhibitory neurons to be functionally identified in the mammalian brain. Per's Canberra achievements catapulted him to superstar status, and enabled him on his return to Oslo in 1963 to establish a laboratory that played a major role over the following decades in characterizing the functional properties of hippocampal synapses. From his laboratory emerged a string of significant advances, including the discovery of long-term potentiation, a form of synaptic plasticity widely believed to support learning and memory, and the introduction of the transverse hippocampal slice, which rapidly became the dominant preparation for investigating the properties of hippocampal neurons. Young researchers, many from the USA and Canada, flocked to his laboratory for postdoctoral training, adding to the steady stream of Norwegian doctoral students, two of whom went on to win the Nobel Prize. Per was also committed to the importance of communicating scientific advances to the general public, and contributed prolifically over the years to the Norwegian media, commentating on advances in neuroscience and their relevance to neurological disorders.

Survey of evaluation policies and procedures in clinical neuropsychology postdoctoral fellowship programs

Objective The objectives of this study were to examine current procedures that are used to evaluate competency development in clinical neuropsychology at the postdoctoral level and to investigate policies and procedures for the management of performance that is below expectations during the postdoctoral fellowship. Method Clinical neuropsychology fellowship program directors were invited via email with multiple reminders to participate in an online survey between 1/26/2023 and 3/31/2023. Results Most programs administer a competency-based written evaluation of fellow performance (92%) and have a written policy for managing performance that is below expectations (86%). However, greater variability was reported regarding the use of other evaluation tools, including fellow self-assessments (46% of programs), program evaluations (57% of programs), supervisor evaluations (73% of programs), and exit interviews (82% of programs). Moreover, there was variability between programs with regard to the specific competencies that were measured and how performance that is below expectations is managed. Conclusions Competency-based evaluations and clear, written policies and procedures for management of performance that is below expectations are recommended. Such tools and policies provide clear expectations for fellowship outcomes, promote regular communication between fellows and supervisors, foster early identification of gaps in training, facilitate program quality improvement, and increase opportunities to support and intervene during the course of fellowship training.

Molecular epidemiology and clinical impact of Klebsiella spp. causing bloodstream infections in Hong Kong

The epidemiological features of the Klebsiella pneumoniae causing bloodstream infections in Hong Kong and their potential threats to human health remained unknown. K.pneumoniae strains collected from four hospitals in Hong Kong during the period of 2009-2018 were subjected to molecular typing, string test, antimicrobial susceptibility testing, whole genome sequencing and analysis. Clinical data of patients from whom these strains were isolated were analyzed retrospectively using univariate and multivariate logistic regression approaches. The 240 Klebsiella spp. strains belonged to 123 different STs and 63 different capsule loci (KLs), with KL1 and KL2 being the major type. 86 out of 212 BSI-KP (40.6%) carried at least one of the virulence genes iuc, iro, rmpA or rmpA2. Virulence plasmid correlated well with the string test positive result, yet 8 strains without rmp genes were also hypermucoviscous, which was due to wzc mutation. The mortality rate of bloodstream infection patients was 43.0%. Univariant analysis showed that factors including renal replacement therapy (FDR adjusted p=0.0007), mechanical ventilation (FDR adjusted p<0.0001) and respiratory sepsis (FDR adjusted p<0.0001) were found to pose the highest risk of death upon infection by Klebsiella spp. This study revealed the high mortality rate and risk factors associated with bloodstream infections caused by K.pneumoniae in Hong Kong, which warrants immediate action to develop effective solution to tackle this problem. Theme Based Research Scheme (T11-104/22-R), Research Impact Fund (R5011-18F) and Postdoctoral Fellowship (PDFS2223-1S09).

Review: Canadian Performance Documents and Debates: A Sourcebook

Dr. Sarah Robbins (Postdoctoral Researcher, University of Toronto) reviews Canadian Performance Documents and Debates: A Sourcebook (2022), edited by Anthony J. Vickery, Glen F. Nichols, and Allana C. Lindgren. Employing an intersectional lens, Dr. Robbins considers what is present and absent in this expansive text of historical ‘Canadian’ artifacts and documents from 1606 through to 1967, the potential for a second volume, and the sourcebook’s value as a teaching tool for instructors aiming to both trouble linear trajectories of history and increase engagement with historical documentation of performance from the lands we now call ‘Canada.’

First person – Nichole Link

ABSTRACT First Person is a series of interviews with the first authors of a selection of papers published in Disease Models &amp; Mechanisms, helping researchers promote themselves alongside their papers. Nichole Link is first author on ‘ A Zika virus protein expression screen in Drosophila to investigate targeted host pathways during development’, published in DMM. Nichole conducted the research described in this article while a postdoctoral researcher in Hugo Bellen's lab at Baylor College of Medicine, Houston, USA. She is now an assistant professor and has her own laboratory at the University of Utah in Salt Lake City, investigating genetic and developmental models of human disease.

ECR Spotlight – Cristina Ottocento

ECR Spotlight is a series of interviews with early-career authors from a selection of papers published in Journal of Experimental Biology and aims to promote not only the diversity of early-career researchers (ECRs) working in experimental biology but also the huge variety of animals and physiological systems that are essential for the ‘comparative’ approach. Cristina Ottocento is an author on ‘ Diet influences resource allocation in chemical defence but not melanin synthesis in an aposematic moth’, published in JEB. Cristina conducted the research described in this article while a PhD Researcher in Johanna Mappes's lab at the University of Jyväskylä, Finland. She is now a Postdoctoral Researcher in the lab of Johanna Mappes at the University of Helsinki, Finland, investigating chemical ecology and chemical communication.

Abstract PR03: CSF-1R antibody targeting therapy with combined metronomic chemotherapy and immune checkpoint blockade enhance a B and T cell response to attenuate metastatic triple negative breast cancer

Abstract Background: Increased macrophage infiltration and elevated levels of Epithelial to Mesenchymal Transition (EMT) gene signatures are associated with a poor outcome following neo-adjuvant chemotherapy in patients with triple negative breast cancer (TNBC). Further, metastatic disease with overall the poorest survival rates has a cold tumor immune microenvironment (TIME), especially in lung and liver metastases. Interestingly, an abundance of macrophages are observed at these metastatic sites. We have extensively characterized multiple preclinical syngeneic Trp53-/- tumor models that have extensive Tumor Associated Macrophage (TAM) infiltration. These tumor models transcriptionally resemble “claudin-low”, “basal-like” and “luminal-like” breast cancers. From these models the “claudin-low” closely phenocopy the high EMT/TAM subtype observed in patients. Objective: Accordingly, we asked if SNDX-ms6352 a novel specific, high affinity monoclonal antibody targeting CSF-1R in combination with Chemotherapy (CTX) and immune checkpoint blockade might provide an alternative approach for treating established lung and liver metastases. Methods: Single cells from primary T12 mammary tumors were introduced either via tail vein injection to obtain lung metastases or portal vein (PV) injection for liver metastases. Mice were injected with BrdU and multiple lung and liver tissues are harvested randomly to identify established metastases. The mice were randomized into treatment groups and administered four weekly treatments of IgG, CTX, SNDX-ms6352, CTX+SNDX-ms6352 or CTX+SNDX-ms6352+aPD1. Tissues were harvested and fixed overnight in 4% PFA then placed in 70% EtOH for paraffin embedding and stained for H&amp;E, Immunohistochemistry (IHC), Immunofluorescence (IF) and Imaging Mass Cytometry (IMC). Results: Following four weekly treatments of IgG, SNDX-ms6352 and CTX+/-SNDX-ms6352 we observed a decrease in lung metastatic burden and an increase in overall survival as compared to IgG, CTX and SNDX-ms6352 alone. Interestingly we also observed increased CD8 T-cell infiltration, but only in the combination treated mice 28 and 56 days post treatment. However, lung metastases recurred in all of the mice several weeks later. Data from IMC showed intra-tumoral heterogeneity with increased PD-L1 and Ki67. Short term treated lung and liver metastases with the addition of aPD1 demonstrated increased CD20+ B and CD8+ T cell expansion and cleared most of the lung and liver metastatic burden. These results suggest that targeting macrophages enhances the immunostimulatory effect of metronomic CTX with immune checkpoint blockade in treating not only primary tumors, but also established lung and liver metastases via the activation of the tumor immune microenvironment. Supported by R01CA148761-12 and American Cancer Society – AutoZone Breast Cancer Postdoctoral Fellowship, PF-22-163-01-MM grants. Citation Format: Diego A Pedroza, Qian Zhu, Weigou Wu, Paul Porter, Xiang H-F Zhang, Jeffrey M Rosen. CSF-1R antibody targeting therapy with combined metronomic chemotherapy and immune checkpoint blockade enhance a B and T cell response to attenuate metastatic triple negative breast cancer [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Advances in Breast Cancer Research; 2023 Oct 19-22; San Diego, California. Philadelphia (PA): AACR; Cancer Res 2024;84(3 Suppl_1):Abstract nr PR03.

Cell scientist to watch – Jakub Sedzinski

ABSTRACT Jakub Sedzinski is an Associate Professor at the University of Copenhagen and the Novo Nordisk Foundation Center for Stem Cell Medicine (reNEW), Denmark. After his undergraduate and Master's degrees in biotechnology at the University of Wroclaw, Poland, he completed his PhD in Prof. Ewa Paluch's lab at the Max Planck Institute of Molecular Cell Biology and Genetics in Dresden, Germany, where he studied biophysical aspects of fundamental cell behaviours. Next, he moved to the University of Texas at Austin in the USA for a postdoctoral fellowship with Prof. John Wallingford. There, he became interested in how cell-level mechanics influence the complex development and maintenance of tissues like the mucociliary epithelium. In 2017, he started his own lab in Copenhagen where he continues to integrate biophysics with cell biology and developmental models in order to elucidate the relationships between cell and tissue mechanics and cell fate acquisition in epithelial tissue dynamics. We spoke with Jakub over Zoom about his career and how his cross-disciplinary approach to research is driven by his fundamental passion for learning new things.

Barriers to finding psychology postdoctoral training opportunities in intensive care settings.

U.S. health organizations, including Division 22 of the American Psychological Association, the Society for Critical Care Medicine, and the American Thoracic Society advocate for psychological treatment that improves long-term outcomes in critical illness survivors. However, limited information exists with regard to psychology training opportunities in intensive care settings. We aim to identify and describe (a) existing psychology programs with training in intensive care settings and (b) barriers to finding these training opportunities. Using aspects of the Arksey and O'Malley Framework and Preferred Reporting Items for Systematic Review and Meta-Analyses Extension for Scoping Reviews reporting checklist as guides, two independent reviewers searched the Association of Psychology Postdoctoral and Internship Centers (APPIC) Directory and Universal Psychology Postdoctoral Directory (UPPD) to identify programs with training experiences in intensive care settings. Searching the APPIC Directory did not reliably or accurately identify training opportunities in intensive care settings. Thus, only programs identified in the more reliable UPPD search were considered for inclusion. After duplicates were removed, searches using the UPPD yielded 31 programs for review. Of those, 22 programs met inclusion, offering heterogeneous training in intensive care settings. These results suggest few opportunities exist for psychology training in intensive care settings and available opportunities are difficult to identify using standard search methods. The identified challenges also emphasize the need for advanced search features for training opportunities within APPIC/UPPD and/or a list of programs offering these training opportunities. Our results highlight the importance of program descriptions that accurately and comprehensively reflect training opportunities-particularly relating to opportunities in intensive care settings. (PsycInfo Database Record (c) 2024 APA, all rights reserved).

‘I can’t do maths’. Can we break this popular phrase? A review of the annual Mathematical Cognition and Learning Society conference and a sneak preview of some recent research

Good mathematical skills are vital for success in school, employment and everyday life, yet many individuals struggle with mathematics, and it is a sad state that saying ‘I can’t do maths’ is a norm. Behind the scenes many researchers and educators are trying to understand why children and adults find mathematics difficult and are designing research-led interventions and programmes to help. In this article I review some of the research that was presented at this years annual Mathematical Cognition and Learning Society (MCLS) conference, an international conference that started only six years ago, but in that time has quickly become the largest in the field. I also present a summary of my postdoctoral work that I’ve been conducting over the last few years, which investigates why many children struggle to learn multiplication facts.

The profile of postdoctoral research fellows in South Africa: Trends over the past two decades

The need for evidence on postdoctoral research fellows, or ‘postdocs’, has become increasingly evident globally, as many countries, including South Africa, lack information on these researchers. We used existing sources of quantitative data to provide a longitudinal profile of postdocs at South African public universities. These sources include national research-and-development surveys and data from the national Higher Education Management Information System. Our focus was on postdocs’ representation and research intensity (i.e. time spent on research) within the national research system, as well as on two key demographic features, namely nationality and gender. We draw comparisons with findings reported for other countries to situate our results within the global science system. Interpretation of our results leads us to comment on global and national developments and policies relevant to postdocs. Significance: This article provides, for the first time, longitudinal, quantitative evidence at the national level about postdocs in South Africa, a category of early-career researcher which has been growing in size and relevance but has remained largely invisible. The findings provide the basis for a critical reflection on current discourses and policies related to postdocs in South Africa. Interpretation of the findings allows us to identify priorities for future research on postdocs in South Africa that would be most useful to inform both national and institutional policy.

Ideals of the good life and good science among high achieving men and women scientists

Traditional gender roles and gender stereotypes assume different life and career priorities among men and women. Meanwhile, the science profession is commonly considered to abide by a universalist ethos and a meritocracy that is independent of gender. We examined whether men and women scientists held different ideals about the good life and about good science. Furthermore, we investigated if those ideals of good life and of good science were linked in the minds of scientists; and if the linkages differed by gender. This study used a structural topic modeling approach to analyze the interview transcripts of 108 women and 92 men elite scientists who had received highly prestigious postdoctoral fellowships during the 1960s and1970s. In the open-ended interviews, the scientists were asked to describe their ideals of good life and of good science. Regarding the good life, we found that women scientists focused more on enjoying life and relationships and less on intellectual stimulation, relative to men scientists. For good science, women scientists focused more on empirical procedural accuracy and less on basic and fundamental breakthroughs, relative to men scientists. Moreover, we found that women scientists exhibited correlations between life and science ideals, whereas the two domains were completely separate for men scientists. In conclusion, a gendered system of life and science ideals existed even among this group of highly promising scientists.