Publishing: Credit where credit is due

Paracrine signals influence patterns of fibrocartilage differentiation in a lyophilized gelatin hydrogel for applications in rotator cuff repair

Rotator cuff injuries present a clinical challenge for repair due to current limitations in functional regeneration of the native tendon-to-bone enthesis. A biomaterial that can regionally instruct unique tissue-specific phenotypes offers potential to promote enthesis repair. We have recently demonstrated the mechanical benefits of a stratified triphasic biomaterial made up of tendon- and bone-mimetic collagen scaffold compartments connected via a continuous hydrogel, and we now explore the potential of a biologically favorable enthesis hydrogel for this application. Here we report in vitro behavior of human mesenchymal stem cells (hMSCs) within thiolated gelatin (Gel-SH) hydrogels in response to chondrogenic stimuli as well as paracrine signals derived from MSC-seeded bone and tendon scaffold compartments. Chondrogenic differentiation media promoted upregulation of cartilage and entheseal fibrocartilage matrix markers COL2, COLX, and ACAN as well as the enthesis-associated transcription factors SCX, SOX9, and RUNX2 in hMSCs within Gel-SH. Similar effects were observed in response to TGF-β3 and BMP-4, enthesis-associated growth factors known to play a role in entheseal development and maintenance. Conditioned media generated by hMSCs seeded in tendon- and bone-mimetic collagen scaffolds influenced patterns of gene expression regarding enthesis-relevant growth factors, matrix markers, and tendon-to-bone transcription factors for hMSCs within the material. Together, these findings demonstrate that a Gel-SH hydrogel provides a permissive environment for enthesis tissue engineering and highlights the significance of cellular crosstalk between adjacent compartments within a spatially graded biomaterial.

Acquired Temozolomide Resistance Instructs Patterns of Glioblastoma Behavior in Gelatin Hydrogels

Acquired drug resistance in glioblastoma (GBM) presents a major clinical challenge and is a key factor contributing to abysmal prognosis, with less than 15 months median overall survival. Aggressive chemotherapy with the frontline therapeutic, temozolomide (TMZ), ultimately fails to kill residual highly invasive tumor cells after surgical resection and radiotherapy. Here, a 3D engineered model of acquired TMZ resistance is reported using two isogenically matched sets of GBM cell lines encapsulated in gelatin methacrylol hydrogels. Response of TMZ-resistant versus TMZ-sensitive GBM cell lines within the gelatin-based extracellular matrix platform is benchmarked and drug response at physiologically relevant TMZ concentrations is further validated. The changes in drug sensitivity, cell invasion, and matrix-remodeling cytokine production are shown as the result of acquired TMZ resistance. This platform lays the foundation for future investigations targeting key elements of the GBM tumor microenvironment to combat GBM's devastating impact by advancing the understanding of GBM progression and treatment response to guide the development of novel treatment strategies.

Gelatin maleimide microgels for hematopoietic progenitor cell encapsulation

Hematopoietic stem cells (HSCs) are the apical cells of the hematopoietic system, giving rise to cells of the blood and lymph lineages. HSCs reside primarily within bone marrow niches that contain matrix and cell-derived signals that help inform stem cell fate. Aspects of the bone marrow microenvironment have been captured in vitro by encapsulating cells within hydrogel matrices that mimic native mechanical and biochemical properties. Hydrogel microparticles, or microgels, are increasingly being used to assemble granular biomaterials for cell culture and noninvasive delivery applications. Here, we report the optimization of a gelatin maleimide hydrogel system to create monodisperse gelatin microgels via a flow-focusing microfluidic process. We report characteristic hydrogel stiffness, stability, and swelling characteristics as well as encapsulation of murine hematopoietic stem and progenitor cells, and mesenchymal stem cells within microgels. Microgels support cell viability, confirming compatibility of the microfluidic encapsulation process with these sensitive bone marrow cell populations. Overall, this work presents a microgel-based gelatin maleimide hydrogel as a foundation for future development of a multicellular artificial bone marrow culture system.

Ten simple rules for computational biologists collaborating with wet lab researchers

Computational biologists are frequently engaged in collaborative data analysis with wet lab researchers. These interdisciplinary projects, as necessary as they are to the scientific endeavor, can be surprisingly challenging due to cultural differences in operations and values. In this Ten Simple Rules guide, we aim to help dry lab researchers identify sources of friction and provide actionable tools to facilitate respectful, open, transparent, and rewarding collaborations.

The impact of affiliation naming proximity on the retrieval efficiency of Chinese universities-affiliated retractions in the Retraction Watch Database

The Retraction Watch Database (RWDB) is widely used to retrieve retraction data. However, its lack of affiliation normalization hinders the retrieval efficiency of retraction data for specific research-performing organizations. A query for a university name in the RWDB may yield retraction data entries for other universities with similar names, giving rise to the issue of affiliation naming proximity. This study assessed the impact of this issue on the retrieval efficiency of retraction records for 2,692 Chinese university names in English. The analysis revealed that the retrieval efficiency of retraction records for 206 Chinese university names can be influenced by 408 university names. As of 2022, the retrieval efficiency of retraction records for 96 Chinese university names was compromised by the involvement of 402 university names, resulting in an overall retraction inflation rate of 37.9% and an average rate of 45.0%. The findings highlight the importance of curating retraction data through affiliation-specific queries in the RWDB, adhering to the official English names of Chinese universities for scholarly publishing, and adopting the Research Organization Registry system for affiliation disambiguation. Given the significance of this issue concerning the English names of universities in non-English-speaking countries, the identified causes of the problem and proposed solutions can offer valuable insights for improving the retrieval of retraction records for non-Chinese universities in the RWDB.

Cell Chirality of Micropatterned Endometrial Microvascular Endothelial Cells

Chirality is an intrinsic cellular property that describes cell polarization biases along the left-right axis, apicobasal axis, or front-rear axes. Cell chirality plays a significant role in the arrangement of organs in the body as well as in the orientation of organelles, cytoskeletons, and cells. Vascular networks within the endometrium, the mucosal inner lining of the uterus, commonly display spiral architectures that rapidly form across the menstrual cycle. Herein, the role of endometrial-relevant extracellular matrix stiffness, composition, and soluble signals on endometrial endothelial cell chirality is systematically examined using a high-throughput microarray. Endometrial endothelial cells display marked patterns of chirality as individual cells and as cohorts in response to substrate stiffness and environmental cues. Vascular networks formed from endometrial endothelial cells also display shifts in chirality as a function of exogenous hormones. Changes in cellular-scale chirality correlate with changes in vascular network parameters, suggesting a critical role for cellular chirality in directing endometrial vessel network organization.

The case for affiliation contribution statements

Author affiliation disclosures are arguably a critical yet poorly understood and largely unregulated phenomenon in scholarly and scientific publishing. First, this paper argues that affiliation attribution practices are burdened by misunderstandings and misuses. Second, it suggests that universities, research institutions and publishers should urgently engage in a conversation aimed at clearly defining expectations and promoting best practices. Third, it introduces affiliation contribution statements as a concrete initiative in the direction of increased accuracy, transparency, and accountability.

Evaluating osteogenic effects associated with the incorporation of ascorbic acid in mineralized collagen scaffolds

Current treatments for craniomaxillofacial (CMF) defects motivate the design of instructive biomaterials that can promote osteogenic healing of complex bone defects. We report methods to promote in vitro osteogenesis of human mesenchymal stem cells (hMSCs) within a model mineralized collagen scaffold via the incorporation of ascorbic acid (vitamin C), a key factor in collagen biosynthesis and bone mineralization. An addition of 5 w/v% ascorbic acid into the base mineralized collagen scaffold significantly changes key morphology characteristics including porosity, macrostructure, and microstructure. This modification promotes hMSC metabolic activity, ALP activity, and hMSC-mediated deposition of calcium and phosphorous. Additionally, the incorporation of ascorbic acid influences osteogenic gene expression (BMP-2, RUNX2, COL1A2) and delays the expression of genes associated with osteoclast activity and bone resorption (OPN, CTSK), though it reduces the secretion of OPG. Together, these findings highlight ascorbic acid as a relevant component for mineralized collagen scaffold design to promote osteogenic differentiation and new bone formation for improved CMF outcomes.

The Coastal Carbon Library and Atlas: Open source soil data and tools supporting blue carbon research and policy

Quantifying carbon fluxes into and out of coastal soils is critical to meeting greenhouse gas reduction and coastal resiliency goals. Numerous 'blue carbon' studies have generated, or benefitted from, synthetic datasets. However, the community those efforts inspired does not have a centralized, standardized database of disaggregated data used to estimate carbon stocks and fluxes. In this paper, we describe a data structure designed to standardize data reporting, maximize reuse, and maintain a chain of credit from synthesis to original source. We introduce version 1.0.0. of the Coastal Carbon Library, a global database of 6723 soil profiles representing blue carbon-storing systems including marshes, mangroves, tidal freshwater forests, and seagrasses. We also present the Coastal Carbon Atlas, an R-shiny application that can be used to visualize, query, and download portions of the Coastal Carbon Library. The majority (4815) of entries in the database can be used for carbon stock assessments without the need for interpolating missing soil variables, 533 are available for estimating carbon burial rate, and 326 are useful for fitting dynamic soil formation models. Organic matter density significantly varied by habitat with tidal freshwater forests having the highest density, and seagrasses having the lowest. Future work could involve expansion of the synthesis to include more deep stock assessments, increasing the representation of data outside of the U.S., and increasing the amount of data available for mangroves and seagrasses, especially carbon burial rate data. We present proposed best practices for blue carbon data including an emphasis on disaggregation, data publication, dataset documentation, and use of standardized vocabulary and templates whenever appropriate. To conclude, the Coastal Carbon Library and Atlas serve as a general example of a grassroots F.A.I.R. (Findable, Accessible, Interoperable, and Reusable) data effort demonstrating how data producers can coordinate to develop tools relevant to policy and decision-making.

Generative design approach to combine architected Voronoi foams with porous collagen scaffolds to create a tunable composite biomaterial

Regenerative biomaterials for musculoskeletal defects must address multi-scale mechanical challenges. Repairing craniomaxillofacial bone defects, which are often large and irregularly shaped, requires close conformal contact between implant and defect margins to aid healing. While mineralized collagen scaffolds can promote mesenchymal stem cell osteogenic differentiation in vitro and bone formation in vivo, their mechanical performance is insufficient for surgical translation. We report a generative design approach to create scaffold-mesh composites by embedding a macro-scale polymeric Voronoi mesh into the mineralized collagen scaffold. The mechanics of architected foam reinforced composites are defined by a rigorous predictive moduli equation. We show biphasic composites localize strain during loading. Further, planar and 3D mesh-scaffold composites can be rapidly shaped to aid conformal fitting. Voronoi-based composites overcome traditional porosity-mechanics relationship limits while enabling rapid shaping of regenerative implants to conformally fit complex defects unique for individual patients. STATEMENT OF SIGNIFICANCE: Biomaterial strategies for (craniomaxillofacial) bone regeneration are often limited by the size and complex geometry of the defects. Voronoi structures are open-cell foams with tunable mechanical properties which have primarily been used computationally. We describe generative design strategies to create Voronoi foams via 3D-printing then embed them into an osteogenic mineralized collagen scaffold to form a multi-scale composite biomaterial. Voronoi structures have predictable and tailorable moduli, permit stain localization to defined regions of the composite, and permit conformal fitting to effect margins to aid surgical practicality and improve host-biomaterial interactions. Multi-scale composites based on Voronoi foams represent an adaptable design approach to address significant challenges to large-scale bone repair.

Acquired temozolomide resistance instructs patterns of glioblastoma behavior in gelatin hydrogels

Acquired drug resistance in glioblastoma (GBM) presents a major clinical challenge and is a key factor contributing to abysmal prognosis, with less than 15 months median overall survival. Aggressive chemotherapy with the frontline therapeutic, temozolomide (TMZ), ultimately fails to kill residual highly invasive tumor cells after surgical resection and radiotherapy. Here, we report a three-dimensional (3D) engineered model of acquired TMZ resistance using two isogenically-matched sets of GBM cell lines encapsulated in gelatin methacrylol hydrogels. We benchmark response of TMZ-resistant vs. TMZ-sensitive GBM cell lines within the gelatin-based extracellular matrix platform and further validate drug response at physiologically relevant TMZ concentrations. We show changes in drug sensitivity, cell invasion, and matrix-remodeling cytokine production as the result of acquired TMZ resistance. This platform lays the foundation for future investigations targeting key elements of the GBM tumor microenvironment to combat GBM's devastating impact by advancing our understanding of GBM progression and treatment response to guide the development of novel treatment strategies.

Teaser

A hydrogel model to investigate the impact of acquired drug resistance on functional response in glioblastoma.

Cell Chirality of Micropatterned Endometrial Microvascular Endothelial Cells

Chirality is an intrinsic cellular property that describes cell polarization biases along the left-right axis, apicobasal axis, or front-rear axes. Cell chirality plays a significant role in the arrangement of organs in the body as well as the orientation of organelles, cytoskeletons, and cells. Vascular networks within the endometrium, the mucosal inner lining of the uterus, commonly display spiral architectures that rapidly form across the menstrual cycle. Herein, we systematically examine the role of endometrial-relevant extracellular matrix stiffness, composition, and soluble signals on endometrial endothelial cell chirality using a high-throughput microarray. Endometrial endothelial cells display marked patterns of chirality as individual cells and as cohorts in response to substrate stiffness and environmental cues. Vascular networks formed from endometrial endothelial cells also display shifts in chirality as a function of exogenous hormones. Changes in cellular-scale chirality correlate with changes in vascular network parameters, suggesting a critical role for cellular chirality in directing endometrial vessel network organization.

Opportunities, challenges and tensions: Open science through a lens of qualitative social psychology

In recent years, there has been a focus in social psychology on efforts to improve the robustness, rigour, transparency and openness of psychological research. This has led to a plethora of new tools, practices and initiatives that each aim to combat questionable research practices and improve the credibility of social psychological scholarship. However, the majority of these efforts derive from quantitative, deductive, hypothesis-testing methodologies, and there has been a notable lack of in-depth exploration about what the tools, practices and values may mean for research that uses qualitative methodologies. Here, we introduce a Special Section of BJSP: Open Science, Qualitative Methods and Social Psychology: Possibilities and Tensions. The authors critically discuss a range of issues, including authorship, data sharing and broader research practices. Taken together, these papers urge the discipline to carefully consider the ontological, epistemological and methodological underpinnings of efforts to improve psychological science, and advocate for a critical appreciation of how mainstream open science discourse may (or may not) be compatible with the goals of qualitative research.

Modulation of Trust in Borderline Personality Disorder by Script-Based Imaginal Exposure to Betrayal

Interpersonal and trust-related difficulties are central features of borderline personality disorder (BPD). In this study, we applied script-driven betrayal imagery to evoke mistrustful behavior in a social reinforcement learning task. In 21 BPD and 20 healthy control (HC) participants, we compared this approach to the standard confederate paradigm used in research studies. The script-driven imagery evoked a transient increase in negative affect and also decreased trusting behavior to a similar degree in both groups. Across conditions, we also replicated previously reported between-group differences in negative affect (increased in BPD) and task behavior (more sensitive to social cues in BPD). These results support the validity of script-driven imagery as an alternative social task stimulus. This script-driven imagery approach is appealing for clinical research studies on reinforcement learning because it eliminates deception, scales easily, and evokes disorder-specific states of social difficulty.

The first author takes it all? Solutions for crediting authors more visibly, transparently, and free of bias

With the seventh edition of the publication manual of the American Psychological Association (APA), the APA style now prescribes bias-free language and encourages accessibility even to non-academic audiences. However, even with the newest guidelines, the way we credit authors in psychology remains anachronistic, intransparent, and prone to conflict. It still relies on a sequence-determines-credit approach in the byline, which concurrently is contradicted by the option to consider the last author as the position of the principal investigator depending on the field or journal. Scholars from various disciplines have argued that relying on such norms introduces a considerable amount of error when stakeholders rely on articles for career-relevant decisions. Given the existing recommendations towards a credit-based system, ignoring those issues will further promote bias that could be avoided with rather minor changes to the way we perceive authorship. In this article, we introduce a set of easy-to-implement changes to the manuscript layout that value contribution rather than position. Aimed at fostering transparency, accountability, and equality between authors, establishing those changes would likely benefit all stakeholders in contemporary psychological science.

Natural differential privacy-a perspective on protection guarantees

We introduce "Natural" differential privacy (NDP)-which utilizes features of existing hardware architecture to implement differentially private computations. We show that NDP both guarantees strong bounds on privacy loss and constitutes a practical exception to no-free-lunch theorems on privacy. We describe how NDP can be efficiently implemented and how it aligns with recognized privacy principles and frameworks. We discuss the importance of formal protection guarantees and the relationship between formal and substantive protections.

Quantifying Intramolecular Basis Set Superposition Errors

We show that medium-sized Gaussian basis sets lead to significant intramolecular basis set superposition errors at Hartree-Fock and density functional levels of theory, with artificial stabilization of compact over extended conformations for a 186 atom deca-peptide. Errors of ∼80 and ∼10 kJ/mol are observed, with polarized double zeta and polarized triple zeta quality basis sets, respectively. Two different procedures for taking the basis set superposition error into account are tested. While both reduce the error, it appears that polarized quadruple zeta basis sets are required to reduce the error below a few kJ/mol. Alternatively, the basis set superposition error can be eliminated using multiresolution methods based on Multiwavelets.

Generative design approach to combine architected Voronoi foams with porous collagen scaffolds to create a tunable composite biomaterial

Regenerative biomaterials for musculoskeletal defects must address multi-scale mechanical challenges. We are developing biomaterials for craniomaxillofacial bone defects that are often large and irregularly shaped. These require close conformal contact between implant and defect margins to aid healing. While we have identified a mineralized collagen scaffold that promotes mesenchymal stem cell osteogenic differentiation in vitro and bone formation in vivo, its mechanical performance is insufficient for surgical translation. We report a generative design approach to create scaffold-mesh composites by embedding a macro-scale polymeric Voronoi mesh into the mineralized collagen scaffold. The mechanics of architected foam reinforced composites are defined by a rigorous predictive moduli equation. We show biphasic composites localize strain during loading. Further, planar and 3D mesh-scaffold composites can be rapidly shaped to aid conformal fitting. Voronoi-based composites overcome traditional porosity-mechanics relationship limits while enabling rapid shaping of regenerative implants to conformally fit complex defects unique for individual patients.

Evidence- and data-driven classification of low back pain via artificial intelligence: Protocol of the PREDICT-LBP study

In patients presenting with low back pain (LBP), once specific causes are excluded (fracture, infection, inflammatory arthritis, cancer, cauda equina and radiculopathy) many clinicians pose a diagnosis of non-specific LBP. Accordingly, current management of non-specific LBP is generic. There is a need for a classification of non-specific LBP that is both data- and evidence-based assessing multi-dimensional pain-related factors in a large sample size. The "PRedictive Evidence Driven Intelligent Classification Tool for Low Back Pain" (PREDICT-LBP) project is a prospective cross-sectional study which will compare 300 women and men with non-specific LBP (aged 18-55 years) with 100 matched referents without a history of LBP. Participants will be recruited from the general public and local medical facilities. Data will be collected on spinal tissue (intervertebral disc composition and morphology, vertebral fat fraction and paraspinal muscle size and composition via magnetic resonance imaging [MRI]), central nervous system adaptation (pain thresholds, temporal summation of pain, brain resting state functional connectivity, structural connectivity and regional volumes via MRI), psychosocial factors (e.g. depression, anxiety) and other musculoskeletal pain symptoms. Dimensionality reduction, cluster validation and fuzzy c-means clustering methods, classification models, and relevant sensitivity analyses, will classify non-specific LBP patients into sub-groups. This project represents a first personalised diagnostic approach to non-specific LBP, with potential for widespread uptake in clinical practice. This project will provide evidence to support clinical trials assessing specific treatments approaches for potential subgroups of patients with non-specific LBP. The classification tool may lead to better patient outcomes and reduction in economic costs.

"Technical" Contributors and Authorship Distribution in Health Science

In health sciences, technical contributions may be undervalued and excluded in the author byline. In this paper, I demonstrate how authorship is a historical construct which perpetuates systemic injustices including technical undervaluation. I make use of Pierre Bourdieu's conceptual work to demonstrate how the power dynamics at play in academia make it very challenging to change the habitual state or "habitus". To counter this, I argue that we must reconceive technical contributions to not be a priori less important based on its nature when assigning roles and opportunities leading to authorship. I make this argument based on two premises. First, science has evolved due to major information and biotechnological innovation; this requires 'technicians' to acquire and exercise a commensurate high degree of both technical and intellectual expertise which in turn increases the value of their contribution. I will illustrate this by providing a brief historical view of work statisticians, computer programmers/data scientists and laboratory technicians. Second, excluding or undervaluing this type of work is contrary to norms of responsibility, fairness and trustworthiness of the individual researchers and of teams in science. Although such norms are continuously tested because of power dynamics, their importance is central to ethical authorship practice and research integrity. While it may be argued that detailed disclosure of contributions (known as contributorship) increases accountability by clearly identifying who did what in the publication, I contend that this may unintentionally legitimize undervaluation of technical roles and may decrease integrity of science. Finally, this paper offers recommendations to promote ethical inclusion of technical contributors.

Can the absolute configuration of cyclic peptides be determined with vibrational circular dichroism?

Cyclic peptides show a wide range of biological activities, among others as antibacterial agents. These peptides are often large and flexible with multiple chiral centers. The determination of the stereochemistry of molecules with multiple chiral centers is a challenging and important task in drug development. Chiroptical spectroscopies such as vibrational circular dichroism (VCD) can distinguish between different stereoisomers. The absolute configuration (AC) of a stereoisomer can be determined by comparing its experimental spectra to computed spectra of stereoisomers with known AC. In this way, the AC of rigid molecules with up to seven chiral centers has been assigned (Bogaerts et al., Phys. Chem. Chem. Phys., 2020, 22, 18014). The question arises whether this is possible with more conformationally flexible molecules such as cyclic peptides. We here investigate to what extent the AC of cyclic peptides can be determined with VCD. More specifically, we investigate the maximum number of chiral centers a cyclic peptide can have in order to be able to unambiguously assign the AC with VCD. We present experimental and computed IR and VCD spectra for a series of eight tetrapeptides and hexapeptides with two, three and four chiral centers. We use our recently developed computational protocol with a conformational search based on sampling with meta-dynamics. We use visual inspection to compare the computed spectra of different stereoisomers with an experimental spectrum of the corresponding cyclic peptide with known AC. We find that the AC of the investigated cyclic peptides with two chiral centers can be unambiguously assigned with VCD. This is however not possible for all of the cyclic peptides with three chiral centers and for none of those with four chiral centers. At best, one can limit the number of possible stereoisomers in those cases. Our work shows that other techniques are needed to assign the AC of cyclic peptides with three or more chiral centers. Our study also constitutes a warning that the spectra of all stereoisomers should be computed before attempting to match to an experimental spectrum, to avoid an accidental erroneous match.

Collecting and communicating perishable data in a post-disaster context: rapid research and rapid dissemination

Context

Puerto Rico experienced four natural disasters in 4 years (2017-2021): Hurricanes Irma and Maria, thousands of earthquakes reaching 6.4 magnitude, and the COVID-19 pandemic. In this context, our team sought to understand the impact of disaster aid distribution on poverty and economic inequality, and their relationship to the spread of COVID-19 across Puerto Rico. Rapid research was required to ensure we could collect perishable data within this ever-changing context.

Challenges

Our mixed methods design relied on both secondary and primary data. Because analyses of the former were to inform where and how to collect the latter, timing was of the essence. The data sources identified were not readily available to the public, and thus required gaining access through direct requests to government agencies. The requests coincided with a transition between administrations after an election. This resulted in unexpected delays. Once in the field, the team had to balance the rapid nature of the research with the mindful work to avoid compounding traumas experienced by participants, heightened risk for re-traumatization and fatigue, the risk of COVID-19, the digital divide, and intermittent electrical and telecommunication services.

Adaptations

In response to the delayed access to secondary data, we adjusted our research question. We continued to collect data as they became available, incorporating some immediately into analyses, and cleaning and storing others for future research opportunities. To overcome ongoing trauma challenges and prevent fatigue, we recruited and hired a large temporary team, including members of communities where we collected data. By recruiting participants and co-researchers at the same time and place, we both collapsed time between these activities and increased our team's contextual competency. To adapt to challenges presented by the pandemic, we created hybrid data collection procedures where some data were collected online, and some in person, while maintaining COVID-19 protections. We used similar adaptations for dissemination.

Lessons

Rapid research needs to be agile. Working within a convergence framework to investigate wicked problems had the unexpected added benefit of providing our team with a variety of disciplinary approaches which proved helpful in adapting to the changing conditions in the field. In addition to the resourcefulness of a transdisciplinary team, it is important to be willing to pivot in response to changes and to collect data where and when you can. To increase participation, opportunities need to be designed with flexibility, mindful of competing demands faced by individuals willing to collaborate. Collecting and analyzing data iteratively and utilizing local resources can enable rapid research that is rigorous and yields rich data.

Contributions

Our team applied the lessons learned to structure a rapid and iterative dissemination plan. We combined member-checking with community-level dissemination, enabling us to hone findings further before presenting to policy makers and media. Rapid research creates opportunities to make data-informed program and policy adjustments when they can be most impactful. Both the media and policy makers pay closer attention to research on current events. Hence, our recommendation is to do more rapid research! The more we do, the better we will get at it, and the more accustomed community leaders, policy makers, and program designers will become to using data to inform decisions.

Managing the "Three Cs" of Academic Literature Authorship: Contributions, Credit, and Conflict

Dissemination of information through publications is central to academic research, as well as professional advancement. Although seemingly a straightforward endeavor, publication authorship may present challenges. Although the International Committee of Medical Journal Editors defines authorship based on 4 required criteria, contemporary interdisciplinary collaborations can complicate authorship determinations. However, communication that occurs early and frequently in the research and writing process can help to prevent or mitigate potential conflicts, while a process for defining authorship contributions can aid in awarding proper credit. The Contributor Roles Taxonomy (CRediT) defines 14 essential roles of manuscript authors that can be utilized to characterize individual author contributions toward any given publication. This information is useful for academic administrators when evaluating contributors of faculty during promotion and tenure decisions. In the era of collaborative scientific, clinical, and pedagogical scholarship, providing faculty development, including statements of credit in the published work, and developing institutional systems to capture and assess contributions are key.

Cavity-Free Continuum Solvation: Implementation and Parametrization in a Multiwavelet Framework

We present a multiwavelet-based implementation of a quantum/classical polarizable continuum model. The solvent model uses a diffuse solute-solvent boundary and a position-dependent permittivity, lifting the sharp-boundary assumption underlying many existing continuum solvation models. We are able to include both surface and volume polarization effects in the quantum/classical coupling, with guaranteed precision, due to the adaptive refinement strategies of our multiwavelet implementation. The model can account for complex solvent environments and does not need a posteriori corrections for volume polarization effects. We validate our results against a sharp-boundary continuum model and find a very good correlation of the polarization energies computed for the Minnesota solvation database.

Evaluation of bacterial attachment on mineralized collagen scaffolds and addition of manuka honey to increase mesenchymal stem cell osteogenesis

The design of biomaterials to regenerate bone is likely to increasingly require modifications that reduce bacterial attachment and biofilm formation as infection during wound regeneration can significantly impede tissue repair and typically requires surgical intervention to restart the healing process. Further, much research on infection prevention in bone biomaterials has focused on modeling of non-resorbable metal alloy materials, whereas an expanding direction of bone regeneration has focused on development of bioresorbable materials. This represents a need for the prevention and understanding of infection in resorbable biomaterials. Here, we investigate the ability of a mineralized collagen biomaterial to natively resist infection and examine how the addition of manuka honey, previously identified as an antimicrobial agent, affects gram positive and negative bacterial colonization and mesenchymal stem cell osteogenesis and vasculature formation. We incorporate manuka honey into these scaffolds via either direct fabrication into the scaffold microarchitecture or via soaking the scaffold in a solution of manuka honey after fabrication. Direct incorporation results in a change in the surface characteristics and porosity of mineralized collagen scaffolds. Soaking scaffolds in honey concentrations higher than 10% had significant negative effects on mesenchymal stem cell metabolic activity. Soaking or incorporating 5% honey had no impact on endothelial cell tube formation. Although solutions of 5% honey reduced metabolic activity of mesenchymal stem cells, MSC-seeded scaffolds displayed increased calcium and phosphorous mineral formation, osteoprotegerin release, and alkaline phosphatase activity. Bacteria cultured on mineralized collagen scaffolds demonstrated surfaces covered in bacteria and no method of preventing infection, and using 10 times the minimal inhibitory concentration of antibiotics did not completely kill bacteria within the mineralized collagen scaffolds, indicating bioresorbable scaffold materials may act to shield bacteria from antibiotics. The addition of 5% manuka honey to scaffolds was not sufficient to prevent P. aeruginosa attachment or consistently reduce the activity of methicillin resistant staphylococcus aureus, and concentrations above 7% manuka honey are likely necessary to impact MRSA. Together, our results suggest bioresorbable scaffolds may create an environment conducive to bacterial growth, and potential trade-offs exist for the incorporation of low levels of honey in scaffolds to increase osteogenic potential of osteoprogenitors while high-levels of honey may be sufficient to reduce gram positive or negative bacteria activity but at the cost of reduced osteogenesis.

A machine learning approach to quantify gender bias in collaboration practices of mathematicians

Collaboration practices have been shown to be crucial determinants of scientific careers. We examine the effect of gender on coauthorship-based collaboration in mathematics, a discipline in which women continue to be underrepresented, especially in higher academic positions. We focus on two key aspects of scientific collaboration-the number of different coauthors and the number of single authorships. A higher number of coauthors has a positive effect on, e.g., the number of citations and productivity, while single authorships, for example, serve as evidence of scientific maturity and help to send a clear signal of one's proficiency to the community. Using machine learning-based methods, we show that collaboration networks of female mathematicians are slightly larger than those of their male colleagues when potential confounders such as seniority or total number of publications are controlled, while they author significantly fewer papers on their own. This confirms previous descriptive explorations and provides more precise models for the role of gender in collaboration in mathematics.

GA, Jensen SR, Eikås RDR, Frediani L. MRChem Multiresolution Analysis Code for Molecular Electronic Structure Calculations: Performance and Scaling Properties

MRChem is a code for molecular electronic structure calculations, based on a multiwavelet adaptive basis representation. We provide a description of our implementation strategy and several benchmark calculations. Systems comprising more than a thousand orbitals are investigated at the Hartree-Fock level of theory, with an emphasis on scaling properties. With our design, terms that formally scale quadratically with the system size in effect have a better scaling because of the implicit screening introduced by the inherent adaptivity of the method: all operations are performed to the requested precision, which serves the dual purpose of minimizing the computational cost and controlling the final error precisely. Comparisons with traditional Gaussian-type orbitals-based software show that MRChem can be competitive with respect to performance.

Amnion and chorion matrix maintain hMSC osteogenic response and enhance immunomodulatory and angiogenic potential in a mineralized collagen scaffold

Craniomaxillofacial (CMF) bone injuries present a major surgical challenge and cannot heal naturally due to their large size and complex topography. We are developing a mineralized collagen scaffold that mimics extracellular matrix (ECM) features of bone. These scaffolds induce in vitro human mesenchymal stem cell (hMSC) osteogenic differentiation and in vivo bone formation without the need for exogenous osteogenic supplements. Here, we seek to enhance pro-regenerative potential via inclusion of placental-derived products in the scaffold architecture. The amnion and chorion membranes are distinct components of the placenta that each have displayed anti-inflammatory, immunomodulatory, and osteogenic properties. While potentially a powerful modification to our mineralized collagen scaffolds, the route of inclusion (matrix-immobilized or soluble) is not well understood. Here we compare the effect of introducing amnion and chorion membrane matrix versus soluble extracts derived from these membranes into the collagen scaffolds on scaffold biophysical features and resultant hMSC osteogenic activity. While inclusion of amnion and chorion matrix into the scaffold microarchitecture during fabrication does not influence their porosity, it does influence compression properties. Incorporating soluble extracts from the amnion membrane into the scaffold post-fabrication induces the highest levels of hMSC metabolic activity and equivalent mineral deposition and elution of the osteoclast inhibitor osteoprotegerin (OPG) compared to the conventional mineralized collagen scaffolds. Mineralized collagen-amnion composite scaffolds elicited enhanced early stage osteogenic gene expression (BGLAP, BMP2), increased immunomodulatory gene expression (CCL2, HGF, and MCSF) and increased angiogenic gene expression (ANGPT1, VEGFA) in hMSCs. Mineralized collagen-chorion composite scaffolds promoted immunomodulatory gene expression in hMSCs (CCL2, HGF, and IL6) while unaffecting osteogenic gene expression. Together, these findings suggest that mineralized collagen scaffolds modified using matrix derived from amnion and chorion membranes represent a promising environment conducive to craniomaxillofacial bone repair.

Perivascular Stromal Cells Instruct Glioblastoma Invasion, Proliferation, and Therapeutic Response within an Engineered Brain Perivascular Niche Model

Glioblastoma (GBM) tumor cells are found in the perivascular niche microenvironment and are believed to associate closely with the brain microvasculature. However, it is largely unknown how the resident cells of the perivascular niche, such as endothelial cells, pericytes, and astrocytes, influence GBM tumor cell behavior and disease progression. A 3D in vitro model of the brain perivascular niche developed by encapsulating brain-derived endothelial cells, pericytes, and astrocytes in a gelatin hydrogel is described. It is shown that brain perivascular stromal cells, namely pericytes and astrocytes, contribute to vascular architecture and maturation. Cocultures of patient-derived GBM tumor cells with brain microvascular cells are used to identify a role for pericytes and astrocytes in establishing a perivascular niche environment that modulates GBM cell invasion, proliferation, and therapeutic response. Engineered models provide unique insight regarding the spatial patterning of GBM cell phenotypes in response to a multicellular model of the perivascular niche. Critically, it is shown that engineered perivascular models provide an important resource to evaluate mechanisms by which intercellular interactions modulate GBM tumor cell behavior, drug response, and provide a framework to consider patient-specific disease phenotypes.

An analysis-ready and quality controlled resource for pediatric brain white-matter research

We created a set of resources to enable research based on openly-available diffusion MRI (dMRI) data from the Healthy Brain Network (HBN) study. First, we curated the HBN dMRI data (N = 2747) into the Brain Imaging Data Structure and preprocessed it according to best-practices, including denoising and correcting for motion effects, susceptibility-related distortions, and eddy currents. Preprocessed, analysis-ready data was made openly available. Data quality plays a key role in the analysis of dMRI. To optimize QC and scale it to this large dataset, we trained a neural network through the combination of a small data subset scored by experts and a larger set scored by community scientists. The network performs QC highly concordant with that of experts on a held out set (ROC-AUC = 0.947). A further analysis of the neural network demonstrates that it relies on image features with relevance to QC. Altogether, this work both delivers resources to advance transdiagnostic research in brain connectivity and pediatric mental health, and establishes a novel paradigm for automated QC of large datasets.

Perish and publish: Dynamics of biomedical publications by deceased authors

The question of whether it is appropriate to attribute authorship to deceased individuals of original studies in the biomedical literature is contentious. Authorship guidelines utilized by journals do not provide a clear consensus framework that is binding on those in the field. To guide and inform the implementation of authorship frameworks it would be useful to understand the extent of the practice in the scientific literature, but studies that have systematically quantified the prevalence of this phenomenon in the biomedical literature have not been performed to date. To address this issue, we quantified the prevalence of publications by deceased authors in the biomedical literature from the period 1990–2020. We screened 2,601,457 peer-reviewed papers from the full text Europe PubMed Central database. We applied natural language processing, stringent filtering and manual curation to identify a final set of 1,439 deceased authors. We then determined these authors published a total of 38,907 papers over their careers with 5,477 published after death. The number of deceased publications has been growing rapidly, a 146-fold increase since the year 2000. This rate of increase was still significant when accounting for the growing total number of publications and pool of authors. We found that more than 50% of deceased author papers were first submitted after the death of the author and that over 60% of these papers failed to acknowledge the deceased authors status. Most deceased authors published less than 10 papers after death but a small pool of 30 authors published significantly more. A pool of 266 authors published more than 90% of their total publications after death. Our analysis indicates that the attribution of deceased authorship in the literature is not an occasional occurrence but a burgeoning trend. A consensus framework to address authorship by deceased scientists is warranted.

Role of Extracellular Matrix Biomolecules on Endometrial Epithelial Cell Attachment and Cytokeratin 18 Expression on Gelatin Hydrogels

The endometrium undergoes profound changes in tissue architecture and composition, both during the menstrual cycle as well as in the context of pregnancy. Dynamic remodeling processes of the endometrial extracellular matrix (ECM) are a major element of endometrial homeostasis, including changes across the menstrual cycle. A critical element of this tissue microenvironment is the endometrial basement membrane, a specialized layer of proteins that separates the endometrial epithelium from the underlying endometrial ECM. Bioengineering models of the endometrial microenvironment that present an appropriate endometrial ECM and basement membrane may provide an improved environment to study endometrial epithelial cell (EEC) function. Here, we exploit a tiered approach using two-dimensional high-throughput microarrays and three-dimensional gelatin hydrogels to define patterns of EEC attachment and cytokeratin 18 (CK18) expression in response to combinations of endometrial basement membrane proteins. We identify combinations (collagen IV + tenascin C; collagen I + collagen III; hyaluronic acid + tenascin C; collagen V; collagen V + hyaluronic acid; collagen III; and collagen I) that facilitate increased EEC attachment, increased CK18 intensity, or both. We also identify significant EEC mediated remodeling of the methacrylamide-functionalized gelatin matrix environment via analysis of nascent protein deposition. Together, we report efforts to tailor the localization of basement membrane-associated proteins and proteoglycans in order to investigate tissue-engineered models of the endometrial microenvironment.

Untangling the network effects of productivity and prominence among scientists

While inequalities in science are common, most efforts to understand them treat scientists as isolated individuals, ignoring the network effects of collaboration. Here, we develop models that untangle the network effects of productivity defined as paper counts, and prominence referring to high-impact publications, of individual scientists from their collaboration networks. We find that gendered differences in the productivity and prominence of mid-career researchers can be largely explained by differences in their coauthorship networks. Hence, collaboration networks act as a form of social capital, and we find evidence of their transferability from senior to junior collaborators, with benefits that decay as researchers age. Collaboration network effects can also explain a large proportion of the productivity and prominence advantages held by researchers at prestigious institutions. These results highlight a substantial role of social networks in driving inequalities in science, and suggest that collaboration networks represent an important form of unequally distributed social capital that shapes who makes what scientific discoveries.

While inequalities in science are common, most efforts to understand them treat scientists as isolated individuals, ignoring the network effects of collaboration. Here, the authors develop models that untangle the network effects of productivity and prominence of individual scientists from their collaboration networks.

Women are credited less in science than men

There is a well-documented gap between the observed number of works produced by women and by men in science, with clear consequences for the retention and promotion of women1. The gap might be a result of productivity differences2-5, or it might be owing to women's contributions not being acknowledged6,7. Here we find that at least part of this gap is the result of unacknowledged contributions: women in research teams are significantly less likely than men to be credited with authorship. The findings are consistent across three very different sources of data. Analysis of the first source-large-scale administrative data on research teams, team scientific output and attribution of credit-show that women are significantly less likely to be named on a given article or patent produced by their team relative to their male peers. The gender gap in attribution is present across most scientific fields and almost all career stages. The second source-an extensive survey of authors-similarly shows that women's scientific contributions are systematically less likely to be recognized. The third source-qualitative responses-suggests that the reason that women are less likely to be credited is because their work is often not known, is not appreciated or is ignored. At least some of the observed gender gap in scientific output may be owing not to differences in scientific contribution, but rather to differences in attribution.

A survey of the state of the practice for research software in the United States

Research software is a critical component of contemporary scholarship. Yet, most research software is developed and managed in ways that are at odds with its long-term sustainability. This paper presents findings from a survey of 1,149 researchers, primarily from the United States, about sustainability challenges they face in developing and using research software. Some of our key findings include a repeated need for more opportunities and time for developers of research software to receive training. These training needs cross the software lifecycle and various types of tools. We also identified the recurring need for better models of funding research software and for providing credit to those who develop the software so they can advance in their careers. The results of this survey will help inform future infrastructure and service support for software developers and users, as well as national research policy aimed at increasing the sustainability of research software.

Are female scientists less inclined to publish alone? The gender solo research gap

In solo research, scientists compete individually for prestige, sending clear signals about their research ability, avoiding problems in credit allocation, and reducing conflicts about authorship. We examine to what extent male and female scientists differ in their use of solo publishing across various dimensions. This research is the first to comprehensively study the “gender solo research gap” among all internationally visible scientists within a whole national higher education system. We examine the gap through mean “individual solo publishing rates” found in “individual publication portfolios” constructed for each Polish university professor. We use the practical significance/statistical significance difference (based on the effect-size r coefficient) and our analyses indicate that while some gender differences are statistically significant, they have no practical significance. Using a partial effects of fractional logistic regression approach, we estimate the probability of conducting solo research. In none of the models does gender explain the variability of the individual solo publishing rate. The strongest predictor of individual solo publishing rate is the average team size, publishing in STEM fields negatively affects the rate, publishing in male-dominated disciplines positively affects it, and the influence of international collaboration is negative. The gender solo research gap in Poland is much weaker than expected: within a more general trend toward team research and international research, gender differences in solo research are much weaker and less relevant than initially assumed. We use our unique biographical, administrative, publication, and citation database (“Polish Science Observatory”) with metadata on all Polish scientists present in Scopus (N = 25,463) and their 158,743 Scopus-indexed articles published in 2009–2018, including 18,900 solo articles.

Bibliometrics as a promising tool for solving publication ethics issues

Publication ethics principles became one of the main aspects of conducting scientific research and presenting its results. Publication ethics challenges cover a wide range of problems of varying importance that involve all participants of publication processes: authors, academic authorities, peer-reviewers, editorial board members, publishers, and funders. All stakeholders put efforts to make modern science and publication processes ethical. This goal is achieved first of all through detailed criteria of publication ethics and extensive author guidelines, as well as by increasing the level of awareness of these criteria in educational programs aimed at prophylactics of research misconduct. However, there is a need for technical facilities for detecting different cases of violation of ethical principles, and bibliometric methods are one of the most promising approaches. The paper summarizes the authors' recent studies on bibliometric perspectives for detecting plagiarism, inappropriate authorship, and official misconduct among editorial board members.

The Scholarly Knowledge Ecosystem: Challenges and Opportunities for the Field of Information

The scholarly knowledge ecosystem presents an outstanding exemplar of the challenges of understanding, improving, and governing information ecosystems at scale. This article draws upon significant reports on aspects of the ecosystem to characterize the most important research challenges and promising potential approaches. The focus of this review article is the fundamental scientific research challenges related to developing a better understanding of the scholarly knowledge ecosystem. Across a range of disciplines, we identify reports that are conceived broadly, published recently, and written collectively. We extract the critical research questions, summarize these using quantitative text analysis, and use this quantitative analysis to inform a qualitative synthesis. Three broad themes emerge from this analysis: the need for multi-sectoral cooperation and coordination, for mixed methods analysis at multiple levels, and interdisciplinary collaboration. Further, we draw attention to an emerging consensus that scientific research in this area should by a set of core human values.

Hydrogels Containing Gradients in Vascular Density Reveal Dose-Dependent Role of Angiocrine Cues on Stem Cell Behavior

Biomaterials that replicate patterns of microenvironmental signals from the stem cell niche offer the potential to refine platforms to regulate stem cell behavior. While significant emphasis has been placed on understanding the effects of biophysical and biochemical cues on stem cell fate, vascular-derived or angiocrine cues offer an important alternative signaling axis for biomaterial-based stem cell platforms. Elucidating dose-dependent relationships between angiocrine cues and stem cell fate are largely intractable in animal models and 2D cell cultures. In this study, microfluidic mixing devices are leveraged to generate 3D hydrogels containing lateral gradients in vascular density alongside murine hematopoietic stem cells (HSCs). Regional differences in vascular density can be generated via embossed gradients in cell, matrix, or growth factor density. HSCs co-cultured alongside vascular gradients reveal spatial patterns of HSC phenotype in response to angiocrine signals. Notably, decreased Akt signaling in high vessel density regions led to increased expansion of lineage-positive hematopoietic cells. This approach offers a combinatorial tool to rapidly screen a continuum of microenvironments with varying vascular, biophysical, and biochemical cues to reveal the influence of local angiocrine signals on HSC fate.

Reporting Policies in Neurosurgical Journals: A Meta-Science Study of the Current State and Case for Standardization

BACKGROUND

Reporting quality within the neurosurgical literature is low, limiting the ability of journals to act as gatekeepers for evidence-based neurosurgical care. Journal policies during article submission aim to improve reporting quality. We conducted a meta-science study characterizing the reporting policies of neurosurgical journals and other related peer-reviewed publications.

METHODS

Journals were retrieved in 7 searches using Journal Citation Reports and Google Scholar. Characteristics, impact metrics, and submission policies were extracted.

RESULTS

Of 486 results, 54 journals were included, including 27 neurosurgical and 27 related topical journals. Thirty-eight (70.4%) adopted authorship guidelines and 20 (37.0%) disclosure standards of the International Council of Medical Journal Editors. Twenty-six (48.1%) required data availability statement and 33 (61.1%) clinical trials registration. Twenty-one (38.9%) required and 11 (20.4%) recommended adherence to reporting guidelines. Twenty (37.0%) endorsed EQUATOR network guidelines. PRISMA was mentioned by 30 (55.6%) journals, CONSORT by 28 (51.9%), and STROBE by 18 (33.3%). Among neurosurgical journals, factors associated with a requirement or recommendation to follow reporting guidelines among neurosurgical journals included impact factor (P = 0.0013), Article Influence Score (P = 0.0236), SCImago h-index (P = 0.0152), SCImago journal rank (P = 0.002), and CiteScore (P = 0.0023), as well as recommendations pertaining to International Council of Medical Journal Editors authorship guidelines (P = 0.0085), ORCID (P = 0.014), clinical trials registration (P = 0.0369), or data availability statement (P = 0.0047). CONSORT, PRISMA, or STROBE delineations were significantly associated with the mention of another guideline (P < 0.01).

CONCLUSIONS

Neurosurgical journal submission policies are inconsistent. Frameworks to improve reporting quality are uncommonly used. Increasing rigor and standardization of reporting policies across journals publishers may improve quality.

Glycosaminoglycan content of a mineralized collagen scaffold promotes mesenchymal stem cell secretion of factors to modulate angiogenesis and monocyte differentiation

Effective design of biomaterials to aid regenerative repair of craniomaxillofacial (CMF) bone defects requires approaches that modulate the complex interplay between exogenously added progenitor cells and cells in the wound microenvironment, such as osteoblasts, osteoclasts, endothelial cells, and immune cells. We are exploring the role of the glycosaminoglycan (GAG) content in a class of mineralized collagen scaffolds recently shown to promote osteogenesis and healing of craniofacial bone defects. We previously showed that incorporating chondroitin-6-sulfate or heparin improved mineral deposition by seeded human mesenchymal stem cells (hMSCs). Here, we examine the effect of varying scaffold GAG content on hMSC behavior, and their ability to modulate osteoclastogenesis, vasculogenesis, and the immune response. We report the role of hMSC-conditioned media produced in scaffolds containing chondroitin-6-sulfate (CS6), chondroitin-4-sulfate (CS4), or heparin (Heparin) GAGs on endothelial tube formation and monocyte differentiation. Notably, endogenous production by hMSCs within Heparin scaffolds most significantly inhibits osteoclastogenesis via secreted osteoprotegerin (OPG), while the secretome generated by CS6 scaffolds reduced pro-inflammatory immune response and increased endothelial tube formation. All conditioned media down-regulated many pro- and anti-inflammatory cytokines, such as IL6, IL-1β, and CCL18 and CCL17 respectively. Together, these findings demonstrate that modifying mineralized collagen scaffold GAG content can both directly (hMSC activity) and indirectly (production of secreted factors) influence overall osteogenic potential and mineral biosynthesis as well as angiogenic potential and monocyte differentiation towards osteoclastic and macrophage lineages. Scaffold GAG content is therefore a powerful stimulus to modulate reciprocal signaling between multiple cell populations within the bone healing microenvironment.