PLoS ONE Research Articles

Open science and conflict of interest policies of medical and health sciences journals before and during the COVID-19 pandemic: A repeat cross-sectional study: Open science policies of medical journals.

To audit the transparent and open science standards of health and medical sciences journal policies and explore the impact of the COVID-19 pandemic. Repeat cross-sectional study. 19 journals listed in Google Scholar's Top Publications for health and medical sciences. Blood, Cell, Circulation, European Heart Journal, Gastroenterology, Journal of Clinical Oncology, Journal of the American College of Cardiology, Nature Genetics, Nature Medicine, Nature Neuroscience, Neuron, PLoS ONE, Proceedings of the National Academy of Sciences, Science Translational Medicine, The British Medical Journal, The Journal of the American Medical Association, The Lancet, The Lancet Oncology, and The New England Journal of Medicine. We used the Transparency and Openness Promotion (TOP) guideline and the International Committee of Medical Journal Editors (ICMJE) requirements for disclosing conflicts of interest (COIs) to evaluate journals standards. TOP scores slightly improved during the COVID-19 pandemic, from a median of 5 (IQR: 2-12.5) out of a possible 24 points in February 2020 to 7 (IQR: 4-12) in May 2021, but overall, scores were very low at both time points. Journal policies scored highest for their adherence to data transparency and scored lowest for preregistration of study protocols and analysis plans and the submission of replication studies. Most journals fulfilled all ICMJE provisions for reporting COIs before (84%; n = 16) and during (95%; n = 18) the COVID-19 pandemic. The COVID-19 pandemic has highlighted the importance of practising open science. However, requirements for open science practices in audited policies were overall low, which may impede progress in health and medical research. As key stakeholders in disseminating research, journals should promote a research culture of greater transparency and more robust open science practices.

OR15-6 Epidemic of Subclinical Ovulatory Disturbances During SARS-COV2 Pandemic—an Experiment of Nature

Abstract During the SARS-COV2 pandemic (COVID-19) many studies have examined changes in women's stress, depression/anxiety, reproduction, plus post-vaccination cycle/flow changes1. Although there are retrospective basal temperature data2, we lack menstrual cycle and ovulation information during the pandemic. This analysis compared two independent, similar-design, convenience/community-based, single-cycle cohort studies 13 years apart: Menstruation Ovulation Study (MOS3, n=301, 2007-8) and MOS2 (n=112) during the pandemic. With MOS as a control, and given evidence subclinicalovulatory disturbances (SOD; short luteal phase/anovulatory menstrual cycles of normal lengths) occur before changed cycle lengths4 5, we hypothesized MOS2 would have increased SOD but similar cycle lengths as MOS. Methods In both studies, recruitment of menstruating women ages 19-35 years, not using systemic or combined hormonal contraceptives (CHC) used posters/eblasts/social media. In MOS, ovulation was assessed by 3-fold increased follicular (FP)-to-luteal (LP/premenstrual) urinary progesterone (PdG); in MOS2, by validated Quantitative Basal Temperature© (QBT)6 7 (normal LP=10+ days). We performed the same interviewer-administered (CaMos©) questionnaire for demographics, SES, and reproduction, measured anthropomorphic variables, plus collected daily Menstrual Cycle Diary© (Diary) for all. FP and LP/premenstrual PdG or salivary progesterone (Ps) samples were respectively collected. Participants in MOS2 were not different from MOS in: average age 29, menarche age 12.5, BMI 24, living situation and education (≥75% university graduates). Cohorts also differed: MOS2 women were less likely to to be White (56% vs 76%), work fulltime, ever use CHC (68% vs 79%) or to be parous (8% vs 20%); they were younger at starting CHC (17.9 vs 18.6 years). Results MOS2 and MOS had similar cycle (30.3 vs 29.9 days, P =.306) and flow lengths (median 6.0 days; P=.055). MOS2 recorded significantly more SOD cycles (>50% anovulatory) vs MOS3 (63% vs 10%; P<.001). MOS2 Diary analyses by Principal Components Analysis showed significantly increased anxiety/depression/frustration (negative moods) and "outside stresses" plus sleep problems and headaches vs MOS (all P<.001). Discussion This is the first evidence that ovulatory disturbances without cycle length changes may be associated with the multidimensional stresses women experience during the pandemic. Increased SOD may also relate to greater nulliparity, younger CHC teen use and more non-White women in MOS2, as well higher prevalence of negative moods, outside stresses and sleep problems. Salivary progesterone, cortisol and estradiol levels remain pending. Prevalent SOD cycles, if persistent/recurrent, risk increased infertility, bone loss5, early heart attacks, and breast and endometrial cancers8. In this 'experiment of nature,' the pandemic was associated with disturbed ovulation rather than menstrual cycles. 1Edelman AB Ob Gyn 2022; 2Nguyen JK PLOS ONE 2021; 3Prior JC IJERPH 2018; 4Prior JC NEJM 1990; 5Li D Epidiol Rev 2014; 6Prior JC Clin Invest. Med 1990; 7Bedford JL Eur J ObGyn Reprod Biol 2009; 8Prior JC DDDM 2020. Presentation: Sunday, June 12, 2022 12:15 p.m. - 12:30 p.m.

In Memoriam : Edward O. Wilson (1929-2021): It All Started with Ants.

In Memoriam : Edward O. Wilson (1929-2021): It All Started with Ants.

Severity in a Norwegian hospitalized injury material (N = 177,663) by two severity measures: threat-to-life and threat of disability

Abstract We conducted a registry-based cohort study of all individuals aged 25-64 years residing in Norway by 1st of January 2008 (N = 2,535,213). This cohort was followed from 2008 through 2014 using inpatient registrations for acute hospitalizations due to all-cause injuries, getting 177,663 cases of hospitalized persons (incidence rate of new cases: 102.1 pr 10,000 person-years at risk). We derived two measures of severity: threat-to-life using the International Classification of Disease-based Injury Severity Score (ICISS) (Stephenson et al 2004; Gedeborg et al 2014), and threat of disability using long-term disability weights (DW) from the Injury-VIBES project (Gabbe et al 2014), also based on the ICD-codes. We found the following distributions of the hospitalized persons (N = 177,663): 1) Threat to life (ICISS): High threat to life: 4,186 (2.4 %); Lower threat to life: 173,477 (97.6%). 2) Threat of disability (Injury Vibes DW): High probability of long-term disability (DW-score < 0.807): 36,573 (20,6 %); Medium probability of long-term disability (DW-score 0.807-0.947): 97,590 (54,9 %); low probability of long-term disability (DW-score >0.947): 43,530 (24.5 %). Correlation between ICISS-score and the Injury Vibes disability weight score was moderate (r = 0.418, p < 0.001). The presentation will end up in a discussion on which of these two severity measures could be used for comparing burden of injuries across countries. References Gabbe BJ, Simpson PM, Lyons RA, et al. (2014) Association between the Number of Injuries Sustained and 12-Months Disability Outcomes: Evidence from the Injury-VIBES Study. PLos ONE, 9(12):e113467. DOI: 10.1371/journal.pone.0113467. Gedeborg R, Warner M, Chen LH, et al. (2014) Internationally comparable diagnosis-specific survival probabilites for calculation of the ICD-10-based Injury Severity Score. J Trauma Acute Care Surg, 76(2):358-65. DOI: 10.1097/ta.0b013e3182a9cd31.

The influence of journal submission guidelines on authors’ reporting of statistics and use of open research practices: Five years later

Changes in statistical practices and reporting have been documented by Giofrè et al. PLOS ONE 12(4), e0175583 (2017), who investigated ten statistical and open practices in two high-ranking journals (Psychological Science [PS] and Journal of Experimental Psychology-General [JEPG]): null hypothesis significance testing; confidence or credible intervals; meta-analysis of the results of multiple experiments; confidence interval interpretation; effect size interpretation; sample size determination; data exclusion; data availability; materials availability; and preregistered design and analysis plan. The investigation was based on an analysis of all papers published in these journals between 2013 and 2015. The aim of the present study was to follow up changes in both PS and JEPG in subsequent years, from 2016 to 2020, adding code availability as a further open practice. We found improvement in most practices, with some exceptions (i.e., confidence interval interpretation and meta-analysis). Despite these positive changes, our results indicate a need for further improvements in statistical practices and adoption of open practices.

(Digital Presentation) Fabrication of NiO-TiO2 Modified Ni Foam and Its Application As Energy Storage Materials

Rechargeable batteries are the most effective and efficient devices that store electricity from various intermediate and renewable sources such as solar and wind power. However, the fast-growing market of portable devices requires the use of hybrid materials which ensures safety, high energy density and higher saving for customers [1-3]. In this work, an energy storage device has been fabricated based on novel NiO-TiO2 film modified 3D Nickel Foam (NF) electrode. Simple sol-gel method was used to fabricate the electrode, where NiCl26H2O and TiO2 were used as precursors. 550 °C was used to calcine the NiO-TiO2 modified NF before it can be used as electrode material. During the fabrication process, Ni-Ti ratio has been varied to 1:1 and 1:2 and a comparative study has been developed on the basis of energy storing capacities. In this work, NiO-TiO2 modified Nickel Foam (NiO-TiO2/NF) was used as working electrode, pencil graphite electrode was also used as counter electrode and Ag/AgCl as reference electrode. To calculate the energy storage capabilities, NiO-TiO2/NF was dipped into NaOH and LiCl electrolytes. NiO-TiO2-NF (1:2) shows higher specific capacity in compare to NiO/NF, TiO2/NF and NiO-TiO2-NF (1:1) electrodes. In addition, with the scan rate increases, energy storing capacity of NiO-TiO2-NF found to be decreased. Thereby, a hybrid NiO-TiO2/NF can be used as future electrode material in the energy storage devices.AcknowledgementsUniversity of Grants Commission of Bangladesh (2021-22) for funding this research.Reference N. Padmanathan, et al., J. Mater. Chem. A, 2016, 4, 4820-4830.J. Islam et al., PLoS ONE, 2021 16(3), e0248142.M. Jamal et al., Sci. Rep., 2019, 9, 4659.

(Digital Presentation) Non-Enzymatic Lactose Sensor Based on Nickel Oxide Nanoparticles Modified Carbon Fiber Cloth Electrode

Lactose (LAC) is the main sugar found mostly in milk and dairy products. LAC content is an important indication of milk quality and health issues in the food business as well as in human and animal health. The development of biosensors for lactose detection has received a lot of attention over the last 20 years due to its importance in the agricultural and healthcare industries [1-3].In this work, an enzyme-free lactose sensor has been developed using a carbon fiber cloth electrode modified with NiO nanoparticles (NiO/CFC). At first, Ni(OH)2 precursor of NiO nanoparticles were electrodeposited on the surface of CFC by applying a constant potential of -1.0V in an electrochemical cell containing 6 mM Ni(NO3)2·6H2O solution where CFC was used as a working, Ag/AgCl (3M KCl) as reference and Pt wire as a counter electrode. Then the electrode was calcined at 100 ℃ in the presence of oxygen for 1 hr. For the confirmation of the growth of NiO nanoparticles on CFC, morphology and chemical composition of the electrode was characterized using SEM, EDX, TEM, XRD, FT-IR and Raman spectroscopy. The electrochemical properties of NiO/CFC were investigated by applying Cyclic Voltammetry, and amperometry in a 0.1M NaOH solution. NiO/CFC exhibits a fast reaction time of less than 5 s with a linear relationship of 0.5 to 3.5 mM (R2 = 0.97) at an applied voltage of +0.65 V (Fig. 1). The sensitivity was found to be 1.73 mA/mM/cm2 with a detection limit of 227 µM. The interference test of the electrode was performed in glucose, ascorbic acid, and uric acid solutions, which indicated insignificant current responses compare to lactose. As a result, it provides a sensitive, simple, and rapid amperometric sensor, which opens the way to developing an enzyme-free sensing platform to detect lactose in milk. Acknowledgments Ministry of Science and Technology of Bangladesh (special allocation 2021-22) for funding this research. References G. Halpin et al., J. Electrochem. Soc., 2022, 169, 037528.M. Jamal et al., Sci. Rep., 2019, 9, 4659.J. Islam et al., PLoS ONE, 2021 16(3), e0248142. Fig. 1. Amperometric current response of the NiO/CFC electrode to sequential additions of lactose ranging from 1 to 3.5 mM into a stirred 0.1 M NaOH solution. Figure 1

(Digital Presentation) Graphene Oxide Modified Pencil Graphite Electrode for the Detection of H2O2

Hydrogen peroxide is a very simple molecule, it is an important chemical and analyte in various industry fields, such as mining, environment, pharmaceutical, food manufacturing and textile applications. Meanwhile, H2O2 is also a kind of toxic by-product of many biological oxidases, based on which H2O2 has been considered to be an indicator of related diseases, such as Parkinson disease, cancer, stroke, arteriosclerosis and Alzheimer disease [1-3]. In addition, H2O2 has been applied in liquid-based fuel cells as an efficient oxidant and has also been employed in organic synthesis. Therefore, it is one of the critical issues to detect H2O2 accurately for industrial needs.In this work reduced graphene oxide-supported tin oxide nano clusters modified pencil graphite electrode (SnO2-rGO/PGE) was used as electrochemical sensing material for H2O2 detection. Cyclic voltammetry and amperometry were used to investigate the catalytic properties of SnO2-rGO/PGE. Hydrothermal synthesis method was used for the fabrication of SnO2 nanoparticles and GO prepared by modified Hummers method. For the detection of H2O2, the nanoparticles were mixed with Nafion and chitosan before drop coating onto the Pencil graphite electrode (PGE) surface. This studies we found a good catalytic activities on 3B pencil that modifier with GO and SnO2nano clusters at pH (7.4). Here, include that the current increasing after using modifier PGE with nanoparticles. Electrochemical studies showed that the sensing platform fabricated from SnO2-rGO possesses fast mass transport, good electrical conductivity and high sensitivity and selectivity for the detection of H2O2.Where, composite SnO2-Go/PGE exhibited amperometric sensitivity of 129 μAmM−1cm-2 and fast response time 2s.The interference study of SnO2-rGO has been found a significant current response for H2O2 compared to the uric acid and ascorbic acid.The electrode can be prepared simply and at low cost, and present a promising tool for sensing H2O2. Here we propose a new, robust and reliable way to detect of H2O2.AcknowledgmentsMinistry of Science and Technology of Bangladesh (special allocation 2021-22) for funding this research.Reference J. Islam et al., PLoS ONE, 2021 16(3), e0248142.Roy, K., et al. Int. J. Environ. Sci. Technol. (2022). DOI: https://doi.org/10.1007/s13762-022-04301-w

Evolution of research trends in artificial intelligence for breast cancer diagnosis and prognosis over the past two decades: A bibliometric analysis.

ObjectiveIn recent years, among the available tools, the concurrent application of Artificial Intelligence (AI) has improved the diagnostic performance of breast cancer screening. In this context, the present study intends to provide a comprehensive overview of the evolution of AI for breast cancer diagnosis and prognosis research using bibliometric analysis.MethodologyTherefore, in the present study, relevant peer-reviewed research articles published from 2000 to 2021 were downloaded from the Scopus and Web of Science (WOS) databases and later quantitatively analyzed and visualized using Bibliometrix (R package). Finally, open challenges areas were identified for future research work.ResultsThe present study revealed that the number of literature studies published in AI for breast cancer detection and survival prediction has increased from 12 to 546 between the years 2000 to 2021. The United States of America (USA), the Republic of China, and India are the most productive publication-wise in this field. Furthermore, the USA leads in terms of the total citations; however, hungry and Holland take the lead positions in average citations per year. Wang J is the most productive author, and Zhan J is the most relevant author in this field. Stanford University in the USA is the most relevant affiliation by the number of published articles. The top 10 most relevant sources are Q1 journals with PLOS ONE and computer in Biology and Medicine are the leading journals in this field. The most trending topics related to our study, transfer learning and deep learning, were identified.ConclusionThe present findings provide insight and research directions for policymakers and academic researchers for future collaboration and research in AI for breast cancer patients.

Response of a grassland species to dry environmental conditions from water stable isotopic monitoring: no evident shift in root water uptake to wetter soil layers

AimsWe aimed at assessing the influence of above- and below-ground environmental conditions over the performance of Centaurea jacea L., a drought-resistant grassland forb species.MethodsTranspiration rate, CO2 assimilation rate, leaf water potential, instantaneous and intrinsic water use efficiency, temperature, relative humidity, vapor pressure deficit and soil water content in one plant and root length density in four plants, all grown in custom-made columns, were monitored daily for 87 days in the lab. The soil water isotopic composition in eleven depths was recorded daily in a non-destructive manner. The isotopic composition of plant transpiration was inferred from gas chamber measurements. Vertical isotopic gradients in the soil column were created by adding labeled water. Daily root water uptake (RWU) profiles were computed using the multi-source mixing model Stable Isotope Analysis in R (Parnell et al. PLoS ONE 5(3):1–5, 2010).ResultsRWU occurred mainly in soil layer 0–15 cm, ranging from 79 to 44%, even when water was more easily available in deeper layers. In wet soil, the transpiration rate was driven mainly by vapor pressure deficit and light intensity. Once soil water content was less than 0.12 cm3 cm− 3, the computed canopy conductance declined, which restricted leaf gas exchange. Leaf water potential dropped steeply to around − 3 MPa after soil water content was below 0.10 cm3 cm− 3.ConclusionOur comprehensive data set contributes to a better understanding of the effects of drought on a grassland species and the limits of its acclimation in dry conditions.

S7.4a Vaccine-inducing lung resident CD4 + memory T cells are protective against Cryptococcus gattii infections

S7.4 Pathogenesis and host defense, September 23, 2022, 10:30 AM - 12:00 PM Cryptococccus gattii is a highly virulent fungal pathogen that can cause cryptococcosis in previously healthy individuals. It is not fully understood how innate and acquired immune responses cooperatively suppress C. gattii infection. Hitherto, we have reported the following findings, (1) Specific environment for exposure of dectin-1 and dectin-2 ligands in cryptococcal cells (PLOS ONE 2019, PMID 31398236), (2) CD11b-mediated immune recognition for C. gattii and capsule dependent immune evasion from CD11b recognition (Eur J Immunol 2021, PMID 33728652), (3) Dendritic cells (DCs)-based vaccine induced lung resident memory Th17 cells and ameliorates C. gattii infection (Mucosal Immunol 2018, PMID 30279512), and (4) Neutrophil and opsonization can mediate fungicidal activity for cryptococcal cells (Med Mycol 2019, PMID 30668754). Based on these findings, we have inferred that induction of lung resident memory T cells (lung TRM) and TRM-driven myeloid cells including granulocytes is necessary for controlling this infection. Currently, we are developing new intranasal (IN) vaccines using highly immunogenic whole cell antigens and characterizing protective lung TRM induced by the vaccines. Just as with component vaccines, whole cell vaccines are also featured for cryptococcal infection because these are highly cross-reactive and protective against each serotype (Biol Pharm Bull 2020, PMID 32009111). We developed two IN vaccines using whole cell antigen and adjuvant. Both vaccines induced IL-5-producing lung TRM and significantly reduced fungal burden in lungs and improved survival rates of mice following C. gattii infection, while not protective against C. neoformans infection. Although immune suppressive agent FTY720 can eliminate most circulating T cells and sustain tissue-resident subset, IN vaccines induced Th2-related immune response including eosinophils and IFN-γ independent granuloma, and reduced the fungal burden in lungs after the infection in the presence of FTY720. Vaccine-mediated protection was completely lost in the Rag-1 knockout mice deficient in T- and B-cells, while the fungal burden was reduced in the Rag-1 knockout mice after receiving the immunized CD4 + T cells in the adoptive transfer experiments. These results suggest that Th2-related lung TRM induced by IN vaccines are also protective against C. gattii infection as well as Th17-related counterparts induced by DC vaccine.

Capturing the Complexity of COVID-19 Research: Trend Analysis in the First Two Years of the Pandemic Using a Bayesian Probabilistic Model and Machine Learning Tools

Publications about COVID-19 have occurred practically since the first outbreak. Therefore, studying the evolution of the scientific publications on COVID-19 can provide us with information on current research trends and can help researchers and policymakers to form a structured view of the existing evidence base of COVID-19 and provide new research directions. This growth rate was so impressive that the need for updated information and research tools become essential to mitigate the spread of the virus. Therefore, traditional bibliographic research procedures, such as systematic reviews and meta-analyses, become time-consuming and limited in focus. This study aims to study the scientific literature on COVID-19 that has been published since its inception and to map the evolution of research in the time range between February 2020 and January 2022. The search was carried out in PubMed extracting topics using text mining and latent Dirichlet allocation modeling and a trend analysis was performed to analyze the temporal variations in research for each topic. We also study the distribution of these topics between countries and journals. 126,334 peer-reviewed articles and 16 research topics were identified. The countries with the highest number of scientific publications were the United States of America, China, Italy, United Kingdom, and India, respectively. Regarding the distribution of the number of publications by journal, we found that of the 7040 sources Int. J. Environ. Res. Public Health, PLoS ONE, and Sci. Rep., were the ones that led the publications on COVID-19. We discovered a growing tendency for eight topics (Prevention, Telemedicine, Vaccine immunity, Machine learning, Academic parameters, Risk factors and morbidity and mortality, Information synthesis methods, and Mental health), a falling trend for five of them (Epidemiology, COVID-19 pathology complications, Diagnostic test, Etiopathogenesis, and Political and health factors), and the rest varied throughout time with no discernible patterns (Therapeutics, Pharmacological and therapeutic target, and Repercussion health services).

Global trends of research on tuberculous pleurisy over the past 15 years: A bibliometric analysis.

Tuberculous pleurisy (TP) is a common type of extrapulmonary tuberculosis (EPTB). With the development of research and changes in TP patient characteristics, an increasing number of studies have revealed the prevalence, risk factors, and novel diagnosis techniques. Thus, this bibliometric analysis was performed to identify global scientific output characteristics and research hotspots and frontiers for TP over the past 15 years. We searched the Web of Science Core Collection (WoSCC) Science Citation Index Expanded (SCI-expanded) for literature published between 2007 and 2021 and recorded their information. The Bibliometrix software package was used for bibliometric indicator analysis, and VOSviewer was used to visualize the trends of and hotspots in TP research. A total of 1,464 original articles were reviewed, and the results indicated that the annual number of publications (Np) focusing on TP has increased over the past 15 years. China had the largest number of papers and the highest H-index, and the United States ranked first for number of citations (Nc). EGYPTIAN KNOWLEDGE BANK and PLOS ONE were the most prolific unit and journal, respectively. The use of the Xpert assay and immune-related biomarker detection to diagnose TP appears to be a recent research hotspot. This bibliometric study demonstrated that the number of publications related to TP have tended to increase. China is a major producer, and the United States is an influential country in this field. Research in the past 15 years has been predominantly clinical research. The diagnosis of TP was the focus of research, and the exploration of novel diagnostic techniques, verification of diagnostic markers, and combination of diagnostic methods have been recent research hotspots. Immune-related biomarkers should be given more attention in the field of TP diagnosis.

Global research trends in extracellular vesicles based on stem cells from 1991 to 2021: A bibliometric and visualized study.

Objective: With the development of extracellular vesicles (EVs) based on stem cells research all over the world, our present study was aiming to discover the global trends in this field. Methods: All publications related to EVs based on stem cells from 1991 to 2021 were collected from the Science Citation Index-Expanded of Web of Science Subsequently, the data were evaluated using the bibliometric methodology. In terms of visualized study, the VOS viewer software was performed to investigate the bibliographic coupling, co-citation, co-authorship, and co-occurrence trends, and last for the publication’s trends involved in the field of EVs based on stem cells. Results: A total of 8,208 publications were retrieved and the relative number of global publications and research interests were increasing every year especially in recent 5 years. China rank top one in terms of total publications, prolific authors, and funds, whereas the USA made the greatest contributions with the most total citations and highest H-index to the global research. Stem cell research therapy contributed the highest publications, whereas the journal of PLOS ONE showed the best total link strength. The Shanghai Jiao Tong University, University of California System, and Harvard University were the most contributive institutions. The global studies could be divided into six clusters as follows: cancer research, musculoskeletal system research, respiratory system research, urinary system and endocrine system research, nerve system research, and cardiovascular system research. All the directions were predicted to still hotspots in near future researches in this field. Conclusion: The total number of publications about EVs based stem cells would be increasing according to the current global trends. China and the USA was the largest contributors in this field. Further efforts should be put in the directions of cancer research, musculoskeletal system research, respiratory system research, urinary system and endocrine system research, nerve system research, as well was cardiovascular system research in this field of EVs based stem cells.

Long-term availability of data associated with articles in PLOS ONE.

The adoption of journal policies requiring authors to include a Data Availability Statement has helped to increase the availability of research data associated with research articles. However, having a Data Availability Statement is not a guarantee that readers will be able to locate the data; even if provided with an identifier like a uniform resource locator (URL) or a digital object identifier (DOI), the data may become unavailable due to link rot and content drift. To explore the long-term availability of resources including data, code, and other digital research objects associated with papers, this study extracted 8,503 URLs and DOIs from a corpus of nearly 50,000 Data Availability Statements from papers published in PLOS ONE between 2014 and 2016. These URLs and DOIs were used to attempt to retrieve the data through both automated and manual means. Overall, 80% of the resources could be retrieved automatically, compared to much lower retrieval rates of 10–40% found in previous papers that relied on contacting authors to locate data. Because a URL or DOI might be valid but still not point to the resource, a subset of 350 URLs and 350 DOIs were manually tested, with 78% and 98% of resources, respectively, successfully retrieved. Having a DOI and being shared in a repository were both positively associated with availability. Although resources associated with older papers were slightly less likely to be available, this difference was not statistically significant, suggesting that URLs and DOIs may be an effective means for accessing data over time. These findings point to the value of including URLs and DOIs in Data Availability Statements to ensure access to data on a long-term basis.

Book Review: Martin Paul Eve, Cameron Neylon, Daniel Paul O’Donnell, Samuel Moore, Robert Gadie, Victoria Odeniyi and Shahina Parvin, Reading Peer Review: PLOS ONE and Institutional Change in Academia

Book Review: Martin Paul Eve, Cameron Neylon, Daniel Paul O’Donnell, Samuel Moore, Robert Gadie, Victoria Odeniyi and Shahina Parvin, Reading Peer Review: PLOS ONE and Institutional Change in Academia

Looking Back to Move Forward: Why Scientific Societies Should Contribute to Making our Science an Equitable, Safe, and Inclusive Space

References Bernard, R.E., and Cooperdock, E.H.G., 2018, No progress on diversity in 40 years: Nature Geoscience, v. 11, p. 292–295, https://www.nature.com/articles/s41561-018-0116-6. Cheney, I., and Shattuck, S., 2020, Picture a Scientist (Film): An Uprising Production. Clancy, K.B., Nelson, R.G., Rutherford, J.N., and Hinde, K., 2014, Survey of academic field experiences (SAFE): Trainees report harassment and assault: PloS ONE, v. 9, p.e102172, https://doi.org/10.1371/journal.pone.0102172. Dowey, N., Barclay, J., Fernando, B., Giles, S., Houghton, J., Jackson, C., Khatwa, A., Lawrence, A., Mills, K., Newton, A., Rogers, S., and Williams, R., 2021, A UK perspective on tackling the geoscience racial diversity crisis in the Global North: Nature Geoscience, v. 14, p. 256–259, https://doi.org/10.1038/s41561-021-00737-w. Goldin, C., and Rouse, C., 2000, Orchestrating impartiality: The impact of “blind” auditions on female musicians: American economic review, v. 90, p. 715–741, https://www.jstor.org/stable/117305. Mattheis, A., Marín-Spiotta, E., Nandihalli S., Schneider, B., and Barnes, R.T., 2022, “Maybe this is just not the place for me:” Gender harassment and discrimination in the geosciences: PLoS ONE, v. 17, e0268562, https://doi.org/10.1371/journal.pone.0268562. Morris, V.R., 2021, Combating racism in the geosciences: Reflections from a black professor: AGU Advances, v. 2, p.e2020AV000358, https://doi.org/10.1029/2020AV000358. Nayeri, F., 2019, When an orchestra was no place for a woman: New York Times, https://www.nytimes.com/2019/12/23/arts/music/women-vienna-philharmonic.html. Osborne, W., and Conant, A., 2003, The Vienna Philharmonic hires its first Asian musician (Website): http://www.osborne-conant.org/vpo-change.htm.

Mitigating the detrimental effects of COVID-19 pandemic on scientific production

Mitigating the detrimental effects of COVID-19 pandemic on scientific production

Bibliometric Analysis of Cathepsin B Research From 2011 to 2021.

Cathepsin B (CTSB) is a lysosomal protease implicated in the progression of various diseases. A large number of CTSB-related studies have been conducted to date. However, there is no comprehensive bibliometric analysis on this subject. In our study, we performed quantitative analysis of CTSB-related publications retrieved from the Science Citation Index Expanded (SCIE) of the Web of Science Core Collection (reference period: 2011–2021). A total of 3,062 original articles and reviews were retrieved. The largest number of publications were from USA (n = 847, 27.66%). The research output of each country showed positive correlation with gross domestic product (GDP) (r = 0.9745, P < 0.0001). Active collaborations between countries/regions were also observed. Reinheckel T and Sloane BF were perhaps the most impactful researchers in the research landscape of CTSB. Plos ONE was the most prevalent (119/3,062, 3.89%) and cited journal (3,021 citations). Comprehensive analysis of the top citations, co-citations, and keywords was performed to acquire the theoretical basis and hotspots of CTSB-related research. The main topics included CTSB-related cancers and inflammatory diseases, CTSB-associated cell death pattern, and the applications of CTSB. These results provide comprehensive insights into the current status of global CTSB-related research especially in pancreas, which is worthy of continued follow-up by practitioners and clinicians in this field.

Data sharing practices across knowledge domains: A dynamic examination of data availability statements in PLOS ONE publications

As the importance of research data gradually grows in sciences, data sharing has come to be encouraged and even mandated by journals and funders in recent years. Following this trend, the data availability statement has been increasingly embraced by academic communities as a means of sharing research data as part of research articles. This article presents a quantitative study of which mechanisms and repositories are used to share research data in PLOS ONE articles. We offer a dynamic examination of this topic from the disciplinary and temporal perspectives based on all statements in English-language research articles published between 2014 and 2020 in the journal. We find a slow yet steady growth in the use of data repositories to share data over time, as opposed to sharing data in the article and/or supplementary materials; this indicates improved compliance with the journal’s data sharing policies. We also find that multidisciplinary data repositories have been increasingly used over time, whereas some disciplinary repositories show a decreasing trend. Our findings can help academic publishers and funders to improve their data sharing policies and serve as an important baseline dataset for future studies on data sharing activities.