Scientific writing of novice researchers: what difficulties and encouragements do they encounter

Abstract Purpose Writing scientific articles is a daunting task for novice researchers. In this qualitative study carried out in 2007, the authors evaluated the experiences of a group of novice researchers engaged in the writing process, to elucidate the main difficulties and sources of encouragement they encountered. Method Sixteen novice researchers were interviewed. Most were women (10), and most were enrolled in programs of medicine (9), followed by nursing (4) and physical therapy (3). These were drawn via convenience sampling from a randomized control trial in which 48 of them were equally assigned to either an online or a face-to-face course of instruction. On completion, interviews were conducted in focus groups of four students each. The interviews were transcribed and read independently by two of the authors, who then encoded the material based on the principles of grounded theory. Initial categories were converted to major emerging themes, which were validated when participants were asked to review the findings. Triangulation of results was carried out by discussing the emerging themes in an online forum with five specialists in college writing education

Laparoscopic Appendectomy Outcomes on the Weekend and During the Week are no Different: A National Study of 151,774 Patients

Background: The "weekend effect” is defined as increased morbidity and mortality for patients admitted on weekends compared with weekdays. It has been observed for several diseases, including myocardial infarction and renal insufficiency; however, it has not yet been investigated for laparoscopic appendectomy in acute appendicitis—one of the most prevalent surgical diagnoses. Methods: The present study is based on the Nationwide Inpatient Sample (NIS) from 1999 to 2008. The following outcomes were compared between patients undergoing laparoscopic appendectomy for acute appendicitis admitted on weekdays versus weekends: severity of appendicitis, intraoperative and postoperative complications, conversion rate, in-hospital mortality, and length of hospital stay. Unadjusted and risk-adjusted generalized linear regression analyses were performed. Results: Overall, 151,774 patients were included, mean age was 39.6years, 52.6% (n=79,801) were male, and 25.3% (n=38,317) were admitted on weekends. After risk adjustment, the conversion rate was lower [odds ratio (OR): 0.94, p=0.004, number needed to harm (NNH): 244], whereas pulmonary complications (OR: 1.12, p=0.028, NNH: 649) and reoperations (OR: 1.21, p=0.013, NNH: 1,028) were slightly higher on weekends than on weekdays. Overall postoperative complications (OR: 1.03, p=0.24), mortality (OR: 1.37, p=0.075) and length of hospital stay (mean on weekday: 2.00days, weekends: 2.01days, p=0.29) were not statistically different. Conclusions: The present investigation provides evidence that no clinically significant "weekend effect” for patients undergoing laparoscopic appendectomy exists. Therefore, hospital or staffing policy changes are not justified based on the findings from this large national stud

Cholecystectomy Concomitant with Laparoscopic Gastric Bypass: A Trend Analysis of the Nationwide Inpatient Sample from 2001 to 2008

Background: Gallstone formation is common in obese patients, particularly during rapid weight loss. Whether a concomitant cholecystectomy should be performed during laparoscopic gastric bypass surgery is still contentious. We aimed to analyze trends in concomitant cholecystectomy and laparoscopic gastric bypass surgery (2001-2008), to identify factors associated with concomitant cholecystectomy, and to compare short-term outcomes after laparoscopic gastric bypass with and without concomitant cholecystectomy. Methods: We used data from adults undergoing laparoscopic gastric bypass for obesity from the Nationwide Inpatient Sample. The Cochran-Armitage trend test was used to assess changes over time. Unadjusted and risk-adjusted generalized linear models were performed to assess predictors of concomitant cholecystectomy and to assess postoperative short-term outcomes. Results: A total of 70,287 patients were included: mean age was 43.1years and 81.6% were female. Concomitant cholecystectomy was performed in 6,402 (9.1%) patients. The proportion of patients undergoing concomitant cholecystectomy decreased significantly from 26.3% in 2001 to 3.7% in 2008 (p for trend < 0.001). Patients who underwent concomitant cholecystectomy had higher rates of mortality (unadjusted odds ratios [OR], 2.16; p = 0.012), overall postoperative complications (risk-adjusted OR, 1.59; p = 0.001), and reinterventions (risk-adjusted OR, 3.83; p < 0.001), less frequent routine discharge (risk-adjusted OR, 0.70; p = 0.05), and longer adjusted hospital stay (median difference, 0.4days; p < 0.001). Conclusions: Concomitant cholecystectomy and laparoscopic gastric bypass surgery have decreased significantly over the last decade. Given the higher rates of postoperative complications, reinterventions, mortality, as well as longer hospital stay, concomitant cholecystectomy should only be considered in patients with symptomatic gallbladder diseas

Application Description and Policy Model in Collaborative Environment for Sharing of Information on Epidemiological and Clinical Research Data Sets

BACKGROUND: Sharing of epidemiological and clinical data sets among researchers is poor at best, in detriment of science and community at large. The purpose of this paper is therefore to (1) describe a novel Web application designed to share information on study data sets focusing on epidemiological clinical research in a collaborative environment and (2) create a policy model placing this collaborative environment into the current scientific social context. METHODOLOGY: The Database of Databases application was developed based on feedback from epidemiologists and clinical researchers requiring a Web-based platform that would allow for sharing of information about epidemiological and clinical study data sets in a collaborative environment. This platform should ensure that researchers can modify the information. A Model-based predictions of number of publications and funding resulting from combinations of different policy implementation strategies (for metadata and data sharing) were generated using System Dynamics modeling. PRINCIPAL FINDINGS: The application allows researchers to easily upload information about clinical study data sets, which is searchable and modifiable by other users in a wiki environment. All modifications are filtered by the database principal investigator in order to maintain quality control. The application has been extensively tested and currently contains 130 clinical study data sets from the United States, Australia, China and Singapore. Model results indicated that any policy implementation would be better than the current strategy, that metadata sharing is better than data-sharing, and that combined policies achieve the best results in terms of publications. CONCLUSIONS: Based on our empirical observations and resulting model, the social network environment surrounding the application can assist epidemiologists and clinical researchers contribute and search for metadata in a collaborative environment, thus potentially facilitating collaboration efforts among research communities distributed around the globe

RECCAP2 Future Component: Consistency and Potential for Regional Assessment to Constrain Global Projections

This is the final version. Available from Wiley via the DOI in this record. Data Availability Statement: All CMIP6 model output datasets analyzed during this study are available online at https://esgf-node.llnl.gov/search/cmip6/ and code required to reproduce figures is available at https://github.com/ChrisJones-MOHC/RECCAP2Future_2023 (ChrisJones-MOHC, 2023) and Zenodo at https://doi.org/10.5281/zenodo.8420250.Projections of future carbon sinks and stocks are important because they show how the world's ecosystems will respond to elevated CO2 and changes in climate. Moreover, they are crucial to inform policy decisions around emissions reductions to stay within the global warming levels identified by the Paris Agreement. However, Earth System Models from the 6th Coupled Model Intercomparison Project (CMIP6) show substantial spread in future projections—especially of the terrestrial carbon cycle, leading to a large uncertainty in our knowledge of any remaining carbon budget (RCB). Here we evaluate the global terrestrial carbon cycle projections on a region‐by‐region basis and compare the global models with regional assessments made by the REgional Carbon Cycle Assessment and Processes, Phase 2 activity. Results show that for each region, the CMIP6 multi‐model mean is generally consistent with the regional assessment, but substantial cross‐model spread exists. Nonetheless, all models perform well in some regions and no region is without some well performing models. This gives confidence that the CMIP6 models can be used to look at future changes in carbon stocks on a regional basis with appropriate model assessment and benchmarking. We find that most regions of the world remain cumulative net sources of CO2 between now and 2100 when considering the balance of fossil‐fuels and natural sinks, even under aggressive mitigation scenarios. This paper identifies strengths and weaknesses for each model in terms of its performance over a particular region including how process representation might impact those results and sets the agenda for applying stricter constraints at regional scales to reduce the uncertainty in global projections.European Union’s Horizon 2020European Union’s Horizon 2020European Union’s Horizon 2020Joint UK BEIS/Defra Met Office Hadley Centre Climate ProgrammeCarbonWatch-NZ Endeavour Research ProgrammeSão Paulo Research FoundationSão Paulo Research FoundationSão Paulo Research FoundationNational Science FoundationAndrew Carnegie Fellow ProgramCNPqKorea Ministry of EnvironmentNatural Environment Research Council (NERC)Natural Environment Research Council (NERC)National Environmental Science Progra

Modeling Reveals Bistability and Low-Pass Filtering in the Network Module Determining Blood Stem Cell Fate

Combinatorial regulation of gene expression is ubiquitous in eukaryotes with multiple inputs converging on regulatory control elements. The dynamic properties of these elements determine the functionality of genetic networks regulating differentiation and development. Here we propose a method to quantitatively characterize the regulatory output of distant enhancers with a biophysical approach that recursively determines free energies of protein-protein and protein-DNA interactions from experimental analysis of transcriptional reporter libraries. We apply this method to model the Scl-Gata2-Fli1 triad—a network module important for cell fate specification of hematopoietic stem cells. We show that this triad module is inherently bistable with irreversible transitions in response to physiologically relevant signals such as Notch, Bmp4 and Gata1 and we use the model to predict the sensitivity of the network to mutations. We also show that the triad acts as a low-pass filter by switching between steady states only in response to signals that persist for longer than a minimum duration threshold. We have found that the auto-regulation loops connecting the slow-degrading Scl to Gata2 and Fli1 are crucial for this low-pass filtering property. Taken together our analysis not only reveals new insights into hematopoietic stem cell regulatory network functionality but also provides a novel and widely applicable strategy to incorporate experimental measurements into dynamical network models

Robust estimation of bacterial cell count from optical density

Optical density (OD) is widely used to estimate the density of cells in liquid culture, but cannot be compared between instruments without a standardized calibration protocol and is challenging to relate to actual cell count. We address this with an interlaboratory study comparing three simple, low-cost, and highly accessible OD calibration protocols across 244 laboratories, applied to eight strains of constitutive GFP-expressing E. coli. Based on our results, we recommend calibrating OD to estimated cell count using serial dilution of silica microspheres, which produces highly precise calibration (95.5% of residuals &lt;1.2-fold), is easily assessed for quality control, also assesses instrument effective linear range, and can be combined with fluorescence calibration to obtain units of Molecules of Equivalent Fluorescein (MEFL) per cell, allowing direct comparison and data fusion with flow cytometry measurements: in our study, fluorescence per cell measurements showed only a 1.07-fold mean difference between plate reader and flow cytometry data

Large expert-curated database for benchmarking document similarity detection in biomedical literature search

Document recommendation systems for locating relevant literature have mostly relied on methods developed a decade ago. This is largely due to the lack of a large offline gold-standard benchmark of relevant documents that cover a variety of research fields such that newly developed literature search techniques can be compared, improved and translated into practice. To overcome this bottleneck, we have established the RElevant LIterature SearcH consortium consisting of more than 1500 scientists from 84 countries, who have collectively annotated the relevance of over 180 000 PubMed-listed articles with regard to their respective seed (input) article/s. The majority of annotations were contributed by highly experienced, original authors of the seed articles. The collected data cover 76% of all unique PubMed Medical Subject Headings descriptors. No systematic biases were observed across different experience levels, research fields or time spent on annotations. More importantly, annotations of the same document pairs contributed by different scientists were highly concordant. We further show that the three representative baseline methods used to generate recommended articles for evaluation (Okapi Best Matching 25, Term Frequency-Inverse Document Frequency and PubMed Related Articles) had similar overall performances. Additionally, we found that these methods each tend to produce distinct collections of recommended articles, suggesting that a hybrid method may be required to completely capture all relevant articles. The established database server located at https://relishdb.ict.griffith.edu.au is freely available for the downloading of annotation data and the blind testing of new methods. We expect that this benchmark will be useful for stimulating the development of new powerful techniques for title and title/abstract-based search engines for relevant articles in biomedical research.Peer reviewe

Design, simulation and HIL testing of an electric propulsion system of an electric scooter with brushless DC motor using field-oriented control Digital Twin of an electric scooter

A motor control algorithm to control a brushless DC motor has been implemented and tested in this master thesis. Model-based development approach has been applied to implement the entire system that includes the control algorithm (Field-Oriented Control) and the model of a brushless DC motor. The model of BLDC motor is implemented in a such a way that any motor’s specification could be given as input and the model would work as a digital twin of that motor. It is a modular system. Certain rotor position sensors are also discussed in this thesis, but the focus is on implementation of the control algorithm with a modular motor model and performing real-time simulation and testing of the model. A sensor-less method is used to measure the speed in this model, using the back-EMF of the motor. The model was deployed on Speedgoat performance machine which has a Xilinx FPGA and a CPU that runs the motor in real-time. Texas Instrument MCU was used to test the control algorithm. The hardware were connected in a loop to perform Hardware-in-the-loop testing and evaluate the results. This was done to test the performance of the control algorithm on the TI MCU. A model-based approach is used with real-time simulation as it helps in testing extreme conditions and various faults in the system without using the actual hardware. The thesis research showed that several extreme conditions can be tested to check the performance of the controller on a hardware connected in a loop, without using the actual motor