bluuebunny/crossref_metadata_2025_split huggingface dataset:
Going against the flow: bumblebees prefer to fly upwind and display more variable kinematics when flying downwind
Authors: Combes Stacey A. , Gravish Nick , Gagliardi Susan F. 
Published: April 2023

ABSTRACT
Foraging insects fly over long distances through complex aerial environments, and many can maintain constant ground speeds in wind, allowing them to gauge flight distance. Although insects encounter winds from all directions in the wild, most lab-based studies have employed still air or headwinds (i.e. upwind flight); additionally, insects are typically compelled to fly in a single, fixed environment, so we know little about their preferences for different flight conditions. We used automated video collection and analysis methods and a two-choice flight tunnel paradigm to examine thousands of foraging flights performed by hundreds of bumblebees flying upwind and downwind. In contrast to the preference for flying with a tailwind (i.e. downwind) displayed by migrating insects, we found that bees prefer to fly upwind. Bees maintained constant ground speeds when flying upwind or downwind in flow velocities from 0 to 2 m s−1 by adjusting their body angle, pitching down to raise their air speed above flow velocity when flying upwind, and pitching up to slow down to negative air speeds (flying backwards relative to the flow) when flying downwind. Bees flying downwind displayed higher variability in body angle, air speed and ground speed. Taken together, bees' preference for upwind flight and their increased kinematic variability when flying downwind suggest that tailwinds may impose a significant, underexplored flight challenge to bees. Our study demonstrates the types of questions that can be addressed with newer approaches to biomechanics research; by allowing bees to choose the conditions they prefer to traverse and automating filming and analysis to examine massive amounts of data, we were able to identify significant patterns emerging from variable locomotory behaviors, and gain valuable insight into the biomechanics of flight in natural environments.
Biopsy-Guided Pathological Response Assessment in Breast Cancer is Insufficient: Additional Pathology Findings of the MICRA Trial
Authors: van Hemert Annemiek K. E. , van Duijnhoven Frederieke H. , van Loevezijn Ariane A. , Loo Claudette E. , Wiersma Terry , Groen Emilie J. , Peeters Marie-Jeanne T. F. D. Vrancken 
Published: April 2023

Abstract
Background
Neoadjuvant systemic treatment (NST) leads to pathologic complete response (pCR) in 10–89% of breast cancer patients depending on subtype. The added value of surgery is uncertain in patients who reach pCR; however, current imaging and biopsy techniques aiming to predict pCR are not accurate enough. This study aims to quantify the residual disease remaining after NST in patients with a favorable response on MRI and residual disease missed with biopsies.

Methods
In the MICRA trial, patients with a favorable response to NST on MRI underwent ultrasound-guided post-NST 14G biopsies followed by surgery. We analyzed pathology reports of the biopsies and the surgical specimens. Primary outcome was the extent of residual invasive disease among molecular subtypes, and secondary outcome was the extent of missed residual invasive disease.

Results
We included 167 patients. Surgical specimen showed residual invasive disease in 69 (41%) patients. The median size of residual invasive disease was 18 mm (interquartile range [IQR] 12–30) in hormone receptor-positive (HR+)/human epidermal growth factor receptor 2-negative (HER2−) patients, 8 mm (IQR 3–15) in HR+/HER2-positive (HER2+) patients, 4 mm (IQR 2–9) in HR-negative (HR−)/HER2+ patients, and 5 mm (IQR 2–11) in triple-negative (TN) patients. Residual invasive disease was missed in all subtypes varying from 4 to 7 mm.

Conclusion
Although the extent of residual invasive disease is small in TN and HER2+ subtypes, substantial residual invasive disease is left behind in all subtypes with 14G biopsies. This may hamper local control and limits adjuvant systemic treatment options. Therefore, surgical excision remains obligatory until accuracy of imaging and biopsy techniques improve.
Nutritional status, nutrient imbalances, food-related behaviors and dietary supplements use among patients with celiac disease on a gluten free diet in Lebanon: a national cross-sectional study
Authors: Hoteit Maha , Chamas Zeinab , Assaf Shaza , Bouhairie Malek Michael , Bahr Abbas , Daccache Romy , Matar Rami , Hallal Mahmoud , Hotayt Samer , Hotayt Bilal 
Published: April 2023

Background: Celiac disease is an autoimmune disorder triggered by gluten, that occurs in susceptible individuals and is associated with dietary restriction and subsequent nutritional deficiencies. This study investigated the diet quality, nutrition imbalances and nutrition status among young children,adolescents and adults with CD who were referred to several hospitals in Lebanon.Methods:A cross-sectional study in 50 individuals (31.74 ± 15.64 years) with CD who follow a gluten free diet was conducted, using biochemical parameters, anthropometric measurements, dietary and physical activity assessments.Results: Of the 50 participants, 38% and 16% were presenting low serum levels of iron and vitamin B12, respectively. The majority of participants were physically inactive and around 40% of them had low muscle mass. A weight loss of 10% to 30% indicating mild to moderate malnutrition was shown in 14% of individuals. The assessment of food-related behaviors shows that 80% of participants were reading nutrition labels and 96% of them were following gluten-free diets (GFD). Some barriers including family ignorance (6%), language of the nutrition labels (20%) and expensive GF products (78%) were limiting the adherence to GFD. The inadequacy of the daily energy intake along with insufficient intakes of calcium and vitamin D were remarked among individuals with CD. However, protein and iron intake were exceeding the recommendations among all age groups, except in males aged 4-8 years and 19-30 years. Half the study participants were using dietary supplements where 38%, 10%, 46%, 18%, 16% and 4% used vitamin D, vitamin B12, iron, calcium, folate and probiotics, respectively.Conclusion: GFD is the key treatment for CD. However, it is not without inadequacies and may cause certain deficiencies such as calcium and vitamin D leading to reduced bone density. This underlines the critical role of dietitians in education and maintenance of healthy GFD among individuals with CD.
Community review: a robust and scalable selection system for resource allocation within open science and innovation communities
Authors: Graham Chris L.B. , Landrain Thomas E. , Vjestica Amber , Masselot Camille , Lawton Elliot , Blondel Leo , Haenal Luca , Greshake Tzovaras Bastian , Santolini Marc 
Published: April 2023

Resource allocation is essential to the selection and implementation of innovative projects in science and technology. With large stakes involved in concentrating large fundings over a few promising projects, current “winner-take-all” models for grant applications are time-intensive endeavours that mobilise significant researcher time in writing extensive project proposals, and rely on the availability of a few time-saturated volunteer experts. Such processes usually carry over several months, resulting in high effective costs compared to expected benefits. Faced with the need for a rapid response to the COVID-19 pandemic in 2020, we devised an agile “community review” system, similar to distributed peer review (DPR) systems, to allocate micro-grants for the fast prototyping of innovative solutions. Here we describe and evaluate the implementation of this community review across 147 projects from the “Just One Giant Lab’s OpenCOVID19 initiative” and “Helpful Engineering” open research communities. The community review process uses granular review forms and requires the participation of grant applicants in the review process. We show that this system is fast, with a median duration of 10 days, scalable, with a median of 4 reviewers per project independent of the total number of projects, and fair, with project rankings highly preserved after the synthetic removal of reviewers. We investigate potential bias introduced by involving applicants in the process, and find that review scores from both applicants and non-applicants have a similar correlation of r=0.28 with other reviews within a project, matching previous observations using traditional approaches. Finally, we find that the ability of projects to apply to several rounds allows to both foster the further implementation of successful early prototypes, as well as provide a pathway to constructively improve an initially failing proposal in an agile manner. This study quantitatively highlights the benefits of a frugal community review system for agile resource allocation.
Multiomic sequencing of paired primary and metastatic small bowel carcinoids
Authors: Postel Mackenzie D. , Darabi Sourat , Howe James R. , Liang Winnie S. , Craig David W. , Demeure Michael J. 
Published: April 2023

Background: Small bowel carcinoids are insidious tumors that are often metastatic when diagnosed. Limited mutation landscape studies of carcinoids indicate that these tumors have a relatively low mutational burden. The development of targeted therapies will depend upon the identification of mutations that drive the pathogenesis and metastasis of carcinoid tumors. Methods: Whole exome and RNA sequencing of 5 matched sets of normal tissue, primary small intestine carcinoid tumors, and liver metastases were investigated. Germline and somatic variants included: single nucleotide variants (SNVs), insertions/deletions (indels), structural variants, and copy number alterations (CNAs). The functional impact of mutations was predicted using Ensembl Variant Effect Predictor. Results: Large-scale CNAs were observed including the loss of chromosome 18 in all 5 metastases and 3/5 primary tumors. Certain somatic SNVs were metastasis-specific; including mutations in ATRX, CDKN1B, MXRA5 (leading to the activation of a cryptic splice site and loss of mRNA), SMARCA2, and the loss of UBE4B. Additional mutations in ATRX, and splice site loss of PYGL, leading to intron retention observed in primary and metastatic tumors. Conclusions: We observed novel mutations in primary/metastatic carcinoid tumor pairs, and some have been observed in other types of neuroendocrine tumors. We confirmed a previously observed loss of chromosome 18 and CDKN1B. Transcriptome sequencing added relevant information that would not have been appreciated with DNA sequencing alone. The detection of several splicing mutations on the DNA level and their consequences at the RNA level suggests that RNA splicing aberrations may be an important mechanism underlying carcinoid tumors.
The utility of salivary CRP and IL-6 as a non-invasive measurement evaluated in patients with COVID-19 with and without diabetes
Authors: Bachtiar Endang , Bachtiar Boy M , Kusumaningrum Ardiana , Sunarto Hari , Soeroso Yuniarti , Sulijaya Benso , Apriyanti Efa , Theodorea Citra Fragrantia , Putra Pratomo Irandi , Yudhistira Yudhistira , Efendi Defi , Lestari Widya 
Published: April 2023

Background: The available evidence suggests that inflammatory responses, in both systemic and oral tissue, contribute to the pathology of COVID-19 disease. Hence, studies of inflammation biomarkers in oral fluids, such as saliva, might be useful to better specify COVID-19 features. Methods: In the current study, we performed quantitative real-time PCR to measure salivary levels of C-reactive protein (CRP) and interleukin-6 (IL-6) in saliva obtained from patients diagnosed with mild COVID-19, in a diabetic group (DG; n = 10) and a non-diabetic group (NDG; n = 13). All participants were diagnosed with periodontitis, while six participants with periodontitis but not diagnosed with COVID-19 were included as controls. Results: We found increases in salivary total protein levels in both the DG and NDG compared to control patients. In both groups, salivary CRP and IL-6 levels were comparable. Additionally, the levels of salivary CRP were significantly correlated with total proteins, in which a strong and moderate positive correlation was found between DG and NDG, respectively. A linear positive correlation was also noted in the relationship between salivary IL-6 level and total proteins, but the correlation was not significant. Interestingly, the association between salivary CRP and IL-6 levels was positive. However, a moderately significant correlation was only found in COVID-19 patients with diabetes, through which the association was validated by a receiver operating curve. Conclusions: These finding suggest that salivary CRP and IL-6 are particularly relevant as potential non-invasive biomarker for predicting diabetes risk in mild cases of COVID-19 accompanied with periodontitis.
Assessment of the level of knowledge about diabetes mellitus among diabetic patients: A cross-sectional study from Nepal
Authors: Adhikari Divas , Dhonju Kiran , Aryal Egesh , Ghimire Sandip , Chapagain Suresh , Malla Bishnu , Sangroula Prativa , Lageju Nimesh 
Published: April 2023

Background Diabetes mellitus is a chronic non-communicable disease (NCD) often associated with poor psychosocial and health outcomes. Available evidence suggests that patients’ knowledge about the disease is fundamental to its treatment and prevention or delaying of complications. Therefore, this study assessed the level of knowledge of diabetes patients on diabetes mellitus and its associated factors. Methods A descriptive cross-sectional study using a translated Nepalese version of the revised Michigan Diabetes Knowledge Scale was conducted among randomly selected patients with diabetes mellitus presenting to the outpatient department (OPD) of Madhyabindu Hospital, Nepal. Data were collected via an interviewer administered questionnaire and analyzed with MS Excel 2016 and IBM SPSS version 25 software. Results Among the 360 participants, 27.2% had good knowledge of diabetes and 72.8% had poor knowledge. Age, level of education, occupation, family history of diabetes, duration of the disease, presence of comorbidity, complications and body mass index (BMI) were significantly associated with knowledge of diabetes mellitus (p-value ≤ 0.05). Conclusions Based on the study findings, it is important that diabetes self-management education and support (DSMES) programs should be implemented and/or strengthened at the Madhyabindu Hospital and targeted communities to improve diabetes patient’s knowledge on their disease condition and self-care practices.
Preserved correlation matrices pinpoint extracellular matrix organization as a critical factor in pancreatic ductal adenocarcinoma
Authors: Menyhart Otília , Bartha Áron , Győrffy Balázs 
Published: April 2023

Background Gene co-expression correlations frequently signal shared biological functions with coordinated regulation. We hypothesized that maintained correlations might be essential for cellular survival, representing potential vulnerabilities of cancer cells. We aimed to reveal correlations preserved in pancreatic ductal adenocarcinomas (PDAC) across normal and tumor tissues. Methods: We searched the NCBI GEO for raw microarray data and the TCGA project for RNA-seq data. The microarray dataset consisted of 248 tumors and 108 normal samples, allowing the analysis of 12,210 genes. The RNA-seq dataset incorporated 177 tumors, four normal samples from TCGA, and 248 normal samples from GTEx, enabling the analysis of 21,479 genes. Genes with an altered expression were identified with a Mann-Whitney U test at p<0.01, and a Pearson correlation was performed to identify preserved correlations. Results: Altogether 371 significant correlations involving 262 genes were preserved across normal samples and tumors in both RNA-seq and gene chip platforms. The identified close-knit gene network is mainly responsible for extracellular matrix organization. Seven genes (SPARC, COL6A3, MMP2, HTRA1, FN1, PALLD, and COL3A1) were heavily overrepresented in maintained correlations, some of them participating in as many as 58 interactions. High expression of 28 genes was linked to poor disease outcome at FDR ≤ 10%, out of which FN1, an extracellular matrix component, was both overrepresented in maintained correlations and associated with worse overall survival (p = 0.00097, FDR ≤ 5%). The growing expression of two genes, MYL12A and MYL12B, across normal tissues, primary, and metastatic tumors may drive the acquisition of motility by cancer cells. Conclusions: Our results propose novel prognostic biomarkers of PDAC and pinpoint fundamental cellular interactions as potential targets for combination therapies. Furthermore, the presence of significant correlations across different data platforms substantiates the validity of our findings.
Dietary knowledge assessment among the patients with type 2 diabetes in Madinah: A cross-sectional study
Authors: Alharbi Mashael , Alharbi Mansour , Surrati Amal , Alhilabi Mashael , alrashdi Ayed , Almokhalafi Majedah 
Published: April 2023

Background: There is a huge burden of nutrition-related non-communicable diseases, and diabetes is one of the leading chronic nutrition-related diseases affecting more than 500 million people globally. Collecting information regarding the awareness of dietary and nutrition knowledge among diabetic patients is the first step to developing a disease prevention program. Thus, this study primarily aims at assessing the dietary awareness of diabetes patients attending the diabetic centre in Madinah governorate, Saudi Arabia. Methods: The study was started in November 2020 and ended in October 2021. The study participants (315) were type 2 diabetes mellitus (T2DM) patients attending a diabetic centre in Madinah, Saudi Arabia. A self-prepared dietary knowledge questionnaire (DKQ) was used in this research. The variables include balanced diet, food type, food choice, carbohydrate, protein, and fat. Knowledge score was, and the total score was leveled/categorized into ‘good’, ‘average’, and ‘poor’. Data were analyzed by SPSS v.26. Results: The study results identified the current knowledge of T2DM patients about different dietary items. The knowledge score of 62.2% of participants showed an average level of dietary knowledge, which is statistically significant. When we separately evaluated their understanding of different dietary components, we found that T2DM patients had poor knowledge of carbohydrates (30.15%), fat, food choices (47.7%), and type (34.6%). However, they had acceptable knowledge of proteins (56.5%). Conclusion: Our participants exhibited acceptable knowledge about proteins but poorer knowledge of other food groups. A healthy, well-balanced diet is essential for excellent glycaemic control. It is recommended to educate and arrange a health education program regarding dietary knowledge, specially designed for diabetic patients so that patients can opt for a healthier lifestyle.
Developing bird friendly transmission power lines in Kenya
Authors: Ngila Peggy , David Chiawo , Owuor Margaret , Wasonga Oliver , Ellwood Elizabeth , Mugo Jane , Masayi Nelly , Ikime Timothy , Chelelgo Stanley , Mugo Dominic 
Published: April 2023

Background: Kenya's rich wildlife is an important natural resource and is vital to the country's economy. However, rapid infrastructure development in key wildlife areas has threatened the survival of numerous species including raptors. Policy: The growing distribution of electricity grids in Kenya poses a significant risk to raptors and populations of other large birds. This research aimed to review the policy gaps in Kenya’s National Energy Policy (2018) examining the strategies for developing bird friendly transmission power lines in Kenya, with a goal to reduce the negative impact on raptor populations and improve their conservation. The findings indicate a high overlap between the ecological niche of raptors with medium and high voltage transmission power lines, with indication of high-risk hotspots for electrocution and collisions. Recommendations: This policy brief therefore proposes the adoption of bird friendly power lines in new transmission infrastructure projects and retrofitting existing power lines with bird friendly devices. This can be achieved through strengthening the legal and regulatory frameworks in the National Energy Policy. This will help prioritize avian conservation in power lines infrastructural development projects including the development of specific policies and guidelines for the placement, orientation, and marking of power lines to reduce the risk of electrocution and collisions of raptor species. Conclusions: Kenya committed to protecting migratory bird species and their habitats by signing the Convention on the Conservation of Migratory Species of Wild Animals in 1999. However, the National Energy Policy of 2018 lacks guidelines for bird-friendly power lines. Addressing this requires collaboration from the government, power companies, research institutions, conservation groups, and local communities. A concerted effort involving public education, targeted funding for research, and stakeholder collaboration can help Kenya meet its conservation obligations and safeguard vital habitats for migratory birds.
Clinical Trial Risk Tool: software application using natural language processing to identify the risk of trial uninformativeness
Authors: Wood Thomas A , McNair Douglas 
Published: April 2023

Background: A large proportion of clinical trials end without delivering results that are useful for clinical, policy, or research decisions. This problem is called “uninformativeness”. Some high-risk indicators of uninformativeness can be identified at the stage of drafting the protocol, however the necessary information can be hard to find in unstructured text documents. Methods: We have developed a browser-based tool which uses natural language processing to identify and quantify the risk of uninformativeness. The tool reads and parses the text of trial protocols and identifies key features of the trial design, which are fed into a risk model. The application runs in a browser and features a graphical user interface that allows a user to drag and drop the PDF of the trial protocol and visualize the risk indicators and their locations in the text. The user can correct inaccuracies in the tool’s parsing of the text. The tool outputs a PDF report listing the key features extracted. The tool is focused HIV and tuberculosis trials but could be extended to more pathologies in future. Results: On a manually tagged dataset of 300 protocols, the tool was able to identify the condition of a trial with 100% area under curve (AUC), presence or absence of statistical analysis plan with 87% AUC, presence or absence of effect estimate with 95% AUC, number of subjects with 69% accuracy, and simulation with 98% AUC. On a dataset of 11,925 protocols downloaded from ClinicalTrials.gov, the tool was able to identify trial phase with 75% accuracy, number of arms with 58% accuracy, and the countries of investigation with 87% AUC. Conclusion: We have developed and validated a natural language processing tool for identifying and quantifying risks of uninformativeness in clinical trial protocols. The software is open-source and can be accessed at the following link: https://app.clinicaltrialrisk.org