bluuebunny/crossref_metadata_2025_split huggingface dataset:
Entropy removal of medical diagnostics
Authors: He Shuhan , Chong Paul , Yoon Byung-Jun , Chung Pei-Hung , Chen David , Marzouk Sammer , Black Kameron C. , Sharp Wilson , Safari Pedram , Goldstein Joshua N. , Raja Ali S. , Lee Jarone 
Published: January 2024

AbstractShannon entropy is a core concept in machine learning and information theory, particularly in decision tree modeling. To date, no studies have extensively and quantitatively applied Shannon entropy in a systematic way to quantify the entropy of clinical situations using diagnostic variables (true and false positives and negatives, respectively). Decision tree representations of medical decision-making tools can be generated using diagnostic variables found in literature and entropy removal can be calculated for these tools. This concept of clinical entropy removal has significant potential for further use to bring forth healthcare innovation, such as quantifying the impact of clinical guidelines and value of care and applications to Emergency Medicine scenarios where diagnostic accuracy in a limited time window is paramount. This analysis was done for 623 diagnostic tools and provided unique insights into their utility. For studies that provided detailed data on medical decision-making algorithms, bootstrapped datasets were generated from source data to perform comprehensive machine learning analysis on these algorithms and their constituent steps, which revealed a novel and thorough evaluation of medical diagnostic algorithms.
FBPP: software to design PCR primers and probes for nucleic acid base detection of foodborne pathogens
Authors: Soliman Mohamed A. , Azab Mohamed S. , Hussein Hala A. , Roushdy Mohamed M. , Abu el-naga Mohamed N. 
Published: January 2024

AbstractFoodborne pathogens can be found in various foods, and it is important to detect foodborne pathogens to provide a safe food supply and to prevent foodborne diseases. The nucleic acid base detection method is one of the most rapid and widely used methods in the detection of foodborne pathogens; it depends on hybridizing the target nucleic acid sequence to a synthetic oligonucleotide (probes or primers) that is complementary to the target sequence. Designing primers and probes for this method is a preliminary and critical step. However, new bioinformatics tools are needed to automate, specific and improve the design sets to be used in the nucleic acid‒base method. Thus, we developed foodborne pathogen primer probe design (FBPP), an open-source, user-friendly graphical interface Python-based application supported by the SQL database for foodborne pathogen virulence factors, for (i) designing primers/probes for detection purposes, (ii) PCR and gel electrophoresis photo simulation, and (iii) checking the specificity of primers/probes.
In silico and in vitro prediction of new synthesized N-heterocyclic compounds as anti-SARS-CoV-2
Authors: Hashem Heba E. , Ahmad Sajjad , Kumer Ajoy , Bakri Youness El 
Published: January 2024

AbstractComputer-aided drug design has been employed to get the medicinal effects against Corona virus from different pyridine derivatives after synthesizing the new compounds. Additionally, various computational studies are also employed between the newly prepared pyridine derivatives and three controls against three proteins (6Y2E, 6M71 and 6M3M). Different methods were employed to synthesize new pyridine derivatives according to the literature using different reaction mediums. MTT was performed for cytotoxicity study and IC50 for inhibitory concentration. Additionally, in-silico studies including DFT, molecular docking, molecular dynamics, MMPBSA, ADME, pharmacokinetics and Lipinski rules were evaluated. The chemical structures of all new compounds were elucidated based on spectroscopic investigation. A molecular docking study demonstrated that compounds 5, 11, and 12 have the best binders of the SARS-CoV-2 main protease enzyme, with energy scores of − 7.5 kcal/mol, − 7.2 kcal/mol, and − 7.9 kcal/mol, respectively. The net binding energy values of the 11-Mpro, 12-Mpro, and 5-Mpro complexes revealed their highly stable nature in terms of both intermolecular interactions and docked conformation across the simulation time. ADME properties, besides the pharmacokinetics and Lipinski rules, showed that all seven newly synthesized compounds follow Lipinski rules with high GI absorption. The In Vitro antiviral study against SARS-CoV-2 using MTT methods confirms that compound 5 has more potential and is safer than other tested compounds. The study shows that the newly synthesized pyridine derivatives have medicinal properties against SARS-CoV-2 without violating Lipinski rules. Compounds 5, 11, and 12, particularly compound 5, may serve as promising potential candidate for COVID-19.
Co-release of cytokines after drug-eluting stent implantation in acute myocardial infarction patients with PCI
Authors: Wan Minying , Hu Kun , Lu Yi , Wang Cheng , Mao Bin , Yang Qing , Zheng Zhenzhong , Wu Hao , Luo Yihong , Maiti Amit K. 
Published: January 2024

AbstractAcute Myocardial Infarction (AMI) after Percutaneous Coronary Intervention (PCI) often requires stent implantation leading to cardiovascular injury and cytokine release. Stent implantation induces cytokines production including TNFα, Hs-CRP, IL-1ß, IL2 receptor, IL6, IL8, and IL10, but their co-release is not extensively established. In 311 PCI patients with Drug-Eluting Stent (DES) implantation, we statistically evaluate the correlation of these cytokines release in various clinical conditions, stent numbers, and medications. We observed that TNFα is moderately correlated with IL-1ß (r2 = 0.59, p = 0.001) in diabetic PCI patients. Similarly, in NSTEMI (Non-ST Segment Elevation) patients, TNFα is strongly correlated with both IL-1ß (r2 = 0.97, p = 0.001) and IL8 (r2 = 0.82, p = 0.001). In CAD (Coronary Artery Disease)-diagnosed patients TNFα is highly correlated (r2 = 0.84, p = 0.0001) with IL8 release but not with IL-1ß. In patients with an increased number of stents, Hs-CRP is significantly coupled with IL8 > 5 pg/ml (t-statistic = 4.5, p < 0.0001). Inflammatory suppressor drugs are correlated as TNFα and IL8 are better suppressed by Metoprolol 23.75 (r2 = 0.58, p < 0.0001) than by Metoprolol 11.87 (r2 = 0.80, p = 0.5306). Increased TNFα and IL-1ß are better suppressed by the antiplatelet drug Brilinta (r2 = 0.30, p < 0.0001) but not with Clopidogrel (r2 = 0.87, p < 0.0001). ACI/ARB Valsartan 80 (r2 = 0.43, p = 0.0011) should be preferred over Benazepril 5.0 (r2 = 0.9291, p < 0.0001) or Olmesartan (r2 = 0.90, p = 0.0001). Thus, the co-release of IL-1ß, IL8 with TNFα, or only IL8 with TNFα could be a better predictor for the outcome of stent implantation in NSTEMI and CAD-diagnosed AMI patients respectively. Cytokine suppressive medications should be chosen carefully to inhibit further cardiovascular damage.
Measurement of IFN-γ and IL-2 for the assessment of the cellular immunity against SARS-CoV-2
Authors: Safont Guillem , Villar-Hernández Raquel , Smalchuk Daria , Stojanovic Zoran , Marín Alicia , Lacoma Alicia , Pérez-Cano Cristina , López-Martínez Anabel , Molina-Moya Bárbara , Solis Alan Jhunior , Arméstar Fernando , Matllo Joan , Díaz-Fernández Sergio , Romero Iris , Casas Irma , Strecker Kevin , Preyer Rosemarie , Rosell Antoni , Latorre Irene , Domínguez Jose 
Published: January 2024

AbstractThe study of specific T-cell responses against SARS-CoV-2 is important for understanding long-term immunity and infection management. The aim of this study was to assess the dual IFN-γ and IL-2 detection, using a SARS-CoV-2 specific fluorescence ELISPOT, in patients undergoing acute disease, during convalescence, and after vaccination. We also evaluated humoral response and compared with T-cells with the aim of correlating both types of responses, and increase the number of specific response detection. Blood samples were drawn from acute COVID-19 patients and convalescent individuals classified according to disease severity; and from unvaccinated and vaccinated uninfected individuals. IgGs against Spike and nucleocapsid, IgMs against nucleocapsid, and neutralizing antibodies were also analyzed. Our results show that IFN-γ in combination with IL-2 increases response detection in acute and convalescent individuals (p = 0.023). In addition, IFN-γ detection can be a useful biomarker for monitoring severe acute patients, as our results indicate that those individuals with a poor outcome have lower levels of this cytokine. In some cases, the lack of cellular immunity is compensated by antibodies, confirming the role of both types of immune responses in infection, and confirming that their dual detection can increase the number of specific response detections. In summary, IFN-γ/IL-2 dual detection is promising for characterizing and assessing the immunization status, and helping in the patient management.
Sea ice-ocean coupling during Heinrich Stadials in the Atlantic–Arctic gateway
Authors: El bani Altuna Naima , Ezat Mohamed M. , Smik Lukas , Muschitiello Francesco , Belt Simon T. , Knies Jochen , Rasmussen Tine L. 
Published: January 2024

AbstractThe variability of Arctic sea-ice during abrupt stadial-interstadial shifts in the last glacial period remain poorly understood. Here, we investigated the millennial-scale relationship, with a focus on Heinrich Stadials (HS), between sea-ice cover and bottom water temperature (BWT) during Marine Isotope Stages (MIS) 3 and 2 (64–13 ka) in the Fram Strait using new molecular sea ice biomarker data and published benthic foraminiferal BWT records. Widespread spring sea-ice cover (SpSIC) dominated the studied interval, especially in mid-late MIS 3 (45–29 ka). Yet, warm interstadials were characterized by relatively more open-ocean conditions compared to cold stadials. At the transition between a HS and the subsequent interstadial, sea ice was tightly linked to BWT with rapid reductions in SpSIC coinciding with lower BWT at the end of HS. The relative timing of the events, especially during HS 1, points to ocean warming as the key controlling factor for sea ice reduction at millennial timescales.
Plant defensive responses to insect eggs are inducible by general egg-associated elicitors
Authors: Lortzing Vivien , Valsamakis Georgios , Jantzen Friederike , Hundacker Janik , Paniagua Voirol Luis R. , Schumacher Fabian , Kleuser Burkhard , Hilker Monika 
Published: January 2024

AbstractEgg deposition by herbivorous insects is well known to elicit defensive plant responses. Our study aimed to elucidate the insect and plant species specificity of these responses. To study the insect species specificity, we treated Arabidopsis thaliana with egg extracts and egg-associated secretions of a sawfly (Diprion pini), a beetle (Xanthogaleruca luteola) and a butterfly (Pieris brassicae). All egg extracts elicited salicylic acid (SA) accumulation in the plant, and all secretions induced expression of plant genes known to be responsive to the butterfly eggs, among them Pathogenesis-Related (PR) genes. All secretions contained phosphatidylcholine derivatives, known elicitors of SA accumulation and PR gene expression in Arabidopsis. The sawfly egg extract did not induce plant camalexin levels, while the other extracts did. Our studies on the plant species specificity revealed that Solanum dulcamara and Ulmus minor responded with SA accumulation and cell death to P. brassicae eggs, i.e. responses also known for A. thaliana. However, the butterfly eggs induced neoplasms only in S. dulcamara. Our results provide evidence for general, phosphatidylcholine-based, egg-associated elicitors of plant responses and for conserved plant core responses to eggs, but also point to plant and insect species-specific traits in plant–insect egg interactions.
Crowdsourced human-based computational approach for tagging peripheral blood smear sample images from Sickle Cell Disease patients using non-expert users
Authors: Rubio José María Buades , Moyà-Alcover Gabriel , Jaume-i-Capó Antoni , Petrović Nataša 
Published: January 2024

AbstractIn this paper, we present a human-based computation approach for the analysis of peripheral blood smear (PBS) images images in patients with Sickle Cell Disease (SCD). We used the Mechanical Turk microtask market to crowdsource the labeling of PBS images. We then use the expert-tagged erythrocytesIDB dataset to assess the accuracy and reliability of our proposal. Our results showed that when a robust consensus is achieved among the Mechanical Turk workers, probability of error is very low, based on comparison with expert analysis. This suggests that our proposed approach can be used to annotate datasets of PBS images, which can then be used to train automated methods for the diagnosis of SCD. In future work, we plan to explore the potential integration of our findings with outcomes obtained through automated methodologies. This could lead to the development of more accurate and reliable methods for the diagnosis of SCD.
Time-course changes in fingernail cortisol levels during pregnancy and postpartum
Authors: Izawa Shuhei , Kawasaki Mikiko , Sugaya Nagisa , Nomura Shusaku 
Published: January 2024

AbstractThe cortisol level in fingernails can reflect the cumulative hormones produced in the body several months prior. However, previous studies have only demonstrated the cross-sectional associations of fingernail cortisol with salivary or hair cortisol, and not longitudinal changes in fingernail cortisol in situations where cortisol levels in the body could be expected to change. Therefore, this study focused on pregnancy as a model for changes in cortisol levels over a prolonged period of time, and investigating the time courses of fingernail cortisol during pregnancy and the postpartum period. We collected nail samples from 30 healthy women during pregnancy and 12 months postpartum to measure the cortisol levels in the nail. Results showed that cortisol levels in fingernail clippings increased from 1 month before childbirth to 4 months postpartum, with the levels peaking at 2 months postpartum. Additionally, we found higher cortisol levels in fingernail clippings in primiparas than in those of multiparas. The time course of fingernail cortisol levels could replicate the longitudinal changes in cortisol in the body, and differences between multiparas and primiparas seemed to be biologically plausible, which could support the concept of fingernail cortisol as a retrospective index of hormone production.
Folate receptor overexpression induces toxicity in a diet-dependent manner in C. elegans
Authors: Shrestha Bideep , Tallila Milla , Matilainen Olli 
Published: January 2024

AbstractFolate receptor (FR) alpha (FOLR1) and beta (FOLR2) are membrane-anchored folate transporters that are expressed at low levels in normal tissues, while their expression is strongly increased in several cancers. Intriguingly, although the function of these receptors in, for example, development and cancer has been studied intensively, their role in aging is still unknown. To address this, we utilized Caenorhabditis elegans, in which FOLR-1 is the sole ortholog of folate receptors. We found that the loss of FOLR-1 does not affect reproduction, physical condition, proteostasis or lifespan, indicating that it is not required for folate transport to maintain health. Interestingly, we found that FOLR-1 is detectably expressed only in uterine-vulval cells, and that the histone-binding protein LIN-53 inhibits its expression in other tissues. Furthermore, whereas knockdown of lin-53 is known to shorten lifespan, we found that the loss of FOLR-1 partially rescues this phenotype, suggesting that elevated folr-1 expression is detrimental for health. Indeed, our data demonstrate that overexpression of folr-1 is toxic, and that this phenotype is dependent on diet. Altogether, this work could serve as a basis for further studies to elucidate the organismal effects of abnormal FR expression in diseases such as cancer.
Comparing deep learning and handcrafted radiomics to predict chemoradiotherapy response for locally advanced cervical cancer using pretreatment MRI
Authors: Jeong Sungmoon , Yu Hosang , Park Shin-Hyung , Woo Dongwon , Lee Seoung-Jun , Chong Gun Oh , Han Hyung Soo , Kim Jae-Chul 
Published: January 2024

AbstractConcurrent chemoradiotherapy (CRT) is the standard treatment for locally advanced cervical cancer (LACC), but its responsiveness varies among patients. A reliable tool for predicting CRT responses is necessary for personalized cancer treatment. In this study, we constructed prediction models using handcrafted radiomics (HCR) and deep learning radiomics (DLR) based on pretreatment MRI data to predict CRT response in LACC. Furthermore, we investigated the potential improvement in prediction performance by incorporating clinical factors. A total of 252 LACC patients undergoing curative chemoradiotherapy are included. The patients are randomly divided into two independent groups for the training (167 patients) and test datasets (85 patients). Contrast-enhanced T1- and T2-weighted MR scans are obtained. For HCR analysis, 1890 imaging features are extracted and a support vector machine classifier with a five-fold cross-validation is trained on training dataset to predict CRT response and subsequently validated on test dataset. For DLR analysis, a 3-dimensional convolutional neural network was trained on training dataset and validated on test dataset. In conclusion, both HCR and DLR models could predict CRT responses in patients with LACC. The integration of clinical factors into radiomics prediction models tended to improve performance in HCR analysis. Our findings may contribute to the development of personalized treatment strategies for LACC patients.
Influence of the breathing pattern on the pulmonary function of endurance-trained athletes
Authors: Sikora Marcin , Mikołajczyk Rafał , Łakomy Olga , Karpiński Jakub , Żebrowska Aleksandra , Kostorz-Nosal Sabina , Jastrzębski Dariusz 
Published: January 2024

AbstractProper functioning of the respiratory system is one of the most important determinants of human health. According to current knowledge, the diaphragmatic breathing pattern seems to be the most favourable. However, recent reports indicate that athletes often have dysfunctional breathing patterns, which may be associated with an increased risk of musculoskeletal injuries. The influence of the type of breathing pattern on the mechanical airways in athletes has not been investigated. The aim of the present study was to determine the characteristics and relationships between breathing patterns and respiratory function in athletes. This study included 69 Polish elite endurance athletes (♂40, ♀29) in different sports disciplines and 44 (♂17, ♀27) healthy nonathletes as a control group. All participants underwent pulmonary function tests (spirometry, plethysmography, diffusion capacity for carbon monoxide) with assessment of breathing patterns by the Hi–Lo test. Inspiratory and expiratory resistance (R) and reactance (X) of the respiratory system at a given frequency (5 Hz, 11 Hz, and 19 Hz) were measured by a noninvasive forced oscillation technique. In this study, almost half of the athletes (44.92%) had dysfunctional breathing patterns, although at a lower rate than that in the control group. Diaphragmatic breathing patterns were characterized by higher spirometric, plethysmographic and DLCO values compared to thoracic or abdominal breathing patterns. Similarly, lower inspiratory reactance at 5 Hz (X5%pred.) was observed in the diaphragmatic pattern compared to the thoracic pattern. A diaphragmatic breathing pattern is associated with better pulmonary function test results. However, this study revealed a dysfunctional breathing pattern in almost half of the athletes. These results suggest that the assessment of breathing patterns and the implementation of breathing exercises in athletes are essential to promote proper breathing patterns.
Changes in global DMS production driven by increased CO2 levels and its impact on radiative forcing
Authors: Zhao Junri , Zhang Yan , Bie Shujun , Bilsback Kelsey R. , Pierce Jeffrey R. , Chen Ying 
Published: January 2024

AbstractOur study highlights the importance of understanding the future changes in dimethyl-sulfide (DMS), the largest natural sulfur source, in the context of ocean acidification driven by elevated CO2 levels. We found a strong negative correlation (R2 = 0.89) between the partial pressure of carbon dioxide (pCO2) and sea-surface DMS concentrations based on global observational datasets, not adequately captured by the Coupled Model Intercomparison Project Phase 6 (CMIP6) Earth System Models (ESMs). Using this relationship, we refined projections of future sea-surface DMS concentrations in CMIP6 ESMs. Our study reveals a decrease in global sea-surface DMS concentrations and the associated aerosol radiative forcing compared to ESMs’ results. These reductions represent ~9.5% and 11.1% of the radiative forcings resulting from aerosol radiation and cloud interactions in 2100 reported by the Intergovernmental Panel on Climate Change Sixth Assessment Report. Thus, future climate projections should account for the climate implications of changes in DMS production due to ocean acidification.
Next-generation study databases require FAIR, EHR-integrated, and scalable Electronic Data Capture for medical documentation and decision support
Authors: Dugas Martin , Blumenstock Max , Dittrich Tobias , Eisenmann Urs , Feder Stephan Christoph , Fritz-Kebede Fleur , Kessler Lucy J. , Klass Maximilian , Knaup Petra , Lehmann Christoph U. , Merzweiler Angela , Niklas Christian , Pausch Thomas M. , Zental Nelly , Ganzinger Matthias 
Published: January 2024

AbstractStructured patient data play a key role in all types of clinical research. They are often collected in study databases for research purposes. In order to describe characteristics of a next-generation study database and assess the feasibility of its implementation a proof-of-concept study in a German university hospital was performed. Key characteristics identified include FAIR access to electronic case report forms (eCRF), regulatory compliant Electronic Data Capture (EDC), an EDC with electronic health record (EHR) integration, scalable EDC for medical documentation, patient generated data, and clinical decision support. In a local case study, we then successfully implemented a next-generation study database for 19 EDC systems (n = 2217 patients) that linked to i.s.h.med (Oracle Cerner) with the local EDC system called OpenEDC. Desiderata of next-generation study databases for patient data were identified from ongoing local clinical study projects in 11 clinical departments at Heidelberg University Hospital, Germany, a major tertiary referral hospital. We compiled and analyzed feature and functionality requests submitted to the OpenEDC team between May 2021 and July 2023. Next-generation study databases are technically and clinically feasible. Further research is needed to evaluate if our approach is feasible in a multi-center setting as well.