bluuebunny/crossref_metadata_2025_split huggingface dataset:
Semantic segmentation of defects based on DCNN and its application on fatigue lifetime prediction for SLM Ti-6Al-4V alloy
Authors: Pan Jinchao , Hu Dianyin , Zhou Liucheng , Huang Di , Wang Ying , Wang Rongqiao 
Published: November 2023

Inevitable defects have an important impact on the fatigue lifetime of additive manufacturing materials. Therefore, it is critical to thoroughly characterize the characteristics of the defects, which requires effective semantic segmentation of the imaged defects. In this paper, a defect dataset for SLM Ti-6Al-4V alloy was obtained by synchrotron radiation computed tomography. Then a semantic segmentation method was developed based on the DeepLabV3 + network to automatically extract defects. Cropping and undersampling were introduced in the dataset pre-processing. A weighted scheme based on the ratio between the number of defect and matrix pixels was applied in the classification layer, and morphological operations were employed in image post-processing to improve the accuracy of identifying small-target defect. Finally, the above method was applied to segment the X-ray computed tomography data for two batches of SLM Ti-6Al-4V materials, and the defect segmentation results were used to predict the fatigue lifetime. The semantic segmentation method performs well with a pixel recognition accuracy of 98.2% for the test dataset, and the error in the predicted fatigue lifetime lies within the scatter band of ±2.2.
This article is part of the theme issue 'Physics-informed machine learning and its structural integrity applications (Part 2)'.
Spot the Difference: Can ChatGPT4-Vision Transform Radiology Artificial Intelligence?
Authors: Kelly Brendan S , Duignan Sophie , Mathur Prateek , Dillon Henry , Lee Edward H , Yeom Kristen W , Keane Pearse , Lawlor Aonghus , Killeen Ronan P 
Published: November 2023

AbstractOpenAI’s flagship Large Language Model ChatGPT can now accept image input (GPT4V). “Spot the Difference” and “Medical” have been suggested as emerging applications. The interpretation of medical images is a dynamic process not a static task. Diagnosis and treatment of Multiple Sclerosis is dependent on identification of radiologic change. We aimed to compare the zero-shot performance of GPT4V to a trained U-Net and Vision Transformer (ViT) for the identification of progression of MS on MRI.170 patients were included. 100 unseen paired images were randomly used for testing. Both U-Net and ViT had 94% accuracy while GPT4V had 85%. GPT4V gave overly cautious non-answers in 6 cases. GPT4V had a precision, recall and F1 score of 0.896, 0.915, 0.905 compared to 1.0, 0.88 and 0.936 for U-Net and 0.94, 0.94, 0.94 for ViT.The impressive performance compared to trained models and a no-code drag and drop interface suggest GPT4V has the potential to disrupt AI radiology research. However misclassified cases, hallucinations and overly cautious non-answers confirm that it is not ready for clinical use. GPT4V’s widespread availability and relatively high error rate highlight the need for caution and education for lay-users, especially those with limited access to expert healthcare.Key pointsEven without fine tuning and without the need for prior coding experience or additional hardware, GPT4V can perform a zero-shot radiologic change detection task with reasonable accuracy.We find GPT4V does not match the performance of established state of the art computer vision models. GPT4V’s performance metrics are more similar to the vision transformers than the convolutional neural networks, giving some possible insight into its underlying architecture.This is an exploratory experimental study and GPT4V is not intended for use as a medical device.Summary statementGPT4V can identify radiologic progression of Multiple Sclerosis in a simplified experimental setting. However GPT4V is not a medical device and its widespread availability and relatively high error rate highlight the need for caution and education for lay-users, especially those with limited access to expert healthcare.
Exploring Emotions in EEG: Deep Learning Approach with Feature Fusion
Authors: Tasaouf Mridula Danastan , Ferdaus Abu Ahmed , Pias Tanmoy Sarkar 
Published: November 2023

AbstractEmotion is an intricate physiological response that plays a crucial role in how we respond and cooperate with others in our daily affairs. Numerous experiments have been evolved to recognize emotion, however still require exploration to intensify the performance. To enhance the performance of effective emotion recognition, this study proposes a subject-dependent robust end-to-end emotion recognition system based on a 1D convolutional neural network (1D-CNN). We evaluate the SJTU1Emotion EEG Dataset SEED-V with five emotions (happy, sad, neural, fear, and disgust). To begin with, we utilize the Fast Fourier Transform (FFT) to decompose the raw EEG signals into six frequency bands and extract the power spectrum feature from the frequency bands. After that, we combine the extracted power spectrum feature with eye movement and differential entropy (DE) features. Finally, for classification, we apply the combined data to our proposed system. Consequently, it attains 99.80% accuracy which surpasses each prior state-of-the-art system.
Demographic and health characteristics associated with fish and n-3 fatty acid supplement intake during pregnancy: results from pregnancy cohorts in the ECHO program
Authors: Oken Emily , Musci Rashelle J. , Westlake Matthew , Gachigi Kennedy , Aschner Judy L. , Barnes Kathrine L. , Bastain Theresa M. , Buss Claudia , Camargo Carlos A. , Cordero Jose F. , Dabelea Dana , Dunlop Anne L. , Ghassabian Akhgar , Hipwell Alison E. , Hockett Christine W. , Karagas Margaret R. , Lugo-Candelas Claudia , Margolis Amy E. , O’Connor Thomas G. , Shuster Coral L. , Straughen Jennifer K. , Lyall Kristen 
Published: November 2023

ABSTRACTObjectiveOmega-3 (n-3) fatty acid consumption during pregnancy is recommended for optimal pregnancy outcomes and offspring health. We examined characteristics associated with self-reported fish or omega-3 supplement intake.DesignPooled pregnancy cohort studies.SettingCohorts participating in the Environmental influences on Child Health Outcomes (ECHO) consortium with births from 1999-2020.ParticipantsA total of 10,800 pregnant people in 23 cohorts with food frequency data on fish consumption; 12,646 from 35 cohorts with information on supplement use.ResultsOverall, 24.6% reported consuming fish never or less than once per month, 40.1% less than once a week, 22.1% 1-2 times per week, and 13.2% more than twice per week. The relative risk (RR) of ever (vs. never) consuming fish was higher in participants who were older (1.14, 95% CI: 1.10, 1.18 for 35-40 vs. <29 years), were other than non-Hispanic White (1.13, 95% CI: 1.08, 1.18 for non-Hispanic Black; 1.05, 95% CI: 1.01, 1.10 for non-Hispanic Asian; 1.06, 95% CI: 1.02, 1.10 for Hispanic), or used tobacco (1.04, 95% CI: 1.01, 1.08). The RR was lower in those with overweight vs. healthy weight (0.97, 95% CI: 0.95, 1.0). Only 16.2% reported omega-3 supplement use, which was more common among individuals with a higher age and education, a lower BMI, and fish consumption (RR 1.5, 95% CI: 1.23, 1.82 for twice-weekly vs. never).ConclusionsOne-quarter of participants in this large nationwide dataset rarely or never consumed fish during pregnancy, and omega-3 supplement use was uncommon, even among those who did not consume fish.
Antibody response to symptomatic infection with SARS-CoV-2 Omicron variant viruses, December 2021—June 2022
Authors: Sandford Ryan , Yadav Ruchi , Noble Emma K. , Sumner Kelsey , Joshi Devyani , Tartof Sara Y. , Wernli Karen J. , Martin Emily T. , Gaglani Manjusha , Zimmerman Richard K. , Talbot H. Keipp , Grijalva Carlos G. , Belongia Edward A. , Carlson Christina , Coughlin Melissa , Flannery Brendan , Pearce Brad , Rogier Eric 
Published: November 2023

ABSTRACTTo describe humoral immune responses to symptomatic SARS-CoV-2 infection, we assessed immunoglobulin G binding antibody levels using a commercial multiplex bead assay against SARS-CoV-2 ancestral spike protein receptor binding domain (RBD) and nucleocapsid protein (N). We measured binding antibody units per mL (BAU/mL) during acute illness within 5 days of illness onset and during convalescence in 105 ambulatory patients with laboratory-confirmed SARS-CoV-2 infection with Omicron variant viruses. Comparing acute- to convalescent phase antibody concentrations, geometric mean anti-N antibody concentrations increased 47-fold from 5.5 to 259 BAU/mL. Anti-RBD antibody concentrations increased 2.5-fold from 1258 to 3189 BAU/mL.
A Formal Model for the Representation of Binary Temporal Relations in Healthcare Applications and an Efficient Algorithm for Logic-Based Temporal Subsumption Testing and Pattern Matching
Authors: Sujansky Walter , Campbell Keith E. 
Published: November 2023

AbstractObjectivesImportant temporal relationships exist among pairs of medically relevant events stored in electronic health records (EHRs), such as “the infection began within two weeks after surgery”. Queries for specific temporal patterns also appear in decision-support rules and data-analysis programs. The accurate matching of such patterns to the patient data in EHRs is critical to the effective performance of decision-support systems, statistical analysis programs, data-abstraction processes, digital phenotyping for machine-learning, and other applications. The correct classification of temporally-qualified concepts in biomedical terminologies and ontologies, such as SNOMED-CT, is also important to ensure the accuracy and completeness of these knowledge-based resources.MethodsIn this paper, we describe an expressive model to formally represent temporal relationships between pairs of events, including “Before”, “During”, “Withinndays after”, and “Withinnhours before ormhours after, but not during”. We also describe a novel logic-based algorithm to deduce whether one such relationship temporally matches (i.e., is subsumed by) another such relationship, which enables the querying of structured time-stamped patient data, the querying of semi-structured narrative patient data, and the classification of logically defined medical concepts. Our model assumes an interval-based notion of time and our algorithm implements a logic-based definition of subsumption.ResultsWe formally prove the correctness of the algorithm based on the properties of temporal intervals and the axioms of propositional logic. We also prove that the algorithm has computational complexity of constant-time (i.e., O(1)) with respect to the size of the database being queried or the knowledge base being classified.ConclusionThe novel model and algorithm described here for temporal representation and reasoning are sound and have the potential to facilitate temporal subsumption testing and pattern matching in a number of medical application domains. Empirical testing is needed to establish the full scope of useful applicability.
Misexpression of inactive genes in whole blood is associated with nearby rare structural variants
Authors: Vanderstichele Thomas , Burnham Katie L , de Klein Niek , Tardaguila Manuel , Howell Brittany , Walter Klaudia , Kundu Kousik , Koeppel Jonas , Lee Wanseon , Tokolyi Alex , Persyn Elodie , Nath Artika P , Marten Jonathan , Petrovski Slavé , Roberts David J , Di Angelantonio Emanuele , Danesh John , Berton Alix , Platt Adam , Butterworth Adam S , Soranzo Nicole , Parts Leopold , Inouye Michael , Paul Dirk S , Davenport Emma E 
Published: November 2023

AbstractGene misexpression is the aberrant transcription of a gene in a context where it is usually inactive. Despite its known pathological consequences in specific rare diseases, we have a limited understanding of its wider prevalence and mechanisms in humans. To address this, we analyzed gene misexpression in 4,568 whole blood bulk RNA sequencing samples from INTERVAL study blood donors. We found that while individual misexpression events occur rarely, in aggregate they were found in almost all samples and over half of inactive genes. Using 2,821 paired whole genome and RNA sequencing samples, we identified that misexpression events are enriched incisfor rare structural variants. We established putative mechanisms through which a subset of SVs lead to gene misexpression, including transcriptional readthrough, transcript fusions and gene inversion. Overall, we develop misexpression as a novel type of transcriptomic outlier analysis and extend our understanding of the variety of mechanisms by which genetic variants can influence gene expression.
Role of desmoplakin in supporting neuronal activity, neurogenic processes, and emotional-related behaviors in the dentate gyrus
Authors: Otsubo Keisuke , Sakashita Naoko , Nishimoto Yuki , Sato Yo , Tsutsui Takehisa , Kobayashi Katsunori , Suzuki Kanzo , Segi-Nishida Eri 
Published: November 2023

AbstractDesmoplakin (Dsp) is a component of desmosomal cell-cell junctions that interacts with the cadherin complex and cytoskeletal intermediate filaments. In addition to its function as an adhesion component, Dsp is involved in various biological processes, such as gene expression, differentiation, and migration. Dsp is specifically expressed in the hippocampal dentate gyrus (DG) in the central nervous system. However, it is unclear how Dsp impacts hippocampal function and its related behaviors. Using an adeno-associated virus knockdown system in mice, we provide evidence that Dsp in the DG maintains hippocampal functions, including neuronal activity and adult neurogenesis, and contributes to anxiolytic-like effects. Dsp protein is mostly localized in mature granule cells in the adult DG. Dsp knockdown in the DG resulted in a lowered expression of an activity-dependent transcription factor FosB, and an increased expression of mature neuronal markers, such as calbindin. In addition, the suppression of Dsp decreases serotonin responsiveness at the DG output mossy fiber synapses and alters adult neurogenic processes in the subgranular zone of the DG. Moreover, DG- specific Dsp knockdown mice showed an increase in anxiety-like behaviors. Taken together, this research uncovers an unexplored function for Dsp in the central nervous system and suggests that Dsp in the DG may function as a regulator to maintain proper neuronal activation and adult neurogenesis, and contribute to the adaptation of emotion-related behavior.
BFCI at #SMM4H 2023: Integration of Machine Learning and TF-IDF for Covid-19 Tweets Analysis
Authors: Nayel Hamada , Ashraf Nsrin , Aldawsari Mohamed 
Published: November 2023

AbstractExtracting information from texts generated by users of social media platforms becomes a crucial task. In this paper, we describe the systems submitted to the SMM4H shared tasks 1 and 2. The aims of these two tasks are binary and multi-class classification of English tweets. We developed a machine learning-based model integrated with TF-IDF as a feature extraction approach. Four classification algorithms have been implemented namely, support vector machines, passive-aggressive classifier, multi-layer perceptron and random forest. For task 1, the passive-aggressive classifier reported f1-score of 63.7%. For task 2, multi-layer perceptron reported f1-score of 71.4%.
Shape variation and sexual dimorphism of the adult human mandible evaluated by geometric morphometrics
Authors: Chalazoniti Aspasia , Lattanzi Wanda , Halazonetis Demetrios J. 
Published: November 2023

AbstractMandibular shape variability and effects of age and sex were explored in an adult human sample using dense landmarking and geometric morphometrics. We segmented 50 male and 50 female mandibular surfaces from CBCT images (age range: 18.9 to 73.7 years). Nine fixed landmarks and 496 sliding semilandmarks were digitized on the mandibular surface, and then slid by minimizing bending energy against the average shape. Principal component analysis extracted the main patterns of shape variation. Sexes were compared with permutation tests and allometry was assessed by regressing on the log of the centroid size. Almost 49 percent of shape variation was described by the first three principal components. Shape variation was related to width, height and length proportions, variation of the angle between ramus and corpus, height of the coronoid process and inclination of the symphysis. Significant sexual dimorphism was detected, both in size and shape. Males were larger than females, had a higher ramus, more pronounced gonial angle, larger inter-gonial width, and more distinct antegonial notch. Accuracy of sexing based on the first two principal components in form space was 91 percent. The degree of edentulism was weakly related to mandibular shape. Age effects were not significant.
Social contact patterns during the early COVID-19 pandemic in Norway: insights from a panel study, April to September 2020
Authors: Veneti Lamprini , Robberstad Bjarne , Steens Anneke , Forland Frode , Winje Brita A. , Vestrheim Didrik F. , Jarvis Christopher I , Gimma Amy , John Edmunds W. , Zandvoort Kevin Van , de Blasio Birgitte Freiesleben 
Published: November 2023

AbstractBackgroundDuring the COVID-19 pandemic, many countries adopted social distance measures and lockdowns of varying strictness. Social contact patterns are essential in driving the spread of respiratory infections, and country-specific measurements are needed. This study aimed to gain insights into changes in social contacts and behaviour during the early pandemic phase in Norway.MethodsWe conducted an online survey among a nationally representative sample of Norwegian adults, including six data collections/waves between April and September 2020, and used survey data from 2017 as baseline. We calculated mean daily contacts, and estimated age-stratified contact matrices that were used to estimate reproduction numbers during the study period.ResultsThe mean daily number of contacts varied between 3.2 (95% CI 3.0-3.4) to 3.9 (95% CI 3.6-4.2) across waves, representing a 67-73% decline compared to pre-pandemic levels. Fewer contacts in the community setting largely drove the reduction; the drop was most prominent among younger adults. Despite gradual easing of social distance measures during the survey period, population contact matrices remained relatively stable and displayed more inter-age group mixing than at baseline. Contacts within households and the community outside schools and workplaces contributed most to social encounters.ConclusionSocial contacts experienced a significant decline during the months following the March 2020 lockdown in Norway, aligning with the implementation of stringent social distancing measures. The findings contribute valuable empirical information into the social behaviour of the Norwegian population during the early pandemic, which can be used to enhance policy-relevant models for addressing future crises when mitigation measures might be implemented.
DormantMycobacterium tuberculosisreactivatesex vivoin blood from HIV infected individuals
Authors: Kalyan Madhur , Agarwal Stuti , Sharma Aman , Verma Indu 
Published: November 2023

AbstractReports of tuberculosis in Human Immunodeficiency Virus infected patients despite high CD4+T-cell counts suggest different mechanisms of reactivation.In vitrodeveloped dormantMycobacterium tuberculosisH37Rv were cultured in HIV blood and normal blood. Colony forming units analysis was performed and expression of mycobacterial Resuscitation Promomoting Factor genes was analyzed by qRT-PCR. Thein vitrodeveloped dormantM. tbresuscitated in HIV blood as evident from increase in CFUs and up-regulation in the expression of mycobacterialrpfgenes. Reactivation of dormant tubercle bacilli following HIV infection in spite of high CD4+T-cell counts could be due to some viral or host factors which needs further studies.
Robust and time-resolved estimation of cardiac sympathetic and parasympathetic indices
Authors: Candia-Rivera Diego , de Vico Fallani Fabrizio , Chavez Mario 
Published: November 2023

AbstractThe time-resolved analysis of heart rate (HR) and heart rate variability (HRV) is crucial for the evaluation of the dynamic changes of autonomic activity under different clinical and behavioral conditions. Standard HRV analysis is performed in the frequency domain because the sympathetic activations tend to increase low-frequency HRV oscillations, while the parasympathetic ones increase high-frequency HRV oscillations. However, a strict separation of HRV in frequency bands may cause biased estimations, especially in the low frequency range. To overcome this limitation, we propose a robust estimator that combines HR and HRV dynamics, based on the correlation of the Poincaré plot descriptors of interbeat intervals from the electrocardiogram. To validate our method, we used electrocardiograms gathered from open databases where standardized paradigms were applied to elicit changes in autonomic activity. Our proposal outperforms the standard spectral approach for the estimation of low- and high-frequency fluctuations in HRV, and its performance is comparable to newer methods. Our method constitutes a valuable, robust, time-resolved, and cost-effective tool for a better understanding of autonomic activity through HR and HRV in healthy state and potentially for pathological conditions.
Guanylate cyclase activity of TIR1/AFB auxin receptors in rapid auxin responses
Authors: Qi Linlin , Kwiatkowski Mateusz , Kulich Ivan , Chen Huihuang , Gao Yongqiang , Yun Ping , Li Lanxin , Shabala Sergey , Farmer Edward E. , Jaworski Krzysztof , Friml Jiří 
Published: November 2023

AbstractThe major developmental signal in plants, auxin is perceived by TIR1/AFB receptors. It triggers transcriptional reprogramming via well-established canonical mechanism but also elusive rapid, non-transcriptional responses. Here we demonstrate that TIR1/AFB receptors have, next to recently identified adenylate cyclase, also guanylate cyclase activity. Auxin perception activates independently the cAMP and cGMP production by TIR1/AFBsin vitroand increases cAMP and cGMP levelsin plantawith a slow and fast dynamics, respectively. Exogenous cGMP but not cAMP application induces rapid cytosolic Ca2+transients and root growth inhibition, suggesting that TIR1/AFB-derived cGMP mediates rapid auxin responses. This unprecedented combination of adenylate and guanylate cyclase activities in a hormone receptor provides a new paradigm for how a single perception mechanism can mediate a multitude of diverse downstream responses.One-Sentence SummaryTIR1/AFB auxin receptors have guanylate cyclase activity, whose product, cGMP mediates rapid non-transcriptional auxin responses.
Hierarchical motion perception as causal inference
Authors: Shivkumar Sabyasachi , DeAngelis Gregory C. , Haefner Ralf M. 
Published: November 2023

AbstractSince motion can only be defined relative to a reference frame, which reference frame guides perception? A century of psychophysical studies has produced conflicting evidence: retinotopic, egocentric, world-centric, or even object-centric. We introduce a hierarchical Bayesian model mapping retinal velocities to perceived velocities. Our model mirrors the structure in the world, in which visual elements move within causally connected reference frames. Friction renders velocities in these reference frames mostly stationary, formalized by an additional delta component (at zero) in the prior. Inverting this model automatically segments visual inputs into groups, groups into supergroups, etc. and “perceives” motion in the appropriate reference frame. Critical model predictions are supported by two new experiments, and fitting our model to the data allows us to infer the subjective set of reference frames used by individual observers. Our model provides a quantitative normative justification for key Gestalt principles providing inspiration for building better models of visual processing in general.