bluuebunny/crossref_metadata_2025_split huggingface dataset:
An annotated human blastocyst dataset to benchmark deep learning architectures for in vitro fertilization
Authors: Kromp Florian , Wagner Raphael , Balaban Basak , Cottin Véronique , Cuevas-Saiz Irene , Schachner Clara , Fancsovits Peter , Fawzy Mohamed , Fischer Lukas , Findikli Necati , Kovačič Borut , Ljiljak Dejan , Martínez-Rodero Iris , Parmegiani Lodovico , Shebl Omar , Min Xie , Ebner Thomas 
Published: May 2023

AbstractMedical Assisted Reproduction proved its efficacy to treat the vast majority forms of infertility. One of the key procedures in this treatment is the selection and transfer of the embryo with the highest developmental potential. To assess this potential, clinical embryologists routinely work with static images (morphological assessment) or short video sequences (time-lapse annotation). Recently, Artificial Intelligence models were utilized to support the embryo selection procedure. Even though they have proven their great potential in different in vitro fertilization settings, there is still considerable room for improvement. To support the advancement of algorithms in this research field, we built a dataset consisting of static blastocyst images and additional annotations. As such, Gardner criteria annotations, depicting a morphological blastocyst rating scheme, and collected clinical parameters are provided. The presented dataset is intended to be used to train deep learning models on static morphological images to predict Gardner’s criteria and clinical outcomes such as live birth. A benchmark of human expert’s performance in annotating Gardner criteria is provided.
Chunking as a rational solution to the speed–accuracy trade-off in a serial reaction time task
Authors: Wu Shuchen , Éltető Noémi , Dasgupta Ishita , Schulz Eric 
Published: May 2023

AbstractWhen exposed to perceptual and motor sequences, people are able to gradually identify patterns within and form a compact internal description of the sequence. One proposal of how sequences can be compressed is people’s ability to form chunks. We study people’s chunking behavior in a serial reaction time task. We relate chunk representation with sequence statistics and task demands, and propose a rational model of chunking that rearranges and concatenates its representation to jointly optimize for accuracy and speed. Our model predicts that participants should chunk more if chunks are indeed part of the generative model underlying a task and should, on average, learn longer chunks when optimizing for speed than optimizing for accuracy. We test these predictions in two experiments. In the first experiment, participants learn sequences with underlying chunks. In the second experiment, participants were instructed to act either as fast or as accurately as possible. The results of both experiments confirmed our model’s predictions. Taken together, these results shed new light on the benefits of chunking and pave the way for future studies on step-wise representation learning in structured domains.
MSRDL: Deep learning framework for service recommendation in mashup creation
Authors: Yu Ting , Liu Hailin , Zhang Lihua , Liu Hongbing 
Published: May 2023

AbstractIn recent years, service-oriented computing technology has developed rapidly. The growing number of services increases the choice burden of software developers when developing service-based systems, such as mashups or applications. How to recommend appropriate services for developers to create mashups has become a basic problem in service-oriented recommendation systems. To solve this problem, people have proposed various methods to recommend services to match the requirements of the new mashups and achieved great success. However, there are also some challenges in feature utilization and text requirement understanding. Therefore, we propose a Mashup-oriented Service Recommendation framework based on Deep Learning, called MSRDL. A content component was designed in MSRDL to generate the representation of mashups and services. Besides, an interaction component was created in MSRDL to model the invocation records between mashups and services. The output features of the two parts are further integrated into MLP to obtain the service recommendation lists. Experimental results on ProgrammableWeb datasets show that our method is superior to the state-of-the-art methods.
Associations of active commuting to school in childhood and physical activity in adulthood
Authors: Kaseva Kaisa , Lounassalo Irinja , Yang Xiaolin , Kukko Tuomas , Hakonen Harto , Kulmala Janne , Pahkala Katja , Rovio Suvi , Hirvensalo Mirja , Raitakari Olli , Tammelin Tuija H. , Salin Kasper 
Published: May 2023

AbstractThis study examined whether active commuting to school in childhood and adolescence predicted active commuting to work and overall physical activity (PA) in adulthood. Participants from the Young Finns Study (N = 2436) were aged 9–18 years in 1980 and followed up until 2018/2020. Their commuting modes to school were assessed with a self-reported questionnaire in 1980. Adulthood PA was assessed through self-reports regarding commuting modes to work (2001–2018), leisure-time physical activity (LTPA) (2001–2018), and objectively measured daily steps (2007–2018/2020). Associations between childhood commuting and adulthood PA were evaluated using regression analyses and multilevel models. Demographic, socioeconomic and environmental covariates were adjusted for in the analyses. Active commuting to school in childhood contributed favourably to LTPA in 2001 (B = .38, p < .001), in 2007 (B = .35, p < .001), and in 2018 (B = .28, p < .01). Active commuting in childhood was associated with higher number of daily aerobic steps (B = 299.00, p = .03) and daily aerobic steps during weekdays in 2011 (B = 312.15, p = .03). In 2018, active commuting associated favourably with daily aerobic steps (B = 370.42, p < .01), daily aerobic steps during weekdays (B = 347.65, p = .01), daily steps during weekends (B = 628.49, p = .02), and daily aerobic steps during weekends (B = 402.69, p = .03). Covariate adjustments attenuated the associations excluding the one between active commuting and LTPA in 2007 (B = .36, p = .01) and daily steps during weekends in 2018 (B = 782.25, p = .04). Active commuting to school in childhood might be one of the PA modes that contribute to PA in adulthood and is therefore encouraged to be promoted from an early age.
Component wave calculation and analysis of the acoustic field in a borehole within a three-phase porous medium
Authors: Liu Lin , Zhang Xiumei , Wang Xiuming , He Xiao , Chen Hao 
Published: May 2023

AbstractThe knowledge of acoustic wave propagation in a borehole embedded in gas hydrate-bearing sediments is of great significance for the exploitation of gas hydrate. A gas hydrate-bearing sediment is a typical three-phase porous medium containing two solids and one fluid. However, until now, the borehole acoustic wavefield and its component waves within such a porous medium have never been calculated. In this work, a real-axis integration method is proposed to calculate the borehole acoustic field embedded in a three-phase porous medium based on the Biot-type three-phase theory. Meanwhile, a component wave approach, combined with the branch-cut integral method and the residue theorem, including residues at leaky poles is proposed to study the borehole wave propagation of a three-phase porous medium. The branch points and poles of the potential acoustic wave function are obtained, which correspond to the normal and leaky modes on various Riemann sheets. On this basis, the excitation intensity and waveforms of each component are obtained. The result shows that the waveform summed up from all individual waves agrees well with the full waveform calculated by real-axis integration, which provides a theoretical basis for the subsequent inversion of reservoir parameters by using the information of various mode waves.
Sputum handling for rheology
Authors: Esteban Enjuto Lydia , Robert de Saint Vincent Matthieu , Maurin Max , Degano Bruno , Bodiguel Hugues 
Published: May 2023

AbstractThe rheology of sputum is viewed as a powerful emerging biophysical marker for monitoring muco-obstructive pulmonary diseases such as cystic fibrosis (CF) and non-CF bronchiectasis (NCFB). However, there is no unified practice to process sputa from collection to analysis, which can lead to highly variable, and sometimes inconsistent results. The main objective of this study is to bring light into the handling of sputum samples to establish a standardised and robust protocol before rheological measurements. Sputum collected from 22 CF and 10 NCFB adults, was divided into control (vortexed and fresh: non-heated and non-frozen) and three treated conditions (either non-vortexed, heated or frozen). In addition, 6 CF expectorations were used to study the dynamics of ageing over 24 h. Sputum’s mechanical properties were measured with a rotational rheometer to obtain their properties at rest, elastic ($$G'$$

G
′

) and viscous moduli ($$G''$$

G

′
′

), and at the onset of flow, critical deformation ($$\gamma _c$$

γ
c

) and critical stress ($$\sigma _c$$

σ
c

). We demonstrate that heating sputum is completely destructive while freezing sputa at $$-80\,\,^{\circ }\hbox {C}$$

-
80

∘

C

has no discernible effect on their rheology. We also show that the variability of rheological measurements largely resulted from the sample’s macroscopic heterogeneity, and can be greatly reduced by non-destructive vortex homogenisation. Finally, we observed contrasted ageing effects as a fonction of purulence: while the viscoelasticity of purulent samples reduced by half within 6 h after collection, semi-purulent samples did not evolve. These results guide towards a robust unified protocol for simple sputum handling in rheometry. We therefore suggest to vortex and snap freeze sputum samples immediately after collection when direct testing is not possible.
Equivalent running leg lengths require prosthetic legs to be longer than biological legs during standing
Authors: Zhang-Lea Janet H. , Tacca Joshua R. , Beck Owen N. , Taboga Paolo , Grabowski Alena M. 
Published: May 2023

AbstractWe aimed to determine a method for prescribing a standing prosthetic leg length (ProsL) that results in an equivalent running biological leg length (BioL) for athletes with unilateral (UTTA) and bilateral transtibial amputations (BTTA). We measured standing leg length of ten non-amputee (NA) athletes, ten athletes with UTTA, and five athletes with BTTA. All athletes performed treadmill running trials from 3 m/s to their maximum speed. We calculated standing and running BioL and ProsL lengths and assessed the running-to-standing leg length ratio (Lratio) at three instances during ground contact: touchdown, mid-stance, and take-off. Athletes with UTTA had 2.4 cm longer standing ProsL than BioL length (p = 0.030), but their ProsL length were up to 3.3 cm shorter at touchdown and 4.1 cm shorter at mid-stance than BioL, at 3–11.5 m/s. At touchdown, mid-stance, and take-off, athletes with BTTA had 0.01–0.05 lower Lratio at 3 m/s (p < 0.001) and 0.03–0.07 lower Lratio at 10 m/s (p < 0.001) in their ProsL compared to the BioL of NA athletes. During running, ProsL were consistently shorter than BioL. To achieve equivalent running leg lengths at touchdown and take-off, athletes with UTTA should set their running-specific prosthesis height so that their standing ProsL length is 2.8–4.5% longer than their BioL length, and athletes with BTTA should set their running-specific prosthesis height so that their standing ProsL lengths are at least 2.1–3.9% longer than their presumed BioL length. Setting ProsL length to match presumed biological dimensions during standing results in shorter legs during running.
Elevated serum uric acid is associated with infertility in women living in America
Authors: Hong Xiang , Zhao Fanqi , Wang Wei , Wu Jingying , Zhu Xiaoqi , Wang Bei 
Published: May 2023

AbstractExcessive uric acid levels may affect several organs and systems in the body. There is limited evidence of the effects of high serum uric acid levels on the female reproductive system. This study used the National Health and Nutrition Examination Survey (NHANES) database to explore the relationship between serum uric acid and female infertility. This cross-sectional study included a total of 2197 eligible subjects using data from NHANES 2013-March 2020 pre-pandemic data. Self-reported infertility (ever experiencing an inability to conceive after 12 months of trying to become pregnant) was the main outcome. Logistic regression models and restricted cubic spline were used to analyze the relationship between serum uric acid and female infertility, and stratified analysis was carried out. A total of 295 women self-reported infertility (13.43%). The median uric acid level for all study subjects was 4.4 mg/dL (interquartile range [IQR]: 3.7, 5.1). Serum uric acid levels were higher in the infertility group than in the control group (4.7 mg/dL [IQR: 4.0, 5.3] vs. 4.4 mg/dL [IQR: 3.7, 5.1], P < 0.001). After adjusting for age, race, marital status, smoking, alcohol, history of pregnancy, history of diabetes, history of hypertension, fasting glucose, total cholesterol, creatinine in refrigerated serum, low-density lipoprotein cholesterol, direct high-density lipoprotein cholesterol, glycohemoglobin, and body mass index confounders, women with serum uric acid levels at Q3 (4.4–5.1 mg/dL) had a 73% (odds ratio [OR] = 1.73, 95% confidence interval [CI] 1.18, 2.54, P = 0.005) higher risk of infertility, and women with uric acid levels at Q4 (5.1–18.0 mg/dL) had an 83% (OR = 1.83, 95% CI 1.22, 2.75, P = 0.003) increased risk of infertility compared to women at Q1 (1.6–3.7 mg/dL). The restricted cubic spline also showed that when serum uric acid levels exceeded the reference value, the risk of infertility gradually increased. We also performed a sensitivity analysis based on the complete dataset and found that the results were robust. Higher serum uric acid levels were significantly associated with an increased risk of female infertility. Women planning a pregnancy should have increased serum uric acid monitoring.
Cross talk between bacterial and human gene networks enriched using ncRNAs in IBD disease
Authors: Elahimanesh Mohammad , Najafi Mohammad 
Published: May 2023

AbstractInflammatory bowel disease (IBD) is a long-term inflammatory immune-mediated gut illness with several extra-intestinal complications. The aims of this study were to identify a novel network-based meta-analysis approach on the basis of the combinations of the differentially expressed genes (DEGs) from microarray data, to enrich the functional modules from human protein–protein interaction (PPI) and gene ontology (GO) data, and to profile the ncRNAs on the genes involved in IBD. The gene expression profiles of GSE126124, GSE87473, GSE75214, and GSE95095 are obtained from the Gene Expression Omnibus (GEO) database based on the study criteria between 2017 and 2022. The DEGs were screened by the R software. DEGs were then used to examine gene ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. The ncRNAs including the miRNAs and ceRNAs were predicted on the PPIs visualized using Cytoscape. Enrichment analysis of genes with differential expression (n = 342) using KEGG and GO showed that the signaling pathways related with staphylococcus aureus and pertussis bacterial infections may stimulate the immune system and exacerbate IBD via the interaction with human proteins including Fibrinogen gamma chain (FGG), Keratin 10 (KRT10), and Toll like receptor 4 (TLR4). By building a ceRNA network, lncRNA XIST and NEAT1 were determined by affecting common miRNAs, hsa-miR-6875-5p, hsa-miR-1908-5p, hsa-miR-186-5p, hsa-miR-6763-5p, hsa-miR-4436a, and hsa-miR-520a-5p. Additionally, the chromosome regions including NM_001039703 and NM_006267, which produce the most potent circRNAs play a significant role in the ceRNA network of IBD. Also, we predicted the siRNAs that would be most effective against the bacterial genes in staphylococcus aureus and pertussis infections. These findings suggested that three genes (FGG, KRT10, and TLR4), six miRNAs (hsa-miR-6875-5p, hsa-miR-1908-5p, hsa-miR-186-5p, hsa-miR-4436a, hsa-miR-520a-5p, and hsa-miR-6763-5p), two lncRNAs (XIST and NEAT1), and chromosomal regions including NM_001039703 and NM_006267 with the production of the most effective circRNAs are involved in the ncRNA-associated ceRNA network of IBD. These ncRNA profiles are related to the described gene functions and may play therapeutic targets in controlling inflammatory bowel disease.
Atrial high-rate episodes intensify R2CHA2DS2-VASc score for prognostic stratification in pacemaker patients
Authors: Li Yi-Pan , Chen Ju-Yi , Chen Tse-Wei , Lu Wei-Da 
Published: May 2023

AbstractPatients with device detected atrial high-rate episodes (AHRE) have an increased risk of MACE. The R2CHA2DS2-VASc, CHADS2, R2CHADS2 and CHA2DS2-VASc score have been investigated for predicting major adverse cardiovascular events (MACE) in different groups of patients. We aimed to evaluate the R2CHA2DS2-VASc score in combination with AHRE ≥ 6 min for predicting MACE in patients with dual-chamber PPM but no prior atrial fibrillation (AF). We retrospectively enrolled 376 consecutive patients undergoing dual-chamber PPM implantation and no prior AF. The primary endpoint was subsequent MACE. For all patients in the cohort, CHADS2, R2CHADS2, CHA2DS2-VASc, R2CHA2DS2-VASc scores and AHRE ≥ or < 6 min were determined. AHRE was recorded as a heart rate > 175 bpm (Medtronic) or > 200 bpm (Biotronik) lasting ≥ 30 s. Multivariate Cox regression analysis with time-dependent covariates was used to determine the independent predictors of MACE. ROC-AUC analysis was performed for CHADS2, R2CHADS2, CHA2DS2-VASc, and R2CHA2DS2-VASc scores and then adding AHRE ≥ 6 min to the four scores. The median age was 77 years, and 107 patients (28.5%) developed AHRE ≥ 6 min. After a median follow-up of 32 months, 46 (12.2%) MACE occurred. Multivariate Cox regression analysis showed that R2CHA2DS2-VASc score (HR, 1.485; 95% CI, 1.212–1.818; p < 0.001) and AHRE ≥ 6 min (HR, 2.125; 95% CI, 1.162–3.887; p = 0.014) were independent predictors for MACE. The optimal R2CHA2DS2-VASc score cutoff value was 4.5 (set at ≥ 5), with the highest Youden index (AUC, 0.770; 95% CI, 0.709–0.831; p < 0.001). ROC-AUC analysis of the four risk scores separately combined with AHRE ≥ 6 min all showed better discriminatory power than the four scores alone (All Z-statistic p < 0.05). In patients with PPM who develop AHRE ≥ 6 min, it is crucial to perform risk assessment with either four scores to further stratify risk for MACE.
Exploring pharmaphylogeny from multiple perspectives: a case study on Lithospermeae
Authors: Yan Yumei , Wei Xinxin , Qiu Bin , Wang Guoping , Zhou Baochang , Zhang Mingxu , Liu Yibo , Li Siqi , Gao Bowen , Li Minhui 
Published: May 2023

AbstractLithospermeae Dumort., a tribe under the subfamily Boraginoidae, is a perennial herb containing approximately 470 species under 26 genera, primarily distributed in temperate and tropical regions. To gain a deeper understanding of the medicinal plants of Lithospermeae and better protect and develop plant medicinal resources, the phytochemistry, pharmacology, and traditional use of Lithospermeae with medicinal value were analyzed. Phylogenetic analysis was carried out based on the internal transcribed spacer sequence. Through spatial analysis and the species distribution model, the spatial distribution pattern of Lithospermeae medicinal plants was analyzed. Meanwhile, the relevant targets and pathways involved in the pharmacological effects of commonly used medicinal plants were predicted using network pharmacology to further explore the genetic origin of Lithospermeae and enrich the pharmaphylogeny of medicinal plants. In this study, the chemical composition, traditional efficacy, and modern pharmacological activity of Lithospermeae were collected for the first time and analyzed in combination with the geographical distribution model, molecular phylogeny, and network pharmacology. Based on our findings, the pharmaphylogeny of Lithospermeae was preliminarily discussed, providing the scientific basis for basic research regarding Lithospermeae. Concurrently, this study explored the relationship between the development of the regional medicinal plant industry and the protection of biodiversity. Furthermore, our findings provide direction and theoretical guidance for the study of the phylogenetic relationships in medicinal plants and the development of Lithospermeae medicinal plant resources.
Stabilization of modulation instability by control field in semiconductor quantum wells
Authors: Nath Monika , Mukherjee Rohit , Borgohain Nitu 
Published: May 2023

AbstractThis article explores the modulation instability of a continuous or quasi-continuous weak probe pulse in a three-level asymmetric double quantum wells under an electromagnetically induced transparency regime, controlled by a strong laser beam. The dynamics of modulation instability reveals that the instability gain as well as its bandwidth is greatly influenced by control field Rabi frequency. The probe pulse is found to be almost stable against modulation instability for higher values of control field Rabi frequency. The results of this investigation may potentially apply for oscillation free generation of supercontinuum in quantum well nanostructures.
Non-invasive identification of combined salinity stress and stalk rot disease caused by Colletotrichum graminicola in maize using Raman spectroscopy
Authors: Higgins Samantha , Joshi Ritu , Juarez Isaac , Bennett John S. , Holman Aidan P. , Kolomiets Michael , Kurouski Dmitry 
Published: May 2023

AbstractFood security is an emerging problem that is faced by our civilization. There are millions of people around the world suffering from various kinds of malnutrition. The number of people that starve will only increase considering the continuous growth of the world’s population. The problem of food security can be addressed by timely detection and identification biotic and abiotic stresses in plants that drastically reduce the crop yield. A growing body of evidence suggests that Raman spectroscopy (RS), an emerging analytical technique, can be used for the confirmatory and non-invasive diagnostics of plant stresses. However, it remains unclear whether RS can efficiently disentangle biotic and abiotic stresses, as well as detect both of them simultaneously in plants. In this work, we modeled a stalk rot disease in corn by inoculating the plant stalks with Colletotrichum graminicola. In parallel, we subjected plants to salt stress, as well as challenging plants with both stalk rot disease and salinity stress simultaneously. After the stresses were introduced, Raman spectra were collected from the stalks to reveal stress-specific changes in the plant biochemistry. We found that RS was able to differentiate between stalk rot disease and salinity stresses with 100% accuracy, as well as predict presence of both of those stresses in plants on early and late stages. These results demonstrate that RS is a robust and reliable approach that can be used for confirmatory, non-destructive and label-free diagnostics of biotic and abiotic stresses in plants.