bluuebunny/crossref_metadata_2025_split huggingface dataset:
A self-knowledge distillation-driven CNN-LSTM model for predicting disease outcomes using longitudinal microbiome data
Authors: Fung Daryl L X , Li Xu , Leung Carson K , Hu Pingzhao 
Published: May 2023

Abstract

Motivation
Human microbiome is complex and highly dynamic in nature. Dynamic patterns of the microbiome can capture more information than single point inference as it contains the temporal changes information. However, dynamic information of the human microbiome can be hard to be captured due to the complexity of obtaining the longitudinal data with a large volume of missing data that in conjunction with heterogeneity may provide a challenge for the data analysis.

Results
We propose using an efficient hybrid deep learning architecture convolutional neural network—long short-term memory, which combines with self-knowledge distillation to create highly accurate models to analyze the longitudinal microbiome profiles to predict disease outcomes. Using our proposed models, we analyzed the datasets from Predicting Response to Standardized Pediatric Colitis Therapy (PROTECT) study and DIABIMMUNE study. We showed the significant improvement in the area under the receiver operating characteristic curve scores, achieving 0.889 and 0.798 on PROTECT study and DIABIMMUNE study, respectively, compared with state-of-the-art temporal deep learning models. Our findings provide an effective artificial intelligence-based tool to predict disease outcomes using longitudinal microbiome profiles from collected patients.

Availability and implementation
The data and source code can be accessed at https://github.com/darylfung96/UC-disease-TL.
Supervised Machine Learning Classifies Inflammatory Bowel Disease Patients by Subtype Using Whole Exome Sequencing Data
Authors: Stafford Imogen S , Ashton James J , Mossotto Enrico , Cheng Guo , Mark Beattie Robert , Ennis Sarah 
Published: May 2023

Abstract

Background
Inflammatory bowel disease [IBD] is a chronic inflammatory disorder with two main subtypes: Crohn’s disease [CD] and ulcerative colitis [UC]. Prompt subtype diagnosis enables the correct treatment to be administered. Using genomic data, we aimed to assess machine learning [ML] to classify patients according to IBD subtype.

Methods
Whole exome sequencing [WES] from paediatric/adult IBD patients was processed using an in-house bioinformatics pipeline. These data were condensed into the per-gene, per-individual genomic burden score, GenePy. Data were split into training and testing datasets [80/20]. Feature selection with a linear support vector classifier, and hyperparameter tuning with Bayesian Optimisation, were performed [training data]. The supervised ML method random forest was utilised to classify patients as CD or UC, using three panels: 1] all available genes; 2] autoimmune genes; 3] ‘IBD’ genes. ML results were assessed using area under the receiver operating characteristics curve [AUROC], sensitivity, and specificity on the testing dataset.

Results
A total of 906 patients were included in analysis [600 CD, 306 UC]. Training data included 488 patients, balanced according to the minority class of UC. The autoimmune gene panel generated the best performing ML model [AUROC = 0.68], outperforming an IBD gene panel [AUROC = 0.61]. NOD2 was the top gene for discriminating CD and UC, regardless of the gene panel used. Lack of variation in genes with high GenePy scores in CD patients was the best classifier of a diagnosis of UC.

Discussion
We demonstrate promising classification of patients by subtype using random forest and WES data. Focusing on specific subgroups of patients, with larger datasets, may result in better classification.
Cardiac magnetic resonance imaging of pericardial diseases: a comprehensive guide
Authors: Antonopoulos Alexios S , Vrettos Apostolos , Androulakis Emmanouil , Kamperou Christina , Vlachopoulos Charalambos , Tsioufis Konstantinos , Mohiaddin Raad , Lazaros George 
Published: May 2023

Abstract
Cardiac magnetic resonance (CMR) imaging has been established as a valuable diagnostic tool in the assessment of pericardial diseases by providing information on cardiac anatomy and function, surrounding extra-cardiac structures, pericardial thickening and effusion, characterization of pericardial effusion, and the presence of active pericardial inflammation from the same scan. In addition, CMR imaging has excellent diagnostic accuracy for the non-invasive detection of constrictive physiology evading the need for invasive catheterization in most instances. Growing evidence in the field suggests that pericardial enhancement on CMR is not only diagnostic of pericarditis but also has prognostic value for pericarditis recurrence, although such evidence is derived from small patient cohorts. CMR findings could also be used to guide treatment de-escalation or up-titration in recurrent pericarditis and selecting patients most likely to benefit from novel treatments such as anakinra and rilonacept. This article is an overview of the CMR applications in pericardial syndromes as a primer for reporting physicians. We sought to provide a summary of the clinical protocols used and an interpretation of the major CMR findings in the setting of pericardial diseases. We also discuss points that are less well clear and delineate the strengths and weak points of CMR in pericardial diseases.
Weight retention and glucose intolerance in early postpartum after gestational diabetes
Authors: Minschart Caro , Myngheer Nele , Maes Toon , De Block Christophe , Van Pottelbergh Inge , Abrams Pascale , Vinck Wouter , Leuridan Liesbeth , Driessens Sabien , Mathieu Chantal , Billen Jaak , Matthys Christophe , Laenen Annouschka , Bogaerts Annick , Benhalima Katrien 
Published: May 2023

Abstract

Objectives
To determine risk factors for early postpartum weight retention (PPWR) and glucose intolerance (GI) in women with gestational diabetes (GDM).

Design and Methods
Prospective, multicentre (n = 8) cohort study in 1201 women with a recent history of GDM. Pregnancy and postpartum characteristics, and data from self-administered questionnaires were collected at the 6-16 weeks postpartum 75 g oral glucose tolerance test.

Results
Of all participants, 38.6% (463) had moderate (&gt;0 and ≤5 kg) and 15.6% (187) had high (&gt;5 kg) PPWR. Independent predictors for early PPWR were excessive gestational weight gain (GWG), lack of breastfeeding, higher dietary fat intake, insulin use during pregnancy, multiparity, lower prepregnancy body mass index (BMI), and lower education degree. Compared to PPWR &lt;5 kg, women with high PPWR had a more impaired postpartum metabolic profile, breastfed less often, had higher depression rates (23.1% [43] vs 16.0% [74], P = .035) and anxiety levels, and lower quality of life. Of all participants, 28.0% (336) had GI (26.1% [313] prediabetes and 1.9% [23] diabetes). Women with high PPWR had more often GI compared to women without PPWR (33.7% [63] vs 24.9% [137], P = .020). Only 12.9% (24) of women with high PPWR perceived themselves at high risk for diabetes but they were more often willing to change their lifestyle than women with moderate PPWR.

Conclusions
Modifiable risk factors such as lifestyle, prepregnancy BMI, GWG, and mental health can be used to identify a subgroup of women with GDM at the highest risk of developing early PPWR, allowing for a more personalized follow-up.
Synthesizing the phylogenetic evidence for mutualism-associated diversification
Authors: Kaur Katrina M , Pennell Matt 
Published: May 2023

Abstract
Mutualisms are associations in which interacting species provide services or resources to each other. It has been suggested that being party to a mutualism can spur the diversification of the interacting species due to several potential hypothesized mechanisms. There is empirical evidence to both support and refute this prediction. However, this evidence comes from a variety of different methodologies, some of which have been found to be unreliable when the phylogenetic model is misspecified, and different data types and it is therefore difficult to weigh together. Here, we synthesize phylogenetic comparative datasets and analyze the data in a consistent manner using both sister-clade comparisons and hidden-trait state-dependent speciation and extinction models. The results are mixed—for the majority of the datasets we find no evidence for an effect on diversification rates in either direction, with several showing significant positive associations and a few showing significant negative associations. In contrast to the generally mixed findings between datasets, we find that qualitative results to be consistent when analyzing taxonomically overlapping datasets using different methods, suggesting that the detected variation in diversification is due to the nature of the mutualism and not due to differences in methodology.
Tectonic evolution of the Yangsan Fault, SE-Korea, by gravity field interpretation
Authors: Choi Sungchan , Kim Sung-Wook , Yoon Jeoung-Seok , Choi Eun-Kyeong 
Published: May 2023

SUMMARY
To estimate the tectonic displacement history of the Yangsan Fault (YSF) in the Cretaceous Gyeongsang Basin (GB), SE-Korea, gravity field measurements were implemented and interpreted. A total of 8000 ground-measured gravity data were compiled and deployed to calculate the Bouguer and residual gravity field. The residual field shows that the mean value in the southern segment of the YSF is very similar to that of the northern segment, meanwhile that of the central segmentation is significantly lower than those of the other segmentations. This implies that the crustal structure and petrophysical properties of the central segment differ significantly from those of the other segments. Applying dip curvature analysis to enhance the image of the residual gravity field, we find that (1) the Gaum fault system (GF) in the western and middle part of the GB extends up to the YSF, where A-type granite outcrops are observed. (2) The middle- and eastern segments of the GF that formed before tectonic motion of the YSF are revealed in turn in areas east of the YSF, which were now covered by the younger sedimentary basin. (3) The middle segment of the GF which occupies between the YSF and the Yeonil tectonic line (YTL) has been displaced approximately 25 km southward from the main GF trace. (4) The easternmost segment is revealed buried in the eastern side of the YTL, which is displaced southward about 18 km from the main GF trace. Comparing all the available geoscientific data sets, we conclude that the right-lateral tectonic movement of the YSF, and the deeply buried middle segment of the GF remained stationary, while the most eastern segment of the GF is reversely moved to the north through left-lateral strike movement of the YTL.
Evolution and phylogenetic distribution of endo-α-mannosidase
Authors: Sobala Łukasz F 
Published: May 2023

Abstract
While glycans underlie many biological processes, such as protein folding, cell adhesion, and cell–cell recognition, deep evolution of glycosylation machinery remains an understudied topic. N-linked glycosylation is a conserved process in which mannosidases are key trimming enzymes. One of them is the glycoprotein endo-α-1,2-mannosidase which participates in the initial trimming of mannose moieties from an N-linked glycan inside the cis-Golgi. It is unique as the only endo-acting mannosidase found in this organelle. Relatively little is known about its origins and evolutionary history; so far it was reported to occur only in vertebrates. In this work, a taxon-rich bioinformatic survey to unravel the evolutionary history of this enzyme, including all major eukaryotic clades and a wide representation of animals, is presented. The endomannosidase was found to be more widely distributed in animals and other eukaryotes. The protein motif changes in context of the canonical animal enzyme were tracked. Additionally, the data show the two canonical vertebrate endomannosidase genes, MANEA and MANEAL, arose at the second round of the two vertebrate genome duplications and one more vertebrate paralog, CMANEAL, is uncovered. Finally, a framework where N-glycosylation co-evolved with complex multicellularity is described. A better understanding of the evolution of core glycosylation pathways is pivotal to understanding biology of eukaryotes in general, and the Golgi apparatus in particular. This systematic analysis of the endomannosidase evolution is one step toward this goal.
Exploration, exploitation, and mode of market entry: acquisition versus internal development by Amazon and Alphabet
Authors: Lee Gwendolyn K , Lieberman Marvin B 
Published: May 2023

Abstract
Research on the tension between exploration and exploitation has made fundamental contributions to our understanding of firm growth via entry into new businesses. While there is consensus about the merits of balancing exploration and exploitation, there has been debate about the best means for achieving balance. In our prior analysis of firms’ choices between acquisition and internal development as entry modes, we found that the role of acquisitions tends to differ inside versus outside a firm’s primary business domain: firms use within-domain acquisitions largely for exploitation, while out-of-domain acquisitions support exploration. To examine these issues in greater depth, we focus here on the historical use of acquisition versus internal development by two major technology firms, Amazon and Alphabet. We show that the two firms have been remarkably different in their use of acquisitions versus internal development. Consistent with our prior analysis, Amazon has emphasized internal development but has used acquisitions to strengthen its existing businesses and to enter new products and services that were (initially) outside Amazon’s primary business domain. In contrast, Alphabet has relied heavily on acquisitions to enter new businesses within its primary domain but has emphasized internal development of “moonshot” businesses outside this domain. These differences illuminate the use of acquisitions in market entry and make clear that there is no single right way to utilize acquisition versus internal development in the pursuit of balance between exploration and exploitation.
Medial Prefrontal Cortex to Medial Septum Pathway Activation Improves Cognitive Flexibility in Rats
Authors: Bortz David M , Feistritzer Catalina M , Grace Anthony A 
Published: May 2023

AbstractBackgroundThe medial prefrontal cortex (mPFC) is necessary for cognitive flexibility and projects to medial septum (MS). MS activation improves strategy switching, a common measure of cognitive flexibility, likely via its ability to regulate midbrain dopamine (DA) neuron population activity. We hypothesized that the mPFC to MS pathway (mPFC-MS) may be the mechanism by which the MS regulates strategy switching and DA neuron population activity.MethodsMale and female rats learned a complex discrimination strategy across 2 different training time points: a constant length (10 days) and a variable length that coincided with each rat meeting an acquisition-level performance threshold (males: 5.3 ± 0.3 days, females: 3.8 ± 0.3 days). We then chemogenetically activated or inhibited the mPFC-MS pathway and measured each rat’s ability to inhibit the prior learned discrimination strategy and switch to a prior ignored discrimination strategy (strategy switching).ResultsActivation of the mPFC-MS pathway improved strategy switching after 10 days of training in both sexes. Inhibition of the pathway produced a modest improvement in strategy switching that was quantitatively and qualitatively different from pathway activation. Neither activation nor inhibition of the mPFC-MS pathway affected strategy switching following the acquisition-level performance threshold training regimen. Activation, but not inhibition, of the mPFC-MS pathway bidirectionally regulated DA neuron activity in the ventral tegmental area and substantia nigra pars compacta, similar to general MS activation.ConclusionsThis study presents a potential top-down circuit from the prefrontal cortex to the midbrain by which DA activity can be manipulated to promote cognitive flexibility.
Environmental Impact Assessment for the Use of an Orally Aerosolized Adenovirus Type-5 Vector-Based COVID-19 Vaccine in Randomized Clinical Trials
Authors: Xia Xin , Tan Zhong-Ming , Wan Peng , Zheng Hao , Tang Rong , Chen Xiao-Qin , Guo Xi-Ling , Zhu Tao , Feng Jia-Lu , Zhong Jin , Li Xiao-Long , Zhang Zhen-Yu , Zhu Feng-Cai , Li Jing-Xin 
Published: May 2023

Abstract

Background
An orally aerosolized adenovirus type-5 vector-based coronavirus disease 2019 (COVID-19) vaccine (Ad5-nCoV) has recently been authorized for boosting immunization in China. Our study aims to assess the environmental impact of the use of aerosolized Ad5-nCoV.

Methods
We collected air samples from rooms, swabs from the desks on which the vaccine nebulizer was set, mask samples from participants, and blood samples of nurses who administered the inoculation in the clinical trials. The viral load of adenovirus type-5 vector in the samples and the antibody levels against the wild-type severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) strain in serum were detected.

Results
Only one (4.00%) air sample collected before initiation of vaccination was positive and most air samples collected during and after vaccination were positive (97.96%, 100%, respectively). All nurses in trial A showed at least 4-fold increase of the neutralizing antibody against SARS-CoV-2 after initiation of the study. In trial B, the proportion of positive mask samples was 72.97% at 30 minutes after vaccination, 8.11% at day 1, and 0% at days 3, 5, and 7.

Conclusions
Vaccination with the orally aerosolized Ad5-nCoV could result in some spillage of the vaccine vector viral particles in the environment and cause human exposure.
Clinical Trials Registration. NCT04840992 and NCT05303584.
Prevalence of Giardia duodenalis among Asian children: a systematic review and meta-analysis
Authors: Kalavani Sara , Matin Sara , Rahmanian Vahid , Meshkin Ahmad , Taghipour Ali , Abdoli Amir 
Published: May 2023

Abstract
Giardia duodenalis is one of the major causes of diarrhea among children. We performed a systematic review and meta-analysis to assess the prevalence of G. duodenalis and associated risk factors among Asian children. We searched online databases (PubMed, Scopus and Web of Science) and Google Scholar search engine for studies published from 1 January 2000 to 15 March 2022 that measured the prevalence of G. duodenalis among Asian children. Accordingly, the pooled prevalence and 95% CIs were estimated using a random-effects meta-analysis model for the included studies. A total of 182 articles from 22 Asian countries met the inclusion criteria. The pooled prevalence of G. duodenalis infection among Asian children was estimated as 15.1% (95% CI 14.1 to 16%). The highest and lowest pooled prevalence values of G. duodenalis infection were estimated for Tajikistan and China as 26.4% (95% CI 22.9 to 30%) and 0.6% (95% CI 0.001 to 1.02%), respectively. The infection had a higher prevalence in males than in females (OR=1.24; 95% CI 1.16 to 1.31; p&lt;0.001), which was statistically significant. Giardiasis is common among Asian children, hence, a prevention and control scheme of this protozoan in children should be considered by health officials and health policymakers, especially in Asian countries where the prevalence is highest.
A Typology of Ontological Insecurity Mechanisms: Russia's Military Engagement in Syria
Authors: von Essen Hugo , Danielson August 
Published: May 2023

Abstract
Because of the novel explanations it generates for states’ security- and identity-related behavior, the concept of ontological security has been used increasingly in the International Relations (IR) literature in recent years. However, the abundance of interpretations of the concept means that it is often used in conflicting ways. To counter the risk of conceptual stretching and provide the foundation for a common research agenda, this article constructs a typology of ontological security mechanisms. Two dimensions of ontological insecurity are highlighted: the sources and the causes of anxiety. We argue that the source of anxiety can be reflexive, relational, or systemic, while the cause of anxiety can be either shame or discontinuity. These two dimensions produce six mechanisms of ontological insecurity that reflect how the concept is used in the contemporary ontological security literature in IR. By specifying these mechanisms, we argue that the typology offers IR scholars the ability to produce even more nuanced and fine-grained explanations of state behavior driven by ontological insecurity. Finally, to demonstrate the utility of this typology, the article provides an illustrative case study of Russia's engagement in the conflict in Syria in 2015–2017.
Reproductive performance and transcriptome analysis of ovaries at different parities in female rabbits
Authors: Chen Yang , Wang Fan , Bai Shaocheng , Chen Xin , Han Xudong , Cai Jiawei , Bao Zhiyuan , Cao Chao , Zhao Bohao , Wu Xinsheng 
Published: May 2023

Abstract
This study investigated the reproductive performance and ovarian molecular regulation associated with parity in commercial rabbit systems. The pregnancy data of 658 female rabbits from the first to sixth parities (P1 to P6) under the same mating pattern were analyzed, showing a significant decrease in the conception rate in P6. Compared to P1 (N = 120) and P2 (N = 105), P6 (N = 99) had significantly lower performance indices in terms of total litter size, live litter size, survival rate at birth, and weight of 3 and 5 wk old kits (P &lt; 0.05). Using H&E staining, we found that the ovarian primordial follicle reservoir of P6 was significantly lower than that of P1 and P2, and the number of atretic follicles at P6 was significantly higher (P &lt; 0.05). Blood (N = 30 per group) and ovaries (N = 6 per group) in P1, P2, and P6 were collected for measurement of the serum anti-oxidant capacity and indices of ovarian function by ELISA. It was found that serum glutathione, ovarian Klotho protein, and telomeres of P1 and P2 were significantly higher than those of P6 (P &lt; 0.05). The serum levels of ROS and MDA at P1 and P2 were significantly lower than those at P6 (P &lt; 0.05). Additionally, transcriptome analysis showed 213 up-regulated and 747 down-regulated differentially expressed genes (DEGs) between P2 and P6 ovaries. Several DEGs were related to reproduction, including CYP21A2, PTGFR, SGK1, PIK3R6, and SRD5A2. These results demonstrate the influence of parity on reproduction in female rabbits, reflected in a loss of follicle reservoir, disordered levels of anti-oxidants, and indices associated with ovarian function and molecular regulation. This study provides a basis for the strategies to increase reproductive rate in female rabbits.
Computationally efficient and data-adaptive changepoint inference in high dimension
Authors: Wang Guanghui , Feng Long 
Published: May 2023

AbstractHigh-dimensional changepoint inference that adapts to various change patterns has received much attention recently. We propose a simple, fast yet effective approach for adaptive changepoint testing. The key observation is that two statistics based on aggregating cumulative sum statistics over all dimensions and possible changepoints by taking their maximum and summation, respectively, are asymptotically independent under some mild conditions. Hence, we are able to form a new test by combining the p-values of the maximum- and summation-type statistics according to their asymptotic null distributions. To this end, we develop new tools and techniques to establish the asymptotic distribution of the maximum-type statistic under a more relaxed condition on componentwise correlations among all variables than those in existing literature. The proposed method is simple to use. It is adaptive to different levels of the sparsity of change signals, and is comparable to or even outperforms existing approaches as revealed by our numerical studies.