bluuebunny/crossref_metadata_2025_split huggingface dataset:
Translocation capacity of some heavy metals in aquatic food chain of crude oil impacted community of Imiringi in Bayelsa state, Nigeria
Authors: Agoro Eni-yimini S , Ikimi Charles G 
Published: December 2022

The translocation capacity of metals (Cd, Cr, As, Pb, and Hg) was determined in water and fish, and in the serum and vitreous humor harvested from New Zealand White (albino) rabbits fed with the processed fish. The sample size comprised 12 male rabbits divided equally into control and experimental groups. Both groups were fed with normal rabbit meal void of detectable metals for 3 months. Only animals grouped under the experimental group were fed fish meal harvested from River Imiringi, Bayelsa State, Nigeria. The metals of interest were estimated using Atomic Absorption Spectroscopy. Similarly, the choice statistical tool was the student t-test analyzed on SPSS version 18–22. The findings revealed that the studied heavy metal concentrations were higher in water and fish sourced from River Imiringi when compared with the World Health Organization’s minimum permissible limits. In the same vein, concentrations of cadmium, chromium, and total arsenic were significantly higher, whereas mercury was lower in fish when compared to that in the water. In addition, vitreous cadmium and lead concentrations were higher in the experimental group when compared with the control group, whereas vitreous chromium was lower. Furthermore, serum cadmium and chromium concentration comparisons were similar to that in the vitreous. The findings are indicative of the translocation capacity of metals from water to fish and then to serum and vitreous humor of rabbits. The increase in metal concentrations and their translocation capacity are potential risks to inhabitants of Imiringi that depends heavily on the river water resources.
Social attention during object engagement: toward a cross-species measure of preferential social orienting
Authors: Weichselbaum Claire , Hendrix Nicole , Albright Jordan , Dougherty Joseph D. , Botteron Kelly N. , Constantino John N. , Marrus Natasha 
Published: December 2022

Abstract
Background
A central challenge in preclinical research investigating the biology of autism spectrum disorder (ASD) is the translation of ASD-related social phenotypes across humans and animal models. Social orienting, an observable, evolutionarily conserved behavior, represents a promising cross-species ASD phenotype given that disrupted social orienting is an early-emerging ASD feature with evidence for predicting familial recurrence. Here, we adapt a competing-stimulus social orienting task from domesticated dogs to naturalistic play behavior in human toddlers and test whether this approach indexes decreased social orienting in ASD.

Methods
Play behavior was coded from the Autism Diagnostic Observation Schedule (ADOS) in two samples of toddlers, each with and without ASD. Sample 1 (n = 16) consisted of community-ascertained research participants, while Sample 2 involved a prospective study of infants at a high or low familial liability for ASD (n = 67). Coding quantified the child’s looks towards the experimenter and caregiver, a social stimulus, while playing with high-interest toys, a non-social stimulus. A competing-stimulus measure of “Social Attention During Object Engagement” (SADOE) was calculated by dividing the number of social looks by total time spent playing with toys. SADOE was compared based on ASD diagnosis and differing familial liability for ASD.

Results
In both samples, toddlers with ASD exhibited significantly lower SADOE compared to toddlers without ASD, with large effect sizes (Hedges’ g ≥ 0.92) driven by a lower frequency of child-initiated spontaneous looks. Among toddlers at high familial likelihood of ASD, toddlers with ASD showed lower SADOE than toddlers without ASD, while SADOE did not differ based on presence or absence of familial ASD risk alone. SADOE correlated negatively with ADOS social affect calibrated severity scores and positively with the Communication and Symbolic Behavior Scales social subscale. In a binary logistic regression model, SADOE alone correctly classified 74.1% of cases, which rose to 85.2% when combined with cognitive development.

Conclusions
This work suggests that a brief behavioral measure pitting a high-interest nonsocial stimulus against the innate draw of social partners can serve as a feasible cross-species measure of social orienting, with implications for genetically informative behavioral phenotyping of social deficits in ASD and other neurodevelopmental disorders.
Development of an image classification pipeline for atherosclerotic plaques assessment using supervised machine learning
Authors: Kunchur Natasha N. , Mostaço-Guidolin Leila B. 
Published: December 2022

Abstract
Background
During atherosclerosis, the narrowing of the arterial lumen is observed through the accumulation of bio compounds and the formation of plaque within artery walls. A non-linear optical imaging modality (NLOM), coherent anti-stokes Raman scattering (CARS) microscopy, can be used to image lipid-rich structures commonly found in atherosclerotic plaques. By matching the lipid’s molecular vibrational frequencies (CH bonds), it is possible to map the accumulation of lipid-rich structures without the need for exogenous labelling and/or processing of the samples. CARS allows for the visualization of the morphological features of plaque. In combination with supervised machine learning, CARS imaged morphological features can be used to characterize the progression of atherosclerotic plaques.

Results
Based on a set of label-free CARS images of atherosclerotic plaques (i.e. foam cell clusters) from a Watanabe heritable hyperlipidemic rabbit model, we developed an automated pipeline to classify atherosclerotic lesions based on their major morphological features. Our method uses image preprocessing to first improve the quality of the CARS-imaged plaque, followed by the segmentation of the plaque using Otsu thresholding, marker-controlled watershed, K-means segmentation and a novel independent foam cell thresholding segmentation. To define relevant morphological features, 27 quantitative features were extracted and further refined by a novel coefficient of variation feature refinement method in accordance with filter-type feature selection. Refined morphological features were supplied into three supervised machine learning algorithms; K-nearest neighbour, support vector machine and decision tree classifier. The classification pipeline showcased the ability to exploit relevant plaque morphological features to accurately classify 3 pre-defined stages of atherosclerosis: early fatty streak development (EFS) and advancing atheroma (AA) with a greater than 85% class accuracy

Conclusions
Through the combination of CARS microscopy and computational methods, a powerful classification tool was developed to identify the progression of atherosclerotic plaque in an automated manner. Using a curated dataset, the classification pipeline demonstrated the ability to differentiate between EFS, EF and AA. Thus, presenting the opportunity to classify the onset of atherosclerosis at an earlier stage of development
eSMC: a statistical model to infer admixture events from individual genomics data
Authors: Wang Yonghui , Zhao Zicheng , Miao Xinyao , Wang Yinan , Qian Xiaobo , Chen Lingxi , Wang Changfa , Li Shuaicheng 
Published: December 2022

Abstract
Background
Inferring historical population admixture events yield essential insights in understanding a species demographic history. Methods are available to infer admixture events in demographic history with extant genetic data from multiple sources. Due to the deficiency in ancient population genetic data, there lacks a method for admixture inference from a single source. Pairwise Sequentially Markovian Coalescent (PSMC) estimates the historical effective population size from lineage genomes of a single individual, based on the distribution of the most recent common ancestor between the diploid’s alleles. However, PSMC does not infer the admixture event.

Results
Here, we proposed eSMC, an extended PSMC model for admixture inference from a single source. We evaluated our model’s performance on both in silico data and real data. We simulated population admixture events at an admixture time range from 5 kya to 100 kya (5 years/generation) with population admix ratio at 1:1, 2:1, 3:1, and 4:1, respectively. The root means the square error is $$\pm 7.61$$

±
7.61

kya for all experiments. Then we implemented our method to infer the historical admixture events in human, donkey and goat populations. The estimated admixture time for both Han and Tibetan individuals range from 60 kya to 80 kya (25 years/generation), while the estimated admixture time for the domesticated donkeys and the goats ranged from 40 kya to 60 kya (8 years/generation) and 40 kya to 100 kya (6 years/generation), respectively. The estimated admixture times were concordance to the time that domestication occurred in human history.

Conclusion
Our eSMC effectively infers the time of the most recent admixture event in history from a single individual’s genomics data. The source code of eSMC is hosted at https://github.com/zachary-zzc/eSMC.
Transcriptome analysis of gene expression profiling from the deep sea in situ to the laboratory for the cold seep mussel Gigantidas haimaensis
Authors: Zhang Hua , Yao Gaoyou , He Maoxian 
Published: December 2022

Abstract
Background
The deep-sea mussel Gigantidas haimaensis is a representative species from the Haima cold seep ecosystem in the South China Sea that establishes endosymbiosis with chemotrophic bacteria. During long-term evolution, G. haimaensis has adapted well to the local environment of cold seeps. Until now, adaptive mechanisms responding to environmental stresses have remained poorly understood.

Results
In this study, transcriptomic analysis was performed for muscle tissue of G. haimaensis in the in situ environment (MH) and laboratory environment for 0 h (M0), 3 h (M3) and 9 h (M9), and 187,368 transcript sequences and 22,924 annotated differentially expressed genes (DEGs) were generated. Based on Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis, these DEGs were enriched with a broad spectrum of biological processes and pathways, including those associated with antioxidants, apoptosis, chaperones, immunity and metabolism. Among these significantly enriched pathways, protein processing in the endoplasmic reticulum and metabolism were the most affected metabolic pathways. These results may imply that G. haimaensis struggles to support the life response to environmental change by changing gene expression profiles.

Conclusion
The present study provides a better understanding of the biological responses and survival strategies of the mussel G. haimaensis from deep sea in situ to the laboratory environment.
Comparison of structural variants detected by PacBio-CLR and ONT sequencing in pear
Authors: Liu Yueyuan , Zhang Mingyue , Wang Runze , Li Benping , Jiang Yafei , Sun Manyi , Chang Yaojun , Wu Jun 
Published: December 2022

Abstract
Background
Structural variations (SVs) have recently become a topic of great interest in the area of genetic diversity and trait regulation. As genomic sequencing technologies have rapidly advanced, longer reads have been used to identify SVs at high resolution and with increased accuracy. It is important to choose a suitable sequencing platform and appropriate sequencing depth for SV detection in the pear genome.

Results
In this study, two types of long reads from sequencing platforms, continuous long reads from Pacific Biosciences (PB-CLR) and long reads from Oxford Nanopore Technologies (ONT), were used to comprehensively analyze and compare SVs in the pear genome. The mapping rate of long reads was higher when the program Minimap2 rather than the other three mapping tools (NGMLR, LRA and Winnowmap2) was used. Three SV detection programs (Sniffles_v2, CuteSV, and Nanovar) were compared, and Nanovar had the highest sensitivity in detecting SVs at low sequencing depth (10–15×). A sequencing depth of 15× was suitable for SV detection in the pear genome using Nanovar. SVs detected by Sniffles_v2 and CuteSV with ONT reads had the high overlap with presence/absence variations (PAVs) in the pear cultivars ‘Bartlett’ and ‘Dangshansuli’, both of them with 38% of insertions and 55% of deletions overlapping with PAVs at sequencing depth of 30×. For the ONT sequencing data, over 37,526 SVs spanning ~ 28 Mb were identified by all three software packages for the ‘Bartlett’ and ‘Dangshansuli’ genomes. Those SVs were annotated and combined with transcriptome profiles derived from ‘Bartlett’ and ‘Dangshansuli’ fruit flesh at 60 days after cross-pollination. Several genes related to levels of sugars, acid, stone cells, and aromatic compounds were identified among the SVs. Transcription factors were then predicted among those genes, and results included bHLH, ERF, and MYB genes.

Conclusion
SV detection is of great significance in exploring phenotypic differences between pear varieties. Our study provides a framework for assessment of different SV software packages and sequencing platforms that can be applied in other plant genome studies. Based on these analyses, ONT sequencing data was determined to be more suitable than PB-CLR for SV detection in the pear genome. This analysis model will facilitate screening of genes related to agronomic traits in other crops.
Procalcitonin to reduce exposure to antibiotics and individualise treatment in hospitalised old patients with pneumonia: a randomised study
Authors: Gavazzi Gaëtan , Drevet Sabine , Debray Matthieu , Bosson Jean Luc , Tidadini Fatah , Paccalin Marc , de Wazieres Benoit , Celarier Thomas , Bonnefoy Marc , Vitrat Virginie 
Published: December 2022

Abstract
Background
Treating pneumonia in old patients remains challenging for clinicians. Moreover, bacterial antimicrobial resistance is a major public health threat.

Objective
The PROPAGE study evaluated the interest of a strategy using serial measurements of procalcitonin (PCT) to reduce the duration of antibiotic therapy in old patients with pneumonia.

Methods
PROPAGE took place from Dec.-2013 to Jun.-2016 in eight French geriatric units. It was a prospective, comparative, randomised, open-label study involving old patients (≥ 80 years) who had initiated antibiotic treatment for pneumonia in the previous 48 h. PCT was monitored in all patients and two decision-making PCT-based algorithms guided antibiotic therapy in patients from the PCT group.

Results
107 patients were randomised (PCT, n = 50; Control, n = 57). Antibiotic therapy exposure was reduced in the PCT group as compared to the Control group (median duration of antibiotic therapy, 8 vs. 10 days [rank-test, p = 0.001]; antibiotic persistence rates on Days 6 and 8, 54% and 44% vs. 91% and 72%) and no significant difference was found in recovery rate (84% vs. 89.5%; Pearson Chi² test, p = 0.402).

Conclusion
Although, the superiority of the strategy was not tested using a composite criterion combining antibiotic therapy duration and recovery rate was not tested due to the small sample size, the present study showed that monitoring associated with PCT-guided algorithm could help shorten antibiotic treatment duration in the very old patients without detrimental effects. Measuring PCT levels between Day 4 and Day 6 could be helpful when making the decision regarding antibiotic discontinuation.

Trial registration
NCT02173613. This study was first registered on 25/06/2014.
Impact of molecular diagnostic tests on diagnostic and treatment delays in tuberculosis: a systematic review and meta-analysis
Authors: Lee Jae Hyoung , Garg Tushar , Lee Jungsil , McGrath Sean , Rosman Lori , Schumacher Samuel G. , Benedetti Andrea , Qin Zhi Zhen , Gore Genevieve , Pai Madhukar , Sohn Hojoon 
Published: December 2022

Abstract
Background
Countries with high TB burden have expanded access to molecular diagnostic tests. However, their impact on reducing delays in TB diagnosis and treatment has not been assessed. Our primary aim was to summarize the quantitative evidence on the impact of nucleic acid amplification tests (NAAT) on diagnostic and treatment delays compared to that of the standard of care for drug-sensitive and drug-resistant tuberculosis (DS-TB and DR-TB).

Methods
We searched MEDLINE, EMBASE, Web of Science, and the Global Health databases (from their inception to October 12, 2020) and extracted time delay data for each test. We then analysed the diagnostic and treatment initiation delay separately for DS-TB and DR-TB by comparing smear vs Xpert for DS-TB and culture drug sensitivity testing (DST) vs line probe assay (LPA) for DR-TB. We conducted random effects meta-analyses of differences of the medians to quantify the difference in diagnostic and treatment initiation delay, and we investigated heterogeneity in effect estimates based on the period the test was used in, empiric treatment rate, HIV prevalence, healthcare level, and study design. We also evaluated methodological differences in assessing time delays.

Results
A total of 45 studies were included in this review (DS = 26; DR = 20). We found considerable heterogeneity in the definition and reporting of time delays across the studies. For DS-TB, the use of Xpert reduced diagnostic delay by 1.79 days (95% CI − 0.27 to 3.85) and treatment initiation delay by 2.55 days (95% CI 0.54–4.56) in comparison to sputum microscopy. For DR-TB, use of LPAs reduced diagnostic delay by 40.09 days (95% CI 26.82–53.37) and treatment initiation delay by 45.32 days (95% CI 30.27–60.37) in comparison to any culture DST methods.

Conclusions
Our findings indicate that the use of World Health Organization recommended diagnostics for TB reduced delays in diagnosing and initiating TB treatment. Future studies evaluating performance and impact of diagnostics should consider reporting time delay estimates based on the standardized reporting framework.
Berlin Registry of Neuroimmunological entities (BERLimmun): protocol of a prospective observational study
Authors: Sperber Pia S. , Brandt Alexander U. , Zimmermann Hanna G. , Bahr Lina S. , Chien Claudia , Rekers Sophia , Mähler Anja , Böttcher Chotima , Asseyer Susanna , Duchow Ankelien Solveig , Bellmann-Strobl Judith , Ruprecht Klemens , Paul Friedemann , Schmitz-Hübsch Tanja 
Published: December 2022

Abstract
Background
Large-scale disease overarching longitudinal data are rare in the field of neuroimmunology. However, such data could aid early disease stratification, understanding disease etiology and ultimately improve treatment decisions. The Berlin Registry of Neuroimmunological Entities (BERLimmun) is a longitudinal prospective observational study, which aims to identify diagnostic, disease activity and prognostic markers and to elucidate the underlying pathobiology of neuroimmunological diseases.

Methods
BERLimmun is a single-center prospective observational study of planned 650 patients with neuroimmunological disease entity (e.g. but not confined to: multiple sclerosis, isolated syndromes, neuromyelitis optica spectrum disorders) and 85 healthy participants with 15 years of follow-up. The protocol comprises annual in-person visits with multimodal standardized assessments of medical history, rater-based disability staging, patient-report of lifestyle, diet, general health and disease specific symptoms, tests of motor, cognitive and visual functions, structural imaging of the neuroaxis and retina and extensive sampling of biological specimen.

Discussion
The BERLimmun database allows to investigate multiple key aspects of neuroimmunological diseases, such as immunological differences between diagnoses or compared to healthy participants, interrelations between findings of functional impairment and structural change, trajectories of change for different biomarkers over time and, importantly, to study determinants of the long-term disease course. BERLimmun opens an opportunity to a better understanding and distinction of neuroimmunological diseases.
Infant feeding practice and gastrointestinal tolerance: a real-world, multi-country, cross-sectional observational study
Authors:   Happy Tummy Consortium, Jalaludin M. Y. , Taher S. W. B. , Kiau H. B. , Hashim S. B. , Yusof M. B. , Khew L. W. , Juffrie M. , Bardosono Saptawati , Galindez G. , Waheed K. A. I. , Gokhale P. , Ibrahim M. N. , Asghar R. , Shirazi H. , Perez M. L. M. , Kesavelu D. , Edris A. , Beleidy A. El , Hodhod M. El , Elzalabany M. , Hussein H. , Shaaban S. Y. , Elmashad A. , Abdelmoez A. , El-Asheer O. M. , Vandenplas Y. , Lavalle Luca , Sauvageot Nicolas , Cercamondi Colin Ivano , Egli Delphine , Jankovic Ivana , Vandenplas Yvan 
Published: December 2022

Abstract
Background
Signs of feeding intolerance, such as gastrointestinal (GI) symptoms, are frequently observed in otherwise healthy formula-fed infants in the first months of life. The primary objective of this observational study was to examine GI tolerance in formula-fed infants (FFI) vs. breastfed infants (BFI) in a real-world setting with a secondary objective being the comparison of infants fed formula with pre- and/or probiotics (FFI_PP) and those fed formula without any pre- and/or probiotics (FFI_noPP) as well as BFI.

Methods
A six-country, cross-sectional study in full-term exclusively/predominantly FFI (n = 2036) and BFI (n = 760) aged 6–16 weeks was conducted using the validated Infant Gastrointestinal Symptom Questionnaire (IGSQ) and a Feeding Practice and Gut Comfort Questionnaire.

Results
The IGSQ composite score in FFI was non-inferior compared to BFI (mean difference [95%CI]: 0.17 [-0.34, 0.67]; non-inferiority p-value < 0.0001) and scores for BFI and FFI were below the threshold of 23, indicating no GI discomfort. Adjusted mean IGSQ scores ± SE were similar in FFI_PP (22.1 ± 0.2) and BFI (22.3 ± 0.3) while FFI_noPP (23.4 ± 0.3) was significantly higher and above 23 indicating some GI discomfort (mean differences [95%CI] FFI_noPP minus FFI_PP and FFI_noPP minus BFI were 1.28 [0.57, 1.98] and 1.09 [0.38, 1.80], respectively; both p < 0.01). Hard stools and difficulty in passing stool were more common in FFI compared to BFI (p < 0.01) but were less common in FFI_PP compared to FFI_noPP (p < 0.01). FFI_PP showed significantly less crying than FFI_noPP and was similar to BFI. Significantly fewer physician-confirmed colic episodes (Rome IV criteria) were reported in FFI_PP compared with FFI_noPP or BFI.

Conclusions
In this real-world observational study, FFI had non-inferior overall GI tolerance compared to BFI. Within FFI, infants receiving formulas with pre- and/or probiotics had a better GI tolerance, improved stooling and less infantile colic compared to those receiving formula without any pre- and/or probiotics and were more similar to BFI.

Trial registration
NCT03703583, 12/10/2018 (https://clinicaltrials.gov/ct2/show/NCT03703583).