bluuebunny/crossref_metadata_2025_split huggingface dataset:
Forest edges increase pollinator network robustness to extinction with declining area
Authors: Ren Peng , Didham Raphael K. , Murphy Mark V. , Zeng Di , Si Xingfeng , Ding Ping 
Published: January 2023

AbstractEdge effects often exacerbate the negative effects of habitat loss on biodiversity. In forested ecosystems, however, many pollinators actually prefer open sunny conditions created by edge disturbances. We tested the hypothesis that forest edges have a positive buffering effect on plant-pollinator interaction networks in the face of declining forest area. In a fragmented land-bridge island system, we recorded ~20,000 plant-pollinator interactions on 41 islands over 3 yr. We show that plant richness and floral resources decline with decreasing forest area at both interior and edge sites, but edges maintain 10-fold higher pollinator abundance and richness regardless of area loss. Edge networks contain highly specialized species, with higher nestedness and lower modularity than interior networks, maintaining high robustness to extinction following area loss while forest interior networks collapse. Anthropogenic forest edges benefit community diversity and network robustness to extinction in the absence of natural gap-phase dynamics in small degraded forest remnants.
Chromosome fusions repatterned recombination rate and facilitated reproductive isolation during Pristionchus nematode speciation
Authors: Yoshida Kohta , Rödelsperger Christian , Röseler Waltraud , Riebesell Metta , Sun Simo , Kikuchi Taisei , Sommer Ralf J. 
Published: January 2023

AbstractLarge-scale genome-structural evolution is common in various organisms. Recent developments in speciation genomics revealed the importance of inversions, whereas the role of other genome-structural rearrangements, including chromosome fusions, have not been well characterized. We study genomic divergence and reproductive isolation of closely related nematodes: the androdioecious (hermaphroditic) modelPristionchus pacificusand its dioecious sister speciesPristionchus exspectatus. A chromosome-level genome assembly ofP. exspectatususing single-molecule and Hi-C sequencing revealed a chromosome-wide rearrangement relative toP. pacificus. Strikingly, genomic characterization and cytogenetic studies including outgroup speciesPristionchus occultusindicated two independent fusions involving the same chromosome, ChrIR, between these related species. Genetic linkage analysis indicated that these fusions altered the chromosome-wide pattern of recombination, resulting in large low-recombination regions that probably facilitated the coevolution between some of the ~14.8% of genes across the entire genomes. Quantitative trait locus analyses for hybrid sterility in all three sexes revealed that major quantitative trait loci mapped to the fused chromosome ChrIR. While abnormal chromosome segregations of the fused chromosome partially explain hybrid female sterility, hybrid-specific recombination that breaks linkage of genes in the low-recombination region was associated with hybrid male sterility. Thus, recent chromosome fusions repatterned recombination rate and drove reproductive isolation duringPristionchusspeciation.
Quality control and removal of technical variation of NMR metabolic biomarker data in ~120,000 UK Biobank participants
Authors: Ritchie Scott C. , Surendran Praveen , Karthikeyan Savita , Lambert Samuel A. , Bolton Thomas , Pennells Lisa , Danesh John , Di Angelantonio Emanuele , Butterworth Adam S. , Inouye Michael 
Published: January 2023

AbstractMetabolic biomarker data quantified by nuclear magnetic resonance (NMR) spectroscopy in approximately 121,000 UK Biobank participants has recently been released as a community resource, comprising absolute concentrations and ratios of 249 circulating metabolites, lipids, and lipoprotein sub-fractions. Here we identify and characterise additional sources of unwanted technical variation influencing individual biomarkers in the data available to download from UK Biobank. These included sample preparation time, shipping plate well, spectrometer batch effects, drift over time within spectrometer, and outlier shipping plates. We developed a procedure for removing this unwanted technical variation, and demonstrate that it increases signal for genetic and epidemiological studies of the NMR metabolic biomarker data in UK Biobank. We subsequently developed an R package, ukbnmr, which we make available to the wider research community to enhance the utility of the UK Biobank NMR metabolic biomarker data and to facilitate rapid analysis.
An RNA-seq time series of the medaka pituitary gland during sexual maturation
Authors: Ager-Wick Eirill , Maugars Gersende , von Krogh Kristine , Fontaine Romain , Weltzien Finn-Arne , Henkel Christiaan 
Published: January 2023

AbstractDirecting both organismal homeostasis and physiological adaptation, the pituitary is a key endocrine gland in all vertebrates. One of its major tasks is to coordinate sexual maturation through the production and release of hormones stimulating gonad development. In order to study its developmental dynamics in the model fish medaka (Oryzias latipes), we sampled both the pituitary and the ovaries of 68 female fish. Of these, 55 spanned the entire course of sexual maturation from prepubertal juveniles to spawning adults. An additional 13 showed either considerably faster or slower growth and development than the majority of fish. We used histological examination of the ovaries to determine a histological maturation stage, and analyzed the pituitary glands using RNA-seq optimized for low input. Taken together, these data reveal the timing of hormone production priorities, and form a comprehensive resource for the study of their regulation.
Investigation of respirable coal mine dust (RCMD) and respirable crystalline silica (RCS) in the U.S. underground and surface coal mines
Authors: Rahimi Elham , Shekarian Younes , Shekarian Naser , Roghanchi Pedram 
Published: January 2023

AbstractDust is an inherent byproduct of mining activities that raises notable health and safety concerns. Cumulative inhalation of respirable coal mine dust (RCMD) and respirable crystalline silica (RCS) can lead to obstructive lung diseases. Despite considerable efforts to reduce dust exposure by decreasing the permissible exposure limits (PEL) and improving the monitoring techniques, the rate of mine workers with respiratory diseases is still high. The root causes of the high prevalence of respiratory diseases remain unknown. This study aimed to investigate contributing factors in RCMD and RCS dust concentrations in both surface and underground mines. To this end, a data management approach is performed on MSHA’s database between 1989 and 2018 using SQL data management. In this process, all data were grouped by mine ID, and then, categories of interests were defined to conduct statistical analysis using the generalized estimating equation (GEE) model. The total number of 12,537 and 9050 observations for respirable dust concentration are included, respectively, in the U.S. underground and surface mines. Several variables were defined in four categories of interest including mine type, geographic location, mine size, and coal seam height. Hypotheses were developed for each category based on the research model and were tested using multiple linear regression analysis. The results of the analysis indicate higher RCMD concentration in underground compared to RCS concentration which is found to be relatively higher in surface coal mines. In addition, RCMD concentration is seen to be higher in the Interior region while RCS is higher in the Appalachia region. Moreover, mines of small sizes show lower RCMD and higher RCS concentrations. Finally, thin-seam coal has greater RCMD and RCS concentrations compared to thicker seams in both underground and surface mines. In the end, it is demonstrated that RCMD and RCS concentrations in both surface and underground mines have decreased. Therefore, further research is needed to investigate the efficacy of the current mass-concentration-based monitoring system.
Biodegradable polymer everolimus-eluting stents versus contemporary drug-eluting stents: a systematic review and meta‑analysis
Authors: Yin Juntao , Li Yang , Chen Yangyang , Wang Chaoyang , Song Xiaoyong 
Published: January 2023

AbstractIn spite of similar efficacy and safety in pilot studies, compared with the contemporary durable polymer drug-eluting stent (DP-DES), the bioabsorbable polymer drug-eluting stent (BP-DES) may be more superior in promoting blood vessel healing. We sought to compare the safety and efficacy of everolimus-eluting BP-DES (BP-EES) with contemporary DP-DES through a meta-analysis. We performed this meta-analysis to provide further evidence of the safety and efficacy of BP-EES. Medline, Embase and the Cochrane library databases were searched for randomized controlled trials comparing clinical efficacy and safety of BP-EES versus contemporary DP-DES. Fifteen RCTs with a total of 15,572 patients were selected. The rate of MACE was 9.4% in patients receiving BP-EES and 7.3% receiving DP-EES (RR 1.13, 95% CI 0.99–1.29, p = 0.05; I2 = 46%). TLF and MI were also similar in both groups. Based on the available data, this review demonstrates that BP-EES displays a clinically comparable efficacy and safety profile to that of contemporary DP-DES at years of follow-up in patients undergoing PCI.
Exploring the hub mechanisms of ischemic stroke based on protein-protein interaction networks related to ischemic stroke and inflammatory bowel disease
Authors: Hu Wei , Li Ping , Zeng Nianju , Tan Sheng 
Published: January 2023

AbstractIschemic stroke is highly concerning because it often leads to severe long-term neurological disability. Among clinical trials, ischemic stroke and inflammatory bowel disease interactions have been increasingly reported in recent years. Therefore, using bioinformatics approaches to explore novel protein interactions between them is of interest. We performed this exploratory analysis by using bioinformatics tools such as string to analyze gene data downloaded from NHGRI-GWAS data related to ischemic stroke and inflammatory bowel disease. We constructed a prospective protein interaction network for ischemic stroke and inflammatory bowel disease, identifying cytokine and interleukin-related signaling pathways, Spliceosome, Ubiquitin–Proteasome System (UPS), Thrombus, and Anticoagulation pathways as the crucial biological mechanisms of the network. Furthermore, we also used data-independent acquisition mass spectrometry (DIA-MS) to detect differential protein expression in eight samples, which also suggested that immune system, signal transduction, and hemostasis-related pathways are key signaling pathways. These findings may provide a basis for understanding the interaction between these two states and exploring possible molecular and therapeutic studies in the future.
Effect of bismuth oxide nanoparticle on the electromagnetic interference shielding and thermal stability of industrial waste based-geopolymer composites
Authors: Maestre Christian V. , Santos Gil Nonato 
Published: January 2023

AbstractGold mine tailings, fly ash, and bagasse ash has been repurposed to produce geopolymer (GP) with enhanced electromagnetic interference shielding efficiency (EMI-SE) and high thermal property. GP has low shielding efficiency compared to concrete. Due to this, an appropriate filler must be incorporated into its matrix to enhance its EMI-SE. For this study, bismuth oxide nanomaterial (BiNP) was utilized as the additive filler. The percent content of BiNP was varied to evaluate its influence on the EMI-SE of GP. Morphology shows that Bi2O3 was embedded in the matrix of GP, and no new aluminu-phyllosilicate minerals were formed. This indicates that some minerals acted only as internal fillers in the matrix. Compressive strength shows synthesized GP composites were more than 20 MPa, with neat GP reaching the maximum strength. Moreover, the EMI-SE of neat GP was 21.2 dB for 20–4500 MHz range. This indicates that GP alone has sufficient characteristics to attenuate EMI radiation. Addition of 5%, 10% and 15% weight of BiNP improves EMI-SE by 4–10%, with 5% BiNP shown to be the optimum ratio. Lastly, the addition of BiNP improves the thermal stability of GP. This study shows that GP incorporated with Bi2O3 can be recommended for small-scale construction and small residential building.
Production of zirconium-88 via proton irradiation of metallic yttrium and preparation of target for neutron transmission measurements at DICER
Authors: Matyskin Artem V. , Stamatopoulos Athanasios , O’Brien Ellen M. , DiGiovine Brad J. , Mocko Veronika , Fassbender Michael E. , Vermeulen C. Etienne , Koehler Paul E. 
Published: January 2023

AbstractA process for the production of tens to hundreds of GBq amounts of zirconium-88 (88Zr) using proton beams on yttrium was developed. For this purpose, yttrium metal targets (≈20 g) were irradiated in a ~16 to 34 MeV proton beam at a beam current of 100–200 µA at the Los Alamos Isotope Production Facility (IPF). The 88Zr radionuclide was produced and separated from the yttrium targets using hydroxamate resin with an elution yield of 94(5)% (1σ). Liquid DCl solution in D2O was selected as a suitable 88Zr sample matrix due to the high neutron transmission of deuterium compared to hydrogen and an even distribution of 88Zr in the sample matrix. The separated 88Zr was dissolved in DCl and 8 µL of the obtained solution was transferred to a tungsten sample can with a 1.2 mm diameter hole using a syringe and automated filling station inside a hot cell. Neutron transmission of the obtained 88Zr sample was measured at the Device for Indirect Capture Experiments on Radionuclides (DICER).
Food protein-derived amyloids do not accelerate amyloid β aggregation
Authors: Rahman M. Mahafuzur , Pires Rodrigo Sanches , Herneke Anja , Gowda Vasantha , Langton Maud , Biverstål Henrik , Lendel Christofer 
Published: January 2023

AbstractThe deposition of proteins in the form of amyloid fibrils is closely associated with several serious diseases. The events that trigger the conversion from soluble functional proteins into insoluble amyloid are not fully understood. Many proteins that are not associated with disease can form amyloid with similar structural characteristics as the disease-associated fibrils, which highlights the potential risk of cross-seeding of disease amyloid by amyloid-like structures encountered in our surrounding. Of particular interest are common food proteins that can be transformed into amyloid under conditions similar to cooking. We here investigate cross-seeding of amyloid-β (Aβ), a peptide known to form amyloid during the development of Alzheimer’s disease, by 16 types of amyloid fibrils derived from food proteins or peptides. Kinetic studies using thioflavin T fluorescence as output show that none of the investigated protein fibrils accelerates the aggregation of Aβ. In at least two cases (hen egg lysozyme and oat protein isolate) we observe retardation of the aggregation, which appears to originate from interactions between the food protein seeds and Aβ in aggregated form. The results support the view that food-derived amyloid is not a risk factor for development of Aβ pathology and Alzheimer’s disease.
Development and evaluation of deep learning algorithms for assessment of acute burns and the need for surgery
Authors: Boissin Constance , Laflamme Lucie , Fransén Jian , Lundin Mikael , Huss Fredrik , Wallis Lee , Allorto Nikki , Lundin Johan 
Published: January 2023

AbstractAssessment of burn extent and depth are critical and require very specialized diagnosis. Automated image-based algorithms could assist in performing wound detection and classification. We aimed to develop two deep-learning algorithms that respectively identify burns, and classify whether they require surgery. An additional aim assessed the performances in different Fitzpatrick skin types. Annotated burn (n = 1105) and background (n = 536) images were collected. Using a commercially available platform for deep learning algorithms, two models were trained and validated on 70% of the images and tested on the remaining 30%. Accuracy was measured for each image using the percentage of wound area correctly identified and F1 scores for the wound identifier; and area under the receiver operating characteristic (AUC) curve, sensitivity, and specificity for the wound classifier. The wound identifier algorithm detected an average of 87.2% of the wound areas accurately in the test set. For the wound classifier algorithm, the AUC was 0.885. The wound identifier algorithm was more accurate in patients with darker skin types; the wound classifier was more accurate in patients with lighter skin types. To conclude, image-based algorithms can support the assessment of acute burns with relatively good accuracy although larger and different datasets are needed.
Candidatus Neoehrlichia mikurensis and Hepatozoon sp. in voles (Microtus spp.): occurrence and evidence for vertical transmission
Authors: Tołkacz Katarzyna , Kowalec Maciej , Alsarraf Mohammed , Grzybek Maciej , Dwużnik-Szarek Dorota , Behnke Jerzy M. , Bajer Anna 
Published: January 2023

AbstractCandidatus Neoehrlichia mikurensis (CNM) and Hepatozoon spp. are important vector-borne parasites of humans and animals. CNM is a relatively recently discovered pathogen of humans. Hepatozoon are parasites of reptiles, amphibians and mammals, commonly found in rodents and carnivores worldwide. The present study aimed to determine the prevalence of CNM and Hepatozoon spp. in three species of Microtus and to assess the occurrence of vertical transmission in naturally-infected voles. Molecular techniques were used to detect pathogen DNA in blood and tissue samples of captured voles and their offspring. The prevalence of CNM in the vole community ranged 24–47% depending on Microtus species. The DNA of CNM was detected in 21% of pups from three litters of six infected Microtus dams (two Microtus arvalis and one M. oeconomus) and in 3/45 embryos (6.6%) from two litters of eight CNM-infected pregnant females. We detected Hepatozoon infection in 14% of M. arvalis and 9% of M. oeconomus voles. Hepatozoon sp. DNA was detected in 48.7% of pups from seven litters (6 M. arvalis and 1 M. oeconomus) and in two embryos (14.3%) obtained from one M. arvalis litter. The high prevalence of CNM infections in the Microtus spp. community may be a result of a relatively high rate of vertical transmission among naturally infected voles. Vertical transmission was also demonstrated for Hepatozoon sp. in M. arvalis and M. oeconomus. Our study underlines the significance of alternative routes of transmission of important vector-borne pathogens.
Accuracy of breathing and radial pulse assessment by non-medical persons: an observational cross-sectional study
Authors: Suzuki Kensuke , Sakaniwa Ryoto , Endo Nobuko , Kubota Miho , Nakazawa Mayumi , Narikawa Kenji , Ogawa Satoo , Yokota Hiroyuki 
Published: January 2023

AbstractEarly recognition of cardiopulmonary arrest (CPA) expedites emergency calls and resuscitation and improves the survival rate of unresponsive individuals. However, the accuracy of breathing and radial artery pulse assessment by non-medical persons is poorly understood. The aim of this study was to determine the accuracy of breathing assessment and radial pulse palpation among 450 non-medical personnel using a high-fidelity simulator. We examined the accuracy of 10 second’s assessment for breathing and radial pulse using a high-fidelity mannequin simulator, included 496 non-medical participants (school teachers) between 2016–2018. For a primary results, the sensitivity for the detection of the presence of the breathing and radial pulse was 96.2% (97.5% for sensitivity and 92.0% for specificity) and 91.7% (99.1% for sensitivity and 56.8% for specificity), respectively. Futher, breathing rate and radial pulse rate were strongly correlated with the assessments, with Spearman’s correlation coefficients of 0.813 (P < 0.001) and 0.719 (P < 0.001), respectively. In contrast, radial pulse strength was weakly correlated with the assessment (coefficient of 0.288, P < 0.001). Our results suggested that non-medical persons would show high accuracy in detecting and measuring respiration and radial pulse, although they did not accurately determine radial pulse strength for the early recognition of CPA.
A novel shape-based approach to identify gestational age-adjusted growth patterns from birth to 11 years of age
Authors: López-Domínguez Lorena , Bassani Diego G. , Bourdon Celine , Massara Paraskevi , Santos Iná S. , Matijasevich Alicia , Barros Aluísio. J. D. , Comelli Elena M. , Bandsma Robert H. J. 
Published: January 2023

AbstractChild growth patterns assessment is critical to design public health interventions. However, current analytical approaches may overlook population heterogeneity. To overcome this limitation, we developed a growth trajectories clustering pipeline that incorporates a shape-respecting distance, baseline centering (i.e., birth-size normalized trajectories) and Gestational Age (GA)-correction to characterize shape-based child growth patterns. We used data from 3945 children (461 preterm) in the 2004 Pelotas Birth Cohort with at least 3 measurements between birth (included) and 11 years of age. Sex-adjusted weight-, length/height- and body mass index-for-age z-scores were derived at birth, 3 months, and at 1, 2, 4, 6 and 11 years of age (INTERGROWTH-21st and WHO growth standards). Growth trajectories clustering was conducted for each anthropometric index using k-means and a shape-respecting distance, accounting or not for birth size and/or GA-correction. We identified 3 trajectory patterns for each anthropometric index: increasing (High), stable (Middle) and decreasing (Low). Baseline centering resulted in pattern classification that considered early life growth traits. GA-correction increased the intercepts of preterm-born children trajectories, impacting their pattern classification. Incorporating shape-based clustering, baseline centering and GA-correction in growth patterns analysis improves the identification of subgroups meaningful for public health interventions.
An automated micro solid phase extraction gas chromatography–mass spectrometry (μSPE-GC–MS) detection method for geosmin and 2-methylisoborneol in drinking water
Authors: Bristow R. L. , Haworth-Duff A. , Young I. S. , Myers P. , Hampson M. R. , Williams J. , Maher S. 
Published: January 2023

AbstractGeosmin and 2-methylisoborneol (2-MIB) are amongst the most common earthy and musty taste and odour (T&O) compounds found in drinking water. With low odour threshold detection limits below 10 ng L−1, and the complexity of raw water matrices, these two compounds provide a significant challenge for water companies globally. In this research, for the first time, a novel and fully automated micro-solid phase-extraction (μSPE) method coupled with gas chromatography (GC)–mass spectrometry (MS) has been developed for the detection of geosmin and 2-MIB for drinking water analysis. The new automated method described herein is environmentally friendly requiring low raw water sample volumes, of 25 mL, and only 50 μL of elution solvent. Our μSPE-GC–MS method exhibits excellent linearity for both compounds (R2 > 0.999) and low limits of detection of 2.0 ng L−1and 4.3 ng L−1for geosmin and 2-MIB, respectively. The method showed excellent recovery rates (95.1–100.1%) and good precision (RSD < 7%) in raw sample matrices. Our approach is fully automated onto a robotic workstation which can be readily integrated into a laboratory workflow for routine water analysis. Furthermore, the method has excellent potential to be incorporated within a portable system for onsite analysis.