bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Souss lagerstätte of the Anti-Atlas, Morocco: discovery of the first Cambrian fossil lagerstätte from Africa
Authors: Geyer Gerd , Landing Ed 
Published: February 2021

AbstractEpisodic low oxygenated conditions on the sea-floor are likely responsible for exceptional preservation of animal remains in the upper Amouslek Formation (lower Cambrian, Stage 3) on the northern slope of the western Anti-Atlas, Morocco. This stratigraphic interval has yielded trilobite, brachiopod, and hyolith fossils with preserved soft parts, including some of the oldest known trilobite guts. The “Souss fossil lagerstätte” (newly proposed designation) represents the first Cambrian fossil lagerstätte in Cambrian strata known from Africa and is one of the oldest trilobite-bearing fossil lagerstätten on Earth. Inter-regional correlation of the Souss fossil lagerstätte in West Gondwana suggests its development during an interval of high eustatic levels recorded by dark shales that occur in informal upper Cambrian Series 2 in Siberia, South China, and East Gondwana.
An evaluation of approaches for rare variant association analyses of binary traits in related samples
Authors: Chen Ming-Huei , Pitsillides Achilleas , Yang Qiong 
Published: February 2021

AbstractRecognizing that family data provide unique advantage of identifying rare risk variants in genetic association studies, many cohorts with related samples have gone through whole genome sequencing in large initiatives such as the NHLBI Trans-Omics for Precision Medicine (TOPMed) program. Analyzing rare variants poses challenges for binary traits in that some genotype categories may have few or no observed events, causing bias and inflation in commonly used methods. Several methods have recently been proposed to better handle rare variants while accounting for family relationship, but their performances have not been thoroughly evaluated together. Here we compare several existing approaches including SAIGE but not limited to related samples using simulations based on the Framingham Heart Study samples and genotype data from Illumina HumanExome BeadChip where rare variants are the majority. We found that logistic regression with likelihood ratio test applied to related samples was the only approach that did not have inflated type I error rates in both single variant test (SVT) and gene-based tests, followed by Firth logistic regression that had inflation in its direction insensitive gene-based test at prevalence 0.01 only, applied to either related or unrelated samples, though theoretically logistic regression and Firth logistic regression do not account for relatedness in samples. SAIGE had inflation in SVT at prevalence 0.1 or lower and the inflation was eliminated with a minor allele count filter of 5. As for power, there was no approach that outperformed others consistently among all single variant tests and gene-based tests.
Tactile sensing biohybrid soft E-skin based on bioimpedance using aloe vera pulp tissues
Authors: Mousa Mostafa A. , Soliman MennaAllah , Saleh Mahmood A. , Radwan Ahmed G. 
Published: February 2021

AbstractSoft and flexible E-skin advances are a subset of soft robotics field where the soft morphology of human skin is mimicked. The number of prototypes that conformed the use of biological tissues within the structure of soft robots—to develop “Biohybrid Soft Robots”—has increased in the last decade. However, no research was conducted to realize Biohybrid E-skin. In this paper, a novel biohybrid E-skin that provides tactile sensing is developed. The biohybrid E-skin highly mimics the human skin softness and morphology and can sense forces as low as 0.01 newton . The tactile sensing feature is augmented through the use of Aloe Vera pulp, embedded in underlying channel, where the change in its bioimpedance is related to the amount of force exerted on the E-skin surface. The biohybrid E-skin employs high biomimicry as the sensorial output is an oscillating signal similar to signals sent from the human sensing neurons to the brain. After investigating different channel geometries, types of filling tissues, and usage of two silicone materials, their frequency-force behaviour is modelled mathematically. Finally, a functional multichannel prototype “ImpEdded Skin” is developed. This prototype could efficiently detect the position of a tactile touch. This work employs the development of discrete sensing system that exhibits morphological computation that consequently enhances performance.
Cecr2 mutant mice as a model for human cat eye syndrome
Authors: Dicipulo Renée , Norton Kacie A. , Fairbridge Nicholas A. , Kibalnyk Yana , Fox Sabrina C. , Hornberger Lisa K. , McDermid Heather E. 
Published: February 2021

AbstractCat eye syndrome (CES), a human genetic disorder caused by the inverted duplication of a region on chromosome 22, has been known since the late 1890s. Despite the significant impact this disorder has on affected individuals, models for CES have not been produced due to the difficulty of effectively duplicating the corresponding chromosome region in an animal model. However, the study of phenotypes associated with individual genes in this region such as CECR2 may shed light on the etiology of CES. In this study we have shown that deleterious loss of function mutations in mouse Cecr2 effectively demonstrate many of the abnormal features present in human patients with CES, including coloboma and specific skeletal, kidney and heart defects. Beyond phenotypic analyses we have demonstrated the importance of utilizing multiple genetic backgrounds to study disease models, as we see major differences in penetrance of Cecr2-related abnormal phenotype between mouse strains, reminiscent of the variability in the human syndrome. These findings suggest that Cecr2 is involved in the abnormal features of CES and that Cecr2 mice can be used as a model system to study the wide range of phenotypes present in CES.
The genomic structure of a human chromosome 22 nucleolar organizer region determined by TAR cloning
Authors: Kim Jung-Hyun , Noskov Vladimir N. , Ogurtsov Aleksey Y. , Nagaraja Ramaiah , Petrov Nikolai , Liskovykh Mikhail , Walenz Brian P. , Lee Hee-Sheung , Kouprina Natalay , Phillippy Adam M. , Shabalina Svetlana A. , Schlessinger David , Larionov Vladimir 
Published: February 2021

AbstractThe rDNA clusters and flanking sequences on human chromosomes 13, 14, 15, 21 and 22 represent large gaps in the current genomic assembly. The organization and the degree of divergence of the human rDNA units within an individual nucleolar organizer region (NOR) are only partially known. To address this lacuna, we previously applied transformation-associated recombination (TAR) cloning to isolate individual rDNA units from chromosome 21. That approach revealed an unexpectedly high level of heterogeneity in human rDNA, raising the possibility of corresponding variations in ribosome dynamics. We have now applied the same strategy to analyze an entire rDNA array end-to-end from a copy of chromosome 22. Sequencing of TAR isolates provided the entire NOR sequence, including proximal and distal junctions that may be involved in nucleolar function. Comparison of the newly sequenced rDNAs to reference sequence for chromosomes 22 and 21 revealed variants that are shared in human rDNA in individuals from different ethnic groups, many of them at high frequency. Analysis infers comparable intra- and inter-individual divergence of rDNA units on the same and different chromosomes, supporting the concerted evolution of rDNA units. The results provide a route to investigate further the role of rDNA variation in nucleolar formation and in the empirical associations of nucleoli with pathology.
Demographic effects of interacting species: exploring stable coexistence under increased climatic variability in a semiarid shrub community
Authors: García-Cervigón Ana I. , Quintana-Ascencio Pedro F. , Escudero Adrián , Ferrer-Cervantes Merari E. , Sánchez Ana M. , Iriondo José M. , Olano José Miguel 
Published: February 2021

AbstractPopulation persistence is strongly determined by climatic variability. Changes in the patterns of climatic events linked to global warming may alter population dynamics, but their effects may be strongly modulated by biotic interactions. Plant populations interact with each other in such a way that responses to climate of a single population may impact the dynamics of the whole community. In this study, we assess how climate variability affects persistence and coexistence of two dominant plant species in a semiarid shrub community on gypsum soils. We use 9 years of demographic data to parameterize demographic models and to simulate population dynamics under different climatic and ecological scenarios. We observe that populations of both coexisting species may respond to common climatic fluctuations both similarly and in idiosyncratic ways, depending on the yearly combination of climatic factors. Biotic interactions (both within and among species) modulate some of their vital rates, but their effects on population dynamics highly depend on climatic fluctuations. Our results indicate that increased levels of climatic variability may alter interspecific relationships. These alterations might potentially affect species coexistence, disrupting competitive hierarchies and ultimately leading to abrupt changes in community composition.
Composition and acquisition of the microbiome in solitary, ground-nesting alkali bees
Authors: Kapheim Karen M. , Johnson Makenna M. , Jolley Maggi 
Published: February 2021

AbstractIncreasing evidence suggests the microbiome plays an important role in bee ecology and health. However, the relationship between bees and their bacterial symbionts has only been explored in a handful of species. We characterized the microbiome across the life cycle of solitary, ground-nesting alkali bees (Nomia melanderi). We find that feeding status is a major determinant of microbiome composition. The microbiome of feeding larvae was similar to that of pollen provisions, but the microbiome of post-feeding larvae (pre-pupae) was similar to that of the brood cell walls and newly-emerged females. Feeding larvae and pollen provisions had the lowest beta diversity, suggesting the composition of larval diet is highly uniform. Comparisons between lab-reared, newly-emerged, and nesting adult females suggest that the hindgut bacterial community is largely shaped by the external environment. However, we also identified taxa that are likely acquired in the nest or which increase or decrease in relative abundance with age. Although Lactobacillus micheneri was highly prevalent in pollen provisions, it was only detected in one lab-reared female, suggesting it is primarily acquired from environmental sources. These results provide the foundation for future research on metagenomic function and development of probiotics for these native pollinators.
A shape-adjusted ellipse approach corrects for varied axonal dispersion angles and myelination in primate nerve roots
Authors: Bartmeyer Petra M. , Biscola Natalia P. , Havton Leif A. 
Published: February 2021

AbstractSegmentation of axons in light and electron micrographs allows for quantitative high-resolution analysis of nervous tissues, but varied axonal dispersion angles result in over-estimates of fiber sizes. To overcome this technical challenge, we developed a novel shape-adjusted ellipse (SAE) determination of axonal size and myelination as an all-inclusive and non-biased tool to correct for oblique nerve fiber presentations. Our new resource was validated by light and electron microscopy against traditional methods of determining nerve fiber size and myelination in rhesus macaques as a model system. We performed detailed segmental mapping and characterized the morphological signatures of autonomic and motor fibers in primate lumbosacral ventral roots (VRs). An en bloc inter-subject variability for the preganglionic parasympathetic fibers within the L7-S2 VRs was determined. The SAE approach allows for morphological ground truth data collection and assignment of individual axons to functional phenotypes with direct implications for fiber mapping and neuromodulation studies.
Immunomodulatory lipid mediator profiling of cerebrospinal fluid following surgery in older adults
Authors: Terrando Niccolò , Park John J. , Devinney Michael , Chan Cliburn , Cooter Mary , Avasarala Pallavi , Mathew Joseph P. , Quinones Quintin J. , Maddipati Krishna Rao , Berger Miles ,   for the MADCO-PC Study Team, Brigman Brian , Browndyke Jeffrey , Bullock William M. , Carter Jessica , Chapman Joseph , Colin Brian , D’Amico Thomas A. , DeOrio James K. , Esclamado Ramon M. , Ferrandino Michael N. , Gadsden Jeffrey , Garrigues Grant E. , Guercio Jason , Habib Ashraf , Harpole David H. , Hartwig Mathew G. , Iboaya Ehimemen , Inman Brant A. , Khan Anver , Lagoo-Deenadayalan Sandhya , Lee Paula S. , Lee Walter T. , Lemm John , Levinson Howard , Mantyh Christopher , McDonagh David L. , Migaly John , Mithani Suhail K. , Moretti Eugene , Moul Judd W. , Newman Mark F. , Ohlendorf Brian , Perez Alexander , Peterson Andrew C. , Preminger Glenn M. , Robertson Cary N. , Roman Sanziana A. , Runyon Scott , Sandler Aaron , Sbahi Faris M. , Scheri Randall P. , Smith S. Kendall , Talbot Leonard , Thacker Julie K. M. , Thomas Jake , Tong Betty C. , Vaslef Steven N. , Waldron Nathan , Wang Xueyuan , Young Christopher 
Published: February 2021

AbstractArachidonic acid (AA), docosahexaenoic acid (DHA), and eicosapentaenoic acid (EPA) derived lipids play key roles in initiating and resolving inflammation. Neuro-inflammation is thought to play a causal role in perioperative neurocognitive disorders, yet the role of these lipids in the human central nervous system in such disorders is unclear. Here we used liquid chromatography–mass spectrometry to quantify AA, DHA, and EPA derived lipid levels in non-centrifuged cerebrospinal fluid (CSF), centrifuged CSF pellets, and centrifuged CSF supernatants of older adults obtained before, 24 h and 6 weeks after surgery. GAGE analysis was used to determine AA, DHA and EPA metabolite pathway changes over time. Lipid mediators derived from AA, DHA and EPA were detected in all sample types. Postoperative lipid mediator changes were not significant in non-centrifuged CSF (p > 0.05 for all three pathways). The AA metabolite pathway showed significant changes in centrifuged CSF pellets and supernatants from before to 24 h after surgery (p = 0.0000247, p = 0.0155 respectively), from before to 6 weeks after surgery (p = 0.0000497, p = 0.0155, respectively), and from 24 h to 6 weeks after surgery (p = 0.0000499, p = 0.00363, respectively). These findings indicate that AA, DHA, and EPA derived lipids are detectable in human CSF, and the AA metabolite pathway shows postoperative changes in centrifuged CSF pellets and supernatants.
Metabolic profiling of historical and modern wheat cultivars using proton nuclear magnetic resonance spectroscopy
Authors: Poudel Rachana , Bhinderwala Fatema , Morton Martha , Powers Robert , Rose Devin J. 
Published: February 2021

AbstractTo determine changes in the grain components between historical and modern wheat (Triticum aestivumL.) cultivars, wholemeal flours from 19 wheat cultivars and 2 landraces released or introduced between 1870 and 2013 and grown over two crop years were extracted using hydroalcoholic solution and analyzed using one dimensional1H NMR spectral profiling. Grain yield, grain volume weight (GVW), and grain protein concentration were also measured. Grain yield increased while protein concentration decreased by release year (p < 0.001). Increasing trends (p < 0.01) were observed for tryptophan, sum of the measured amino acids, chlorogenic acid, ferulic acid, vanillic acid, and sum of the measured phenolic acids. Grain yield, phenolic acids, and tryptophan were mainly associated with modern cultivars, whereas grain protein concentration and GVW were associated with historical cultivars. The findings from this study showed changes in concentration of grain components over a century of breeding that may have implications for grain quality and human health.
Western listeners detect boundary hierarchy in Indian music: a segmentation study
Authors: Popescu Tudor , Widdess Richard , Rohrmeier Martin 
Published: February 2021

AbstractHow are listeners able to follow and enjoy complex pieces of music? Several theoretical frameworks suggest links between the process of listening and the formal structure of music, involving a division of the musical surface into structural units at multiple hierarchical levels. Whether boundaries between structural units are perceivable to listeners unfamiliar with the style, and are identified congruently between naïve listeners and experts, remains unclear. Here, we focused on the case of Indian music, and asked 65 Western listeners (of mixed levels of musical training; most unfamiliar with Indian music) to intuitively segment into phrases a recording of sitar ālāp of two different rāga-modes. Each recording was also segmented by two experts, who identified boundary regions at section and phrase levels. Participant- and region-wise scores were computed on the basis of "clicks" inside or outside boundary regions (hits/false alarms), inserted earlier or later within those regions (high/low "promptness"). We found substantial agreement—expressed as hit rates and click densities—among participants, and between participants' and experts' segmentations. The agreement and promptness scores differed between participants, levels, and recordings. We found no effect of musical training, but detected real-time awareness of grouping completion and boundary hierarchy. The findings may potentially be explained by underlying general bottom-up processes, implicit learning of structural relationships, cross-cultural musical similarities, or universal cognitive capacities.
Association between low potassium intake and the number of teeth in Korean adults: based on the national data (2013–2015)
Authors: Kim Eun-Jeong , Lee Hye-Ju 
Published: February 2021

AbstractGeneral health and oral health are very closely related. This study aimed to analyze the nutritional factors associated with the number of present teeth in Korean elderly adults. A total of 6,356 individuals were surveyed from the sixth Korean National Health and Nutrition Examination Survey conducted from 2013–2015. The number of existing teeth was divided into three categories: 0–10, 11–20, and over 21, and the nutrition survey covers eating habits, food frequency and food intake using face-to-face interviews. Multiple logistic regression analysis was performed to evaluate the association between nutrient intake and the number of existing teeth after adjusting for socio-demographic factors and general and oral health behaviors and status. As age increases, the number of teeth decreases. Individuals with more teeth had a significantly higher mean daily intake of protein, calcium, phosphorus, potassium and riboflavin (p < 0.05). After adjusting for sociodemographic factors in model 1 and the lower number of teeth in model 2, the strength of the association between the number of teeth and daily calcium intake remained significant. Statistically significant associations were present for dietary potassium intake in models 1 and 2 and in the 11–20 teeth group in model 3 (p < 0.05). We demonstrated a significant association between calcium and potassium intake and the number of teeth.
The G127V variant of the prion protein interferes with dimer formation in vitro but not in cellulo
Authors: Sangeetham Sudheer Babu , Engelke Anna Dorothee , Fodor Elfrieda , Krausz Sarah Laura , Tatzelt Jörg , Welker Ervin 
Published: February 2021

AbstractScrapie prion, PrPSc, formation is the central event of all types of transmissible spongiform encephalopathies (TSEs), while the pathway with possible intermediates and their mechanism of formation from the normal isoform of prion (PrP), remains not fully understood. Recently, the G127V variant of the human PrP is reported to render the protein refractory to transmission of TSEs, via a yet unknown mechanism. Molecular dynamics studies suggested that this mutation interferes with the formation of PrP dimers. Here we analyze the dimerization of 127G and 127VPrP, in both in vitro and a mammalian cell culture system. Our results show that while molecular dynamics may capture the features affecting dimerization in vitro, G127V inhibiting dimer formation of PrP, these are not evidenced in a more complex cellular system.
Accurate spectra for high energy ions by advanced time-of-flight diamond-detector schemes in experiments with high energy and intensity lasers
Authors: Salvadori Martina , Consoli F. , Verona C. , Cipriani M. , Anania M. P. , Andreoli P. L. , Antici P. , Bisesto F. , Costa G. , Cristofari G. , De Angelis R. , Di Giorgio G. , Ferrario M. , Galletti M. , Giulietti D. , Migliorati M. , Pompili R. , Zigler A. 
Published: February 2021

AbstractTime-Of-Flight (TOF) methods are very effective to detect particles accelerated in laser-plasma interactions, but they show significant limitations when used in experiments with high energy and intensity lasers, where both high-energy ions and remarkable levels of ElectroMagnetic Pulses (EMPs) in the radiofrequency-microwave range are generated. Here we describe a novel advanced diagnostic method for the characterization of protons accelerated by intense matter interactions with high-energy and high-intensity ultra-short laser pulses up to the femtosecond and even future attosecond range. The method employs a stacked diamond detector structure and the TOF technique, featuring high sensitivity, high resolution, high radiation hardness and high signal-to-noise ratio in environments heavily affected by remarkable EMP fields. A detailed study on the use, the optimization and the properties of a single module of the stack is here described for an experiment where a fast diamond detector is employed in an highly EMP-polluted environment. Accurate calibrated spectra of accelerated protons are presented from an experiment with the femtosecond Flame laser (beyond 100 TW power and ~ 1019 W/cm2intensity) interacting with thin foil targets. The results can be readily applied to the case of complex stack configurations and to more general experimental conditions.
Temperature and species-dependent regulation of browning in retrobulbar fat
Authors: Rajaii Fatemeh , Kim Dong Won , Pan Jianbo , Mahoney Nicholas R. , Eberhart Charles G. , Qian Jiang , Blackshaw Seth 
Published: February 2021

AbstractRetrobulbar fat deposits surround the posterior retina and optic nerve head, but their function and origin are obscure. We report that mouse retrobulbar fat is a neural crest-derived tissue histologically and transcriptionally resembles interscapular brown fat. In contrast, human retrobulbar fat closely resembles white adipose tissue. Retrobulbar fat is also brown in other rodents, which are typically housed at temperatures below thermoneutrality, but is white in larger animals. We show that retrobulbar fat in mice housed at thermoneutral temperature show reduced expression of the brown fat marker Ucp1, and histological properties intermediate between white and brown fat. We conclude that retrobulbar fat can potentially serve as a site of active thermogenesis, that this capability is both temperature and species-dependent, and that this may facilitate regulation of intraocular temperature.