bluuebunny/crossref_metadata_2025_split huggingface dataset:
Natural 2D layered mineral cannizzarite with anisotropic optical responses
Authors: Dasgupta Arindam , Yang Xiaodong , Gao Jie 
Published: June 2022

AbstractCannizzarite is a naturally occurring mineral formed by van der Waals (vdW) stacking of alternating layers of PbS-like and Bi2S3-like two-dimensional (2D) materials. Although the PbS-type and Bi2S3-type 2D material layers are structurally isotropic individually, the forced commensuration between these two types of layers while forming the heterostructure of cannizzarite induces strong structural anisotropy. Here we demonstrate the mechanical exfoliation of natural cannizzarite mineral to obtain thin vdW heterostructures of PbS-type and Bi2S3-type atomic layers. The structural anisotropy induced anisotropic optical properties of thin cannizzarite flakes are explored through angle-resolved polarized Raman scattering, linear dichroism, and polarization-dependent anisotropic third-harmonic generation. Our study establishes cannizzarite as a new natural vdW heterostructure-based 2D material with highly anisotropic optical properties for realizing polarization-sensitive linear and nonlinear photonic devices for future on-chip optical computing and optical information processing.
Splitting tensile strength and microstructure of xanthan gum-treated loess
Authors: Jiang Tong , Zhao Jin-di , Zhang Jun-ran 
Published: June 2022

AbstractThe tensile strength of loess is closely related to geological disasters. As eco-friendly materials, biopolymers have an excellent strengthening effect on the mechanical properties of soil. The effect of different initial dry densities and xanthan gum (XG) contents on the microstructure and mechanical behavior of XG-treated loess was studied with a series of microscopic tests and splitting tensile tests based on the particle image velocimetry technique. The results show that the XG became concentrated and agglomerated during dehydration, forming bridge links between soil particles and covering their surfaces. The XG-treated loess had a significant concentration of micropores and mesopores, with greater peak pore size distribution values than untreated loess. The specimens’ load–displacement curves with different XG contents and initial dry densities showed strain-softening. The displacement vector field indicated that specimens’ primary cracks were radial–vertical, and the secondary cracks were well-developed. The strain-softening phenomenon was more significant with increased XG content and initial dry density, and the specimens’ splitting tensile strength and brittleness increased. XG treatment gave the soils stronger cementation and a denser structure, helping to increase strength and brittleness. This research provides a scientific basis and practical experience for applying XG in geotechnical engineering.
Utilisation of Oxford Nanopore sequencing to generate six complete gastropod mitochondrial genomes as part of a biodiversity curriculum
Authors: De Vivo Mattia , Lee Hsin-Han , Huang Yu-Sin , Dreyer Niklas , Fong Chia-Ling , de Mattos Felipe Monteiro Gomes , Jain Dharmesh , Wen Yung-Hui Victoria , Mwihaki John Karichu , Wang Tzi-Yuan , Machida Ryuji J. , Wang John , Chan Benny K. K. , Tsai Isheng Jason 
Published: June 2022

AbstractHigh-throughput sequencing has enabled genome skimming approaches to produce complete mitochondrial genomes (mitogenomes) for species identification and phylogenomics purposes. In particular, the portable sequencing device from Oxford Nanopore Technologies (ONT) has the potential to facilitate hands-on training from sampling to sequencing and interpretation of mitogenomes. In this study, we present the results from sampling and sequencing of six gastropod mitogenomes (Aplysia argus, Cellana orientalis, Cellana toreuma, Conus ebraeus, Conus miles and Tylothais aculeata) from a graduate level biodiversity course. The students were able to produce mitogenomes from sampling to annotation using existing protocols and programs. Approximately 4 Gb of sequence was produced from 16 Flongle and one MinION flow cells, averaging 235 Mb and N50 = 4.4 kb per flow cell. Five of the six 14.1–18 kb mitogenomes were circlised containing all 13 core protein coding genes. Additional Illumina sequencing revealed that the ONT assemblies spanned over highly AT rich sequences in the control region that were otherwise missing in Illumina-assembled mitogenomes, but still contained a base error of one every 70.8–346.7 bp under the fast mode basecalling with the majority occurring at homopolymer regions. Our findings suggest that the portable MinION device can be used to rapidly produce low-cost mitogenomes onsite and tailored to genomics-based training in biodiversity research.
Increased erosion of high-elevation land during late Cenozoic: evidence from detrital thermochronology off-shore Greenland
Authors: Olivetti Valerio , Cattò Silvia , Zattin Massimiliano 
Published: June 2022

AbstractMountain regions at high altitudes show deeply incised glacial valleys that coexist with a high-standing low-relief landscape, whose origin is largely debated. Whether the plateaus contributed to sediment production during the late Cenozoic is a currently debated issue in glacial geomorphology and paleoclimatology. In this study, we used detrital apatite fission-track dating of marine sediments to trace provenance and spatial variation in focused erosion over the last 7 million years. The decomposition of age distributions into populations reveals that, moving upwards through the sections, two young populations get younger, while two older populations get progressively older. We interpreted these trends as the effect of glacial erosion on the valley floors and an increased sediment contribution from the high elevations. To test this hypothesis, we compared the measured ages with synthetic age distributions, which represented a change in the elevation of focused erosion. We conclude that the central-eastern Greenland region is the main source of sediments, and in addition to enhanced valley incision, sediments have also been sourced from progressively higher elevations since 7 Ma. The ageing trend provides an unusual case in detrital thermochronology and a strong evidence that intensified Quaternary glaciations amplify the erosional process both in valley bottoms and at high elevations.
Correlations of FRMD7 gene mutations with ocular oscillations
Authors: Huang Lijuan , Zhou Yunyu , Chen Wencong , Lin Ping , Xie Yan , He Kaiwen , Zhang Shasha , Wu Yuyu , Li Ningdong 
Published: June 2022

AbstractMutations in the FERM domain containing 7 (FRMD7) gene have been proven to be responsible for infantile nystagmus (IN). The purpose of this study is to investigate FRMD7 gene mutations in patients with IN, and to evaluate the nystagmus intensity among patients with and without FRMD7 mutations. The affected males were subdivided into three groups according to whether or not having FRMD7 mutations and the types of mutations. Fifty-two mutations were detected in FRMD7 in 56 pedigrees and 34 sporadic patients with IN, including 28 novel and 24 previous reported mutations. The novel identified mutations further expand the spectrum of FRMD7 mutations. The parameters of nystagmus intensity and the patients’ best corrected visual acuity were not statistically different among the patients with and without identified FRMD7 mutations, and also not different among patients with different mutant types. The FERM-C domain, whose amino acids are encoded by exons 7, 8 and 9, could be the harbor region for most mutations. Loss-of-function is suggested to be the common molecular mechanism for the X-linked infantile nystagmus.
Sensitive and accurate DNA metabarcoding of parasitic helminth mock communities using the mitochondrial rRNA genes
Authors: Chan Abigail Hui En , Saralamba Naowarat , Saralamba Sompob , Ruangsittichai Jiraporn , Chaisiri Kittipong , Limpanont Yanin , Charoennitiwat Vachirapong , Thaenkham Urusa 
Published: June 2022

AbstractNext-generation sequencing technologies have accelerated the pace of helminth DNA metabarcoding research, enabling species detection in bulk community samples. However, finding suitable genetic markers with robust species-level resolution and primers targeting a broad species range among parasitic helminths are some of the challenges faced. This study aimed to demonstrate the potential use of the mitochondrial 12S and 16S rRNA genes for parasitic helminth (nematodes, trematodes, cestodes) DNA metabarcoding. To demonstrate the robustness of the 12S and 16S rRNA genes for DNA metabarcoding, we determined the proportion of species successfully recovered using mock helminth communities without environment matrix and mock helminth communities artificially spiked with environmental matrices. The environmental matrices are human fecal material, garden soil, tissue, and pond water. Our results revealed the robustness of the mitochondrial rRNA genes, through the high sensitivity of the 12S rRNA gene, and the effectiveness of the 12S and 16S primers targeting platyhelminths. With the mitochondrial rRNA genes, a broad range of parasitc helminths were successfully detected to the species level. The potential of the mitochondrial rRNA genes for helminth DNA metabarcoding was demonstrated, providing a valuable gateway for future helminth DNA metabarcoding applications like helminth detection and biodiversity studies.
Identification of miRNAs of Strongyloides stercoralis L1 and iL3 larvae isolated from human stool
Authors: Pomari Elena , Malerba Giovanni , Veschetti Laura , Franceschi Alessandra , Moron Dalla Tor Lucas , Deiana Michela , Degani Monica , Mistretta Manuela , Patuzzo Cristina , Ragusa Andrea , Mori Antonio , Bisoffi Zeno , Buonfrate Dora 
Published: June 2022

AbstractStrongyloidiasis is a neglected tropical disease caused by the soil-transmitted nematode by Strongyloides stercoralis, that affects approximately 600 million people worldwide. In immunosuppressed individuals disseminated strongyloidiasis can rapidly lead to fatal outcomes. There is no gold standard for diagnosing strongyloidiasis, and infections are frequently misdiagnosed. A better understanding of the molecular biology of this parasite can be useful for example for the discovery of potential new biomarkers. Interestingly, recent evidence showed the presence of small RNAs in Strongyloididae, but no data was provided for S. stercoralis. In this study, we present the first identification of miRNAs of both L1 and iL3 larval stages of S. stercoralis. For our purpose, the aims were: (i) to analyse the miRNome of L1 and iL3 S. stercoralis and to identify potential miRNAs of this nematode, (ii) to obtain the mRNAs profiles in these two larval stages and (iii) to predict potential miRNA target sites in mRNA sequences. Total RNA was isolated from L1 and iL3 collected from the stool of 5 infected individuals. For the miRNAs analysis, we used miRDeep2 software and a pipeline of bio-informatic tools to construct a catalog of a total of 385 sequences. Among these, 53% were common to S. ratti, 19% to S. papillosus, 1% to Caenorhabditis elegans and 44% were novel. Using a differential analysis between the larval stages, we observed 6 suggestive modulated miRNAs (STR-MIR-34A-3P, STR-MIR-8397-3P, STR-MIR-34B-3P and STR-MIR-34C-3P expressed more in iL3, and STR-MIR-7880H-5P and STR-MIR-7880M-5P expressed more in L1). Along with this analysis, we obtained also the mRNAs profiles in the same samples of larvae. Multiple testing found 81 statistically significant mRNAs of the total 1553 obtained (FDR < 0.05; 32 genes expressed more in L1 than iL3; 49 genes expressed more in L3 than iL1). Finally, we found 33 predicted mRNA targets of the modulated miRNAs, providing relevant data for a further validation to better understand the role of these small molecules in the larval stages and their valuein clinical diagnostics.
Rapid but specific perceptual learning partially explains individual differences in the recognition of challenging speech
Authors: Banai Karen , Karawani Hanin , Lavie Limor , Lavner Yizhar 
Published: June 2022

AbstractPerceptual learning for speech, defined as long-lasting changes in speech recognition following exposure or practice occurs under many challenging listening conditions. However, this learning is also highly specific to the conditions in which it occurred, such that its function in adult speech recognition is not clear. We used a time-compressed speech task to assess learning following either brief exposure (rapid learning) or additional training (training-induced learning). Both types of learning were robust and long-lasting. Individual differences in rapid learning explained unique variance in recognizing natural-fast speech and speech-in-noise with no additional contribution for training-induced learning (Experiment 1). Rapid learning was stimulus specific (Experiment 2), as in previous studies on training-induced learning. We suggest that rapid learning is key for understanding the role of perceptual learning in online speech recognition whereas longer training could provide additional opportunities to consolidate and stabilize learning.
Cell type matching in single-cell RNA-sequencing data using FR-Match
Authors: Zhang Yun , Aevermann Brian , Gala Rohan , Scheuermann Richard H. 
Published: June 2022

AbstractReference cell atlases powered by single cell and spatial transcriptomics technologies are becoming available to study healthy and diseased tissue at single cell resolution. One important use of these data resources is to compare cell types from new dataset with cell types in the reference atlases to evaluate their phenotypic similarities and differences, for example, for identifying novel cell types under disease conditions. For this purpose, rigorously-validated computational algorithms are needed to perform these cell type matching tasks that can compare datasets from different experiment platforms and sample types. Here, we present significant enhancements to FR-Match (v2.0)—a multivariate nonparametric statistical testing approach for matching cell types in query datasets to reference atlases. FR-Match v2.0 includes a normalization procedure to facilitate cross-platform cluster-level comparisons (e.g., plate-based SMART-seq and droplet-based 10X Chromium single cell and single nucleus RNA-seq and spatial transcriptomics) and extends the pipeline to also allow cell-level matching. In the use cases evaluated, FR-Match showed robust and accurate performance for identifying common and novel cell types across tissue regions, for discovering sub-optimally clustered cell types, and for cross-platform and cross-sample cell type matching.
TGR5 agonists induce peripheral and central hypersensitivity to bladder distension
Authors: Caldwell Ashlee , Grundy Luke , Harrington Andrea M. , Garcia-Caraballo Sonia , Castro Joel , Bunnett Nigel W. , Brierley Stuart M. 
Published: June 2022

AbstractThe mechanisms underlying chronic bladder conditions such as interstitial cystitis/bladder pain syndrome (IC/BPS) and overactive bladder syndrome (OAB) are incompletely understood. However, targeting specific receptors mediating neuronal sensitivity to specific stimuli is an emerging treatment strategy. Recently, irritant-sensing receptors including the bile acid receptor TGR5, have been identified within the viscera and are thought to play a key role in neuronal hypersensitivity. Here, in mice, we identify mRNA expression of TGR5 (Gpbar1) in all layers of the bladder as well as in the lumbosacral dorsal root ganglia (DRG) and in isolated bladder-innervating DRG neurons. In bladder-innervating DRG neurons Gpbar1 mRNA was 100% co-expressed with Trpv1 and 30% co-expressed with Trpa1. In vitro live-cell calcium imaging of bladder-innervating DRG neurons showed direct activation of a sub-population of bladder-innervating DRG neurons with the synthetic TGR5 agonist CCDC, which was diminished in Trpv1−/− but not Trpa1−/− DRG neurons. CCDC also activated a small percentage of non-neuronal cells. Using an ex vivo mouse bladder afferent recording preparation we show intravesical application of endogenous (5α-pregnan-3β-ol-20-one sulphate, Pg5α) and synthetic (CCDC) TGR5 agonists enhanced afferent mechanosensitivity to bladder distension. Correspondingly, in vivo intravesical administration of CCDC increased the number of spinal dorsal horn neurons that were activated by bladder distension. The enhanced mechanosensitivity induced by CCDC ex vivo and in vivo was absent using Gpbar1−/− mice. Together, these results indicate a role for the TGR5 receptor in mediating bladder afferent hypersensitivity to distension and thus may be important to the symptoms associated with IC/BPS and OAB.
Glutamine and norepinephrine in follicular fluid synergistically enhance the antioxidant capacity of human granulosa cells and the outcome of IVF-ET
Authors: Wang Lulu , Zhou Chengliang , Sun Junyan , Zhang Qiuwan , Lai Dongmei 
Published: June 2022

AbstractAn increasing number of studies demonstrate that changes in neurotransmitters metabolic levels in follicular fluid are directly related to oocyte maturation, fertilization, the quality of embryo and pregnancy rates. However, the relationship between the intra-follicular neurotransmitters and the function of granulosa cells (GCs), and the outcome of in vitro fertilization-embryo transfer (IVF-ET) is not clear. Human follicular fluid and cumulus GCs were harvested from large follicles obtained from patients undergoing IVF. Neurotransmitters and steroid hormones in follicular fluid were measured through liquid chromatography-tandem mass spectrometry (LC–MS/MS) and high-performance liquid chromatography-mass spectrometry (HPLC–MS/MS). Based on the content of glutamine (Gln) in follicular fluid, the samples were divided into two groups: high Gln level group and low Gln level group. The expression of proliferation-, steroidogenesis- and antioxidant-related genes in GCs was detected by qRT-PCR. In vitro, KGN cells were used to further verify the effects of Gln and NE on GCs function. Primary and secondary outcomes were the number of mature and retrieved oocytes, and the ratio of high-quality embryos, respectively. Gln (46.75 ± 7.74 μg/mL) and norepinephrine (NE, 0.20 ± 0.07 μg/mL) were abundant neurotransmitters in follicular fluid, and exhibited a significantly positive correlation (R = 0.5869, P < 0.005). In high Gln level group, the expression of proliferation, steroidogenesis and antioxidant-related genes in GCs were higher than those in low Gln level group, and the contents of estriol and E2 in follicular fluid were more abundant. Moreover, the concentrations of Gln and NE in follicular fluid showed significantly positive correlation with IDH1 expression in GCs (R = 0.3822, R = 0.4009, P < 0.05). Importantly, a significantly positive correlation was observed between IDH1 expression in GCs and the ratio of higher-quality/cleaved embryos (R = 0.4480, P < 0.05). In vitro studies further demonstrated that Gln and NE played synergistically function in improving GCs proliferation and E2 production by upregulating IDH1 expression. These data demonstrate that Gln and NE in follicular fluid might play significant positive roles in GCs function, and may be potential predictors for selecting optimal quality oocytes and evaluating the quality of embryonic development.
Bee pollen in zebrafish diet affects intestinal microbiota composition and skin cutaneous melanoma development
Authors: Di Chiacchio Isabela M. , Gómez-Abenza Elena , Paiva Isadora M. , de Abreu Danilo J. M. , Rodríguez-Vidal Juan Francisco , Carvalho Elisângela E. N. , Carvalho Stephan M. , Solis-Murgas Luis David , Mulero Victoriano 
Published: June 2022

AbstractBee pollen is recommended as dietary supplement due to immunostimulating functions including antioxidant, anti-inflammatory and anti-carcinogenic properties. Nevertheless, the effectiveness of such properties is still not well understood. As diet can be associated with animal performance, microbiota modulation and potentially factor for cancer, this study aimed to analyze if bee pollen could influence growth, gut microbial and skin cutaneous melanoma development in zebrafish. Control diets based on commercial flakes and Artemia were compared with the same diet supplemented with bee pollen. Fish weight gain, increased length, intestinal bacteria metagenomics analysis, serum amyloid A gene expression and cutaneous melanoma transplantation assays were performed. Bee pollen affected microbiota composition and melanoma development. Differential abundance revealed higher abundance in the control group for Aeromonadaceae family, Aeromonas and Pseudomonas genus, A. sobria, A. schubertii, A. jandaei and P. alcaligenes species compared with pollen diet group. Pollen group presented higher abundance for Chromobacterium genus and for Gemmobacter aquaticus, Flavobacterium succinicans and Bifidobacterium breve compared with control group. Unexpectedly, fish fed with bee pollen showed higher tumor growth rate and larger tumor size than control group. This is the first study to report intestinal microbial changes and no protective cancer properties after bee pollen administration.
Demographic characteristics shape patterns of dawn swarming during roost switching in tree-dwelling Daubenton’s bat
Authors: Ružinská Romana , Lőbbová Denisa , Kaňuch Peter 
Published: June 2022

AbstractFrequent roost switching in fission–fusion societies of tree-dwelling bats is closely associated with swarming behaviour entailing ritualised night-time displays around the roost tree and/or at the roost entrance to signal its actual location, particularly immediately prior to sunrise. However, effects of demographic characteristics of individuals in this social behaviour remain unanswered. Using passive integrated transponders (PIT) and automatic readers, we recorded swarming activity of members of a Daubenton’s bat (Myotis daubentonii) maternity colony in the vicinity of their roosts. In total, 59,622 activity events of 281 PIT-tagged individuals were recorded on ten monitored roosts during three summer seasons. We found a gradual increase of swarming activity from midnight to sunrise in old adult females, whereas young females and juveniles primarily swarmed later at dawn. We attribute this difference to the learning status of younger bats, which are not yet able to perform a defined pattern of swarming activity, whereas older bats likely take a more active role in signalling the position of the roost. Old males exhibited the least swarming activity at maternity roosts, which mostly occurred between crepuscular periods, presumably due to their solitary lives. A negative correlation between genetic distance and swarming activity suggests an important role of kinship in the formation of the maternity colony as well as group cohesion during roost switching.