bluuebunny/crossref_metadata_2025_split huggingface dataset:
Chiral fermion reversal in chiral crystals
Authors: Li Hang , Xu Sheng , Rao Zhi-Cheng , Zhou Li-Qin , Wang Zhi-Jun , Zhou Shi-Ming , Tian Shang-Jie , Gao Shun-Ye , Li Jia-Jun , Huang Yao-Bo , Lei He-Chang , Weng Hong-Ming , Sun Yu-Jie , Xia Tian-Long , Qian Tian , Ding Hong 
Published: December 2019

AbstractIn materials chiral fermions such as Weyl fermions are characterized by nonzero chiral charges, which are singular points of Berry curvature in momentum space. Recently, new types of chiral fermions beyond Weyl fermions have been discovered in structurally chiral crystals CoSi, RhSi and PtAl. Here, we have synthesized RhSn single crystals, which have opposite structural chirality to the CoSi crystals we previously studied. Using angle-resolved photoemission spectroscopy, we show that the bulk electronic structures of RhSn are consistent with the band calculations and observe evident surface Fermi arcs and helical surface bands, confirming the existence of chiral fermions in RhSn. It is noteworthy that the helical surface bands of the RhSn and CoSi crystals have opposite handedness, meaning that the chiral fermions are reversed in the crystals of opposite structural chirality. Our discovery establishes a direct connection between chiral fermions in momentum space and chiral lattices in real space.
Estimating heritability and genetic correlations from large health datasets in the absence of genetic data
Authors: Jia Gengjie , Li Yu , Zhang Hanxin , Chattopadhyay Ishanu , Boeck Jensen Anders , Blair David R. , Davis Lea , Robinson Peter N. , Dahlén Torsten , Brunak Søren , Benson Mikael , Edgren Gustaf , Cox Nancy J. , Gao Xin , Rzhetsky Andrey 
Published: December 2019

AbstractTypically, estimating genetic parameters, such as disease heritability and between-disease genetic correlations, demands large datasets containing all relevant phenotypic measures and detailed knowledge of family relationships or, alternatively, genotypic and phenotypic data for numerous unrelated individuals. Here, we suggest an alternative, efficient estimation approach through the construction of two disease metrics from large health datasets: temporal disease prevalence curves and low-dimensional disease embeddings. We present eleven thousand heritability estimates corresponding to five study types: twins, traditional family studies, health records-based family studies, single nucleotide polymorphisms, and polygenic risk scores. We also compute over six hundred thousand estimates of genetic, environmental and phenotypic correlations. Furthermore, we find that: (1) disease curve shapes cluster into five general patterns; (2) early-onset diseases tend to have lower prevalence than late-onset diseases (Spearman’s ρ = 0.32, p < 10–16); and (3) the disease onset age and heritability are negatively correlated (ρ = −0.46, p < 10–16).
Cryo-EM structure of a 40 kDa SAM-IV riboswitch RNA at 3.7 Å resolution
Authors: Zhang Kaiming , Li Shanshan , Kappel Kalli , Pintilie Grigore , Su Zhaoming , Mou Tung-Chung , Schmid Michael F. , Das Rhiju , Chiu Wah 
Published: December 2019

AbstractSpecimens below 50 kDa have generally been considered too small to be analyzed by single-particle cryo-electron microscopy (cryo-EM). The high flexibility of pure RNAs makes it difficult to obtain high-resolution structures by cryo-EM. In bacteria, riboswitches regulate sulfur metabolism through binding to the S-adenosylmethionine (SAM) ligand and offer compelling targets for new antibiotics. SAM-I, SAM-I/IV, and SAM-IV are the three most commonly found SAM riboswitches, but the structure of SAM-IV is still unknown. Here, we report the structures of apo and SAM-bound SAM-IV riboswitches (119-nt, ~40 kDa) to 3.7 Å and 4.1 Å resolution, respectively, using cryo-EM. The structures illustrate homologies in the ligand-binding core but distinct peripheral tertiary contacts in SAM-IV compared to SAM-I and SAM-I/IV. Our results demonstrate the feasibility of resolving small RNAs with enough detail to enable detection of their ligand-binding pockets and suggest that cryo-EM could play a role in structure-assisted drug design for RNA.
Near 100% CO selectivity in nanoscaled iron-based oxygen carriers for chemical looping methane partial oxidation
Authors: Liu Yan , Qin Lang , Cheng Zhuo , Goetze Josh W. , Kong Fanhe , Fan Jonathan A. , Fan Liang-Shih 
Published: December 2019

AbstractChemical looping methane partial oxidation provides an energy and cost effective route for methane utilization. However, there is considerable CO2 co-production in current chemical looping systems, rendering a decreased productivity in value-added fuels or chemicals. In this work, we demonstrate that the co-production of CO2 can be dramatically suppressed in methane partial oxidation reactions using iron oxide nanoparticles embedded in mesoporous silica matrix. We experimentally obtain near 100% CO selectivity in a cyclic redox system at 750–935 °C, which is a significantly lower temperature range than in conventional oxygen carrier systems. Density functional theory calculations elucidate the origins for such selectivity and show that low-coordinated lattice oxygen atoms on the surface of nanoparticles significantly promote Fe–O bond cleavage and CO formation. We envision that embedded nanostructured oxygen carriers have the potential to serve as a general materials platform for redox reactions with nanomaterials at high temperatures.
High-resolution behavioral time series of Japanese quail within their social environment
Authors: Caliva Jorge Martín , Alcala Rocio Soledad , Guzmán Diego Alberto , Marin Raúl Héctor , Kembro Jackelyn Melissa 
Published: December 2019

AbstractThe behavioral dynamics within a social group not only could depend on individual traits and social-experience of each member, but more importantly, emerges from inter-individual interactions over time. Herein, we first present a dataset, as well as the corresponding original video recordings, of the results of 4 behavioral tests associated with fear and aggressive response performed on 106 Japanese quail. In a second stage, birds were housed with conspecifics that performed similarly in the behavioral tests in groups of 2 females and 1 male. By continuously monitoring each bird in these small social groups, we obtained time series of social and reproductive behavior, and high-resolution locomotor time series. This approach provides the opportunity to perform precise quantification of the temporal dynamics of behavior at an individual level within different social scenarios including when an individual showing continued aggressive behaviors is present. These unique datasets and videos are publicly available in Figshare and can be used in further analysis, or for comparison with existing or future data sets or mathematical models across different taxa.
Eyasi Plateau Paleontological Expedition, Laetoli, Tanzania, fossil specimen database 1998–2005
Authors: Reed Denné , Harrison Terry , Kwekason Amandus 
Published: December 2019

AbstractThe Eyasi Plateau Paleontological Expedition (EPPE) Laetoli specimen database contains 13716 records of plant and animal fossils (ca. 28248 specimens) collected by EPPE field teams working at Laetoli, Tanzania between 1998 and 2005. This dataset is a digital version of the original hard-copy specimen catalog, and it documents the discovery, stratigraphic provenience and taxonomic diversity of Plio-Pleistocene fauna and flora in northern Tanzania between 4.4 Ma and >200 ka. Laetoli is renowned for the discovery of important hominin fossils, including the lectotype for Australopithecus afarensis, one of our early hominin ancestors, the first record of Paranthropus aethiopicus outside Kenya-Ethiopia, and an early record of our own species Homo sapiens. This database is one of the few publicly available palaeoanthropological fossil datasets and serves as an example for expanding open access to primary fossil occurrence data in palaeoanthropology. The taxonomic identifications appearing in this dataset are the original field identifications and are provisional. Any taxonomic analysis employing this dataset should refer to updated taxonomic identifications published by specialists.
TOFF, a database of traits of fish to promote advances in fish aquaculture
Authors: Lecocq Thomas , Benard Alain , Pasquet Alain , Nahon Sarah , Ducret Alex , Dupont-Marin Kevin , Lang Iris , Thomas Marielle 
Published: December 2019

AbstractFunctional traits can be valuable pieces of information for aquaculture research and management. Although fish traits have been the focus of an abundant research, trait datasets for these organisms are difficult to access and often unpractical to achieve meta-analyses without a time-consuming extensive review. Already available large-scale compilations include trait information for many fish species but not as detailed as required for aquaculture purpose. Here, we introduce the TOFF (i.e. Traits OF Fish), a database focusing on fish functional traits that aims at bringing together behavioral, morphological, phenological, and physiological traits always coupled to environmental measurement context into a single open-source access repository. TOFF hosts data from published field and experimental studies. Here, we release data for 228 traits for 174 species extracted from 165 publications and present a collaborative platform. We ultimately aim at providing an inclusive and accessible data resource to facilitate advances in aquaculture development.
Hybrid de novo whole-genome assembly and annotation of the model tapeworm Hymenolepis diminuta
Authors: Nowak Robert M. , Jastrzębski Jan P. , Kuśmirek Wiktor , Sałamatin Rusłan , Rydzanicz Małgorzata , Sobczyk-Kopcioł Agnieszka , Sulima-Celińska Anna , Paukszto Łukasz , Makowczenko Karol G. , Płoski Rafał , Tkach Vasyl V. , Basałaj Katarzyna , Młocicki Daniel 
Published: December 2019

AbstractDespite the use of Hymenolepis diminuta as a model organism in experimental parasitology, a full genome description has not yet been published. Here we present a hybrid de novo genome assembly based on complementary sequencing technologies and methods. The combination of Illumina paired-end, Illumina mate-pair and Oxford Nanopore Technology reads greatly improved the assembly of the H. diminuta genome. Our results indicate that the hybrid sequencing approach is the method of choice for obtaining high-quality data. The final genome assembly is 177 Mbp with contig N50 size of 75 kbp and a scaffold N50 size of 2.3 Mbp. We obtained one of the most complete cestode genome assemblies and annotated 15,169 potential protein-coding genes. The obtained data may help explain cestode gene function and better clarify the evolution of its gene families, and thus the adaptive features evolved during millennia of co-evolution with their hosts.
Transcriptome and chromatin accessibility in porcine intestinal epithelial cells upon Zearalenone exposure
Authors: Wang Haifei , Jin Jian , Wu Jiayun , Qu Huan , Wu Shenglong , Bao Wenbin 
Published: December 2019

AbstractZearalenone (ZEA) is one of the main mycotoxins widely spread in contaminated cereal crops, which poses a great threat to food safety as well as human and animal health. Biological control strategies are emerging as important solutions to eliminate mycotoxin contaminations. However, molecular mechanisms underlying ZEA cytotoxic effects are only partly understood. Noncoding RNAs and chromatin accessibilities are important regulators of gene expression and implicate in a variety of biological processes. Here, we established a study model of porcine intestinal epithelial cells upon ZEA exposure and presented a RNA-seq dataset for mRNA, microRNA, and lncRNA profiling in 18 experimental samples. In addition, chromatin accessibilities of four samples were also explored by ATAC-seq. This dataset will shed new light on gene expression profiling and transcriptional regulation of animal cells in the response to ZEA exposure, which further contributes to detecting biomarkers and drug targets for predicting and controlling ZEA contamination.
Diversity of Streptomyces spp. from mangrove forest of Sarawak (Malaysia) and screening of their antioxidant and cytotoxic activities
Authors: Law Jodi Woan-Fei , Chan Kok-Gan , He Ya-Wen , Khan Tahir Mehmood , Ab Mutalib Nurul-Syakima , Goh Bey-Hing , Lee Learn-Han 
Published: December 2019

AbstractStreptomycetes have been the center of attraction within scientific community owing to their capability to produce various bioactive compounds, for instance, with different antimicrobial, anticancer, and antioxidant properties. The search for novel Streptomyces spp. from underexplored area such as mangrove environment has been gaining attention since these microorganisms could produce pharmaceutically important metabolites. The aim of this study is to discover the diversity of Streptomyces spp. from mangrove in Sarawak and their bioactive potentials — in relation to antioxidant and cytotoxic activities. A total of 88 Streptomyces isolates were successfully recovered from the mangrove soil in Kuching, state of Sarawak, Malaysia. Phylogenetic analysis of all the isolates and their closely related type strains using 16S rRNA gene sequences resulted in 7 major clades in the phylogenetic tree reconstructed based on neighbour-joining algorithm. Of the 88 isolates, 18 isolates could be considered as potentially novel species according to the 16S rRNA gene sequence and phylogenetic analyses. Preliminary bioactivity screening conducted on the potential novel Streptomyces isolates revealed significant antioxidant activity and notable cytotoxic effect against tested colon cancer cell lines (HCT-116, HT-29, Caco-2, and SW480), with greater cytotoxicity towards SW480 and HT-29 cells. This study highlighted that the Sarawak mangrove environment is a rich reservoir containing streptomycetes that could produce novel secondary metabolites with antioxidant and cytotoxic activities.
Antioxidant constituents of three selected red and green color Amaranthus leafy vegetable
Authors: Sarker Umakanta , Oba Shinya 
Published: December 2019

AbstractRed color (A. tricolor) genotypes are an excellent source of pigments, such as betalain (1122.47 ng g−1 FW), β-xanthin (585.22 ng g−1 FW), β-cyanin (624.75 ng g−1 FW), carotenoids (55.55 mg 100 g−1 FW), and antioxidant phytochemicals, such as vitamin C (122.43 mg 100 g−1 FW), TFC (312.64 RE µg g−1 DW), TPC (220.04 GAE µg g−1 DW), TAC (DPPH and ABTS+) (43.81 and 66.59 TEAC µg g−1 DW) compared to green color (A. lividus) genotype. Remarkable phenolic acids, such as salicylic acid, vanillic acid, protocatechuic acid, gallic acid, gentisic acid, β-resorcylic acid, p-hydroxybenzoic acid, syringic acid, ellagic acid, chlorogenic acid, sinapic acids, trans-cinnamic acid, m-coumaric acid, caffeic acid, p-coumaric acid, ferulic acid, and flavonoids, such as rutin, hyperoside, isoquercetin, myricetin, quercetin, apigenin, kaempferol, and catechin were observed in the red color amaranth genotypes, which was much higher compared to the green color amaranth genotype. We newly identified four flavonoids such as quercetin, catechin, myricetin, and apigenin in amaranth. Among the three selected advanced genotypes studied the red color genotype VA13 and VA3 had abundant antioxidant pigments, phytochemicals, phenolic acids, flavonoids, and antioxidant activity could be selected for extracting colorful juice. Correlation study revealed that all antioxidant constituents of red color amaranth had strong antioxidant activity. The present investigation revealed that two red color genotypes had an excellent source of antioxidants that demand detail pharmacological study.
Surface Grafted MSI-78A Antimicrobial Peptide has High Potential for Gastric Infection Management
Authors: Parreira Paula , Monteiro Claudia , Graça Vanessa , Gomes Joana , Maia Sílvia , Gomes Paula , Gonçalves Inês C. , Martins M. Cristina L. 
Published: December 2019

AbstractAs we approach the end of the antibiotic era, newer therapeutic options, such as antimicrobial peptides (AMPs), are in urgent demand. AMP surface grafting onto biomaterials has been described as a good strategy to overcome problems associated with their in vivo stability. Helicobacter pylori is among the bacteria that pose greatest threat to human health, being MSI-78A one of the few bactericidal AMPs against this bacterium. Here, we report that MSI-78A grafted onto model surfaces (Self-Assembled Monolayers –SAMs), in a concentration of 30.3 ± 1.2 ng/cm2 determined by quartz crystal microbalance with dissipation (QCM-D), was able to kill, by contact, 98% of planktonic H. pylori in only 2 h. This fact was not verified against the control bacteria (Staphylococcus epidermidis), although the minimal inhibitory concentration (MIC) of MSI-78A in solution is much lower for S. epidermidis (2 μg/mL) than for H. pylori (64 μg/mL). Our results also demonstrated that, in opposite to other bacteria, H. pylori cells were attracted to ethylene glycol terminated (antiadhesive) surfaces, which can explain the high bactericidal potential of grafted MSI-78A. This proof of concept study establishes the foundations for development of MSI-78A grafted nanoparticles for gastric infection management within a targeted nanomedicine concept.
Diel and tidal pCO2 × O2 fluctuations provide physiological refuge to early life stages of a coastal forage fish
Authors: Cross Emma L. , Murray Christopher S. , Baumann Hannes 
Published: December 2019

AbstractCoastal ecosystems experience substantial natural fluctuations inpCO2and dissolved oxygen (DO) conditions on diel, tidal, seasonal and interannual timescales. Rising carbon dioxide emissions and anthropogenic nutrient input are expected to increase thesepCO2and DO cycles in severity and duration of acidification and hypoxia. How coastal marine organisms respond to naturalpCO2 × DO variability and future climate change remains largely unknown. Here, we assess the impact of static and cyclingpCO2 × DO conditions of various magnitudes and frequencies on early life survival and growth of an important coastal forage fish,Menidia menidia. Static low DO conditions severely decreased embryo survival, larval survival, time to 50% hatch, size at hatch and post-larval growth rates. Static elevatedpCO2did not affect most response traits, however, a synergistic negative effect did occur on embryo survival under hypoxic conditions (3.0 mg L−1). CyclingpCO2 × DO, however, reduced these negative effects of static conditions on all response traits with the magnitude of fluctuations influencing the extent of this reduction. This indicates that fluctuations inpCO2and DO may benefit coastal organisms by providing periodic physiological refuge from stressful conditions, which could promote species adaptability to climate change.
The C-Fern (Ceratopteris richardii) genome: insights into plant genome evolution with the first partial homosporous fern genome assembly
Authors: Marchant D. Blaine , Sessa Emily B. , Wolf Paul G. , Heo Kweon , Barbazuk W. Brad , Soltis Pamela S. , Soltis Douglas E. 
Published: December 2019

AbstractFerns are notorious for possessing large genomes and numerous chromosomes. Despite decades of speculation, the processes underlying the expansive genomes of ferns are unclear, largely due to the absence of a sequenced homosporous fern genome. The lack of this crucial resource has not only hindered investigations of evolutionary processes responsible for the unusual genome characteristics of homosporous ferns, but also impeded synthesis of genome evolution across land plants. Here, we used the model fern speciesCeratopteris richardiito address the processes (e.g., polyploidy, spread of repeat elements) by which the large genomes and high chromosome numbers typical of homosporous ferns may have evolved and have been maintained. We directly compared repeat compositions in species spanning the green plant tree of life and a diversity of genome sizes, as well as both short- and long-read-based assemblies ofCeratopteris. We found evidence consistent with a single ancient polyploidy event in the evolutionary history ofCeratopterisbased on both genomic and cytogenetic data, and on repeat proportions similar to those found in large flowering plant genomes. This study provides a major stepping-stone in the understanding of land plant evolutionary genomics by providing the first homosporous fern reference genome, as well as insights into the processes underlying the formation of these massive genomes.
The Impact of Comorbidity Burden on The Association between Vascular Access Type and Clinical Outcomes among Elderly Patients Undergoing Hemodialysis
Authors: Jhee Jong Hyun , Hwang Seun Deuk , Song Joon Ho , Lee Seoung Woo 
Published: December 2019

AbstractThe optimal vascular access type for elderly hemodialysis patients is controversial. We evaluated the impact of comorbidity burden on the association between vascular access type and mortality risk among 23,100 hemodialysis patients aged ≥65 years from the Korean Society of Nephrology End-Stage Renal Disease registry data. Subjects were stratified into tertiles according to the simplified Charlson comorbidity index (sCCI), and the survival and hospitalization rates were compared with respect to vascular access type: arteriovenous fistula (AVF), arteriovenous graft (AVG), and central venous catheter (CVC). Among all tertiles of sCCI, CVC use showed highest risk of mortality than AVF use. In the lowest to middle tertile, no difference was observed in survival rates between the use of AVF and AVG. However, in the highest tertile, AVG use showed higher risk of mortality than AVF use. When subjects were classified according to a combination of sCCI tertile and access type (AVF vs. AVG), patients with the highest CCI with AVG showed 1.75-folded increased risk of mortality than those with the lowest sCCI with AVF. Hospitalization rates due to access malfunction were highest in patients with CVC in all sCCI tertiles. In the highest tertile, patients with AVG showed increased rates of hospitalization compared to those with AVF due to access malfunction. However, hospitalization rates due to access infection were highest in patients with AVG in all tertiles. The use of AVF may be of benefit and switching to AVF should be considered in elderly hemodialysis patients with a high burden of comorbidity.