bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evidence of nematic order and nodal superconducting gap along [110] direction in RbFe2As2
Authors: Liu Xi , Tao Ran , Ren Mingqiang , Chen Wei , Yao Qi , Wolf Thomas , Yan Yajun , Zhang Tong , Feng Donglai 
Published: March 2019

AbstractUnconventional superconductivity often intertwines with various forms of order, such as the nematic order which breaks the rotational symmetry of the lattice. Here we report a scanning tunneling microscopy study on RbFe2As2, a heavily hole-doped Fe-based superconductor (FeSC). We observe significant symmetry breaking in its electronic structure and magnetic vortex which differentiates the (π, π) and (π, -π) directions of the unfolded Brillouin zone. It is thus a novel nematic state, distinct from the nematicity of undoped/lightly-doped FeSCs which breaks the (π, 0)/(0, π) equivalence. Moreover, we observe a clear V-shaped superconducting gap. The gap is suppressed on surface Rb vacancies and step edges, and the suppression is particularly strong at the [110]-oriented edges. This is possibly due to a $${{d}}_{{{x}}^2 - {{y}}^2}$$

d

x

2

-

y

2

like pairing component with nodes along the [110] directions. Our results thus highlight the intimate connection between nematicity and superconducting pairing in iron-based superconductors.
High-resolution structure determination of sub-100 kDa complexes using conventional cryo-EM
Authors: Herzik Mark A. , Wu Mengyu , Lander Gabriel C. 
Published: March 2019

AbstractDetermining high-resolution structures of biological macromolecules amassing less than 100 kilodaltons (kDa) has been a longstanding goal of the cryo-electron microscopy (cryo-EM) community. While the Volta phase plate has enabled visualization of specimens in this size range, this instrumentation is not yet fully automated and can present technical challenges. Here, we show that conventional defocus-based cryo-EM methodologies can be used to determine high-resolution structures of specimens amassing less than 100 kDa using a transmission electron microscope operating at 200 keV coupled with a direct electron detector. Our ~2.7 Å structure of alcohol dehydrogenase (82 kDa) proves that bound ligands can be resolved with high fidelity to enable investigation of drug-target interactions. Our ~2.8 Å and ~3.2 Å structures of methemoglobin demonstrate that distinct conformational states can be identified within a dataset for proteins as small as 64 kDa. Furthermore, we provide the sub-nanometer cryo-EM structure of a sub-50 kDa protein.
Genome maps across 26 human populations reveal population-specific patterns of structural variation
Authors: Levy-Sakin Michal , Pastor Steven , Mostovoy Yulia , Li Le , Leung Alden K. Y. , McCaffrey Jennifer , Young Eleanor , Lam Ernest T. , Hastie Alex R. , Wong Karen H. Y. , Chung Claire Y. L. , Ma Walfred , Sibert Justin , Rajagopalan Ramakrishnan , Jin Nana , Chow Eugene Y. C. , Chu Catherine , Poon Annie , Lin Chin , Naguib Ahmed , Wang Wei-Ping , Cao Han , Chan Ting-Fung , Yip Kevin Y. , Xiao Ming , Kwok Pui-Yan 
Published: March 2019

AbstractLarge structural variants (SVs) in the human genome are difficult to detect and study by conventional sequencing technologies. With long-range genome analysis platforms, such as optical mapping, one can identify large SVs (>2 kb) across the genome in one experiment. Analyzing optical genome maps of 154 individuals from the 26 populations sequenced in the 1000 Genomes Project, we find that phylogenetic population patterns of large SVs are similar to those of single nucleotide variations in 86% of the human genome, while ~2% of the genome has high structural complexity. We are able to characterize SVs in many intractable regions of the genome, including segmental duplications and subtelomeric, pericentromeric, and acrocentric areas. In addition, we discover ~60 Mb of non-redundant genome content missing in the reference genome sequence assembly. Our results highlight the need for a comprehensive set of alternate haplotypes from different populations to represent SV patterns in the genome.
Variable outcomes of human heart attack recapitulated in genetically diverse mice
Authors: Salimova Ekaterina , Nowak Kristen J. , Estrada Ana C. , Furtado Milena B. , McNamara Elyshia , Nguyen Quang , Balmer Lois , Preuss Christoph , Holmes Jeffrey W. , Ramialison Mirana , Morahan Grant , Rosenthal Nadia A. 
Published: March 2019

AbstractClinical variation in patient responses to myocardial infarction (MI) has been difficult to model in laboratory animals. To assess the genetic basis of variation in outcomes after heart attack, we characterized responses to acute MI in the Collaborative Cross (CC), a multi-parental panel of genetically diverse mouse strains. Striking differences in post-MI functional, morphological, and myocardial scar features were detected across 32 CC founder and recombinant inbred strains. Transcriptomic analyses revealed a plausible link between increased intrinsic cardiac oxidative phosphorylation levels and MI-induced heart failure. The emergence of significant quantitative trait loci for several post-MI traits indicates that utilizing CC strains is a valid approach for gene network discovery in cardiovascular disease, enabling more accurate clinical risk assessment and prediction.
Inter-chromosomal coupling between vision and pigmentation genes during genomic divergence
Authors: Hench Kosmas , Vargas Marta , Höppner Marc P. , McMillan W. Owen , Puebla Oscar 
Published: March 2019

AbstractRecombination between loci underlying mate choice and ecological traits is a major evolutionary force acting against speciation with gene flow. The evolution of linkage disequilibrium between such loci is therefore a fundamental step in the origin of species. Here, we show that this process can take place in the absence of physical linkage in hamlets—a group of closely related reef fishes from the wider Caribbean that differ essentially in colour pattern and are reproductively isolated through strong visually-based assortative mating. Using full-genome analysis, we identify four narrow genomic intervals that are consistently differentiated among sympatric species in a backdrop of extremely low genomic divergence. These four intervals include genes involved in pigmentation (sox10), axial patterning (hoxc13a), photoreceptor development (casz1) and visual sensitivity (SWSandLWSopsins) that develop islands of long-distance and inter-chromosomal linkage disequilibrium as species diverge. The relatively simple genomic architecture of species differences facilitates the evolution of linkage disequilibrium in the presence of gene flow.
Assessing metastatic potential of breast cancer cells based on EGFR dynamics
Authors: Liu Yen-Liang , Chou Chao-Kai , Kim Mirae , Vasisht Rohan , Kuo Yu-An , Ang Phyllis , Liu Cong , Perillo Evan P. , Chen Yu-An , Blocher Katherine , Horng Hannah , Chen Yuan-I , Nguyen Duc Trung , Yankeelov Thomas E. , Hung Mien-Chie , Dunn Andrew K. , Yeh Hsin-Chih 
Published: March 2019

AbstractDerailed transmembrane receptor trafficking could be a hallmark of tumorigenesis and increased tumor invasiveness, but receptor dynamics have not been used to differentiate metastatic cancer cells from less invasive ones. Using single-particle tracking techniques, we developed a phenotyping asssay named Transmembrane Receptor Dynamics (TReD), studied the dynamics of epidermal growth factor receptor (EGFR) in seven breast epithelial cell lines and developed a phenotyping assay named Transmembrane Receptor Dynamics (TReD). Here we show a clear evidence that increased EGFR diffusivity and enlarged EGFR confinement size in the plasma membrane (PM) are correlated with the enhanced metastatic potential in these cell lines. By comparing the TReD results with the gene expression profiles, we found a clear negative correlation between the EGFR diffusivities and the breast cancer luminal differentiation scores (r = −0.75). Upon the induction of epithelial-mesenchymal transition (EMT), EGFR diffusivity significantly increased for the non-tumorigenic MCF10A (99%) and the non-invasive MCF7 (56%) cells, but not for the highly metastatic MDA-MB-231 cell. We believe that the reorganization of actin filaments during EMT modified the PM structures, causing the receptor dynamics to change. TReD can thus serve as a new biophysical marker to probe the metastatic potential of cancer cells and even to monitor the transition of metastasis.
Early-Life Exposure to the Chinese Famine Is Associated with Higher Methylation Level in the INSR Gene in Later Adulthood
Authors: Wang Zhenghe , Song Jieyun , Li Yanhui , Dong Bin , Zou Zhiyong , Ma Jun 
Published: March 2019

AbstractWe examined the association between the China famine exposure in early life and DNA methylation of INSR (hg18, chr19:7110130-7110574) and CPT1A (hg18, chr11: 68286513-68286952) related to growth and metabolism in 235 subjects selected from two provinces in China. The subjects were categorized into prenatal famine-exposed group and non-exposed group based on their birthdates. DNA methylation at the INSR gene locus was assayed from peripheral white blood cells using the Sequenom’s MassARRAY system. Two dependent samples t-test was used to compare the difference between the exposed group and non-exposed group. DNA methylation level of INSR was higher among individuals who exposed to the China famine in the fetus than that of non-exposed group (d = 3.3%, P = 0.006). A significant interaction between famine exposure and province was observed for INSR (Pinteraction < 0.001). DNA methylation level of INSR was positively associated with triglyceride (β = 0.011, P = 0.021), and negatively associated with high-density lipoprotein cholesterol (β = −0.039, P = 0.021). Moreover, exposed group had higher meat consumption than non-exposed group in severe exposure area. Prenatal exposure to the China famine plus later life eating habits might regulate epigenome.
The Reaction of Dimerization by Itself Reduces the Noise Intensity of the Protein Monomer
Authors: Liu Feng-You , Lo Shih-Chiang , Shu Che-Chi 
Published: March 2019

AbstractBecause of the small particle number of intracellular species participating in genetic circuits, stochastic fluctuations are inevitable. This intracellular noise is detrimental to precise regulation. To maintain the proper function of a cell, some natural motifs attenuate the noise at the protein level. In many biological systems, the protein monomer is used as a regulator, but the protein dimer also exists. In the present study, we demonstrated that the dimerization reaction reduces the noise intensity of the protein monomer. Compared with two common noise-buffering motifs, the incoherent feedforward loop (FFL) and negative feedback control, the coefficient of variation (COV) in the case of dimerization was 25% less. Furthermore, we examined a system with direct interaction between proteins and other ligands. Both the incoherent FFL and negative feedback control failed to buffer the noise, but the dimerization was effective. Remarkably, the formation of only one protein dimer was sufficient to cause a 7.5% reduction in the COV.
Genetic polymorphism and phylogenetic differentiation of the Huaxia Platinum System in three Chinese minority ethnicities
Authors: Liu Jing , Wang Zheng , He Guanglin , Wang Mengge , Hou Yiping 
Published: March 2019

AbstractShort tandem repeats (STRs) with features of high polymorphism and abundant evolution information play a significant role in genetic applications such as human forensics, anthropology and population genetics. The Huaxia Platinum System was specifically exploited to allow coamplification of all markers in the expanded Combined DNA Index System and the Chinese National Database. Herein, in continuation of our previous studies, 493 unrelated individuals were firstly genotyped to investigate the efficacy of this novel system in three minority ethnicities of China (Hui, Tibetan and Uygur). Additionally, genetic relationships among our three investigated populations and other previously published populations were analyzed using pairwise genetic distances, multidimensional scaling (MDS), principal component analysis (PCA), cladogram and STRUCTURE. The combined match probabilities (CMP) for the Hui, Tibetan and Uygur groups were 1.6894 × 10−27, 6.1666 × 10−27 and 5.0655 × 10−27, respectively, and the combined powers of exclusion (CPE) were 0.999999999646627, 0.999999999304935 and 0.999999999433994. Population comparison analysis manifested that the Hui and Tibetan populations had genetic affinities with the Han, Yi and Korean populations, while the Uygur group had a close relationship with the Kazakh population. The aforementioned results suggested that the Huaxia Platinum System is a polymorphic and effective tool that is appropriate for personal identification and population genetics.
Differences in monocyte: lymphocyte ratio and Tuberculosis disease progression in genetically distinct populations of macaques
Authors: Sibley Laura , Gooch Karen , Wareham Alice , Gray Susan , Chancellor Andrew , Dowall Stuart , Bate Simon , Marriott Anthony , Dennis Mike , White Andrew D. , Marsh Philip D. , Fletcher Helen , Sharpe Sally 
Published: March 2019

AbstractMonocyte:lymphocyte ratio (M:L) has been identified as a risk factor in development of TB disease in children and those undergoing treatment for HIV in co-infected individuals. Retrospective analysis was performed using M:L data collected from TB modelling studies performed in Rhesus macaques of Indian genotype (RM), cynomolgus macaque of Chinese genotype (CCM) and cynomolgus macaque of Mauritian genotype (MCM), which found that the more susceptible populations (RM and MCM) had higher M:L ratios than the least susceptible population (CCM). Following Mycobacterium tuberculosis exposure, significant increases in M:L ratio were observed in susceptible RM and MCM within 12 weeks of TB infection, whereas M:L in CCM remained stable, suggesting that changes in M:L ratio may also act as a biomarker of TB disease progression. The frequency of PPD-specific interferon gamma (IFNγ) secreting cells (SFU) were compared, with the more susceptible macaque populations showing an association between M:L and IFNγ SFU frequency. Investigation of the genes associated with monocyte-derived antigen presenting cells revealed differences between RM and CCM, highlighting differences in their monocyte populations, as well as overall M:L ratio. Differences in M:L ratio between macaque populations could be used to explore immunological mechanisms in susceptible populations that would complement human population studies.
New molecular insights on the response of the green alga Tetraselmis suecica to nitrogen starvation
Authors: Lauritano Chiara , De Luca Daniele , Amoroso Mariano , Benfatto Salvatore , Maestri Simone , Racioppi Claudia , Esposito Francesco , Ianora Adrianna 
Published: March 2019

AbstractMicroalgae are currently considered one of the most promising resources for biofuel production, aquaculture feedstock and new pharmaceuticals. Among them, green algae of the genusTetraselmisare extensively studied for their lipid accumulation in nutrient-starvation conditions. In this paper, we present the full-transcriptome ofTetraselmis suecicaand differential expression analysis between nitrogen-starved and -repleted conditions (at stationary phase) focusing not only on lipid metabolism but giving new insights on nutrient starvation responses. Transcripts involved in signal transduction pathways, stress and antioxidant responses and solute transport were strongly up-regulated whenT.suecicawas cultured under nitrogen starvation. On the contrary, transcripts involved in amino acid synthesis, degradation of sugars, secondary metabolite synthesis, as well as photosynthetic activity were down-regulated under the same conditions. Among differentially expressed transcripts, a polyketide synthase and three lipoxygenases (involved in the synthesis of secondary metabolites with antipredator, anticancer and anti-infective activities) were identified, suggesting the potential synthesis of bioactive compounds by this microalga. In addition, the transcript for a putative nitrilase, enzyme used in nitrile bioremediation, is here reported for the first time forT. suecica. These findings give new insights onT. suecicaresponses to nutrient starvation and on possible biotechnological applications for green algae.
Entrainment of superoxide rhythm by menadione in HCT116 colon cancer cells
Authors: Kizhuveetil Uma , Palukuri Meghana V. , Sharma Priyanshu , Karunagaran Devarajan , Rengaswamy Raghunathan , Suraishkumar G. K. 
Published: March 2019

AbstractReactive oxygen species (ROS) are primary effectors of cytotoxicity induced by many anti-cancer drugs. Rhythms in the pseudo-steady-state (PSS) levels of particular intracellular ROS in cancer cells and their relevance to drug effectiveness are unknown thus far. We report that the PSS levels of intracellular superoxide (SOX), an important ROS, exhibit an inherent rhythm in HCT116 colon cancer cells, which is entrained (reset) by the SOX inducer, menadione (MD). This reset was dependent on the expression of p53, and it doubled the sensitivity of the cells to MD. The period of oscillation was found to have a linear correlation with MD concentration, given by the equation, T, in h = 23.52 − 1.05 [MD concentration in µM]. Further, we developed a mathematical model to better understand the molecular mechanisms involved in rhythm reset. Biologically meaningful parameters were obtained through parameter estimation techniques; the model can predict experimental profiles of SOX, establish qualitative relations between interacting species in the system and serves as an important tool to understand the profiles of various species. The model was also able to successfully predict the rhythm reset in MD treated hepatoma cell line, HepG2.
Species-specific alterations in Anopheles mosquito olfactory responses caused by Plasmodium infection
Authors: Stanczyk N. M. , Brugman V. A. , Austin V. , Sanchez-Roman Teran F. , Gezan S. A. , Emery M. , Visser T. M. , Dessens J. T. , Stevens W. , Smallegange R. C. , Takken W. , Hurd H. , Caulfield John , Birkett M. , Pickett J. , Logan J. G. 
Published: March 2019

AbstractMosquitoes infected with malaria parasites have demonstrated altered behaviour that may increase the probability of parasite transmission. Here, we examine the responses of the olfactory system in Plasmodium falciparum infected Anopheles gambiae, Plasmodium berghei infected Anopheles stephensi, and P. berghei infected An. gambiae. Infected and uninfected mosquitoes showed differential responses to compounds in human odour using electroantennography coupled with gas chromatography (GC-EAG), with 16 peaks triggering responses only in malaria-infected mosquitoes (at oocyst, sporozoite or both stages). A selection of key compounds were examined with EAG, and responses showed differences in the detection thresholds of infected and uninfected mosquitoes to compounds including lactic acid, tetradecanoic acid and benzothiazole, suggesting that the changes in sensitivity may be the reason for differential attraction and biting at the oocyst and sporozoite stages. Importantly, the different cross-species comparisons showed varying sensitivities to compounds, with P. falciparum infected An. gambiae differing from P. berghei infected An. stephensi, and P. berghei infected An. gambiae more similar to the P. berghei infected An. stephensi. These differences in sensitivity may reflect long-standing evolutionary relationships between specific Plasmodium and Anopheles species combinations. This highlights the importance of examining different species interactions in depth to fully understand the impact of malaria infection on mosquito olfactory behaviour.
Examining the relationship between body mass index and adverse cardio-metabolic profiles among Australian Indigenous and non-Indigenous young adults
Authors: Sevoyan Arusyak , Davison Belinda , Rumbold Alice , Moore Vivienne , Singh Gurmeet 
Published: March 2019

AbstractAustralian Indigenous young people have a 10-fold excess of deaths from ischaemic heart disease compared with non-Indigenous Australians, yet the reasons behind this remain understudied. This paper aims to describe cardio-metabolic profiles among Australian Indigenous (n = 459) and non-Indigenous (n = 117) young adults (21–27 years). The association between body size and an adverse cardio-metabolic profile (≥3 abnormal cardio-metabolic markers) is assessed by gender and urban/rural residence, employing regression analyses. The prevalence of obesity was highest among urban Indigenous participants, both males and females (22% and 23%, respectively). Overall, BMI showed a significant positive association with an adverse cardio-metabolic profile. Moreover, adverse cardio-metabolic profile was present in a substantial proportion of Indigenous participants even in overweight and normal BMI categories. Among females, this could reflect elevated waist circumference, which was present in half of those of normal weight. Remote Indigenous females had the highest predicted probability of having an adverse cardio-metabolic profile across all BMI categories (13% for underweight, 54% for normal BMI, 93% for overweight, and 99% for obese). Our findings highlight the associations between obesity and adverse cardio-metabolic profiles among Indigenous and non-Indigenous youth. Culturally-relevant strategies that address lifestyle risks, including access to healthy food, are urgently needed in this age group.
Novel Hg2+-Selective Signaling Probe Based on Resorufin Thionocarbonate and its μPAD Application
Authors: Choi Myung Gil , Park So Young , Park Ka Young , Chang Suk-Kyu 
Published: March 2019

AbstractIn this study, a novel resorufin thionocarbonate-based Hg2+-selective signaling probe (RT) for microfluidic paper-based analytical device (μPAD) applications is reported. The designed probe, RT, was readily synthesized by the one-step reaction of resorufin with phenyl thionochloroformate. The RT probe displayed a prominent color change from yellow to pink and a marked turn-on fluorescence signaling behavior exclusively toward the Hg2+ ion. The signaling of RT was due to Hg2+-induced hydrolysis of the phenyl thionocarbonate moiety to form the parent resorufin dye, which restored its spectroscopic properties. In addition, RT exhibited the Hg2+-selective signaling behavior without interference by coexisting environmentally relevant metal ions. The detection limit for Hg2+ in simulated wastewater samples was estimated to be 5.8 × 10−8 M. In particular, an RT-equipped μPAD prepared using a wax printing technique enabled simple and convenient determination of Hg2+ ions in simulated wastewater samples, with a detection limit of 5.9 × 10−6 M.
Zero-reflection acoustic metamaterial with a negative refractive index
Authors: Park Choon Mahn , Lee Sang Hun 
Published: March 2019

AbstractWaves are reflected to varying degrees at the boundary between two different media. A reduction of this reflection is important for many materials, including acoustic metamaterials. Here, we theoretically develop a balanced acoustic metamaterial that exhibits zero reflection between the metamaterial and air over its entire refractive index range, regardless of the sign of the refractive index. The metamaterial is realized using unit cell structures containing membranes and open tubes, and the material performance is verified experimentally, demonstrating sound reflectance of less than 10% in the frequency region that satisfies the homogeneous medium condition. The zero-reflection characteristic of the acoustic balanced metamaterial can improve the performance of new acoustic devices such as the invisibility cloak and super-lens and can also contribute to basic research of acoustic metamaterials.