bluuebunny/crossref_metadata_2025_split huggingface dataset:
The thermoacidophilic methanotroph Methylacidiphilum fumariolicum SolV oxidizes subatmospheric H2 with a high-affinity, membrane-associated [NiFe] hydrogenase
Authors: Schmitz Rob A , Pol Arjan , Mohammadi Sepehr S , Hogendoorn Carmen , van Gelder Antonie H , Jetten Mike S M , Daumann Lena J , Op den Camp Huub J M 
Published: February 2020

Abstract
The trace amounts (0.53 ppmv) of atmospheric hydrogen gas (H2) can be utilized by microorganisms to persist during dormancy. This process is catalyzed by certain Actinobacteria, Acidobacteria, and Chloroflexi, and is estimated to convert 75 × 1012 g H2 annually, which is half of the total atmospheric H2. This rapid atmospheric H2 turnover is hypothesized to be catalyzed by high-affinity [NiFe] hydrogenases. However, apparent high-affinity H2 oxidation has only been shown in whole cells, rather than for the purified enzyme. Here, we show that the membrane-associated hydrogenase from the thermoacidophilic methanotroph Methylacidiphilum fumariolicum SolV possesses a high apparent affinity (Km(app) = 140 nM) for H2 and that methanotrophs can oxidize subatmospheric H2. Our findings add to the evidence that the group 1h [NiFe] hydrogenase is accountable for atmospheric H2 oxidation and that it therefore could be a strong controlling factor in the global H2 cycle. We show that the isolated enzyme possesses a lower affinity (Km = 300 nM) for H2 than the membrane-associated enzyme. Hence, the membrane association seems essential for a high affinity for H2. The enzyme is extremely thermostable and remains folded up to 95 °C. Strain SolV is the only known organism in which the group 1h [NiFe] hydrogenase is responsible for rapid growth on H2 as sole energy source as well as oxidation of subatmospheric H2. The ability to conserve energy from H2 could increase fitness of verrucomicrobial methanotrophs in geothermal ecosystems with varying CH4 fluxes. We propose that H2 oxidation can enhance growth of methanotrophs in aerated methane-driven ecosystems. Group 1h [NiFe] hydrogenases could therefore contribute to mitigation of global warming, since CH4 is an important and extremely potent greenhouse gas.
Neurology-related protein biomarkers are associated with cognitive ability and brain volume in older age
Authors: Harris Sarah E. , Cox Simon R. , Bell Steven , Marioni Riccardo E. , Prins Bram P. , Pattie Alison , Corley Janie , Muñoz Maniega Susana , Valdés Hernández Maria , Morris Zoe , John Sally , Bronson Paola G. , Tucker-Drob Elliot M. , Starr John M. , Bastin Mark E. , Wardlaw Joanna M. , Butterworth Adam S. , Deary Ian J. 
Published: February 2020

AbstractIdentifying biological correlates of late life cognitive function is important if we are to ascertain biomarkers for, and develop treatments to help reduce, age-related cognitive decline. Here, we investigated the associations between plasma levels of 90 neurology-related proteins (Olink® Proteomics) and general fluid cognitive ability in the Lothian Birth Cohort 1936 (LBC1936, N = 798), Lothian Birth Cohort 1921 (LBC1921, N = 165), and the INTERVAL BioResource (N = 4451). In the LBC1936, 22 of the proteins were significantly associated with general fluid cognitive ability (β between −0.11 and −0.17). MRI-assessed total brain volume partially mediated the association between 10 of these proteins and general fluid cognitive ability. In an age-matched subsample of INTERVAL, effect sizes for the 22 proteins, although smaller, were all in the same direction as in LBC1936. Plasma levels of a number of neurology-related proteins are associated with general fluid cognitive ability in later life, mediated by brain volume in some cases.
Single-cell RNA-sequencing of differentiating iPS cells reveals dynamic genetic effects on gene expression
Authors: Cuomo Anna S. E. , Seaton Daniel D. , McCarthy Davis J. , Martinez Iker , Bonder Marc Jan , Garcia-Bernardo Jose , Amatya Shradha , Madrigal Pedro , Isaacson Abigail , Buettner Florian , Knights Andrew , Natarajan Kedar Nath ,   HipSci Consortium, Agu Chukwuma A. , Alderton Alex , Danecek Petr , Denton Rachel , Durbin Richard , Gaffney Daniel J. , Goncalves Angela , Halai Reena , Harper Sarah , Kirton Christopher M. , Kolb-Kokocinski Anja , Leha Andreas , McCarthy Shane A. , Memari Yasin , Patel Minal , Birney Ewan , Casale Francesco Paolo , Clarke Laura , Harrison Peter W. , Kilpinen Helena , Streeter Ian , Denovi Davide , Meleckyte Ruta , Moens Natalie , Watt Fiona M. , Ouwehand Willem H. , Lamond Angus I. , Bensaddek Dalila , Beales Philip , Vallier Ludovic , Marioni John C. , Chhatriwala Mariya , Stegle Oliver 
Published: February 2020

AbstractRecent developments in stem cell biology have enabled the study of cell fate decisions in early human development that are impossible to study in vivo. However, understanding how development varies across individuals and, in particular, the influence of common genetic variants during this process has not been characterised. Here, we exploit human iPS cell lines from 125 donors, a pooled experimental design, and single-cell RNA-sequencing to study population variation of endoderm differentiation. We identify molecular markers that are predictive of differentiation efficiency of individual lines, and utilise heterogeneity in the genetic background across individuals to map hundreds of expression quantitative trait loci that influence expression dynamically during differentiation and across cellular contexts.
Temporal dynamics of protein complex formation and dissociation during human cytomegalovirus infection
Authors: Hashimoto Yutaka , Sheng Xinlei , Murray-Nerger Laura A. , Cristea Ileana M. 
Published: February 2020

AbstractThe co-evolution and co-existence of viral pathogens with their hosts for millions of years is reflected in dynamic virus-host protein-protein interactions (PPIs) that are intrinsic to the spread of infections. Here, we investigate the system-wide dynamics of protein complexes throughout infection with the herpesvirus, human cytomegalovirus (HCMV). Integrating thermal shift assays and mass spectrometry quantification with virology and microscopy, we monitor the temporal formation and dissociation of hundreds of functional protein complexes and the dynamics of host-host, virus-host, and virus-virus PPIs. We establish pro-viral roles for cellular protein complexes and translocating proteins. We show the HCMV receptor integrin beta 1 dissociates from extracellular matrix proteins, becoming internalized with CD63, which is necessary for virus production. Moreover, this approach facilitates characterization of essential viral proteins, such as pUL52. This study of temporal protein complex dynamics provides insights into mechanisms of HCMV infection and a resource for biological and therapeutic studies.
H3K4 methylation at active genes mitigates transcription-replication conflicts during replication stress
Authors: Chong Shin Yen , Cutler Sam , Lin Jing-Jer , Tsai Cheng-Hung , Tsai Huai-Kuang , Biggins Sue , Tsukiyama Toshio , Lo Yi-Chen , Kao Cheng-Fu 
Published: February 2020

AbstractTranscription-replication conflicts (TRCs) occur when intensive transcriptional activity compromises replication fork stability, potentially leading to gene mutations. Transcription-deposited H3K4 methylation (H3K4me) is associated with regions that are susceptible to TRCs; however, the interplay between H3K4me and TRCs is unknown. Here we show that H3K4me aggravates TRC-induced replication failure in checkpoint-defective cells, and the presence of methylated H3K4 slows down ongoing replication. Both S-phase checkpoint activity and H3K4me are crucial for faithful DNA synthesis under replication stress, especially in highly transcribed regions where the presence of H3K4me is highest and TRCs most often occur. H3K4me mitigates TRCs by decelerating ongoing replication, analogous to how speed bumps slow down cars. These findings establish the concept that H3K4me defines the transcriptional status of a genomic region and defends the genome from TRC-mediated replication stress and instability.
The Immobilization of Soil Cadmium by the Combined Amendment of Bacteria and Hydroxyapatite
Authors: Zeng Xiaoxi , Xu Hong , Lu Jijie , Chen Qimin , Li Wen , Wu Ling , Tang Jianxin , Ma Liang 
Published: February 2020

AbstractThe remediation of heavy metal-contaminated soils has attracted increased attention worldwide. The immobilization of metals to prevent their uptake by plants is an efficient way to remediate contaminated soils. This work aimed to seek the immobilization of cadmium in contaminated soils via a combination method. Flask experiments were performed to investigate the effects of hydroxyapatite (HAP) and theCupriavidussp. strain ZSK on soil pH and DTPA-extractable cadmium. Pot experiments were carried out to study the effects of the combined amendment on three plant species. The results showed that HAP has no obvious influence on the growth of the strain. With increasing concentrations of HAP, the soil pH increased, and the DTPA-extractable Cd decreased. Via the combined amendment of the strain and HAP (SH), the DTPA-extractable Cd in the soil decreased by 58.2%. With the combined amendment of the SH, the cadmium accumulation in ramie, dandelion, and daisy decreased by 44.9%, 51.0%, and 38.7%, respectively. Moreover, the combined amendment somewhat benefitted the growth of the three plant species and significantly decreased the biosorption of cadmium. These results suggest that the immobilization by the SH combination is a potential method to decrease the available cadmium in the soil and the cadmium accumulation in plants.
Long-term dynamic topographic support during post-orogenic crustal thinning revealed by stable isotope (δ18O) paleo-altimetry in eastern Pyrenees
Authors: Huyghe Damien , Mouthereau Frédéric , Ségalen Loïc , Furió Marc 
Published: February 2020

AbstractUnderstanding the geodynamic and Earth surface processes at the origin of post-collisional surface uplift in mountain ranges requires reconstruction of paleo-elevation. Here, we focus on the topographic evolution of the Cerdanya Basin in the eastern Pyrenees formed by post-orogenic extension during the Late Miocene. Stable isotope (δ18O) analyses of small rodent teeth and biogenic carbonates show the basin uplifted by 500 m since 6.5 Ma. These new paleoaltitudes constraints when combined with the regional geology and geophysical data reveal the anomalously high topography of the region is the result of density changes in the sublithospheric mantle associated with crustal thinning and then opening of Gulf of Lion during the Chattian-early Burdigalian.
Subclinical hypothyroidism and anxiety may contribute to metabolic syndrome in Sichuan of China: a hospital-based population study
Authors: Li Rui-cen , Zhang Lingyun , Luo Han , Lei Yali , Zeng Li , Zhu Jingqiang , Tang Huairong 
Published: February 2020

AbstractThe prevalence of Metabolic syndrome (MetS) in Sichuan of China has not yet been estimated. Meanwhile the association among anxiety, subclinical hypothyroidism (SCH) and MetS was less well-studied. The data was retrieved retrospectively from Health Promotion Center of West China Hospital database between 2014 and 2017. Internal validation by randomizing into training and testing panel by 9:1 and external validation with National Health and Nutrition Examination Survey (NHNES) were conducted. 19006 subjects were included into analysis, and 3530 (18.6%) of them were diagnosed with MetS. In training panel, age, sex (male), SCH (presence), SAS score, alcohol (Sometimes & Usual) and smoking (Active) were identified as independent risk factors for MetS, which was confirmed in testing panel internally. NHNES data validated externally the association between free thyroxine (fT4) and MetS components. The C-indices of predicting MetS nomogram were 0.705 (95% CI: 0.696–0.714) and 0.728 (95% CI: 0.701–0.754) in training and testing panel respectively. In conclusion, MetS prevalence was 18.6% in Sichuan. SCH and anxiety may be associated with MetS independently. A risk scale-based nomogram with accurate and objective prediction ability was provided for check-up practice, but more cohort validation was needed.
Anthropometry, body shape in early-life and risk of premenopausal breast cancer among Latin American women: results from the PRECAMA study
Authors: His Mathilde , Biessy Carine , Torres-Mejía Gabriela , Ángeles-Llerenas Angélica , Alvarado-Cabrero Isabel , Sánchez Gloria Inés , Borrero Mauricio , Porras Carolina , Rodriguez Ana Cecilia , Garmendia Maria Luisa , Olivier Magali , Porter Peggy L. , Lin MingGang , Gunter Marc J. , Romieu Isabelle , Rinaldi Sabina ,   PRECAMA team, Tejeda Jenny , Navarro Edgar , Jaramillo Roberto , Rodas Cortes Yorlany , Angel Alberto , Ossa Carlos Andres , Arias William H. , Bedoya Gabriel , Cock-Rada Alicia Maria , Echeverri Carolina , Herazo Fernando , Díaz-Yunez Israel , Hernández Angel , Cortes Bernal , Gonzalez Paula , Ocampo Rebecca , Guillen Diego , Moyano Leonor , Soto Jose Luis , Donato Elizabeth , Guenthoer Jamie , Donn Thomas , Wirtala Kelly , Loucks Hailey 
Published: February 2020

AbstractCumulating evidence in Caucasian women suggests a positive association between height and premenopausal breast cancer risk and a negative association with overall adiposity; however data from Latin America are scarce. We investigated the associations between excess adiposity, body shape evolution across life, and risk of premenopausal breast cancer among 406 cases (women aged 20–45) and 406 matched population-based controls from Chile, Colombia, Costa Rica, and Mexico. Negative associations between adult adiposity and breast cancer risk were observed in adjusted models (body mass index (BMI): Odds ratio (OR) per 1 kg/m2 = 0.93; 95% confidence interval = 0.89–0.96; waist circumference (WC): OR per 10 cm = 0.81 (0.69–0.96); hip circumference (HC): OR per 10 cm = 0.80 (0.67–0.95)). Height and leg length were not associated with risk. In normal weight women (18.5 ≤ BMI < 25), women with central obesity (WC > 88 cm) had an increased risk compared to women with normal WC (OR = 3.60(1.47–8.79)). Residuals of WC over BMI showed positive associations when adjusted for BMI (OR per 10 cm = 1.38 (0.98–1.94)). Body shape at younger ages and body shape evolution were not associated with risk. No heterogeneity was observed by receptor status. In this population of Latin American premenopausal women, different fat distributions in adulthood were differentially associated with risk of breast cancer.
Direct light-induced propulsion of vessels filled with a suspension of graphene particles and methanol
Authors: Strek W. , Wiewiorski P. , Mista W. , Tomala R. 
Published: February 2020

AbstractThe direct propulsion of glassy capsule filled with solution of methanol and disperse graphene foam (GF) particles under irradiation with infrared LED is reported. The vertical propulsion occurred after irradiation of transparent glassy bottom. The velocity of propulsion was dependent of light irradiation power. It was observed that with irradiation the GF particles moved violently and vertically with direction of lighting. It was found that upon light irradiation there is generated efficiently hydrogen upon solution surface. The mechanism of propulsion effect was discussed in terms of the explosive hydrogen-oxygen reaction.
Spin Hydrodynamic Generation in the Charged Subatomic Swirl
Authors: Guo Xingyu , Liao Jinfeng , Wang Enke 
Published: February 2020

AbstractRecently there have been significant interests in the spin hydrodynamic generation phenomenon from multiple disciplines of physics. Such phenomenon arises from global polarization effect of microscopic spin by macroscopic fluid rotation and is expected to occur in the hot quark-gluon fluid (the “subatomic swirl”) created in relativistic nuclear collisions. This was indeed discovered in experiments which however revealed an intriguing puzzle: a polarization difference between particles and anti-particles. We suggest a novel application of a general connection between rotation and magnetic field: a magnetic field naturally arises along the fluid vorticity in the charged subatomic swirl. We establish this mechanism as a new way for generating long-lived in-medium magnetic field in heavy ion collisions. Due to its novel feature, this new magnetic field provides a nontrivial explanation to the puzzling observation of a difference in spin hydrodynamic generation for particles and anti-particles in heavy ion collisions.
Genotype-independent association between vitamin D deficiency and polycystic ovarian syndrome in Lahore, Pakistan
Authors: Lone Nasira M. , Riaz Saba , Eusaph Amna Z. , Mein Charles A. , Wozniak Eva L. , Xenakis Theodoros , Wu Zhenqiang , Younis Sidra , Jolliffe David A. , Junaid Kashaf , Martineau Adrian R. 
Published: February 2020

AbstractBoth vitamin D deficiency and single nucleotide polymorphisms (SNPs) in the gene encoding the vitamin D receptor (VDR) have been widely reported to associate with susceptibility to polycystic ovarian syndrome (PCOS). A case-control study was conducted to study the influence of vitamin D status and genotpye for 24 SNPs in four genes in the vitamin D pathway (VDR, DBP, CYP27B1, CYP24A1) on PCOS. Statistical analyses were conducted to identify phenotypic and genotypic factors associated with risk of PCOS and to test for interactions between genotype and vitamin D status. PCOS was independently associated with lower age, higher body mass index, lower waist-hip ratio, vitamin D deficiency (serum 25-hydroxyvitamin D concentration <10 ng/mL), lack of outdoor exercise, increased fasting glucose and a family history of PCOS in at least one first degree relative. No statistically significant association was observed between the genotype of any SNP investigated and risk of PCOS, either as a main effect or in interaction with vitamin D status. We report a strong and independent association between vitamin D deficiency and risk of PCOS in Pakistan, that was not modified by genetic variation in the vitamin D pathway.
Regulation of bone metabolism by megakaryocytes in a paracrine manner
Authors: Lee Young-Sun , Kwak Mi Kyung , Moon Sung-Ah , Choi Young Jin , Baek Ji Eun , Park Suk Young , Kim Beom-Jun , Lee Seung Hun , Koh Jung-Min 
Published: February 2020

AbstractMegakaryocytes (MKs) play key roles in regulating bone metabolism. To test the roles of MK-secreted factors, we investigated whether MK and promegakaryocyte (pro-MK) conditioned media (CM) may affect bone formation and resorption. K562 cell lines were differentiated into mature MKs. Mouse bone marrow macrophages were differentiated into mature osteoclasts, and MC3T3-E1 cells were used for osteoblastic experiments. Bone formation was determined by a calvaria bone formation assayin vivo. Micro-CT analyses were performed in the femurs of ovariectomized female C57B/L6 and Balb/c nude mice after intravenous injections of MK or pro-MK CM. MK CM significantly reducedin vitrobone resorption, largely due to suppressed osteoclastic resorption activity. Compared with pro-MK CM, MK CM suppressed osteoblastic differentiation, but stimulated its proliferation, resulting in stimulation of calvaria bone formation. In ovariectomized mice, treatment with MK CM for 4 weeks significantly increased trabecular bone mass parameters, such as bone volume fraction and trabecular thickness, in nude mice, but not in C57B/L6 mice. In conclusion, MKs may secrete anti-resorptive and anabolic factors that affect bone tissue, providing a novel insight linking MKs and bone cells in a paracrine manner. New therapeutic agents against metabolic bone diseases may be developed from MK-secreted factors.
Coherent Mid-IR Supercontinuum Generation using Tapered Chalcogenide Step-Index Optical Fiber: Experiment and modelling
Authors: Saini Than Singh , Tuan Tong Hoang , Suzuki Takenobu , Ohishi Yasutake 
Published: February 2020

AbstractMid-infrared region of electromagnetic spectrum has increased a lot of scientific and technical interest because of its utility to figure out the molecular fingerprints. Current mid-infrared light sources including quantum cascade lasers, thermal-emitters, and synchrotron radiation are not suitable for various potential applications where we require coherent, portable and broadband light sources. During the current decade, several efforts have been put forwarded to extend the spectral range of the supercontinuum. However, the coherent mid-infrared supercontinuum spectrum in the mid-infrared region has been demonstrated rarely. Here, we demonstrate a coherent mid-infrared supercontinuum using a tapered chalcogenide fiber pumped at various wavelength ranging from 2 µm to 2.6 µm. Experimental observations show that the supercontinuum spectrum extending from ~1.6 µm to 3.7 µm can be achieved using a 3 cm long tapered chalcogenide step-index optical fiber pumped with femtosecond laser pulses at 2.6 µm. To the best of our knowledge, using short pump wavelengths at 2 µm to 2.6 µm in an all-normal dispersion engineered chalcogenide glass fiber, the coherent supercontinuum spectrum has been reported first time. Such coherent broadband light source has its key prominence for the various prospective applications in the fields of bio-medical, sensing, and multiplex coherent anti-Stokes Raman scattering microspectroscopy.
Three-layer heterogeneous mammographic phantoms for Monte Carlo simulation of normalized glandular dose coefficients in mammography
Authors: Chang Tien-Yu , Lai Kuan-Jen , Tu Chun-Yuan , Wu Jay 
Published: February 2020

AbstractNormalized glandular dose (DgN) coefficients obtained using homogeneous breast phantoms are commonly used in breast dosimetry for mammography. However, glandular tissue is heterogeneously distributed in the breast. This study aimed to construct three-layer heterogeneous mammographic phantoms (THEPs) to examine the effect of glandular distribution on DgN coefficient. Each layer of THEPs was set to 25%, 50%, or 75% glandular fraction to emulate heterogeneous glandular distribution. Monte Carlo simulation was performed to attain mean glandular dose (MGD) and air kerma at 22–36 kVp and W/Al, W/Rh, and W/Ag target–filter combinations. The heterogeneous DgN coefficient was calculated as functions of the mean glandular fraction (MGF), breast thickness, tube voltage, and half-value layer. At 50% MGF, the heterogeneous DgN coefficients for W/Al, W/Rh, and W/Ag differed by 40.3%, 36.7%, and 31.2%. At 9-cm breast thickness, the DgN values of superior and inferior glandular distributions were 25.4% higher and 29.2% lower than those of uniform distribution. The proposed THEPs can be integrated with conventional breast dosimetry to consider the heterogeneous glandular distribution in clinical practice.