bluuebunny/crossref_metadata_2025_split huggingface dataset:
Photoinduced hydrogen release from hydrogen boride sheets
Authors: Kawamura Reiya , Cuong Nguyen Thanh , Fujita Takeshi , Ishibiki Ryota , Hirabayashi Toru , Yamaguchi Akira , Matsuda Iwao , Okada Susumu , Kondo Takahiro , Miyauchi Masahiro 
Published: October 2019

AbstractHydrogen boride nanosheets (HB sheets) are facilely synthesized via ion-exchange treatment on magnesium diboride (MgB2) in an acetonitrile solution. Optical absorption and fluorescence spectra of HB sheets indicate that their bandgap energy is 2.8 eV. According to first-principles calculations, optical absorption seen at 2.8 eV is assigned to the electron transition between the σ-bonding states of B and H orbitals. In addition, density functional theory (DFT) calculations suggest the other allowed transition from the σ-bonding state of B and H orbitals to the antibonding state with the gap of 3.8 eV. Significant gaseous H2 release is found to occur only under photoirradiation, which causes the electron transition from the σ-bonding state to the antibonding state even under mild ambient conditions. The amount of H2 released from the irradiated HB sheets is estimated to be 8 wt%, indicating that the sheets have a high H2-storage capacity compared with previously reported metal H2-storage materials.
Unexpected large evasion fluxes of carbon dioxide from turbulent streams draining the world’s mountains
Authors: Horgby Åsa , Segatto Pier Luigi , Bertuzzo Enrico , Lauerwald Ronny , Lehner Bernhard , Ulseth Amber J. , Vennemann Torsten W. , Battin Tom J. 
Published: October 2019

AbstractInland waters, including streams and rivers, are active components of the global carbon cycle. Despite the large areal extent of the world’s mountains, the role of mountain streams for global carbon fluxes remains elusive. Using recent insights from gas exchange in turbulent streams, we found that areal CO2evasion fluxes from mountain streams equal or exceed those reported from tropical and boreal streams, typically regarded as hotspots of aquatic carbon fluxes. At the regional scale of the Swiss Alps, we present evidence that emitted CO2derives from lithogenic and biogenic sources within the catchment and delivered by the groundwater to the streams. At a global scale, we estimate the CO2evasion from mountain streams to 167 ± 1.5 Tg C yr−1, which is high given their relatively low areal contribution to the global stream and river networks. Our findings shed new light on mountain streams for global carbon fluxes.
Tankyrase inhibition preserves osteoarthritic cartilage by coordinating cartilage matrix anabolism via effects on SOX9 PARylation
Authors: Kim Sukyeong , Han Sangbin , Kim Yeongjae , Kim Hyeon-Seop , Gu Young-Ran , Kang Donghyun , Cho Yongsik , Kim Hyeonkyeong , Lee Jeeyeon , Seo Yeyoung , Chang Moon Jong , Chang Chong Bum , Kang Seung-Baik , Kim Jin-Hong 
Published: October 2019

AbstractOsteoarthritis (OA) is a prevalent degenerative disease, which involves progressive and irreversible destruction of cartilage matrix. Despite efforts to reconstruct cartilage matrix in osteoarthritic joints, it has been a difficult task as adult cartilage exhibits marginal repair capacity. Here we report the identification of tankyrase as a regulator of the cartilage anabolism axis based on systems-level factor analysis of mouse reference populations. Tankyrase inhibition drives the expression of a cartilage-signature matrisome and elicits a transcriptomic pattern that is inversely correlated with OA progression. Furthermore, tankyrase inhibitors ameliorate surgically induced OA in mice, and stem cell transplantation coupled with tankyrase knockdown results in superior regeneration of cartilage lesions. Mechanistically, the pro-regenerative features of tankyrase inhibition are mainly triggered by uncoupling SOX9 from a poly(ADP-ribosyl)ation (PARylation)-dependent protein degradation pathway. Our findings provide insights into the development of future OA therapies aimed at reconstruction of articular cartilage.
Biological process activity transformation of single cell gene expression for cross-species alignment
Authors: Ding Hongxu , Blair Andrew , Yang Ying , Stuart Joshua M. 
Published: October 2019

AbstractThe maintenance and transition of cellular states are controlled by biological processes. Here we present a gene set-based transformation of single cell RNA-Seq data into biological process activities that provides a robust description of cellular states. Moreover, as these activities represent species-independent descriptors, they facilitate the alignment of single cell states across different organisms.
Morphometrics of eight Chinese cavefish species
Authors: Lunghi Enrico , Zhao Yang , Sun Xueying , Zhao Yahui 
Published: October 2019

AbstractChinese cavefishes are a bizarre and interesting vertebrate taxa, but one with relatively little research. China holds the highest global cavefish diversity, accounting for about one-third of known species. Sinocyclocheilus is the largest genus of cavefishes in the world and is endemic to the south of China. The distribution of Sinocyclocheilus species is very narrow, and sometimes they inhabit just a single cave; this feature increases the vulnerability to extinction. With this study we provide the first comprehensive dataset related to the morphometrics of eight Sinocyclocheilus species. In addition to enhancing our knowledge on these poorly known species we aim to provide a dataset useful for future comparative analyses aiming to better understand the adaptive ability of cavefishes.
Characterization and prediction of acute and sustained response to psychedelic psilocybin in a mindfulness group retreat
Authors: Smigielski Lukasz , Kometer Michael , Scheidegger Milan , Krähenmann Rainer , Huber Theo , Vollenweider Franz X. 
Published: October 2019

AbstractMeditation and psychedelics have played key roles in humankind’s search for self-transcendence and personal change. However, neither their possible synergistic effects, nor related state and trait predictors have been experimentally studied. To elucidate these issues, we administered double-blind the model psychedelic drug psilocybin (315 μg/kg PO) or placebo to meditators (n = 39) during a 5-day mindfulness group retreat. Psilocybin increased meditation depth and incidence of positively experienced self-dissolution along the perception-hallucination continuum, without concomitant anxiety. Openness, optimism, and emotional reappraisal were predictors of the acute response. Compared with placebo, psilocybin enhanced post-intervention mindfulness and produced larger positive changes in psychosocial functioning at a 4-month follow-up, which were corroborated by external ratings, and associated with magnitude of acute self-dissolution experience. Meditation seems to enhance psilocybin’s positive effects while counteracting possible dysphoric responses. These findings highlight the interactions between non-pharmacological and pharmacological factors, and the role of emotion/attention regulation in shaping the experiential quality of psychedelic states, as well as the experience of selflessness as a modulator of behavior and attitudes. A better comprehension of mechanisms underlying most beneficial psychedelic experiences may guide therapeutic interventions across numerous mental conditions in the form of psychedelic-assisted applications.
Genomic Prediction of 16 Complex Disease Risks Including Heart Attack, Diabetes, Breast and Prostate Cancer
Authors: Lello Louis , Raben Timothy G. , Yong Soke Yuen , Tellier Laurent C. A. M. , Hsu Stephen D. H. 
Published: October 2019

AbstractWe construct risk predictors using polygenic scores (PGS) computed from common Single Nucleotide Polymorphisms (SNPs) for a number of complex disease conditions, using L1-penalized regression (also known as LASSO) on case-control data from UK Biobank. Among the disease conditions studied are Hypothyroidism, (Resistant) Hypertension, Type 1 and 2 Diabetes, Breast Cancer, Prostate Cancer, Testicular Cancer, Gallstones, Glaucoma, Gout, Atrial Fibrillation, High Cholesterol, Asthma, Basal Cell Carcinoma, Malignant Melanoma, and Heart Attack. We obtain values for the area under the receiver operating characteristic curves (AUC) in the range ~0.58–0.71 using SNP data alone. Substantially higher predictor AUCs are obtained when incorporating additional variables such as age and sex. Some SNP predictors alone are sufficient to identify outliers (e.g., in the 99th percentile of polygenic score, or PGS) with 3–8 times higher risk than typical individuals. We validate predictors out-of-sample using the eMERGE dataset, and also with different ancestry subgroups within the UK Biobank population. Our results indicate that substantial improvements in predictive power are attainable using training sets with larger case populations. We anticipate rapid improvement in genomic prediction as more case-control data become available for analysis.
Development and application of affordable SNP typing approaches to genotype Mycobacterium tuberculosis complex strains in low and high burden countries
Authors: Cancino-Muñoz Irving , Gil-Brusola Ana , Torres-Puente Manuela , Mariner-Llicer Carla , Dogba John , Akinseye Victor , Adesokan Kehinde , Kwaghe Ayi , Ejeh Francis , Cadmus Simeon , Comas Iñaki 
Published: October 2019

AbstractThe Mycobacterium tuberculosis complex (MTBC) comprises the species that causes tuberculosis (TB) which affects 10 million people every year. A robust classification of species, lineages, and sub-lineages is important to explore associations with drug resistance, epidemiological patterns or clinical outcomes. We present a rapid and easy-to-follow methodology to classify clinical TB samples into the main MTBC clades. Approaches are based on the identification of lineage and sub-lineage diagnostic SNP using a real-time PCR high resolution melting assay and classic Sanger sequencing from low-concentrated, low quality DNA. Thus, suitable for implementation in middle and low-income countries. Once we validated our molecular procedures, we characterized a total of 491 biological samples from human and cattle hosts, representing countries with different TB burden. Overall, we managed to genotype ~95% of all samples despite coming from unpurified and low-concentrated DNA. Our approach also allowed us to detect zoonotic cases in eight human samples from Nigeria. To conclude, the molecular techniques we have developed, are accurate, discriminative and reproducible. Furthermore, it costs less than other classic typing methods, resulting in an affordable alternative method in TB laboratories.
The extent, frequency and ecological functions of food wasting by parrots
Authors: Sebastián-González Esther , Hiraldo Fernando , Blanco Guillermo , Hernández-Brito Dailos , Romero-Vidal Pedro , Carrete Martina , Gómez-Llanos Eduardo , Pacífico Erica C. , Díaz-Luque José A. , Dénes Francisco V. , Tella José L. 
Published: October 2019

AbstractAnecdotic citations of food wasting have been described for parrots, but we lack a comprehensive knowledge about the extent of this behaviour, and its ecological and evolutionary implications. Here, we combine experimental and observational approaches to evaluate the spatial, temporal, typological and taxonomic extent of food wasting by parrots, to identify the ecological and evolutionary factors driving food wasting, and to assess the incidence of two ecological functions derived from food wasting, such as food facilitation to other animal species and secondary seed dispersal. We found that food wasting is a widespread behaviour found in all the studied parrot species. However, the proportion of food wasted differed among species and throughout the year. Parrots wasted more food during the non-breeding season, when they relied on exotic plants and on unripe fruits or seeds. We also recorded 86 animal species feeding on the food wasted by parrots, 27 of which potentially acted as secondary seed dispersers. Overall, our study emphasizes the universality of food wasting among parrots, and the important implications that this behaviour may have for the species involved (i.e., the parrot, the plant, the other species feeding on wasted food), and for the functioning of the whole ecosystem.
Genetic structure of Mycoplasma ovipneumoniae informs pathogen spillover dynamics between domestic and wild Caprinae in the western United States
Authors: Kamath Pauline L. , Manlove Kezia , Cassirer E. Frances , Cross Paul C. , Besser Thomas E. 
Published: October 2019

AbstractSpillover diseases have significant consequences for human and animal health, as well as wildlife conservation. We examined spillover and transmission of the pneumonia-associated bacterium Mycoplasma ovipneumoniae in domestic sheep, domestic goats, bighorn sheep, and mountain goats across the western United States using 594 isolates, collected from 1984 to 2017. Our results indicate high genetic diversity of M. ovipneumoniae strains within domestic sheep, whereas only one or a few strains tend to circulate in most populations of bighorn sheep or mountain goats. These data suggest domestic sheep are a reservoir, while the few spillovers to bighorn sheep and mountain goats can persist for extended periods. Domestic goat strains form a distinct clade from those in domestic sheep, and strains from both clades are found in bighorn sheep. The genetic structure of domestic sheep strains could not be explained by geography, whereas some strains are spatially clustered and shared among proximate bighorn sheep populations, supporting pathogen establishment and spread following spillover. These data suggest that the ability to predict M. ovipneumoniae spillover into wildlife populations may remain a challenge given the high strain diversity in domestic sheep and need for more comprehensive pathogen surveillance.
Modulating cellular cytotoxicity and phototoxicity of fluorescent organic salts through counterion pairing
Authors: Broadwater Deanna , Bates Matthew , Jayaram Mayank , Young Margaret , He Jianzhou , Raithel Austin L. , Hamann Thomas W. , Zhang Wei , Borhan Babak , Lunt Richard R. , Lunt Sophia Y. 
Published: October 2019

AbstractLight-activated theranostics offer promising opportunities for disease diagnosis, image-guided surgery, and site-specific personalized therapy. However, current fluorescent dyes are limited by low brightness, high cytotoxicity, poor tissue penetration, and unwanted side effects. To overcome these limitations, we demonstrate a platform for optoelectronic tuning, which allows independent control of the optical properties from the electronic properties of fluorescent organic salts. This is achieved through cation-anion pairing of organic salts that can modulate the frontier molecular orbital without impacting the bandgap. Optoelectronic tuning enables decoupled control over the cytotoxicity and phototoxicity of fluorescent organic salts by selective generation of mitochondrial reactive oxygen species that control cell viability. We show that through counterion pairing, organic salt nanoparticles can be tuned to be either nontoxic for enhanced imaging, or phototoxic for improved photodynamic therapy.
Adsorptive removal of mercury from water by adsorbents derived from date pits
Authors: Al-Ghouti Mohammad A. , Da’ana Dana , Abu-Dieyeh Mohammed , Khraisheh Majeda 
Published: October 2019

AbstractThe current work presented here focuses on the remediation of mercury from water using modified low-cost materials. Modified date pits, low cost, minimal pretreatment steps and locally abundant agricultural waste materials were effectively employed as an adsorbent for remediating Hg2+ from aqueous media. Physical and chemical modification were developed such as thermal roasting (RDP), sulfur (SMRDP) and silane (SIMRDP) based modifications. Results showed that maximum adsorption by RDP was at pH 6, AC and both modifications was at pH 4. Furthermore, RDP has exothermic adsorption mechanism while AC, SMRDP, and SIMRDP have endothermic. All adsorbents except SIMRDP have spontaneous adsorption process. SEM analysis showed that the surface morphology of RDP was not significantly affected by different treatments while surface of AC was affected. The investigation for good adsorbents for Hg2+ uptake from different anthropogenic sources has been carried out by many investigators worldwide towards having a safe environment. In the current study, the highest Hg2+ adsorption of SMRDP was relatively high compared to other known adsorbents.
Bases of Bacterial Sodium Channel Selectivity Among Organic Cations
Authors: Wang Yibo , Finol-Urdaneta Rocio K. , Ngo Van Anh , French Robert J. , Noskov Sergei Yu. 
Published: October 2019

AbstractHille’s (1971) seminal study of organic cation selectivity of eukaryotic voltage-gated sodium channels showed a sharp size cut-off for ion permeation, such that no ion possessing a methyl group was permeant. Using the prokaryotic channel, NaChBac, we found some similarity and two peculiar differences in the selectivity profiles for small polyatomic cations. First, we identified a diverse group of minimally permeant cations for wildtype NaChBac, ranging in sizes from ammonium to guanidinium and tetramethylammonium; and second, for both ammonium and hydrazinium, the charge-conserving selectivity filter mutation (E191D) yielded substantial increases in relative permeability (PX/PNa). The relative permeabilities varied inversely with relative Kd calculated from 1D Potential of Mean Force profiles (PMFs) for the single cations traversing the channel. Several of the cations bound more strongly than Na+, and hence appear to act as blockers, as well as charge carriers. Consistent with experimental observations, the E191D mutation had little impact on Na+ binding to the selectivity filter, but disrupted the binding of ammonium and hydrazinium, consequently facilitating ion permeation across the NaChBac-like filter. We concluded that for prokaryotic sodium channels, a fine balance among filter size, binding affinity, occupancy, and flexibility seems to contribute to observed functional differences.
Abnormally Methylated FMR1 in Absence of a Detectable Full Mutation in a U.S.A Patient Cohort Referred for Fragile X Testing
Authors: Hensel Charles H. , Vanzo Rena J. , Martin Megan M. , Ling Ling , Aliaga Solange M. , Bui Minh , Francis David I. , Twede Hope , Field Michael H. , Morison Jonathon W. , Amor David J. , Godler David E. 
Published: October 2019

AbstractIn 2016, Methylation-Specific Quantitative Melt Analysis (MS-QMA) on 3,340 male probands increased diagnostic yield from 1.60% to 1.84% for fragile X syndrome (FXS) using a pooling approach. In this study probands from Lineagen (UT, U.S.A.) of both sexes were screened using MS-QMA without sample pooling. The cohorts included: (i) 279 probands with no FXS full mutation (FM: CGG > 200) detected by AmplideX CGG sizing; (ii) 374 negative and 47 positive controls. MS-QMA sensitivity and specificity in controls approached 100% for both sexes. For male probands with no FM detected by standard testing (n = 189), MS-QMA identified abnormal DNA methylation (mDNA) in 4% normal size (NS: < 44 CGGs), 6% grey zone (CGG 45–54) and 12% premutation (CGG 54–199) alleles. The abnormal mDNA was confirmed by AmplideX methylation sensitive (m)PCR and EpiTYPER tests. In contrast, no abnormal mDNA was detected in 89 males with NS alleles from the general population. For females, 11% of 43 probands with NS alleles by the AmplideX sizing assay had abnormal mDNA by MS-QMA, with FM / NS mosaicism confirmed by AmplideX mPCR. FMR1 MS-QMA analysis can cost-effectively screen probands of both sexes for methylation and FM mosaicism that may be missed by standard testing.
Clostridium difficile clade 3 (RT023) have a modified cell surface and contain a large transposable island with novel cargo
Authors: Shaw Helen Alexandra , Khodadoost Ladan , Preston Mark D. , Corver Jeroen , Mullany Peter , Wren Brendan W. 
Published: October 2019

AbstractThe major global pathogen Clostridium difficile (recently renamed Clostridioides difficile) has large genetic diversity including multiple mobile genetic elements. In this study, whole genome sequencing of 86 strains from the poorly characterised clade 3, predominantly PCR ribotype (RT)023, of C. difficile revealed distinctive surface architecture characteristics and a large mobile genetic island. These strains have a unique sortase substrate phenotype compared with well-characterised strains of C. difficile, and loss of the phage protection protein CwpV. A large genetic insertion (023_CTnT) comprised of three smaller elements (023_CTn1-3) is present in 80/86 strains analysed in this study, with genes common among other bacterial strains in the gut microbiome. Novel cargo regions of 023_CTnT include genes encoding a sortase, putative sortase substrates, lantibiotic ABC transporters and a putative siderophore biosynthetic cluster. We demonstrate the excision of 023_CTnT and sub-elements 023_CTn2 and 023_CTn3 from the genome of RT023 reference strain CD305 and the transfer of 023_CTn3 to a non-toxigenic C. difficile strain, which may have implications for the use of non-toxigenic C. difficile strains as live attenuated vaccines. Finally, we show that the genes within the island are expressed in a regulated manner in C. difficile RT023 strains conferring a distinct “niche adaptation”.
Sex determination using circulating cell-free fetal DNA in small volume of maternal plasma in elephants
Authors: Vincze Boglárka , Gáspárdy András , Biácsi Alexandra , Papp Endre Ákos , Garamvölgyi László , Sós Endre , Cseh Sándor , Kovács Gábor , Pádár Zsolt , Zenke Petra 
Published: October 2019

AbstractThe genetic sexing of animals having long gestation periods offers significant benefits in regard to breeding management among their populations living in captivity. In our study, a new increased-sensitivity PCR method for fetal sexing was developed and tested successfully on elephants, from only a small volume of maternal plasma. Suitable sensitivity was obtained by using short, reduced amplicon lengths with fluorescent labelling for capillary electrophoresis detection. The fundamental principle for this technique was based on the detection of two Y-specific markers (AmelYandSRY), the presence of which indicates the mother is carrying a male fetus and the absence of these markers designates a female fetus. As a reaction control, the X-chromosomal marker (PlpX) was used. To the best of our knowledge, this is the first report on this topic, confirming the presence of fetal cell-free DNA from the plasma of a pregnant captive elephant, and demonstrating a new opportunity for non-invasive assessment in fetal sex determination.
Complex interactions between sperm viability and female fertility
Authors: Tourmente Maximiliano , Archer C. Ruth , Hosken David J. 
Published: October 2019

AbstractSperm viability is a major male fitness component, with higher sperm viability associated with enhanced sperm competitiveness. While many studies have focussed on sperm viability from the male fitness standpoint, its impact on female fitness is less clear. Here we used a panel of 32 isogenic Drosophila simulans lines to test for genetic variation in sperm viability (percentage of viable cells). We then tested whether sperm viability affected female fitness by mating females to males from low or high sperm viability genotypes. We found significant variation in sperm viability among genotypes, and consistent with this, sperm viability was highly repeatable within genotypes. Additionally, females mated to high sperm viability males laid more eggs in the first seven hours after mating, and produced more offspring in total. However, the early increase in oviposition did not result in more offspring in the 8 hours following mating, suggesting that mating with high sperm-viability genotypes leads to egg wastage for females shortly after copulation. Although mating with high sperm-viability males resulted in higher female fitness in the long term, high quality ejaculates would result in a short-term female fitness penalty, or at least lower realised fitness, potentially generating sexual conflict over optimal sperm viability.