bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Prototype Antibody-based Biosensor for Measurement of Salivary MMP-8 in Periodontitis using Surface Acoustic Wave Technology
Authors: Taylor John J. , Jaedicke Katrin M. , van de Merwe Rachel C. , Bissett Susan M. , Landsdowne Nichola , Whall Kerry M. , Pickering Kimberley , Thornton Vivienne , Lawson Victoria , Yatsuda Hiromi , Kogai Takashi , Shah Deepan , Athey Dale , Preshaw Philip M. 
Published: July 2019

AbstractPeriodontitis is an economically important disease which is highly prevalent worldwide. Current diagnostic approaches are time-consuming and require interpretation of multiple aspects of clinical and radiographic assessment. Chair-side monitoring of inflammatory mediators of periodontitis could provide immediate information about disease activity, which can inform patient management. We aimed to develop a novel prototype biosensor to measure salivary matrix metalloproteinase-8 (MMP-8) using specific antibodies and surface acoustic wave (SAW) technology. The analytical performance of the prototype biosensor was compared to standard enzyme-linked immunosorbent assay (ELISA) using unstimulated saliva samples obtained from patients with periodontitis before and after non-surgical treatment (N = 58), patients with gingivitis (N = 54) and periodontally healthy volunteers (N = 65). Receiver operator characteristic (ROC) analysis for distinguishing periodontitis from health revealed an almost identical performance between the sensor and ELISA assays (area under curve values (AUC): ELISA 0.93; SAW 0.89). Furthermore, both analytical approaches yielded readouts which distinguished between heath, gingivitis and periodontitis, correlated identically with clinical measures of periodontal disease and recorded similar post-treatment decreases in salivary MMP-8 in periodontitis. The assay time for our prototype device is 20 minutes. The prototype SAW biosensor is a novel and rapid method of monitoring periodontitis which delivers similar analytical performance to conventional laboratory assays.
A principled strategy for mapping enhancers to genes
Authors: Kim Dongkyeong , An Hongjoo , Shearer Randall S. , Sharif Mohamed , Fan Chuandong , Choi Jin-ok , Ryu Sun , Park Yungki 
Published: July 2019

AbstractMapping enhancers to genes is a fundamental goal of modern biology. We have developed an innovative strategy that maps enhancers to genes in a principled manner. We illustrate its power by applying it toMyrf. Despite being a master regulator of oligodendrocytes, oligodendrocyte enhancers governingMyrfexpression remain elusive. Since chromatin conformation capture studies have shown that a gene and its enhancer tend to be found in the same topologically associating domain (TAD), we started with the delineation of theMyrfTAD. A genome-wide map of putative oligodendrocyte enhancers uncovered 6 putative oligodendrocyte enhancers in theMyrfTAD, narrowing down the search space forMyrfenhancers from the entire genome to 6 loci in a principled manner. Epigenome editing experiments revealed that two of them governMyrfexpression for oligodendrocyte development. Our new method is simple, principled, and powerful, providing a systematic way to find enhancers that regulate the expression of a gene of interest. Since it can be applied to most cell types, it would greatly facilitate our effort to unravel transcriptional regulatory networks of diverse cell types.
Neutralized chimeric DNA probe for the improvement of GC-rich RNA detection specificity on the nanowire field-effect transistor
Authors: Chou Wei-Cheng , Hu Wen-Pin , Yang Yuh-Shyong , Chan Hardy Wai-Hong , Chen Wen-Yih 
Published: July 2019

AbstractSilicon nanowire (SiNW) field-effect transistors (FETs) is a powerful tool in genetic molecule analysis because of their high sensitivity, short detection time, and label-free detection. In nucleic acid detection, GC-rich nucleic acid sequences form self- and cross-dimers and stem-loop structures, which can easily obtain data containing signals from nonspecific DNA binding. The features of GC-rich nucleic acid sequences cause inaccuracies in nucleic acid detection and hinder the development of precision medicine. To improve the inaccurate detection results, we used phosphate-methylated (neutral) nucleotides to synthesize the neutralized chimeric DNA oligomer probe. The probe fragment originated from a primer for the detection of hepatitis C virus (HCV) genotype 3b, and single-mismatched and perfect-matched targets were designed for single nucleotide polymorphisms (SNP) detection on the SiNW FET device. Experimental results revealed that the HCV-3b chimeric neutralized DNA (nDNA) probe exhibited better performance for SNP discrimination in 10 mM bis-tris propane buffer at 25 °C than a regular DNA probe. The SNP discrimination of the nDNA probe could be further improved at 40 °C on the FET device. Consequently, the neutralized chimeric DNA probe could successfully distinguish SNP in the detection of GC-rich target sequences under optimal operating conditions on the SiNW FET device.
An upper bound for the background rate of human extinction
Authors: Snyder-Beattie Andrew E. , Ord Toby , Bonsall Michael B. 
Published: July 2019

AbstractWe evaluate the total probability of human extinction from naturally occurring processes. Such processes include risks that are well characterized such as asteroid impacts and supervolcanic eruptions, as well as risks that remain unknown. Using only the information that Homo sapiens has existed at least 200,000 years, we conclude that the probability that humanity goes extinct from natural causes in any given year is almost guaranteed to be less than one in 14,000, and likely to be less than one in 87,000. Using the longer track record of survival for our entire genus Homo produces even tighter bounds, with an annual probability of natural extinction likely below one in 870,000. These bounds are unlikely to be affected by possible survivorship bias in the data, and are consistent with mammalian extinction rates, typical hominin species lifespans, the frequency of well-characterized risks, and the frequency of mass extinctions. No similar guarantee can be made for risks that our ancestors did not face, such as anthropogenic climate change or nuclear/biological warfare.
Inhibition of the Akt1-mTORC1 Axis Alters Venous Remodeling to Improve Arteriovenous Fistula Patency
Authors: Guo Xiangjiang , Fereydooni Arash , Isaji Toshihiko , Gorecka Jolanta , Liu Shirley , Hu Haidi , Ono Shun , Alozie Michelle , Lee Shin Rong , Taniguchi Ryosuke , Yatsula Bogdan , Nassiri Naiem , Zhang Lan , Dardik Alan 
Published: July 2019

AbstractArteriovenous fistulae (AVF) are the most common access created for hemodialysis, but up to 60% do not sustain dialysis within a year, suggesting a need to improve AVF maturation and patency. In a mouse AVF model, Akt1 regulates fistula wall thickness and diameter. We hypothesized that inhibition of the Akt1-mTORC1 axis alters venous remodeling to improve AVF patency. Daily intraperitoneal injections of rapamycin reduced AVF wall thickness with no change in diameter. Rapamycin decreased smooth muscle cell (SMC) and macrophage proliferation; rapamycin also reduced both M1 and M2 type macrophages. AVF in mice treated with rapamycin had reduced Akt1 and mTORC1 but not mTORC2 phosphorylation. Depletion of macrophages with clodronate-containing liposomes was also associated with reduced AVF wall thickness and both M1- and M2-type macrophages; however, AVF patency was reduced. Rapamycin was associated with improved long-term patency, enhanced early AVF remodeling and sustained reduction of SMC proliferation. These results suggest that rapamycin improves AVF patency by reducing early inflammation and wall thickening while attenuating the Akt1-mTORC1 signaling pathway in SMC and macrophages. Macrophages are associated with AVF wall thickening and M2-type macrophages may play a mechanistic role in AVF maturation. Rapamycin is a potential translational strategy to improve AVF patency.
A protein-RNA interaction atlas of the ribosome biogenesis factor AATF
Authors: Kaiser Rainer W. J. , Ignarski Michael , Van Nostrand Eric L. , Frese Christian K. , Jain Manaswita , Cukoski Sadrija , Heinen Heide , Schaechter Melanie , Seufert Lisa , Bunte Konstantin , Frommolt Peter , Keller Patrick , Helm Mark , Bohl Katrin , Höhne Martin , Schermer Bernhard , Benzing Thomas , Höpker Katja , Dieterich Christoph , Yeo Gene W. , Müller Roman-Ulrich , Fabretti Francesca 
Published: July 2019

AbstractAATF is a central regulator of the cellular outcome upon p53 activation, a finding that has primarily been attributed to its function as a transcription factor. Recent data showed that AATF is essential for ribosome biogenesis and plays a role in rRNA maturation. AATF has been implicated to fulfil this role through direct interaction with rRNA and was identified in several RNA-interactome capture experiments. Here, we provide a first comprehensive analysis of the RNA bound by AATF using CLIP-sequencing. Interestingly, this approach shows predominant binding of the 45S pre-ribosomal RNA precursor molecules. Furthermore, AATF binds to mRNAs encoding for ribosome biogenesis factors as well as snoRNAs. These findings are complemented by an in-depth analysis of the protein interactome of AATF containing a large set of proteins known to play a role in rRNA maturation with an emphasis on the protein-RNA-complexes known to be required for the generation of the small ribosomal subunit (SSU). In line with this finding, the binding sites of AATF within the 45S rRNA precursor localize in close proximity to the SSU cleavage sites. Consequently, our multilayer analysis of the protein-RNA interactome of AATF reveals this protein to be an important hub for protein and RNA interactions involved in ribosome biogenesis.
Comparison of five glomerular filtration rate estimating equations as predictors of acute kidney injury after cardiovascular surgery
Authors: Jo Jun-Young , Ryu Seung Ah , Kim Jong-Il , Lee Eun-Ho , Choi In-Cheol 
Published: July 2019

AbstractWe aimed to compare the ability of preoperative estimated glomerular filtration rate (eGFR), calculated using five different equations, to predict adverse renal outcomes after cardiovascular surgery. Cohorts of 4,125 adult patients undergoing elective cardiovascular surgery were evaluated. Preoperative eGFR was calculated using the Cockcroft-Gault, Modification of Diet in Renal Disease (MDRD) II, re-expressed MDRD II, Chronic Kidney Disease Epidemiology Collaboration, and Mayo quadratic (Mayo) equations. The primary outcome was postoperative acute kidney injury (AKI), defined by Kidney Disease: Improving Global Outcomes Definition and Staging criteria based on changes in serum creatinine concentrations within 7 days. The MDRD II and Cockcroft-Gault equations yielded the highest (88.1 ± 26.7 ml/min/1.73 m2) and lowest (79.6 ± 25.5 ml/min/1.73 m2) mean eGFR values, respectively. Multivariable analysis showed that a preoperative decrease in renal function according to all five equations was independently associated with an increased risk of postoperative AKI. The area under the receiver operating characteristics curve for predicting postoperative AKI was highest for the Mayo equation (0.713). Net improvements in reclassification and integrated discrimination were higher for the Mayo equation than for the other equations. The Mayo equation was the most accurate in predicting postoperative AKI in patients undergoing cardiovascular surgery.
Proton-free electron-trapping feature of titanium dioxide nanoparticles without the characteristic blue color
Authors: Yan Yan , Shi Weidong , Peng Wei , Lin Yuhan , Zhang Chunxi , Li Lailai , Sun Young , Ju Huanxin , Zhu Junfa , Ma Wanhong , Zhao Jincai 
Published: July 2019

AbstractMost solar-energy conversion applications are based on trapping and transferring photoinduced electrons on oxide semiconductor nanoparticles, such as titanium dioxide, and broad UV-vis absorption (400~800 nm) and monotonic IR absorption (1100~3000 cm−1) signals have long been considered signatures of the electron-trapping state on titanium dioxide nanoparticles. Here we show that, under proton-free conditions and using iodide ions in acetonitrile as the hole scavenger, the intrinsic electron-trapping feature of titanium dioxide nanoparticles does not exhibit the characteristic UV-vis absorption and infrared absorption signatures. Further electron spin resonance studies identify the proton-free electron-trapping state as the lattice octahedral Ti6c3+ species, differing from the traditional proton-participating surface tetrahedral Ti4c3+ species. Synchronized radiation ultraviolet photoelectron spectroscopy results also show that the internal electron-trapping state without protons has a larger Ti3d binding energy (1.8 eV) than the blue electron-trapping state (1.3 eV) that forms when protons participate and thus shows different electron transfer abilities.
The protective role of CsNPs and CurNPs against DNA damage, oxidative stress, and histopathological and immunohistochemical alterations induced by hydroxyapatite nanoparticles in male rat kidney
Authors: Mosa Israa F. , Yousef Mokhtar I. , Kamel Maher , Mosa Osama F. , Helmy Yasser 
Published: July 2019

AbstractHydroxyapatite nanoparticles (HAP-NPs) are an inorganic component of natural bone and are mainly used in the tissue engineering field due to their bioactivity, osteoconductivity, biocompatibility, non-inflammatory, and non-toxicity properties. However, the current toxicity data for HAP-NPs regarding human health are limited, and only a few results from basic studies have been published. Therefore, the present study was designed to investigate the beneficial role of chitosan nanoparticles (CsNPs) and curcumin nanoparticles (CurNPs) in alleviating nephrotoxicity induced by HAP-NPs in male rats. The results showed that HAP-NPs caused a reduction in antioxidant enzymes and induced lipid peroxidation, nitric oxide production and DNA oxidation. Moreover, HAP-NP administration was associated with intense histologic changes in kidney architecture and immunoreactivity to proliferating cell nuclear antigen (PCNA). However, the presence of CsNPs and/or CurNPs along with HAP-NPs reduced the levels of oxidative stress through improving the activities of antioxidant enzymes. Also, the rats administered the nanoparticles showed a moderate improvement in glomerular damage which matched that of the control group and showed mild positive reactions to PCNA–ir in glomeruli and renal tubules in the cortical and medullary portions. These novel insights confirm that the presence of chitosan and curcumin in nanoforms has powerful biological effects with enhanced bioactivity and bioavailability phenomena compared to their microphase counterparts. Also, they were able to ameliorate the nephrotoxicity induced by HAP-NPs.
Feedback from OB stars on their parent cloud: gas exhaustion rather than gas ejection
Authors: Watkins E. J. , Peretto N. , Marsh K. , Fuller G. A. 
Published: July 2019

Context.Stellar feedback from high-mass stars shapes the interstellar medium, and thereby impacts gas that will form future generations of stars. However, due to our inability to track the time evolution of individual molecular clouds, quantifying the exact role of stellar feedback on their star formation history is an observationally challenging task.Aims.In the present study, we take advantage of the unique properties of the G316.75-00.00 massive-star forming ridge to determine how stellar feedback from O-stars impacts the dynamical stability of massive filaments. The G316.75 ridge is 13.6 pc long and contains 18 900M⊙of H2gas, half of which is infrared dark and half of which infrared bright. The infrared bright part has already formed four O-type stars over the past 2 Myr, while the infrared dark part is still quiescent. Therefore, by assuming the star forming properties of the infrared dark part represent the earlier evolutionary stage of the infrared bright part, we can quantify how feedback impacts these properties by contrasting the two.Methods.We used publicly availableHerschel/HiGAL and molecular line data to measure the ratio of kinetic to gravitational energy per-unit-length,αvirline, across the entire ridge. By using both dense (i.e. N2H+and NH3) and more diffuse (i.e.13CO) gas tracers, we were able to computeαvirlinefor a range of gas volume densities (~1 × 102–1 × 105cm−3).Results.This study shows that despite the presence of four embedded O-stars, the ridge remains gravitationally bound (i.e.αvirline≤ 2) nearly everywhere, except for some small gas pockets near the high-mass stars. In fact,αvirlineis almost indistinguishable for both parts of the ridge. These results are at odds with most hydrodynamical simulations in which O-star-forming clouds are completely dispersed by stellar feedback within a few cloud free-fall times. However, from simple theoretical calculations, we show that such feedback inefficiency is expected in the case of high-gas-density filamentary clouds.Conclusions.We conclude that the discrepancy between numerical simulations and the observations presented here originates from different cloud morphologies and average densities at the time when the first O-stars form. In the case of G316.75, we speculate that the ridge could arise from the aftermath of a cloud-cloud collision, and that such filamentary configuration promotes the inefficiency of stellar feedback. This does very little to the dense gas already present, but potentially prevents further gas accretion onto the ridge. These results have important implications regarding, for instance, how stellar feedback is implemented in cosmological and galaxy scale simulations.
Cometary compositions compared with protoplanetary disk midplane chemical evolution
Authors: Eistrup Christian , Walsh Catherine , van Dishoeck Ewine F. 
Published: July 2019

Context.Comets are planetesimals left over from the formation of planets in the solar system. With a growing number of observed molecular abundances in many comets, and an improved understanding of chemical evolution in protoplanetary disk midplanes, comparisons can be made between models and observations that could potentially constrain the formation histories of comets.Aims.Our aim is to carry out the first statistical comparison between cometary volatile ice abundances and modelled evolving abundances in a protoplanetary disk midplane.Methods.Aχ2-method was used to determine maximum likelihood surfaces for 14 different comets that formed at a given time (up to 8 Myr) and place (out to beyond the CO iceline) in the pre-solar nebula midplane. This was done using observed volatile abundances for the 14 comets and the evolution of volatile abundances from chemical modelling of disk midplanes. Two assumptions for the chemical modelling starting conditions (cloud inheritance or chemical reset), as well as two different sets of cometary molecules (parent species, with or without sulphur species) were investigated.Results.Considering all parent species (ten molecules) in the reset scenario,χ2likelihood surfaces show a characteristic trail in the parameter space with high likelihood of formation around 30 AU at early times and 12 AU at later times for ten comets. This trail roughly traces the vicinity of the CO iceline in time.Conclusions.A statistical comparison between observed and modelled chemical abundances in comets and comet-forming regions could be a powerful tool for constraining cometary formation histories. The formation histories for all comets were constrained to the vicinity of the CO iceline, assuming that the chemistry was partially reset early in the pre-solar nebula. This is found, both when considering carbon-, oxygen-, and sulphur-bearing molecules (ten in total), and when only considering carbon- and oxygen-bearing molecules (seven in total). Since these 14 comets did not previously fall into the same taxonomical categories together, this chemical constraint may be proposed as an alternative taxonomy for comets. Based on the most likely time for each of these comets to have formed during the disk chemical evolution, a formation time classification for the 14 comets is suggested.
Thermal evolution and quiescent emission of transiently accreting neutron stars
Authors: Potekhin A. Y. , Chugunov A. I. , Chabrier G. 
Published: July 2019

Aims.We study the long-term thermal evolution of neutron stars in soft X-ray transients (SXTs), taking the deep crustal heating into account consistently with the changes of the composition of the crust. We collect observational estimates of average accretion rates and thermal luminosities of such neutron stars and compare the theory with observations.Methods.We performed simulations of thermal evolution of accreting neutron stars, considering the gradual replacement of the original nonaccreted crust by the reprocessed accreted matter, the neutrino and photon energy losses, and the deep crustal heating due to nuclear reactions in the accreted crust. We also tested and compared results for different modern theoretical models. We updated a compilation of the observational estimates of the thermal luminosities in quiescence and average accretion rates in the SXTs and compared the observational estimates with the theoretical results.Results.The long-term thermal evolution of transiently accreting neutron stars is nonmonotonic. The quasi-equilibrium temperature in quiescence reaches a minimum and then increases toward the final steady state. The quasi-equilibrium thermal luminosity of a neutron star in an SXT can be substantially lower at the minimum than in the final state. This enlarges the range of possibilities for theoretical interpretation of observations of such neutron stars. The updates of the theory and observations leave the previous conclusions unchanged, namely that the direct Urca process operates in relatively cold neutron stars and that an accreted heat-blanketing envelope is likely present in relatively hot neutron stars in the SXTs in quiescence. The results of the comparison of theory with observations favor suppression of the triplet pairing type of nucleon superfluidity in the neutron-star matter.