bluuebunny/crossref_metadata_2025_split huggingface dataset:
Multi-Omic Data Integration Allows Baseline Immune Signatures to Predict Hepatitis B Vaccine Response in a Small Cohort
Authors: Shannon Casey P. , Blimkie Travis M. , Ben-Othman Rym , Gladish Nicole , Amenyogbe Nelly , Drissler Sibyl , Edgar Rachel D. , Chan Queenie , Krajden Mel , Foster Leonard J. , Kobor Michael S. , Mohn William W. , Brinkman Ryan R. , Le Cao Kim-Anh , Scheuermann Richard H. , Tebbutt Scott J. , Hancock Robert E.W. , Koff Wayne C. , Kollmann Tobias R. , Sadarangani Manish , Lee Amy Huei-Yi 
Published: November 2020

BackgroundVaccination remains one of the most effective means of reducing the burden of infectious diseases globally. Improving our understanding of the molecular basis for effective vaccine response is of paramount importance if we are to ensure the success of future vaccine development efforts.MethodsWe applied cutting edge multi-omics approaches to extensively characterize temporal molecular responses following vaccination with hepatitis B virus (HBV) vaccine. Data were integrated across cellular, epigenomic, transcriptomic, proteomic, and fecal microbiome profiles, and correlated to final HBV antibody titres.ResultsUsing both an unsupervised molecular-interaction network integration method (NetworkAnalyst) and a data-driven integration approach (DIABLO), we uncovered baseline molecular patterns and pathways associated with more effective vaccine responses to HBV. Biological associations were unravelled, with signalling pathways such as JAK-STAT and interleukin signalling, Toll-like receptor cascades, interferon signalling, and Th17 cell differentiation emerging as important pre-vaccination modulators of response.ConclusionThis study provides further evidence that baseline cellular and molecular characteristics of an individual’s immune system influence vaccine responses, and highlights the utility of integrating information across many parallel molecular datasets.
Metabolomics Profiling and Diagnosis Biomarkers Searching for Drug-Induced Liver Injury Implicated to Polygonum multiflorum: A Cross-Sectional Cohort Study
Authors: Huang Ying , Zhao Xu , Zhang Zi-teng , Chen Shuai-shuai , Li Shan-shan , Shi Zhuo , Jing Jing , Huang Ang , Guo Yu-ming , Bai Zhao-fang , Zou Zheng-sheng , Xiao Xiao-he , Wang Jia-bo , Niu Ming 
Published: November 2020

Aim:The diagnosis of drug-induced liver injury (DILI) remains a challenge and the cases ofPolygonum multiflorumThunb. (PM) induced DILI (PM-DILI) have received much attention This study aimed to identify a simple and high-efficiency approach to PM-DILI diagnosis via metabolomics analysis.Methods:Plasma metabolites in 13 PM-DILI patients were profiled by liquid chromatography along with high-resolution mass spectrometry. Meanwhile, the metabolic characteristics of the PM-DILI were compared with that of autoimmune hepatitis (AIH), hepatitis B (HBV), and healthy volunteers.Results:Twenty-four metabolites were identified to present significantly different levels in PM-DILI patients compared with HBV and AIH groups. These metabolites were enriched into glucose, amino acids, and sphingolipids metabolisms. Among these essential metabolites, the ratios of P-cresol sulfate vs. phenylalanine and inosine vs. bilirubin were further selected using a stepwise decision tree to construct a classification model in order to differentiate PM-DILI from HBV and AIH. The model was highly effective with sensitivity of 92.3% and specificity of 88.9%.Conclusions:This study presents an integrated view of the metabolic features of PM-DILI induced by herbal medicine, and the four-metabolite decision tree technique imparts a potent tool in clinical diagnosis.
Comparative Analysis of the Global Transcriptomic Response to Oxidative Stress of Bacillus anthracis htrA-Disrupted and Parental Wild Type Strains
Authors: Zaide Galia , Elia Uri , Cohen-Gihon Inbar , Israeli Ma’ayan , Rotem Shahar , Israeli Ofir , Ehrlich Sharon , Cohen Hila , Lazar Shirley , Beth-Din Adi , Shafferman Avigdor , Zvi Anat , Cohen Ofer , Chitlaru Theodor 
Published: November 2020

We previously demonstrated that the HtrA (High Temperature Requirement A) protease/chaperone active in the quality control of protein synthesis, represents an important virulence determinant of Bacillus anthracis. Virulence attenuation of htrA-disrupted Bacillus anthracis strains was attributed to susceptibility of ΔhtrA strains to stress insults, as evidenced by affected growth under various stress conditions. Here, we report a comparative RNA-seq transcriptomic study generating a database of differentially expressed genes in the B. anthracis htrA-disrupted and wild type parental strains under oxidative stress. The study demonstrates that, apart from protease and chaperone activities, HtrA exerts a regulatory role influencing expression of more than 1000 genes under stress. Functional analysis of groups or individual genes exhibiting strain-specific modulation, evidenced (i) massive downregulation in the ΔhtrA and upregulation in the WT strains of various transcriptional regulators, (ii) downregulation of translation processes in the WT strain, and (iii) downregulation of metal ion binding functions and upregulation of sporulation-associated functions in the ΔhtrA strain. These modulated functions are extensively discussed. Fifteen genes uniquely upregulated in the wild type strain were further interrogated for their modulation in response to other stress regimens. Overexpression of one of these genes, encoding for MazG (a nucleoside triphosphate pyrophosphohydrolase involved in various stress responses in other bacteria), in the ΔhtrA strain resulted in partial alleviation of the H2O2-sensitive phenotype.
Quantitative behavior study of velocity, radius and topological charge on skyrmion/edge interaction dynamics on Co/Pt nanotrack
Authors: Andrade Santece Isaac , Carlos Souza Gomes Josiel , Toscano Danilo , Gama Monteiro Jr. Maxwel , Almeida de Mendonça João Paulo , Irineu Levartoski de Araujo Clodoaldo , Sato Fernando , De Andrade Leonel Sidiney , Zimmermann Coura Pablo 
Published: November 2020

Skyrmions are considered promising candidates to be the information carriers in the next generation of data storage and logic devices, due to its stability and easy control under the application of an electric current. For future technological applications in spintronic devices, it is important to study the properties behavior of these topological excitations during its movement on magnetic nanotracks, specially because in ferromagnetic materials they suffer a kind of magnus effect which tends to spell the skyrmion through the borders, preventing its transport throughout the nanotrack. We used micromagnetic simulations to study the dynamics of a skyrmion on a magnetic nanotrack induced by a spin polarized electric current. We considered thin magnetic nanotrack made of cobalt and platinum multilayers, whose magnetic state is perpendicular to the track plane and contain a single Néel-type Skyrmion. To describe this magnetic system, we used a Hamiltonian containing exchange, Dzyaloshinskii-Moriya, perpendicular magnetic anisotropy and dipole-dipole interactions. In our study we observed the well-known Skyrmion Hall effect and changes in the structure of the skyrmion when it approaches of the border. This alteration can be measured by determining the radius and the topological charge of the Skyrmion. Our simulation results show that both the radius and the topological charge decrease when it approaches of the border. Our study also demonstrates that the skyrmion-border interaction is repulsive, but there is a minimum distance from the border at which the interaction becomes attractive. If the skyrmion exceeds this critical position yc, it will be attracted and annihilated at the border of the nanotrack. We also performed simulations to obtain the limit value jc of the applied current density that the skyrmion can be transported along of the nanotrack without escaping from the side edge. From a technological point of view for possible applications in spintronic devices, the estimate of jc is of crucial importance.
Emission properties of intrinsic and extrinsic defects in Cu2SnS3 thin films and solar cells
Authors: Kanai Ayaka , Sugiyama Mutsumi 
Published: November 2020

Abstract
Intrinsic and extrinsic defects around the p–n interface in Cu2SnS3 (CTS) solar cells were evaluated using low-temperature photoluminescence (LT-PL) measurements. The intrinsic defects were investigated based on the PL-dependence of CTS films on the excitation power and temperature. Donor–acceptor pair recombination was observed with shallow acceptors (copper vacancies, V
Cu) located approximately 18 meV above the valence band maximum and typical donors located 72 and 112 meV below the conduction band minimum (CBM). The PL spectra of various CTS solar cell structures were measured to identify the Cd-related defects formed by Cd diffusion from the CdS layer. A new LT-PL peak was observed at 0.87 eV for the CdS/CTS solar cells, corresponding to D–A pair recombination with Cd on Cu site donors located 62 meV below the CBM. A p–n homojunction may form in CTS by V
Cu passivation by Cd diffusion and suppressed interface recombination.
Analysis and revision of the Miocene boreal faunae of bivalve mollusks of the South Sakhalin
Authors: ХУДИК В.Д. , ЗАХАРОВ Ю.Д. 
Published: November 2020

Приведены результаты изучения остатков фаун двустворчатых моллюсков из миоценовых отложений Южного Сахалина. Их анализ позволил выделить три бореальных комплекса моллюсков: невельский, раннечеховский и курасийский, фиксирующие периоды похолодания климата в миоцене региона. Изучение неогеновых представителей родов Lucinoma и Mya позволило обозначить среди них ряд таксонов, имеющих стратиграфическое значение. Установленное присутствие тепловодных двустворок в фаунах позднечеховского времени Южного Сахалина, очевидно, отражает собой начальный этап тенденции нарастающего потепления климата в миоцене региона с климатическим оптимумом в верхнедуйско-сертунайское время. Высказывается следующее мнение: неустойчивые климатические условия в позднем палеогене – раннем неогене северной части Япономорского региона могли быть основной причиной возникновения здесь одного из мощных центров эволюции морских малакофаун бореальных районов северной Пацифики.
The results on the studying of the faunae of bivalve mollusks remains from miocene deposits of the South Sakhalin are presented. The analysis of the last ones allowed distinguishing the following three boreal assemblages of mollusks: Nevelskiy, early Chekhovskiy and Kurasiiskiy, recording the period of climatic cooling in miocene of the region. Studying of Neogene representatives of Lucinoma and Mya generas allowed identifying some taxa among them which have stratigraphic significance. The detected presence of warm water bivalves in the faunae of the late Chekhovsky time of the South Sakhalin appears to reflect the initial stage of the tendency of the intensifying climate warming happened during miocene, with climatic optimum during the Verkhneduysky – Sertunaysky times. An opinion is expressed that the unstable climatic conditions in the northern part of the Japan Sea region during late Paleogene – early Neogene could have been the main reason for originating of one of the high-potential centers of evolution of the marine malacofaunae of boreal regions of the North Pacific.
Influence of inter-annual variability of river runoff on the bottom sediments of the Razdolnaya River estuary, Primorye, Russia
Authors: ШУЛЬКИН В.М. 
Published: November 2020

Изучены вариации гранулометрического и химического состава верхнего двухсантиметрового слоя донных отложений эстуария р. Раздольная, отобранных трижды в течение 2015–2019 гг., когда водный и твердый стоки реки выросли в 2–3 и 5–6 раз соответственно по сравнению с 2014 г. Показано, что значительный вынос осадочного материала сопровождается увеличением на 10–20 % доли пелитовых (<0,01мм) фракций в отложениях внешней части эстуария в северной части Амурского залива. Вариации гранулометрического состава являются главным контролирующим фактором и определяют 67 % общей изменчивости химического состава осадков эстуария. Еще 20 % изменчивости обусловлены примесью загрязненных отложений залива, содержащих повышенную концентрацию Сорг., Hg, Zn, Pb, Cd, Ag, Cu, Mo, V, а также восстановительным диагенезом, приводящим к обеднению осадков марганцем и кобальтом на разрезе река–море. Установить влияние коагуляционных процессов в зоне смешения на валовый состав донных отложений эстуария р. Раздольная не удалось.
Grain size and chemical composition have been studied of the upper 2 cm layer of bottom sediments of the Razdolnaya River estuary sampled thrice in 2015–2019. It was a period when the river runoff increased by 2–3 and 5–6 times for the water and suspended solids, respectively, compared to 2014. It has been shown that significant subtraction of sedimentary material is accompanied by 10–20 % increase of pellite fractions (grain size <0.01 mm) in the deposits of the outer part of anestuary in the North part of the Amur Bay. Grain size composition is the main controlling factor determining 67 % of the total variability of the chemical composition of estuarine bottom sediments. Another 20 % of variability are due to the admix of polluted sediments of the Amur Bay, containing an increased concentration of Corg., Hg, Zn, Pb, Cd, Ag, Cu, Mo, V, as well as diagenesis, leading to depletion of sediments by the Mn and Co on a river-sea section. It is not possible to establish the influence of coagulation processes in the mixing zone on total concentration of trace elements in the bottom sediments of Razdolnaya River estuary.
Perawatan Luka Diabetes Mellitus Menggunakan Teknik Modern Dressing
Authors: Dimantika Alberikus , Sugiyarto Sugiyarto , Setyorini Yuyun 
Published: November 2020

Background: The most common complication in patients with diabetes mellitus tippe 2 (DM) is diabetic ulcers, where the tissue deformity occurs either partially (Partial Thickness) or completely (Full Thickness). If not handled properly and appropriately, ulcers can become infected. Where leg ulcers, infection, neuroarthropathy and peripheral artery disease are the causes of gangrene and lower limb amputations. The aim of this study is to determine the effectiveness of wound healing in the treatment of diabetes mellitus wounds using modern dressing techniques. Methods: the literature review (LR) method uses meta-analysis where the data used is a database of searches using MEDLINE (PubMed), Google Scholar, Science Direct, Surgery Science and Sci-Hub. Reports published from 2010-2020 that focused on modern wound care dressings for wound healing of type 2 diabetes mellitus were identified. Results: Based on the analysis of the journal, there are nursing implications that have been compared from 10 journals, it was found that the treatment of type two diabetes mellitus wounds using modern dressing techniques is more effective in wound healing, by accelerating granulation and healing of the various types of dressings used, each of which has advantages. in terms of wound healing type 2 diabetes mellitus. Conclusion: The use of modern dressing techniques is effective in wound healing in the treatment of type 2 diabetes mellitus wounds. Researchers suggest that they be able to conduct research related to modern wound care dressings such as the use of alginate dressings, foam dressings, hydrogel dressings, moisture dressings, silver dressings, hydrophilic polyurethane foam dressings, acellular matrix dressings, and others related to wound care using modern dressing techniques. . Further research needs to be done by paying attention to the latest evidence-based practice journals to enrich knowledge about wound care with modern dressing techniques for diabetes mellitus wounds.
A Template-based Approach to the Photometric Classification of SN 1991bg-like Supernovae in the SDSS-II Supernova Survey
Authors: Perrefort Daniel , Zhang Yike , Galbany Lluís , Wood-Vasey W. M. , González-Gaitán Santiago 
Published: November 2020

Abstract
The use of SNe Ia to measure cosmological parameters has grown significantly over the past two decades. However, there exists a significant diversity in the SN Ia population that is not well understood. Overluminous SN 1991T-like and subluminous SN 1991bg-like objects are two characteristic examples of peculiar SNe. The identification and classification of such objects is an important step in studying what makes them unique from the remaining SN population. With the upcoming Vera C. Rubin Observatory promising on the order of a million new SNe over a 10 year survey, spectroscopic classifications will be possible for only a small subset of observed targets. As such, photometric classification has become an increasingly important concern in preparing for the next generation of astronomical surveys. Using observations from the Sloan Digital Sky Survey II (SDSS-II) SN Survey, we apply here an empirically based classification technique targeted at the identification of SN 1991bg-like SNe in photometric data sets. By performing dedicated fits to photometric data in the rest-frame redder and bluer bandpasses, we classify 16 previously unidentified 91bg-like SNe. Using SDSS-II host galaxy measurements, we find that these SNe are preferentially found in host galaxies with an older average stellar age than the hosts of normal SNe Ia. We also find that these SNe are found at a further physical distance from the center of their host galaxies. We find no statistically significant bias in host galaxy mass or specific star formation rate for these targets.
Constraining the Kilonova Rate with Zwicky Transient Facility Searches Independent of Gravitational Wave and Short Gamma-Ray Burst Triggers
Authors: Andreoni Igor , Kool Erik C. , Carracedo Ana Sagués , Kasliwal Mansi M. , Bulla Mattia , Ahumada Tomás , Coughlin Michael W. , Anand Shreya , Sollerman Jesper , Goobar Ariel , Kaplan David L. , Loveridge Tegan T. , Karambelkar Viraj , Cooke Jeff , Bagdasaryan Ashot , Bellm Eric C. , Cenko S. Bradley , Cook David O. , De Kishalay , Dekany Richard , Delacroix Alexandre , Drake Andrew , Duev Dmitry A. , Fremling Christoffer , Golkhou V. Zach , Graham Matthew J. , Hale David , Kulkarni S. R. , Kupfer Thomas , Laher Russ R. , Mahabal Ashish A. , Masci Frank J. , Rusholme Ben , Smith Roger M. , Tzanidakis Anastasios , Sistine Angela Van , Yao Yuhan 
Published: November 2020

Abstract
The first binary neutron star merger, GW170817, was accompanied by a radioactivity-powered optical/infrared transient called a kilonova. To date, no compelling kilonova has been found in all-sky optical surveys, independently of short gamma-ray burst and gravitational-wave triggers. In this work, we searched the first 23 months of the Zwicky Transient Facility (ZTF) data stream for candidate kilonovae in the form of rapidly evolving transients. We combined ZTF alert queries with forced point-spread-function photometry and nightly flux stacking to increase our sensitivity to faint and fast transients. Automatic queries yielded >11,200 candidates, 24 of which passed quality checks and selection criteria based on a grid of kilonova models tailored for both binary neutron star and neutron star–black hole mergers. None of the candidates in our sample was deemed a possible kilonova after thorough vetting. The sources that passed our selection criteria are dominated by Galactic cataclysmic variables. We identified two fast transients at high Galactic latitude, one of which is the confirmed afterglow of long-duration GRB 190106A, the other is a possible cosmological afterglow. Using a survey simulation code, we constrained the kilonova rate for a range of models including top-hat, linearly decaying light curves, and synthetic light curves obtained with radiative transfer simulations. For prototypical GW170817-like kilonovae, we constrain the rate to be

Gpc−3 yr−1 (95% confidence). By assuming a population of kilonovae with the same geometry and composition of GW170817 observed under a uniform viewing angle distribution, we obtained a constraint on the rate of R < 4029 Gpc−3 yr−1.
Magnetic Cloud and Sheath in the Ground-level Enhancement Event of 2000 July 14. I. Effects on the Solar Energetic Particles
Authors: Wu S.-S. , Qin G. 
Published: November 2020

Abstract
Ground-level enhancements generally accompany fast interplanetary coronal mass ejections (ICMEs), and ICME-driven shocks are sources of solar energetic particles (SEPs). Observations of the GLE event of 2000 July 14 show that a very fast and strong magnetic cloud (MC) is behind the ICME shock and the proton intensity-time profiles observed at 1 au had a rapid two-step decrease near the sheath and MC. Therefore, we study the effect of sheath and MC on SEPs accelerated by an ICME shock by numerically solving the focused transport equation. The shock is regarded as a moving source of SEPs with an assumed particle distribution function. The sheath and MC are set to thick spherical caps with enhanced magnetic field, and the turbulence levels in the sheath and MC are set to be higher and lower than those of the ambient solar wind, respectively. The simulation results of proton intensity-time profiles agree well with the observations in energies ranging from ∼1 to ∼100 MeV, and the two-step decrease is reproduced when the sheath and MC arrived at the Earth. The simulation results show that the sheath-MC structure reduced the proton intensities for about 2 days after the shock passed through the Earth. It is found that the sheath contributed most of the decrease while the MC facilitated the formation of the second step decrease. The simulation also infers that the coordination of magnetic field and turbulence in sheath-MC structure can produce a stronger reduction of SEP intensities.
Supermassive Black Hole Fueling in IllustrisTNG: Impact of Environment
Authors: Bhowmick Aklant K. , Blecha Laura , Thomas July 
Published: November 2020

Abstract
We study the association between active galactic nuclei (AGNs) and environment at scales of 0.01–1

h

−
1

Mpc in the IllustrisTNG simulated universe (TNG100). We identify supermassive black hole (BH) pairs and multiples within scales of 0.01, 0.1, and 1

h

−
1

Mpc and examine their AGN activity in relation to randomly selected pairs and multiples. The number density of BHs in TNG100 is n = 0.06 h
3 Mpc−3 at z ≲ 1.5 (n = 0.02 h
3 Mpc−3 at z = 3). About ∼10% and ∼1% of these BHs live in pairs and multiples, respectively, within 0.1

h

−
1

Mpc scales. These systems have enhanced likelihood (up to factors of 3–6) of containing high Eddington ratio (η ≳ 0.7) AGNs compared to random pairs and multiples. Conversely, the likelihood of an AGN to live in 0.1

h

−
1

Mpc scale BH systems is also higher (by factors ∼4 for η ≳ 0.7) compared to random pairs and multiples. ∼10% of ultra-hard X-ray selected AGNs in TNG100 have detectable 2–10 keV AGN companions on 0.1

h

−
1

Mpc scales, consistent with observations. On larger spatial scales (∼1

h

−
1

Mpc), however, no significant enhancements in AGN activity exist, even at high Eddington ratios. This implies that small-scale (≲0.1

h

−
1

Mpc) AGN enhancement is likely driven by galaxy interactions and mergers. Nonetheless, the overall percentage of AGNs living in ≲0.1

h

−
1

Mpc scale multiples is still subdominant (≲40%). Furthermore, the associated Eddington ratio enhancements of BH systems (as well as merging BHs) is only up to factors of ∼2–3. Our results support the existence of merger-AGN connection in TNG100. However, it plays a relatively minor role in fueling the AGN population.