bluuebunny/crossref_metadata_2025_split huggingface dataset:
Serum total IgE may be a biomarker among chronic pulmonary aspergillosis patients with elevated serum total IgE levels: A cohort study with pathological evaluations
Authors: Watanabe Shizuka , Suzuki Junko , Suzukawa Maho , Takeda Keita , Imoto Sahoko , Kitani Masashi , Fukami Takeshi , Sasaki Yuka , Hebisawa Akira , Matsui Hirotoshi 
Published: January 2022

Abstract

High serum total immunoglobulin E (IgE) levels have been reported in chronic pulmonary aspergillosis (CPA). However, researchers have not verified if they reflect the disease activity. We aimed to compare the serum total IgE levels in CPA cases with high serum IgE during an exacerbation or when stable and examined the IgE expression patterns in the lesions via immunofluorescence staining. From April 2016 to September 2019, we extracted CPA cases with elevated serum total IgE levels based on the criteria of the Infectious Diseases Society of America. We retrospectively analyzed serum total IgE levels and other parameters and eventually extracted 32 cases. The patients’ serum total IgE levels were significantly higher in the exacerbation period than in the stable period (P &lt; .0001). The median rate of change was 1.76 times (quartile 1.41–3.25). In addition, we used surgical specimens of CPA cases with high serum total IgE levels, normal serum total IgE CPA cases, and control surgical specimens and performed immunofluorescence staining with IgE, mast cell tryptase, CD138, and 4,6-diamidino-2-phenylindole. We observed multiple mast cells and plasma cells in the CPA cases regardless of the serum total IgE level. In contrast, multiple IgE-positive cells co-stained with tryptase were observed in CPA cases with high serum total IgE levels. This finding suggested that serum total IgE could serve as a biomarker for evaluating disease severity. Immunofluorescence staining suggested that IgE may play a role in pathogenesis through activation of mast cells by cross-linking in cases of CPA with high serum total IgE levels.

Lay summary
High serum total IgE levels are common in chronic pulmonary aspergillosis. This novel study indicated that serum total IgE is a possible biomarker of the disease activity in the aforementioned condition. Immunofluorescence staining indicated a possible role of IgE in disease pathogenesis.
Invasive mold infection of the gastrointestinal tract: A case series of 22 immunocompromised patients from a single academic center
Authors: Quintero Orlando , Allard Libby , Ho Dora 
Published: January 2022

Abstract

Invasive mold infection (IMI) of the gastrointestinal (GI) tract is a rare complication in immunocompromised patients that carries a high mortality rate. It is most often described in the setting of disseminated disease. Early diagnosis and treatment are critical in its management, but this is rarely obtained, leading to delayed therapy. To describe the clinical characteristics, treatment and outcomes of this infection, we reviewed all the cases of adult patients with histopathological findings from autopsy or surgical specimens that demonstrated fungal invasion into the GI tract at Stanford Hospital & Clinics from January 1997 to August 2020. Twenty-two patients that met criteria were identified and they were all immunocompromised, either due to their underlying medical conditions or the treatments that they received. The most common underlying disease was hematological malignancies (63.6%) and the most common symptoms were abdominal pain, GI bleeding and diarrhea. A majority of patients (72.7%) had disseminated invasive mold infection, while the rest had isolated GI tract involvement. In 2/3 of our cases, the fungal genus or species was confirmed based on culture or PCR results. Given the very high mortality associated with GI mold infection, this diagnosis should be considered when evaluating immunocompromised patients with concerning GI signs and symptoms. A timely recognition of the infection, prompt initiation of appropriate antifungal therapy as well as surgical intervention if feasible, are key to improve survival from this devastating infection.

Lay summary
Patients with a weakened immune system can suffer from mold infections in the bowel, which are difficult to diagnose and have very high death rate. We examined such cases in our institution in order to learn about their clinical and microbiological features. This study can further improve our understanding of these infections in order to improve patient outcome.
Paeonol enhances treatment of fluconazole and amphotericin B against oropharyngeal candidiasis through HIF-1α related IL-17 signaling
Authors: Pan Min , Wang Qirui , Liu Yulong , Xiao Nan , Niu Xiaojia , Wu Daqiang , Wang Tianming , Yan Guiming , Shao Jing 
Published: January 2022

Abstract
Oropharyngeal candidiasis (OPC) is an oral infection mainly caused by Candida albicans, a dimorphic human opportunistic pathogen that can proliferate and invade the superficial oral epithelium using its hyphae. The filamentation of C. albicans is a hallmark of biofilm formation, accompanied by the occurrence of a hypoxic microenvironment. Paeonol (PAE) is a traditional medicine with multiple properties. In a previous study, we demonstrated the synergism of PAE plus Fluconazole (FLU) or Amphotericin B (AmB) against C. albicans in vitro and in vivo. This study aimed to explore the therapeutic mechanisms of drug combinations on OPC. In an established OPC mouse model, the culture of hypoxia was observed by calcofluor white and hypoxyprobe staining. The expression and levels of IL-17 signaling-associated genes and proteins (IL-17A and IL-23) were evaluated in tissue homogenates and EC109 cells. The results show that compared with the single therapy, PAE plus FLU or AmB can decrease fungal burden, restore mucosal integrity, and reduce the hypoxic microenvironment and inflammation in the OPC mice. Relative to infected mice, the drug combinations can also rectify the abnormal expression of hypoxia inducible factor (hif)-1α, il-17a, and il-23 mRNA. Meanwhile, compared with the infected EC109 cells treated with a single drug, PAE plus FLU or AmB significantly inhibited the mRNA and protein expression of HIF-1α, IL-17A, and IL-23. Taken together, the possible mechanism of PAE plus FLU or AmB can be attributed to the regulation of hypoxia-associated IL-17 signaling in OPC treatment.
Compact object mergers in hierarchical triples from low-mass young star clusters
Authors: Trani Alessandro A , Rastello Sara , Carlo Ugo N Di , Santoliquido Filippo , Tanikawa Ataru , Mapelli Michela 
Published: January 2022

Abstract
A binary star orbited by an outer companion constitutes a hierarchical triple system. The outer body may excite the eccentricity of the inner binary through the von Zeipel-Lidov-Kozai (ZLK) mechanism, triggering the gravitational wave (GW) coalescence of the inner binary when its members are compact objects. Here, we study a sample of hierarchical triples with an inner black hole (BH) – BH binary, BH – neutron star (NS) binary, and BH – white dwarf (WD) binary, formed via dynamical interactions in low-mass young star clusters. Our sample of triples was obtained self-consistently from direct N-body simulations of star clusters which included up-to-date stellar evolution. We find that the inner binaries in our triples cannot merge via GW radiation alone, and the ZLK mechanism is essential to trigger their coalescence. Contrary to binaries assembled dynamically in young star clusters, binary BHs merging in triples have preferentially low mass ratios (q ≃ 0.3) and higher primary masses ($m_{\rm p} \gtrsim 40 {\, \rm M_\odot }$). We derive a local merger rate density of 0.60, 0.11 and $0.5 {-1} \, \rm Gpc^{-3}$ for BH-BH, BH-NS and BH-WD binaries, respectively. Additionally, we find that merging binaries have high eccentricities across the GW spectrum, including the LIGO-Virgo-KAGRA (LVK), LISA, and DECIGO frequencies. About 7 per cent of BH-BH and 60 per cent of BH-NS binaries will have detectable eccentricities in the LVK band. Our results indicate that the eccentricity and the mass spectrum of merging binaries are the strongest features for the identification of GW mergers from triples.
Thethesanproject: properties of the intergalactic medium and its connection to reionization-era galaxies
Authors: Garaldi E , Kannan R , Smith A , Springel V , Pakmor R , Vogelsberger M , Hernquist L 
Published: January 2022

ABSTRACTThe high-redshift intergalactic medium (IGM) and the primeval galaxy population are rapidly becoming the new frontier of extragalactic astronomy. We investigate the IGM properties and their connection to galaxies at z ≥ 5.5 under different assumptions for the ionizing photon escape and the nature of dark matter, employing our novel thesan radiation-hydrodynamical simulation suite, designed to provide a comprehensive picture of the emergence of galaxies in a full reionization context. Our simulations have realistic ‘late’ reionization histories, match available constraints on global IGM properties, and reproduce the recently observed rapid evolution of the mean free path of ionizing photons. We additionally examine high-z Lyman-α transmission. The optical depth evolution is consistent with data, and its distribution suggests an even-later reionization than simulated, although with a strong sensitivity to the source model. We show that the effects of these two unknowns can be disentangled by characterizing the spectral shape and separation of Lyman-α transmission regions, opening up the possibility to observationally constrain both. For the first time in simulations, thesan reproduces the modulation of the Lyman-α flux as a function of galaxy distance, demonstrating the power of coupling a realistic galaxy formation model with proper radiation hydrodynamics. We find this feature to be extremely sensitive on the timing of reionization, while being relatively insensitive to the source model. Overall, thesan produces a realistic IGM and galaxy population, providing a robust framework for future analysis of the high-z Universe.
Siloxyl radical initiated HCN polymerization: computation of N-heterocycles formation and surface passivation
Authors: Fioroni Marco , DeYonker Nathan J 
Published: January 2022

ABSTRACT
In this work, by means of quantum chemistry (Density Functional Theory (DFT), PW6B95/def2-TZVPP; DLPNO-CCSD(T)/CBS), HCN polymerization [(HCN)1 − 4] initiated and catalysed by a siloxyl radical (Si-O•) on a model silica surface is analysed. Linear HCN polymers (pHCN) are obtained by a radical initiated mechanism at a SiO• site and are characterized by a -(HC-N)- skeleton due to radical localization on the terminal N atom and radical attack on the C centre. NC heterocycles are formed by cyclization of the linear SiO-(HCN)3 − 4 and are always thermodynamically preferred over their linear counterparts, acting as thermodynamic sinks. Of particular interest to the astrochemistry community is the formation of the N-heterocycle 1,3,5-triazine that can be released into the gas phase at relatively low T (ΔG† = 23.3 kcal/mol). Full hydrogenation of SiO-(HCN•) follows two reaction channels with products: (a) SiO-CH3 + •NH2 or (b) amino-methanol + Si•, though characterized by slow kinetics. Nucleophilic addition of H2O to the electron-rich SiO-(HCN•) shows an unfavourable thermodynamics as well as a high-activation energy. The cleavage of the linear (HCN)1−4 from the SiO• site also shows a high thermodynamic energy penalty (ΔG≥82.0 kcal/mol). As a consequence, the silicate surface will be passivated by a chemically active ‘pHCN brush’ modifying the surface physico-chemical properties. The prospect of surface-catalysed HCN polymers exhibiting a high degree of chemical reactivity and proposed avenues for the formation of 1,3,5-triazine and amino-methanol opens exciting new chemical pathways to Complex Organic Matter formation in astrochemistry.
The RapidXMM upper limit server: X-ray aperture photometry of the XMM-Newton archival observations
Authors: Ruiz A , Georgakakis A , Gerakakis S , Saxton R , Kretschmar P , Akylas A , Georgantopoulos I 
Published: January 2022

ABSTRACT
This paper presents the construction of the RapidXMM database that is available through the XMM-Newton Science Archive and offers access to upper limits and aperture photometry across the field of view of the XMM-Newton Pointed and Slew Survey observations. The feature of RapidXMM is speed. It enables the fast retrieval of X-ray upper limits and photometry products in three energy bands (0.2–2, 2–12, and 0.2–12 keV) for large numbers of input sky positions. This is accomplished using the Hierarchical Equal Area Iso Latitude pixelation of the sphere (HEALPix). The pre-calculated upper-limits and associated X-ray photometry products are reprojected into the HEALPix grid of cells before being ingested into the RapidXMM database. This results in tables of upper limits and aperture photometry within HEALPix cells of size ≈3 arcsec (Pointed observations) and 6 arcsec (Slew Survey). The database tables are indexed by the unique integer number of the HEALPix cells. This reduces spatial nearest-neighbour queries by sky position to an integer-matching exercise and significantly accelerates the retrieval of results. We describe in detail the processing steps that lead from the science products available in the XMM-Newton archive to a database optimized for sky queries. We also present two simple show-case applications of RapidXMM for scientific studies – searching for variable X-ray sources and stacking analysis of X-ray faint populations.
NGC 2004 #115: a black hole imposter containing three luminous stars
Authors: El-Badry Kareem , Burdge Kevin B , Mróz Przemek 
Published: January 2022

ABSTRACT
NGC 2004 #115 is a recently identified black hole (BH) candidate in the Large Magellanic Cloud (LMC) containing a B star orbiting an unseen companion in a 2.9 d orbit and a Be star tertiary. We show that the unseen companion is not a 25 M⊙ BH, but a $(2\!-\!3)\, {\rm M}_{\odot }$ luminous star. Analysing the Optical Gravitational Lensing Experiment (OGLE) and MAssive Compact Halo Object (MACHO) light curves of the system, we detect ellipsoidal variability with amplitude 10 times larger than would be expected if the companion were a 25 M⊙ BH, ruling out the low inclination required for a massive companion. The light curve also shows a clear reflection effect that is well modelled with a $2.5\, {\rm M}_{\odot }$ main-sequence secondary, ruling out a lower mass BH or neutron star companion. We consider and reject models in which the system is a binary containing a stripped star orbiting the Be star: only a triple model with an outer Be star can explain both the observed light curve and radial velocities. Our results imply that the B star, whose slow projected rotation velocity and presumed tidal synchronization were interpreted as evidence for a low inclination (and thus a high companion mass), is far from being tidally synchronized: despite being in a 2.9 d orbit that is fully or nearly circularized (e &lt; 0.04), its surface rotation period appears to be at least 20 d. We offer cautionary notes on the interpretation of dormant BH candidates in binaries.
On the possible contribution of cationic oxygenated carbon chains CnO+, HCnO+, and OCnO+ (n = 4–9) to the diffuse interstellar bands
Authors: Jacovella U , Buntine Jack T , Cotter Mariah , Muller Giel , Scholz Michael S , Dartois Emmanuel 
Published: January 2022

ABSTRACT
Only four of the diffuse interstellar bands (DIBs) are currently accounted for, ascribed to electronic transitions of C$_{60}^+$. Investigations into carriers of other DIBs historically focus on charged and neutral hydrocarbons, and little information is available regarding oxygenated carbon and hydrocarbon species that result from the two most abundant heavy elements in the interstellar medium, C and O. In this study, we assess whether CnO+, HCnO+, and OCnO+ (n = 4–9) cations are viable candidates to account for DIBs using both density-functional theory (DFT) and coupled cluster single-double and perturbative triple theory, CCSD(T). For these species, the linear structures are the most stable isomers with the lowest dissociation threshold corresponding to CO loss. Optical absorptions of the oxygenated carbon chain cations are characterized by calculated vertical excitation wavelengths and their corresponding oscillator strengths using the equation-of-motion CCSD (EOM-CCSD) method. Aside from HC4O+ and HC2n +1O+, all of the species considered in this study have calculated electronic transitions that lie in the visible or near-infrared spectral regions. Minimal column densities necessary for these cations to account for DIBs have been estimated. Based on present results and the known column densities for neutral oxygenated carbon chains in TMC-1, the growth rate of charged O-bearing carbon chains via ion-neutral reaction mechanisms is judged to be too low to form a sufficient population to give rise to DIBs.
Global comparison of awake and asleep mapping procedures in glioma surgery: An international multicenter survey
Authors: Gerritsen Jasper K W , Broekman Marike L D , De Vleeschouwer Steven , Schucht Philippe , Jungk Christine , Krieg Sandro M , Nahed Brian V , Berger Mitchel S , Vincent Arnaud J P E 
Published: January 2022

Abstract

Background
Mapping techniques are frequently used to preserve neurological function during glioma surgery. There is, however, no consensus regarding the use of many variables of these techniques. Currently, there are almost no objective data available about potential heterogeneity between surgeons and centers. The goal of this survey is therefore to globally identify, evaluate and analyze the local mapping procedures in glioma surgery.

Methods
The survey was distributed to members of the neurosurgical societies of the Netherlands (Nederlandse Vereniging voor Neurochirurgie—NVVN), Europe (European Association of Neurosurgical Societies—EANS), and the United States (Congress of Neurological Surgeons—CNS) between December 2020 and January 2021 with questions about awake mapping, asleep mapping, assessment of neurological morbidity, and decision making.

Results
Survey responses were obtained from 212 neurosurgeons from 42 countries. Overall, significant differences were observed for equipment and its settings that are used for both awake and asleep mapping, intraoperative assessment of eloquent areas, the use of surgical adjuncts and monitoring, anesthesia management, assessment of neurological morbidity, and perioperative decision making. Academic practices performed awake and asleep mapping procedures more often and employed a clinical neurophysiologist with telemetric monitoring more frequently. European neurosurgeons differed from US neurosurgeons regarding the modality for cortical/subcortical mapping and awake/asleep mapping, the use of surgical adjuncts, and anesthesia management during awake mapping.

Discussion
This survey demonstrates the heterogeneity among surgeons and centers with respect to their procedures for awake mapping, asleep mapping, assessing neurological morbidity, and decision making in glioma patients. These data invite further evaluations for key variables that can be optimized and may therefore benefit from consensus.
Diverse Anatexis in the Main Central Thrust Zone, Eastern Nepal: Implications for Melt Evolution and Exhumation Process of the Himalaya
Authors: Liu Shuaiqi , Zhang Guibin , Zhang Lifei , Wang Shuzhen , Upreti Bishal N , Adhikari Danda P , Wu Chenguang , Wang Jiaxing 
Published: January 2022

Abstract
Sitting between the Greater Himalayan sequence (GHS) and Lesser Himalayan sequence (LHS), the Main Central Thrust zone (MCTZ) has experienced multiple episodes of anatexis, which presents an opportunity to explore the nature of partial melting and its response to Himalayan orogenic processes. A series of deformed rocks, including migmatites, gneisses, and leucosomes were collected across the MCT at Arun Valley, eastern Nepal. We investigated the bulk rock major and trace elements, Sr-Nd isotopes, mineral chemistry, zircon geochronology and Hf isotopes, and conducted phase equilibria modeling. The protolith boundary between the GHS and LHS is recognized on the basis of Sr–Nd isotopes with εNd(0) of −16.7 to −8.0 for the GHS and −31.2 to −23.9 for the LHS. Samples from both the GHS and LHS have undergone partial melting, as revealed by in situ leucosomes at outcrops and melt inclusions at thin-section scale. Leucosomes separated from their host rocks are divided into four groups: those derived from hydration melting, muscovite dehydration melting, amphibole dehydration melting, and feldspar accumulation. Phase equilibria modeling results for the GHS migmatite show isothermal decompression from peak P–T conditions of 11 kbar and 795°C, accompanied by muscovite dehydration melting evolving into biotite dehydration melting. In contrast, rocks from the LHS are modeled to have undergone hydration melting at P–T conditions of 9 kbar and 685°C. Zircon U–Pb geochronology suggests that long-lived partial melting (35–13 Ma) occurred in the MCTZ. Moreover, anatectic zircon Hf isotopes show that the protoliths for partial melting changed from the GHS to the LHS with εHf(t) of −19.4 to −5.7 during the early Miocene, and lower values of −42.5 to −16.7 during the middle to late Miocene. These zircon geochemical results indicate that hydrous metasediments from the LHS were progressively accreted to the base of the GHS, resulting in hydration melting of both the GHS and LHS assisted by MCT. The timing of activity of the MCT is constrained to 25–13 Ma, coeval with movement of the South Tibetan detachment system. Integration of petrogenetic modeling, the chronology of partial melting, and metamorphic P–T paths allows us to propose that thickened Himalayan crust was heated from the middle to late Eocene, and widespread anatexis occurred during the Oligocene to middle Miocene, forming a large-scale melt channel. The hot GHS channel flow moved upward in association with the synchronous activity of the MCT system, triggered intense dehydration of LHS metasediments, resulting in fluid-present melting in both the GHS and LHS during middle to late Miocene, and the formation of leucogranite with mixture features of GHS and LHS. Furthermore, with the cooling of the melt channel, duplexing has gradually operated since the middle to late Miocene in the shallow crust.
High-throughput methods for genome editing: the more the better
Authors: Huang Yong , Shang Meiqi , Liu Tingting , Wang Kejian 
Published: January 2022

Abstract
During the last decade, targeted genome-editing technologies, especially clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR-associated protein (Cas) technologies, have permitted efficient targeting of genomes, thereby modifying these genomes to offer tremendous opportunities for deciphering gene function and engineering beneficial traits in many biological systems. As a powerful genome-editing tool, the CRISPR/Cas systems, combined with the development of next-generation sequencing and many other high-throughput techniques, have thus been quickly developed into a high-throughput engineering strategy in animals and plants. Therefore, here, we review recent advances in using high-throughput genome-editing technologies in animals and plants, such as the high-throughput design of targeted guide RNA (gRNA), construction of large-scale pooled gRNA, and high-throughput genome-editing libraries, high-throughput detection of editing events, and high-throughput supervision of genome-editing products. Moreover, we outline perspectives for future applications, ranging from medication using gene therapy to crop improvement using high-throughput genome-editing technologies.