bluuebunny/crossref_metadata_2025_split huggingface dataset:
The landscape of isoform switches in sepsis: a multicenter cohort study
Authors: Chen Lin , Chen Kun , Hong Yucai , Xing Lifeng , Zhang Jianjun , Zhang Kai , Zhang Zhongheng 
Published: June 2022

AbstractSepsis is caused by an uncontrolled inflammatory response, whose underlying mechanisms are not fully understood. It is well known that the majority of human genes can be expressed as alternative isoforms. While isoform switching is implicated in many diseases and is particularly prominent in cancer, it has never been reported in the context of sepsis. Patients presented to the emergency department of three tertiary care hospitals from January 2020 to December 2020 were enrolled. Clinical variables and genome-wide transcriptome of peripheral blood mononuclear cells (PBMC) were obtained. Isoform switching analysis were performed to identify significant isoform switches and relevant biological consequences. A total of 48 subjects with sepsis, involving 42 survivors and 6 non-survivors, admitted to the emergency department of three tertiary care hospitals were enrolled in this study. PBMCs were extracted for RNA sequencing (RNA-seq). Patients (n = 4) with mild stroke or acute coronary syndrome without infection were enrolled in this study as controls. The most frequent functional changes resulting from isoform switching were changes affecting the open reading frame, protein domains and intron retention. Many genes without differences in gene expression showed significant isoform switching. Many genes with significant isoform switches ($$|dIF|$$|dIF|> 0.1) were associated with higher mortality risk, including PIGS, CASP3, LITAF, HBB and RUVBL2. The study for the first time described the landscape of isoform switching in sepsis, including differentially expressed isoform fractions between patients with and without sepsis and survivors and nonsurvivors. The biological consequences of isoform switching, including protein domain loss, signal peptide gain, and intron retention, were identified.
A preliminary study of suppression of candida infection by miconazole mucoadhesive tablets in oral or oropharyngeal cancer patients undergoing radiotherapy
Authors: Soutome Sakiko , Otsuru Mitsunobu , Kawashita Yumiko , Yoshimatsu Masako , Funahara Madoka , Murata Maho , Ukai Takashi , Umeda Masahiro , Saito Toshiyuki 
Published: June 2022

AbstractElevated numbers of candida in the oral cavity often lead to oral candidiasis development in patients undergoing radiotherapy for oral or oropharyngeal cancer. This study aimed to verify the effect of miconazole mucoadhesive tablets on suppression of oral candida infection during radiotherapy. For this preliminary interventional study, miconazole mucoadhesive tablets were attached to the oral mucosa for 14 days from when grade 2 oral mucositis appeared in patients with oral or oropharyngeal cancer receiving radiotherapy, and the incidence of oral candidiasis was investigated. Various clinical factors were examined; univariate and multivariate Cox regression analyses were performed to investigate and compare the efficacy of this drug in preventing oral candidiasis with results of our previous study as historical control. Miconazole mucoadhesive tablets were administered to 18 patients, and oral candidiasis was observed in one patient (5.6%) after treatment completion. Among 144 historical control patients, 43 (29.9%) developed oral candidiasis. Multivariate Cox regression showed that miconazole mucoadhesive tablets significantly reduced oral candidiasis development during radiotherapy (p = 0.049, Hazard ratio 0.136, 95% confidence interval 0.019–0.994). This preliminary study suggests the efficacy of miconazole mucoadhesive tablets in preventing oral candidiasis in oral or oropharyngeal cancer patients treated with radiotherapy.Trial registration: Japan Registry of Clinical Trials (jRCT), jRCTs071190023. Registered 3 September, 2019.
Effectiveness of a multi-loop traction device for colorectal endoscopic submucosal dissection performed by trainees: a pilot study
Authors: Jinushi Ryuhei , Tashima Tomoaki , Terada Rie , Miyaguchi Kazuya , Katsuda Hiromune , Ogawa Tomoya , Nakano Yuya , Saito Yoichi , Fujita Akashi , Tanisaka Yuki , Mizuide Masafumi , Mashimo Yumi , Kawasaki Tomonori , Ryozawa Shomei 
Published: June 2022

AbstractColorectal endoscopic submucosal dissection (ESD) is a difficult procedure, and its introduction to trainees has been debated. Although the criteria for performing colorectal ESD vary among institutions, it is often allowed after gaining experience performing surgeries in animals and upper gastrointestinal ESD. This pilot study aimed to compare the treatment outcomes of ESD performed by trainees using the multi-loop traction device (MLTD group) and those of conventional ESD performed by experts (control group). It also aimed to determine whether the MLTD can be used to safely introduce colorectal ESD to trainees. We included 26 colorectal ESD patients (13 in the MLTD group and 13 in the control group) treated at our hospital from October to December 2021. There were no significant differences in the procedure time (50 min vs. 30 min), dissection speed (19.9 mm2/min vs. 28.7 mm2/min), and intraoperative perforation (0% vs. 0%) of the two groups. Furthermore, the rate of ESD self-completion in the MLTD group was 100%. Therefore, the use of the MLTD allowed the safe introduction of colorectal ESD, even among endoscopists with no experience performing colorectal ESD. Consequently, the use of the MLTD may replace animal and upper gastrointestinal ESD when introducing colorectal ESD to trainees.
Association between germline variants and somatic mutations in colorectal cancer
Authors: Barfield Richard , Qu Conghui , Steinfelder Robert S. , Zeng Chenjie , Harrison Tabitha A. , Brezina Stefanie , Buchanan Daniel D. , Campbell Peter T. , Casey Graham , Gallinger Steven , Giannakis Marios , Gruber Stephen B. , Gsur Andrea , Hsu Li , Huyghe Jeroen R. , Moreno Victor , Newcomb Polly A. , Ogino Shuji , Phipps Amanda I. , Slattery Martha L. , Thibodeau Stephen N. , Trinh Quang M. , Toland Amanda E. , Hudson Thomas J. , Sun Wei , Zaidi Syed H. , Peters Ulrike 
Published: June 2022

AbstractColorectal cancer (CRC) is a heterogeneous disease with evidence of distinct tumor types that develop through different somatically altered pathways. To better understand the impact of the host genome on somatically mutated genes and pathways, we assessed associations of germline variations with somatic events via two complementary approaches. We first analyzed the association between individual germline genetic variants and the presence of non-silent somatic mutations in genes in 1375 CRC cases with genome-wide SNPs data and a tumor sequencing panel targeting 205 genes. In the second analysis, we tested if germline variants located within previously identified regions of somatic allelic imbalance were associated with overall CRC risk using summary statistics from a recent large scale GWAS (n≃125 k CRC cases and controls). The first analysis revealed that a variant (rs78963230) located within a CNA region associated with TLR3 was also associated with a non-silent mutation within gene FBXW7. In the secondary analysis, the variant rs2302274 located in CDX1/PDGFRB frequently gained/lost in colorectal tumors was associated with overall CRC risk (OR = 0.96, p = 7.50e-7). In summary, we demonstrate that an integrative analysis of somatic and germline variation can lead to new insights about CRC.
Biofinder detects biological remains in Green River fish fossils from Eocene epoch at video speed
Authors: Misra Anupam K. , Rowley Sonia J. , Zhou Jie , Acosta-Maeda Tayro E. , Dasilveira Luis , Ravizza Gregory , Ohtaki Kenta , Weatherby Tina M. , Trimble A. Zachary , Boll Patrick , Porter John N. , McKay Christopher P. 
Published: June 2022

AbstractThe “Search for life”, which may be extinct or extant on other planetary bodies is one of the major goals of NASA planetary exploration missions. Finding such evidence of biological residue in a vast planetary landscape is an enormous challenge. We have developed a highly sensitive instrument, the “Compact Color Biofinder”, which can locate minute amounts of biological material in a large area at video speed from a standoff distance. Here we demonstrate the efficacy of the Biofinder to detect fossils that still possess strong bio-fluorescence signals from a collection of samples. Fluorescence images taken by the Biofinder instrument show that all Knightia spp. fish fossils analysed from the Green River formation (Eocene, 56.0–33.9 Mya) still contain considerable amounts of biological residues. The biofluorescence images support the fact that organic matter has been well preserved in the Green River formation, and thus, not diagenetically replaced (replaced by minerals) over such a significant timescale. We further corroborated results from the Biofinder fluorescence imagery through Raman and attenuated total reflection Fourier-transform infrared (ATR-FTIR) spectroscopies, scanning electron microscopy, energy dispersive X-ray spectroscopy (SEM–EDS), and fluorescence lifetime imaging microscopy (FLIM). Our findings confirm once more that biological residues can survive millions of years, and that using biofluorescence imaging effectively detects these trace residues in real time. We anticipate that fluorescence imaging will be critical in future NASA missions to detect organics and the existence of life on other planetary bodies.
Lipopolysaccharide-induced murine lung injury results in long-term pulmonary changes and downregulation of angiogenic pathways
Authors: Tsikis S. T. , Fligor S. C. , Hirsch T. I. , Pan A. , Yu L. J. , Kishikawa H. , Joiner M. M. , Mitchell P. D. , Puder M. 
Published: June 2022

AbstractAcute respiratory distress syndrome is the most severe form of acute lung injury (ALI) and is associated with significant mortality. Lipopolysaccharide (LPS)-induced injury is a valuable murine model of ALI but there is a paucity of data on lung regeneration and the role of angiogenic signaling involving vascular endothelial growth factor (VEGF). Eight-week-old male C57BL/6J mice were randomized to receive intratracheal instillation of either LPS or isovolumetric phosphate buffered saline as a vehicle control. Mice were observed at a single follow-up time-point that was either short-term (24 h or 4 days) or long-term (7 days or 4 weeks). On pulmonary function testing, LPS-treated mice had increased compliance at 4 weeks post-instillation, which correlated with decreased vascularization and with time-dependent, progressive decrease in alveolarization. Treadmill exercise tolerance testing demonstrated impaired performance at 24 h, 4 days and 4 weeks following LPS exposure. On lung protein analysis, LPS instillation decreased VEGF expression at up to 4 weeks, and decreased activation of its key receptor, VEGFR2 at 7 days and 4 weeks post-instillation. Together, these data provide insight on long-term pulmonary functional outcomes 4 weeks after ALI and identify angiogenic proteins as possible therapeutic targets following lung injury.
The tumor mutational landscape of BRCA2-deficient primary and metastatic prostate cancer
Authors: Kensler Kevin H. , Baichoo Shakuntala , Pathania Shailja , Rebbeck Timothy R. 
Published: June 2022

AbstractCarriers of germlineBRCA2pathogenic sequence variants have elevated aggressive prostate cancer risk and are candidates for precision oncology treatments. We examined whetherBRCA2-deficient (BRCA2d) prostate tumors have distinct genomic alterations compared withBRCA2-intact (BRCA2i) tumors. Among 2536 primary and 899 metastatic prostate tumors from the ICGC, GENIE, and TCGA databases, we identified 138 primary and 85 metastaticBRCA2dtumors. Total tumor mutation burden (TMB) was higher among primaryBRCA2dtumors, although pathogenic TMB did not differ by tumorBRCA2status. Pathogenic and total single nucleotide variant (SNV) frequencies atKMT2Dwere higher inBRCA2dprimary tumors, as was the total SNV frequency atKMT2DinBRCA2dmetastatic tumors. Homozygous deletions atNEK3,RB1, andAPCwere enriched inBRCA2dprimary tumors, andRB1deletions in metastaticBRCA2dtumors as well.TMPRSS2-ETV1fusions were more common inBRCA2dtumors. These results identify somatic alterations that hallmark etiological and prognostic differences betweenBRCA2dandBRCA2iprostate tumors.
Comparative metagenomics reveals expanded insights into intra- and interspecific variation among wild bee microbiomes
Authors: Shell Wyatt A. , Rehan Sandra M. 
Published: June 2022

AbstractThe holobiont approach proposes that species are most fully understood within the context of their associated microbiomes, and that both host and microbial community are locked in a mutual circuit of co-evolutionary selection. Bees are an ideal group for this approach, as they comprise a critical group of pollinators that contribute to both ecological and agricultural health worldwide. Metagenomic analyses offer comprehensive insights into an organism’s microbiome, diet, and viral load, but remain largely unapplied to wild bees. Here, we present metagenomic data from three species of carpenter bees sampled from around the globe, representative of the first ever carpenter bee core microbiome. Machine learning, co-occurrence, and network analyses reveal that wild bee metagenomes are unique to host species. Further, we find that microbiomes are likely strongly affected by features of their local environment, and feature evidence of plant pathogens previously known only in honey bees. Performing the most comprehensive comparative analysis of bee microbiomes to date we discover that microbiome diversity is inversely proportional to host species social complexity. Our study helps to establish some of the first wild bee hologenomic data while offering powerful empirical insights into the biology and health of vital pollinators.
Critical role of orbital hybridization in the Dzyaloshinskii-Moriya interaction of magnetic interfaces
Authors: Zhu Lijun , Zhu Lujun , Ma Xin , Li Xiaoqin , Buhrman Robert A. 
Published: June 2022

AbstractDzyaloshinskii-Moriya interaction (DMI), an interfacial spin-orbit coupling (ISOC)-related effect, has become foundational for spintronic research and magnetic memory and computing technologies. However, the underlying mechanism of DMI, including the quantitative role of ISOC, has remained a long-standing unsettled problem due to the great challenge in quantifying and widely tuning ISOC strength in a strong DMI material system. Here, we find that DMI, ISOC, and orbital hybridization at the model magnetic interface Au1-xPtx/Co can be quantified and tuned significantly at the same time through the composition of the Au1-xPtx, without varying the bulk SOC and the electronegativity. From this ability, we establish that the widespread expectation that DMI should scale in linear proportion to ISOC breaks down at the Au1-xPtx/Co interface where degree of orbital hybridization varies with the Au1-xPtx composition and that the unexpected DMI behaviors can be understood well by the critical role of orbital hybridization. Our study provides a quantitative frame for comprehensively understanding interfacial DMI of various magnetic interfaces and establishes orbital hybridization as a new degree of freedom for controlling DMI in high-performance chiral domain wall/skyrmion devices and ultrafast magnetic tunnel junctions.
Short vs. long chains competition during “grafting to” process from melt
Authors: Chiarcos Riccardo , Antonioli Diego , Gianotti Valentina , Laus Michele , Munaò Gianmarco , Milano Giuseppe , De Nicola Antonio , Perego Michele 
Published: June 2022

A preferential grafting of short chains occurs during the “grafting to” reaction of hydroxy terminated P(S-st-MMA) blends consisting of short and long chains. The enrichment is enhanced when the chain length difference increases.
A self‐contained self‐protected ±70 V voltage‐to‐current converter with ±0.2% non‐linearity
Authors: Xiao Zhiming , Zhai Dengfu , Yang Junzhong , Yang Sen , Wu Weiguo , Hu Weibo , Luo Feng 
Published: June 2022

AbstractThis paper presents a self‐protected wide‐range bi‐directional voltage‐to‐current (V–I) converter. The proposed V–I converter is a self‐contained cell that operates independently and implements high precision conversion with a transconductance set by resistors. Compared with conventional structures, the proposed scheme features safety and reliability. The conversion range is widened since the internal biasing current is not starved and is adaptively set based on the input voltage. The proposed V–I structure was fabricated in a 0.18‐µm Bipolar‐CMOS‐DMOS (BCD) process with a die area of 0.0825 mm2. The measured non‐linearity across an input voltage range from −70 to 70 V was within ±0.2%. The total harmonic distortion was −63 dB at 1 kHz and the delay of conversion was within 3 µs.
Analytical modelling of one cage rotor induction motor for electric submersible pumps
Authors: Rezaee‐Alam Farhad , Nazari Marashi Abbas , Dehafarin Abolfazl , Kanzi Khalil , Roozbehani Sam 
Published: June 2022

AbstractA new hybrid analytical model (HAM) based on conformal mapping (CM) method and magnetic equivalent circuit (MEC) model is presented in this paper for electromagnetic modelling of cage rotor induction motors (CRIMs) used in electric submersible pumps (ESPs). For every operating point, the iron parts are modelled with a non‐linear MEC model to calculate the equivalent virtual currents, which represent the influence of magneto motive force (MMF) drops and MMF sources in stator and rotor cores. The effects of the equivalent virtual currents on the air‐gap magnetic field are then considered using the CM method and Hague's solution. This approach for calculating the air‐gap field is also used to prepare a 3‐D lookup table (3‐D LUT) for each element of inductance matrix and derivative of inductance matrix in terms of rotor position. These LUTs are then used for transient modelling and analysis of CRIM under no‐load and loading conditions. The accuracy of proposed HAM is validated by comparing the results obtained through HAM with corresponding results obtained from finite element method and experiment set‐up.
Gravitoturbulent dynamo in global simulations of gaseous disks
Authors: Béthune William , Latter Henrik 
Published: June 2022

Context. The turbulence driven by gravitational instabilities (GIs) can amplify magnetic fields in massive gaseous disks. This GI dynamo may appear in young circumstellar disks, whose weak ionization challenges other amplification routes, as well as in active galactic nuclei. Although regarded as a large-scale dynamo, only local simulations have so far described its kinematic regime.
Aims. We study the GI dynamo in global magnetohydrodynamic (MHD) models of accretion disks, focusing on its kinematic phase.
Methods. We perform resistive MHD simulations with the PLUTO code for different radiative cooling times and electrical resistivities. A weak magnetic field seeds the dynamo, and we adopt mean-field and heuristic models to capture its essence.
Results. We recover the same induction process leading to magnetic field amplification as previously identified in local simulations. The dynamo is, however, global in nature, connecting distant annuli of the disk via a large-scale dynamo mode of a fixed growth rate. This large-scale amplification can be described by a mean-field model that does not rely on conventional α-Ω effects. When varying the disk parameters we find an optimal resistivity that facilitates magnetic amplification, whose magnetic Reynolds number, ℛm ≲ 10, is substantially smaller than in local simulations. Unlike local simulations, we find an optimal cooling rate and the existence of global oscillating dynamo modes. The nonlinear saturation of the dynamo puts the disk in a strongly magnetized turbulent state on the margins of the effective range of GI. In our simulations, the accretion power eventually exceeds the threshold required by local thermal balance against cooling, leaving the long-term nonlinear outcome of the GI dynamo uncertain.
The interstellar medium of high-redshift galaxies: Gathering clues from C III] and [C II] lines
Authors: Markov V. , Carniani S. , Vallini L. , Ferrara A. , Pallottini A. , Maiolino R. , Gallerani S. , Pentericci L. 
Published: June 2022

Context.A tight relation between [C II] 158 μm line luminosity and the star formation rate (SFR) has been observed for local galaxies. At high redshift (z > 5), galaxies instead deviate downwards from the local Σ[C II]− ΣSFRrelation. This deviation might be caused by different interstellar medium (ISM) properties in galaxies at early epochs.Aims.To test this hypothesis, we combined the [C II] and SFR data with C III] 1909 Å line observations and our physical models. We additionally investigated how ISM properties, such as burstiness,κs, total gas density,n, and metallicity,Z, affect the deviation from the Σ[C II]− ΣSFRrelation in these sources.Methods.We present the VLT/X-shooter observations targeting the C III]λ1909 line emission in three galaxies at 5.5 < z < 7.0. We include archival X-shooter data of two other sources at 5.5 < z < 7.0 and the VLT/MUSE archival data of six galaxies atz ∼ 2. We extend our sample of galaxies with eleven star-forming systems at 6 < z < 7.5, with either C III] or [C II] detection reported in the literature.Results.We detected C III]λλ1907, 1909 line emission in HZ10 and we derived the intrinsic, integrated flux of the C III]λ1909 line. We constrained the ISM properties for our sample of galaxies,κs,n, andZ, by applying our physically motivated model based on the MCMC algorithm. For the most part, high-zstar-forming galaxies show subsolar metallicities. The majority of the sources have log(κs) ≳ 1, that is, they overshoot the Kennicutt–Schmidt (KS) relation by about one order of magnitude.Conclusions.Our findings suggest that the whole KS relation might be shifted upwards at early times. Furthermore, all the high-zgalaxies of our sample lie below the Σ[C II]− ΣSFRlocal relation. The total gas density,n, shows the strongest correlation with the deviation from the local Σ[C II]− ΣSFRrelation, namely, low-density high-zsystems have lower [C II] surface brightness, in agreement with theoretical models.
Wideband Acoustic Absorbance in Otosclerosis: Does Stapedotomy Restore Normal Tympanic Cavity Function?*
Authors: Durante Alessandra Spada , Nascimento Polyana Cristiane , Almeida Katia de , Servilha Thamyris Rosati , Marçal Gil Junqueira , Neto Osmar Mesquita de Sousa 
Published: June 2022

Abstract
Introduction Otosclerosis is characterized by the fixation of the stapes to the oval window, thereby impairing acoustic signal absorbance. A commonly used surgical technique for improving hearing in cases of otosclerosis is stapedotomy. However, it is unclear whether this surgery restores all the physical characteristics of the tympano-ossicular system.
Objective To evaluate the tympano-ossicular system in individuals with fenestral otosclerosis pre and poststapedotomy using wideband tympanometry.
Method A total of 47 individuals and 71 ears were assessed. The subjects were divided into three groups: presurgery otosclerosis; postsurgery; and a control group of normal-hearing adults. A handheld tympanometer with a wideband module (226–8,000 Hz) was used to take measurements at ambient pressure and under pressurized conditions. The level of statistical significance adopted was p ≤ 0.05.
Results Acoustic absorbance at 226 Hz was low for all groups. At frequencies in the range 630 to 5,040 Hz, each group had a characteristic absorbance curve, allowing them to be distinguished from one another. In the presurgery group, absorbance values were below normal levels, with energy absorbance below 10%. Low energy absorbance was most evident at 1,000 Hz in the presurgery group, but this was not observed in the postsurgery group. Although there was an improvement in hearing, the surgery failed to restore the tympano-ossicular system to normal.
Conclusion Wideband acoustic absorbance proved able to differentiate normal ears and otosclerotic ears pre and postsurgery, under both ambient pressure and pressurized conditions.