bluuebunny/crossref_metadata_2025_split huggingface dataset:
Spectral analysis of the AMXP IGR J17591–2342 during its 2018 outburst
Authors: Manca A , Gambino A F , Sanna A , Jaisawal G K , Di Salvo T , Iaria R , Mazzola S M , Marino A , Anitra A , Bozzo E , Riggio A , Burderi L 
Published: December 2022

ABSTRACT
The Accreting Millisecond X-ray Pulsar IGR J17591–2342 is a Low Mass X-ray Binary (LMXB) system that went in outburst on 2018 August and it was monitored by the NICER observatory and partially by other facilities. We aim to study how the spectral emission of this source evolved during the outburst by exploiting the whole X-ray data repository of simultaneous observations. The continuum emission of the combined broad-band spectra is on average well described by an absorbed Comptonization component scattering blackbody-distributed photons peaking at (0.8 ± 0.5) keV by a moderately optically thick corona (τ = 2.3 ± 0.5) with temperature of (34 ± 9) keV. A blackbody component with temperature and radial size of (0.8 ± 0.2) keV and (3.3 ± 1.5) km, respectively, is required by some of the spectra and suggests that part of the central emission, possibly a fraction of the neutron star surface, is not efficiently scattered by the corona. The continuum at low energies is characterized by significant residuals suggesting the presence of an absorption edge of O viii and of emission lines of Ne ix ions. Moreover, broad Fe i and Fe xxv Kα emission lines are detected at different times of the outburst, suggesting the presence of reflection in the system.
Importance of intracluster scattering and relativistic corrections from tSZ effect with cosmic infrared background
Authors: Acharya Sandeep Kumar , Chluba Jens 
Published: December 2022

ABSTRACT
The Sunyaev–Zeldovich effect towards clusters of galaxies has become a standard probe of cosmology. It is caused by the scattering of photons from the cosmic microwave background (CMB) by the hot cluster electron gas. In a similar manner, other photon backgrounds can be scattered when passing through the cluster medium. This problem has been recently considered for the radio and the cosmic infrared background. Here, we revisit the discussion of the cosmic infrared background (CIB) including several additional effects that were omitted before. We discuss the intracluster scattering of the CIB and the role of relativistic temperature corrections to the individual cluster and all-sky averaged signals. We show that the all-sky CIB distortion introduced by the scattering of the photon field was underestimated by a factor of ≃1.5 due to neglecting the intracluster scattering contribution. The CIB photons can scatter with the thermal electrons of both the parent halo or another halo, meaning that there are two ways to gain energy. Therefore, energy is essentially transferred twice from the thermal electrons to the CIB. We carefully clarify the origin of various effects in the calculation of the average CIB and also scattered signals. The single-cluster CIB scattering signal also exhibits a clear redshift dependence, which can be used in cosmological analyses, as we describe both analytically and numerically. This may open a new way for cosmological studies with future CMB experiments.
Gravitationally lensed quasars in Gaia – IV. 150 new lenses, quasar pairs, and projected quasars
Authors: Lemon C , Anguita T , Auger-Williams M W , Courbin F , Galan A , McMahon R , Neira F , Oguri M , Schechter P , Shajib A , Treu T , Agnello A , Spiniello C 
Published: December 2022

ABSTRACT
We report the spectroscopic follow-up of 175 lensed quasar candidates selected using Gaia Data Release 2 observations following Paper III of this series. Systems include 86 confirmed lensed quasars and a further 17 likely lensed quasars based on imaging and/or similar spectra. We also confirm 11 projected quasar pairs and 11 physical quasar pairs, while 25 systems are left as unclassified quasar pairs – pairs of quasars at the same redshift, which could be either distinct quasars or potential lensed quasars. Especially interesting objects include eight quadruply imaged quasars of which two have BAL sources, an apparent triple, and a doubly lensed LoBaL quasar. The source redshifts and image separations of these new lenses range between 0.65–3.59 and 0.78–6.23 arcsec, respectively. We compare the known population of lensed quasars to an updated mock catalogue at image separations between 1 and 4 arcsec, showing a very good match at z &lt; 1.5. At z &gt; 1.5, only 47 per cent of the predicted number are known, with 56 per cent of these missing lenses at image separations below 1.5 arcsec. The missing higher redshift, small-separation systems will have fainter lensing galaxies, and are partially explained by the unclassified quasar pairs and likely lenses presented in this work, which require deeper imaging. Of the 11 new reported projected quasar pairs, 5 have impact parameters below 10 kpc, almost tripling the number of such systems, which can probe the innermost regions of quasar host galaxies through absorption studies. We also report four new lensed galaxies discovered through our searches, with source redshifts ranging from 0.62 to 2.79.
Mutations in the non-codingRNU4ATACgene affect the homeostasis and function of the Integrator complex
Authors: Almentina Ramos Shidi Fatimat , Cologne Audric , Delous Marion , Besson Alicia , Putoux Audrey , Leutenegger Anne-Louise , Lacroix Vincent , Edery Patrick , Mazoyer Sylvie , Bordonné Rémy 
Published: December 2022

AbstractVarious genetic diseases associated with microcephaly and developmental defects are due to pathogenic variants in the U4atac small nuclear RNA (snRNA), a component of the minor spliceosome essential for the removal of U12-type introns from eukaryotic mRNAs. While it has been shown that a few RNU4ATAC mutations result in impaired binding of essential protein components, the molecular defects of the vast majority of variants are still unknown. Here, we used lymphoblastoid cells derived from RNU4ATAC compound heterozygous (g.108_126del;g.111G&gt;A) twin patients with MOPD1 phenotypes to analyze the molecular consequences of the mutations on small nuclear ribonucleoproteins (snRNPs) formation and on splicing. We found that the U4atac108_126del mutant is unstable and that the U4atac111G&gt;A mutant as well as the minor di- and tri-snRNPs are present at reduced levels. Our results also reveal the existence of 3’-extended snRNA transcripts in patients’ cells. Moreover, we show that the mutant cells have alterations in splicing of INTS7 and INTS10 minor introns, contain lower levels of the INTS7 and INTS10 proteins and display changes in the assembly of Integrator subunits. Altogether, our results show that compound heterozygous g.108_126del;g.111G&gt;A mutations induce splicing defects and affect the homeostasis and function of the Integrator complex.
A versatile and convenient tool for regulation of DNA strand displacement and post-modification on pre-fabricated DNA nanodevices
Authors: Liao Yangwei , Hu Hao , Tang Xiaofeng , Qin Yang , Zhang Wei , Dong Kejun , Yan Bei , Mu Yaoqin , Li Longjie , Ming Zhihao , Xiao Xianjin 
Published: December 2022

Abstract
Toehold-mediated strand displacement and its regulatory tools are fundamental for DNA nanotechnology. However, current regulatory tools all need to change the original sequence of reactants, making the regulation inconvenient and cumbersome. More importantly, the booming development of DNA nanotechnology will soon promote the production of packaged and batched devices or circuits with specified functions. Regarding standardized, packaged DNA nanodevices, access to personalized post-modification will greatly help users, whereas none of the current regulatory tools can provide such access, which has greatly constrained DNA nanodevices from becoming more powerful and practical. Herein, we developed a novel regulation tool named Cap which has two basic functions of subtle regulation of the reaction rate and erasability. Based on these functions, we further developed three advanced functions. Through integration of all functions of Cap and its distinct advantage of working independently, we finally realized personalized tailor-made post-modification on pre-fabricated DNA circuits. A pre-fabricated dual-output DNA circuit was successfully transformed into an equal-output circuit, a signal-antagonist circuit and a covariant circuit according to our requirements. Taken together, Cap is easy to design and generalizable for all strand displacement-based DNA nanodevices. We believe the Cap tool will be widely used in regulating reaction networks and personalized tailor-made post-modification of DNA nanodevices.
Plasma endotrophin, reflecting tissue fibrosis, is associated with graft failure and mortality in KTRs: results from two prospective cohort studies
Authors: Kremer Daan , Alkaff Firas F , Post Adrian , Knobbe Tim J , Tepel Martin , Thaunat Olivier , Berger Stefan P , van den Born Jacob , Genovese Federica , Karsdal Morten A , Rasmussen Daniel G K , Bakker Stephan J L 
Published: December 2022

ABSTRACTBackgroundFibrosis is a suggested cause of graft failure and mortality among kidney transplant recipients (KTRs). Accumulating evidence suggests that collagen type VI is tightly linked to fibrosis and may be a marker of systemic fibrosis and ageing. We studied whether plasma endotrophin, a pro-collagen type VI fragment, is associated with graft failure and mortality among KTRs.MethodsIn cohort A (57% male, age 53 ± 13 years), we measured plasma endotrophin in 690 prevalent KTRs ≥1 year after transplantation. The non-overlapping cohort B included 500 incident KTRs with serial endotrophin measurements before and after kidney transplantation to assess trajectories and intra-individual variation of endotrophin.ResultsIn cohort A, endotrophin was higher in KTRs compared with healthy controls. Concentrations were positively associated with female sex, diabetes, cardiovascular disease, markers of inflammation and kidney injury. Importantly, endotrophin was associated with graft failure {hazard ratio [HR] per doubling 1.87 [95% confidence interval (CI) 1.07–3.28]} and mortality [HR per doubling 2.59 (95% CI 1.73–3.87)] independent of potential confounders. Data from cohort B showed that endotrophin concentrations strongly decrease after transplantation and remain stable during post-transplantation follow-up [intra-individual coefficient of variation 5.0% (95% CI 3.7–7.6)].ConclusionsPlasma endotrophin is strongly associated with graft failure and mortality among KTRs. These findings suggest a key role of abnormal extracellular matrix turnover and fibrosis in graft and patient prognosis among KTRs and highlight the need for (interventional) studies targeting the profibrotic state of KTRs. The intra-individual stability after transplantation indicates potential use of endotrophin as a biomarker and outcome measure of fibrosis.Trial registrationClinicalTrials.gov NCT02811835.
Efficacy and safety of interleukin-1 blockers in kidney transplant recipients with familial Mediterranean fever: a propensity score–matched cohort study
Authors: Mirioglu Safak , Dirim Ahmet Burak , Bektas Murat , Demir Erol , Tor Yavuz Burak , Ozluk Yasemin , Kilicaslan Isin , Oto Ozgur Akin , Yalcinkaya Yasemin , Caliskan Yasar , Artim-Esen Bahar , Yazici Halil , Inanc Murat , Turkmen Aydin , Gul Ahmet , Sever Mehmet Sukru 
Published: December 2022

ABSTRACT

Background
Data on use of interleukin (IL)-1 blockers in kidney transplant recipients (KTRs) with familial Mediterranean fever (FMF) are very limited. We aimed to evaluate the efficacy and safety of anakinra and canakinumab in the transplantation setting.

Methods
In this retrospective cohort study, we included KTRs who suffered from AA amyloidosis caused by FMF and treated with anakinra or canakinumab (study group, n = 36). Using propensity score matching, we selected 36 patients without FMF or amyloidosis from our database of 696 KTRs as the control group. Primary outcomes were patient and graft survival. Biopsy-confirmed graft rejection, changes in estimated glomerular filtration rate (eGFR), high-sensitivity CRP (hsCRP), erythrocyte sedimentation rate (ESR), proteinuria and number of monthly attacks were secondary outcomes.

Results
All KTRs with FMF began IL-1 blocker therapy with anakinra and nine (25%) were switched to canakinumab. Overall death was more frequent in the study group (19.4% vs 0%) (P = .005); however, overall graft loss was comparable between study (27.8%) and control groups (36.1%) (P = .448). Five- and 10-year graft survival rates were significantly higher in the study group (94.4% and 83.3%, respectively) than in the control group (77.8% and 63.9%, respectively) (P = .014 and P &lt; .001, respectively). Rejections were numerically lower in study group (8.3% vs 25%), but it did not reach to statistical significance (P = .058). When compared with the pre-treatment period, with IL-1 blockers, the number of attacks per month (P &lt; .001), and eGFR (P = .004), hsCRP (P &lt; .001) and ESR (P = .026) levels were lower throughout the follow-up, whereas proteinuria levels were not.

Conclusions
Anakinra and canakinumab are effective in KTRs suffering from FMF; however, the mortality rate may be of concern.
Hepatic Resection vs Particle Therapy as an Initial Treatment for Single Hepatocellular Carcinoma: Bi-Institutional Propensity Score-Matched Analysis
Authors: Omiya Satoshi , Komatsu Shohei , Terashima Kazuki , Yamasaki Nobuaki , Matsuo Yoshiro , Toyama Hirochika , Tokumaru Sunao , Okimoto Tomoaki , Fukumoto Takumi 
Published: December 2022

Background:
Curative treatment for hepatocellular carcinoma (HCC) is limited to hepatic resection (HR), radiofrequency ablation, and liver transplantation, while the value of particle therapy (PT) as an initial treatment remains unclear. This study aimed to compare the outcomes of HR and PT for single HCC.

Study Design:
A total of 554 patients with single HCC without vascular invasion were enrolled from January 2000 to December 2015. Patients underwent either HR (n = 279) or PT (n = 275) as initial treatments. A one-to-one propensity score matching (PSM) analysis was performed to evaluate the overall survival (OS) and progression-free survival (PFS) after dividing patients according to liver function as assessed by the modified albumin-bilirubin (mALBI) grade.

Results:
The median OS (130 vs. 85 month, p = 0.001) and PFS (47 vs. 30 month, p = 0.004) of HR were also significantly better than that of PT in the PSM cohort with mALBI grade 1/2a (n = 145 per group). Meanwhile, in a PSM cohort with mALBI grade 2b/3 (n = 53 per group), there were no significant differences in median OS and PFS between HR and PT.

Conclusion:
HR may be preferable as an initial treatment for patients with single HCC without vascular invasion, especially those with preserved liver function. PT can be an acceptable alternative to HR for patients without surgical indication and/or impaired liver function.
Proposal to reclassify Aquiflexum aquatile into a novel genus as Cognataquiflexum aquatile gen. nov., comb. nov., and description of Cognataquiflexum nitidum sp. nov. and Cognataquiflexum rubidum sp. nov., isolated from freshwater lakes on the Tibetan Plateau
Authors: Gao Peixin , Lu Huibin , Phurbu Dorji , Wu Qinglong , Xing Peng 
Published: December 2022

Thousands of lakes harbouring different characteristics (pH, salinity, temperature) are located on the Tibetan Plateau, and the mining of microbial resources inhabited in these lakes has great value. Two Gram-stain-negative, aerobic, rod-shaped, non-motile strains (LQ15WT and AIY15WT) were isolated from freshwater lakes on the Tibetan Plateau. Comparisons based on the 16S rRNA gene sequences showed that both strains LQ15WT and AIY15WT share 16S rRNA gene sequence similarities 98.4 % with

Aquiflexum aquatile

Z0201T, but only about 95.0 % with

Aquiflexum balticum

DSM 16537T. The 16S rRNA gene sequence similarity between strains LQ15WT and AIY15WT was 98.9 %. The phylogenetic tree reconstructed based on 16S rRNA gene sequences also showed that strains LQ15WT and AIY15WT take

A. aquatile

Z0201T as their closest neighbour and these three strains form a tight cluster. In the phylogenomic tree, the genus

Aquiflexum

was splited into two clusters by

Mariniradius saccharolyticus

. Strains LQ15WT, AIY15WT and

A. aquatile

Z0201T still formed a close cluster, and

A. balticum

DSM 16537T and

Aquiflexum lacus

CUG 91378T formed another cluster. The calculated OrthoANIu, average amino acid identity and digital DNA–DNA hybridization values among strains LQ15WT, AIY15WT,

A. aquatile

Z0201T,

A. balticum

DSM 16537T and

A. lacus

CUG 91378T were less than 91.0, 92.9 and 42.1 %, respectively. The major respiratory quinones of both strains LQ15WT and AIY15WT were MK-7 (32 %) and MK-8 (68 %), and their major fatty acids were iso-C15 : 0, C18 : 1
ω9c, summed feature 3 and summed feature 9. The predominant polar lipids of both strains were phosphatidylethanolamine, unidentified aminophospholipids, unidentified phospholipids and lipids. Strain AIY15WT also contained phosphatidylglycerol and unidentified glycolipid. Considering the distinct phylogenetic relationships and chemotaxonomic characteristics between strains

A. aquatile

Z0201T and

A. balticum

DSM 16537T, it is proposed to reclassify

A. aquatile

into a novel genus Cognataquiflexum gen. nov. as Cognataquiflexum aquatile comb. nov., and strains LQ15WT and AIY15WT should represent two independent novel species of the genus Cognataquiflexum, for which the names Cognataquiflexum nitidum sp. nov. (type strain: LQ15WT=CICC 24711T=JCM 34222T) and Cognataquiflexum rubidum sp. nov. (type strain: AIY15WT=CICC 24708T=JCM 34612T) are proposed.
Predicting Adverse Events in the Cardiothoracic Surgery Intensive Care Unit Using Machine Learning: Results and Challenges
Authors: Amal Saeed , Kramer Robert , Sawyer Douglas , Rabb Jaime B , Maurais Alanna S , Ross Cathy S. , Iribarne Alexander , Winslow Raimond L 
Published: December 2022

AbstractIt is highly important to anticipate impending problems in patients in the cardiothoracic intensive care unit (CTICU) and be proactive with respect to prediction of adverse events, enabling interventions to prevent them. In order to develop models that predict the occurrence of adverse events after cardiac surgery, a dataset of 9,237 patients was constructed of a single center’s Society of Thoracic Surgeons (STS) internal database. 1,383 of those patients had developed at least one of seven defined adverse events for this analysis. For the control set, we randomly picked 1,383 patients from the group who did not develop any adverse event. The ensemble learning algorithm, random forest, was applied and outperformed the best reported logistic regression models for similar task (c-statistic of ∼0.81), by achieving an AUC of 0.86 with a 95% CI of [0.81-0.90], specificity of 0.72, sensitivity of 0.82, PPV of 0.78 and NPV of 0.77. In the future, we plan to run a similar evaluation process on a multicenter dataset, and then use this static prediction model as a context for using time-evolving data to develop algorithms for real-time feedback to care teams. In acute care settings, such as the operating room and intensive care unit, the ability to anticipate potentially fatal complications will be enhanced by using supervised machine learning algorithms.
Identifying the neurodevelopmental and psychiatric signatures of genomic disorders associated with intellectual disability
Authors: Donnelly Nicholas A , Cunningham Adam C , Bracher-Smith Matthew , Chawner Samuel , Stochl Jan , Ford Tamsin , Raymond F Lucy , Escott-Price Valentina , van den Bree Marianne BM 
Published: December 2022

AbstractIntroductionGenomic conditions can be associated with developmental delay, intellectual disability and physical and mental health symptoms, but are individually rare and variable, which limits the use of standard clinical guidelines. A simple screening tool to identify young people with genetic conditions associated with neurodevelopmental disorders (ND-GC) who could benefit from further support would be of considerable value. We used machine learn approaches to address this question.MethodsA total of 489 individuals were included: 376 with a ND-GC, mean age=9.33, 63% male) and 113 unaffected siblings; mean age=10.35, 50% male). Primary carers completed detailed assessments of behavioural, neurodevelopmental and psychiatric symptoms and physical health conditions. Machine learning techniques (elastic net regression, random forests, support vector machines and artificial neural networks) were used to develop classifiers of ND-GC status using a limited set of variables. Exploratory Graph Analysis was used to understand associations within the final variable set.ResultsWe identified a set of 30 variables best discriminating between ND-GC carriers and control individuals, which formed 4 dimensions: Anxiety, Motor Development, Insomnia and Depression. All methods showed high discrimination accuracy with Linear Support Vector machines outperforming other methods (AUROC between 0.959 and 0.971).ConclusionsIn this study we developed models that identified a compact set of psychiatric and physical health measures that differentiate individuals with a ND-GC from controls and highlight the structure within these measures. This work is a step toward developing of a screening instrument to select young people with ND-GCs who might benefit from further specialist assessment.
Babesia microti with multiple resistance mutations detected in an immunocompromised patient receiving atovaquone prophylaxis
Authors: Holbrook Nolan R. , Klontz Erik H. , Adams Gordon C. , Schnittman Samuel R. , Issa Nicolas C. , Bond Sheila A. , Branda John A. , Lemieux Jacob E. 
Published: December 2022

AbstractWe reportBabesia microtigenomic sequences with multiple mutations in the atovaquone-target region of cytochrome b and the azithromycin-associated ribosomal protein L4, including newly identified mutations. The parasite was sequenced from an immunocompromised patient on prophylactic atovaquone forPneumocystispneumonia for several weeks before the diagnosis of babesiosis.
Predicting transcription factor activity using prior biological information
Authors: Estabrook Joseph , Yashar William M. , Holly Hannah D. , Somers Julia , Nikolova Olga , Barbur Özgün , Braun Theodore P. , Demir Emek 
Published: December 2022

ABSTRACTTranscription factors are critical regulators of cellular gene expression programs. Disruption of normal transcription factor regulation is associated with a broad range of diseases. In order to understand the mechanisms that underly disease pathogenesis, it is critical to detect aberrant transcription factor activity. We have developed Priori, a computational method to predict transcription factor activity from RNA sequencing data. Priori has several key advantages over existing methods. Priori utilizes literature-supported regulatory relationship information to identify known transcription factor target genes. Using these transcriptional relationships, Priori uses linear models to determine the impact and direction of transcription factor regulation on the expression of its target genes. In our work, we evaluated the ability of Priori and 16 other methods to detect aberrant activity from 124 single-gene perturbation experiments. We show that Priori identifies perturbed transcription factors with greater sensitivity and specificity than other methods. Furthermore, our work demonstrates that Priori can be used to discover significant determinants of survival in breast cancer as well as identify mediators of drug response in leukemia from primary patient samples.