bluuebunny/crossref_metadata_2025_split huggingface dataset:
CUT&RUNTools 2.0: a pipeline for single-cell and bulk-level CUT&RUN and CUT&Tag data analysis
Authors: Yu Fulong , Sankaran Vijay G , Yuan Guo-Cheng 
Published: July 2021

Abstract

Motivation
Genome-wide profiling of transcription factor binding and chromatin states is a widely-used approach for mechanistic understanding of gene regulation. Recent technology development has enabled such profiling at single-cell resolution. However, an end-to-end computational pipeline for analyzing such data is still lacking.

Results
Here, we have developed a flexible pipeline for analysis and visualization of single-cell CUT&Tag and CUT&RUN data, which provides functions for sequence alignment, quality control, dimensionality reduction, cell clustering, data aggregation and visualization. Furthermore, it is also seamlessly integrated with the functions in original CUT&RUNTools for population-level analyses. As such, this provides a valuable toolbox for the community.

Availability and implementation
https://github.com/fl-yu/CUT-RUNTools-2.0.

Supplementary information
Supplementary data are available at Bioinformatics online.
Small vs. large eggs: comparative population connectivity and demographic history along a depth gradient in deep-sea crangonid Argis shrimps
Authors: Fujita Junta , Drumm David T , Iguchi Akira , Tominaga Osamu , Kai Yoshiaki , Yamashita Yoh 
Published: July 2021

Abstract
The crangonid shrimps Argis hozawai, A. lar and A. toyamaensis, co-distributed in the Sea of Japan, exhibit intriguing differences in geographical and bathymetric distributions and in reproductive biology. Argis hozawai (150–250 m depth) and A. lar (200–300 m) are broadly distributed in the north-western Pacific Ocean and spawn relatively large numbers of small eggs, whereas A. toyamaensis (250–2000 m) is distributed in the Sea of Japan and spawns a small number of large eggs. We examined the relationship between egg size and dispersal patterns in the deep sea by comparing genetic population structures using mitochondrial DNA sequence variation. We found little or no genetic divergence within the Sea of Japan for A. hozawai and A. lar, whereas there was a slight but significantly higher genetic differentiation in A. toyamaensis. This suggests that A. toyamaensis has lower dispersal ability than A. hozawai and A. lar, and therefore might maximize larval survival through larger size at hatching, with either direct or abbreviated larval development, to adapt to the deep-sea environment in the Sea of Japan. We also detected the effects of drastic environmental changes during the Pleistocene glacial periods on their demographic processes in the Sea of Japan.
Comparison of risk prediction models in infarct-related cardiogenic shock
Authors: Freund Anne , Pöss Janine , de Waha-Thiele Suzanne , Meyer-Saraei Roza , Fuernau Georg , Eitel Ingo , Feistritzer Hans-Josef , Rubini Maria , Huber Kurt , Windecker Stephan , Montalescot Gilles , Oldroyd Keith , Noc Marko , Zeymer Uwe , Ouarrak Taoufik , Schneider Steffen , Baran David A , Desch Steffen , Thiele Holger 
Published: July 2021

AbstractAimsSeveral prediction models have been developed to allow accurate risk assessment and provide better treatment guidance in patients with infarct-related cardiogenic shock (CS). However, comparative data between these models are still scarce. The objective of the study is to externally validate different risk prediction models in infarct-related CS and compare their predictive value in the early clinical course.Methods and resultsThe Simplified Acute Physiology Score (SAPS) II Score, the CardShock score, the IABP-SHOCK II score, and the Society for Cardiovascular Angiography and Intervention (SCAI) classification were each externally validated in a total of 1055 patients with infarct-related CS enrolled into the randomized CULPRIT-SHOCK trial or the corresponding registry. The primary outcome was 30-day all-cause mortality. Discriminative power was assessed by comparing the area under the curves (AUC) in case of continuous scores. In direct comparison of the continuous scores in a total of 161 patients, the IABP-SHOCK II score revealed best discrimination [area under the curve (AUC = 0.74)], followed by the CardShock score (AUC = 0.69) and the SAPS II score, giving only moderate discrimination (AUC = 0.63). All of the three scores revealed acceptable calibration by Hosmer–Lemeshow test. The SCAI classification as a categorical predictive model displayed good prognostic assessment for the highest risk group (Stage E) but showed poor discrimination between Stages C and D with respect to short-term-mortality.ConclusionBased on the present findings, the IABP-SHOCK II score appears to be the most suitable of the examined models for immediate risk prediction in infarct-related CS. Prospective evaluation of the models, further modification, or even development of new scores might be necessary to reach higher levels of discrimination.
Left atrial appendage thrombus and cerebrovascular events post-transcatheter aortic valve implantation
Authors: van Wiechen Maarten P , Faure Marguerite E , Hokken Thijmen W , Ooms Joris F , de Ronde-Tillmans Marjo J , Hirsch Alexander , Daemen Joost , de Jaegere Peter P , Budde Ricardo P J , Van Mieghem Nicolas M 
Published: July 2021

AbstractAimsTo elucidate the frequency and clinical impact of left atrial appendage thrombus (LAAT) in patients set for transcatheter aortic valve implantation (TAVI).Methods and resultsAll patients undergoing TAVI between January 2014 and June 2020 with analysable multislice computed tomography (MSCT) for LAAT were included. Baseline and procedural characteristics were collected, pre-procedural MSCT’s were retrospectively analysed for LAAT presence. The primary endpoint was defined as the cumulative incidence of any cerebrovascular event (stroke or transient ischaemic attack) within the first year after TAVI. A Cox proportional hazards model was used to identify predictors.A total of 1050 cases had analysable MSCT. Median age was 80 [interquartile range (IQR) 74–84], median Society of Thoracic Surgeons’ Predicted Risk Of Mortality (STS-PROM) was 3.4% (IQR 2.3–5.5). Thirty-six percent were on oral anticoagulant therapy for atrial fibrillation (AF). LAAT was present in 48 (4.6%) of cases. Patients with LAAT were at higher operative risk [STS-PROM: 4.9% (2.9–7.1) vs. 3.4% (2.3–5.5), P = 0.01], had worse systolic left ventricular function [EF 52% (35–60) vs. 55% (45–65), P = 0.01] and more permanent pacemakers at baseline (35% vs. 10%, P &lt; 0.01). All patients with LAAT had a history of AF and patients with LAAT were more often on vitamin K antagonist-treatment than patients without LAAT [43/47 (91%) vs. 232/329 (71%), P &lt; 0.01]. LAAT [hazard ratio (HR) 2.94 (1.39–6.22), P &lt; 0.01] and the implantation of more than one valve [HR 4.52 (1.79–11.25), P &lt; 0.01] were independent predictors for cerebrovascular events.ConclusionPatients with MSCT-identified LAAT were at higher risk for cerebrovascular events during the first year after TAVI.
Mycobacterium tuberculosis (MTB) antigen-induced upregulation of interleukin-35 expression in patients with MTB infection: In vitro blockade of the effects of interleukin-35 on T lymphocyte subsets
Authors: Jiang Hongbin , Cui Beinian , Zhang Jun 
Published: July 2021

ABSTRACT
Immunosuppressive interleukin-35 (IL-35) serum concentrations were analyzed in patients with active pulmonary Mycobacterium tuberculosis (MTB) infections (PTB), PTB patients after two months treatment (stable PTB) and healthy controls. IL-35 concentrations were highest in active PTB followed by stable PTB cases and lowest in healthy control participants (all P &lt; 0.01). The same trents were found for supernatants of isolated blood mononuclear cells (PBMCs), with additional enhancements after MTB antigen stimulation only for PBMCs of active and stable PTB patients (P &lt; 0.001), for EBI3 and IL-12a transcriptions in PBMCs (P &lt; 0.001) and percentages of EBI3 expressing (CD4 + CD25 + Foxp3+) regulatory T cells (Treg) (P &lt; 0.001). IL-35 antibody applications significantly reversed MTB antigen stimulated IL-35 and IL-10 expression in PBMCs of active and stable PTB patients, and reduced Foxp3 expression in CD4 + CD25 + cells and EBI3 expression in Treg cells, but had no effects on healthy control cells. The percentages of Th1 and Th17 cells in CD4 + cells were enhanced after MTB antigen stimulation of cells taken from active and stable PTB patients, which were partly increased only for Th1 cells after IL-35 antibody exposure. MTB antigen-driven upregulation of IL-35 may lead to reduced immune surveillance in PTB patients.
Structure of the northwestern North Anatolian Fault Zone imaged via teleseismic scattering tomography
Authors: Rost S , Houseman G A , Frederiksen A W , Cornwell D G , Kahraman M , Altuncu Poyraz S , Teoman U M , Thompson D A , Türkelli N , Gülen L , Utkucu M , Wright T J 
Published: July 2021

SUMMARYInformation on fault zone structure is essential for our understanding of earthquake mechanics, continental deformation and seismic hazard. We use the scattered seismic wavefield to study the subsurface structure of the North Anatolian Fault Zone (NAFZ) in the region of the 1999 İzmit and Düzce ruptures using data from an 18-month dense deployment of seismometers with a nominal station spacing of 7 km. Using the forward- and back-scattered energy that follows the direct P-wave arrival from teleseismic earthquakes, we apply a scattered wave inversion approach and are able to resolve changes in lithospheric structure on a scale of 10 km or less in an area of about 130 km by 100 km across the NAFZ. We find several crustal interfaces that are laterally incoherent beneath the surface strands of the NAFZ and evidence for contrasting crustal structures either side of the NAFZ, consistent with the presence of juxtaposed crustal blocks and ancient suture zones. Although the two strands of the NAFZ in the study region strike roughly east–west, we detect strong variations in structure both north–south, across boundaries of the major blocks, and east–west, parallel to the strike of the NAFZ. The surface expression of the two strands of the NAFZ is coincident with changes on main interfaces and interface terminations throughout the crust and into the upper mantle in the tomographic sections. We show that a dense passive network of seismometers is able to capture information from the scattered seismic wavefield and, using a tomographic approach, to resolve the fine scale structure of crust and lithospheric mantle even in geologically complex regions. Our results show that major shear zones exist beneath the NAFZ throughout the crust and into the lithospheric mantle, suggesting a strong coupling of strain at these depths.
The assessment of Pseudomonas aeruginosa lectin LecA binding characteristics of divalent galactosides using multiple techniques
Authors: Zaree Pouya , Sastre Torano Javier , de Haan Cornelis A M , Scheltema Richard A , Barendregt Arjan , Thijssen Vito , Yu Guangyun , Flesch Frits , Pieters Roland J 
Published: July 2021

Abstract
Pseudomonas aeruginosa is a widespread opportunistic pathogen that is capable of colonizing various human tissues and is resistant to many antibiotics. LecA is a galactose binding tetrameric lectin involved in adhesion, infection and biofilm formation. This study reports on the binding characteristics of mono- and divalent (chelating) ligands to LecA using different techniques. These techniques include affinity capillary electrophoresis, bio-layer interferometry, native mass spectrometry and a thermal shift assay. Aspects of focus include: affinity, selectivity, binding kinetics and residence time. The affinity of a divalent ligand was determined to be in the low-nanomolar range for all of the used techniques and with a ligand residence time of approximately 7 h, while no strong binding was seen to related lectin tetramers. Each of the used techniques provides a unique and complementary insight into the chelation based binding mode of the divalent ligand to the LecA tetramer.
Finding Fault in the Law of Unfair Dismissal: The Insubstantiality of Reasons for Dismissal
Authors: Collins Philippa M 
Published: July 2021

Abstract
The question of whether an Employment Tribunal should accept the employer’s reason for a dismissal has received little attention in studies of the law of unfair dismissal. This shortage of analysis continues even though this stage holds the potential to decide the outcome of the case. The current approach to the interpretation of the five potentially fair reasons for a dismissal is to leave them undefined, allowing employers broad scope to rely upon almost any reason to justify their decision to dismiss an employee. This piece demonstrates how the established view of this stage of the fairness process is a missed opportunity and fails to deliver the full potential of the law of unfair dismissal as it was drafted. In order to protect the fundamental right not to be unjustifiably dismissed, a threshold of substantiality should run throughout the reasons for dismissal—assessed objectively by the Tribunal judge. The assertion of such a threshold is particularly necessary under the open-ended ‘some other substantial reason’ category. The piece turns then to disciplinary dismissals, arguing that the current approach results in fair dismissals, first, for minor misconduct and, second, because of conduct with no connection to the employment relationship. Two solutions to these particular problems will be put forward: a tailored legislative amendment and a contractual reading of the existing section. Both approaches would introduce an element of substantive fairness that is currently absent and place some confines on the scope of the employer’s managerial prerogative by restraining the reasons for which they may fairly dismiss.
SARS-CoV-2 coinfection with additional respiratory virus does not predict severe disease: a retrospective cohort study
Authors: Chekuri Sweta , Szymczak Wendy A , Goldstein D Yitzchak , Nori Priya , Marrero Rolon Rebecca , Spund Brian , Singh-Tan Sumeet , Mohrmann Laurel , Assa Andrei , Southern William N , Baron Sarah W 
Published: July 2021

AbstractBackgroundThe coronavirus disease 2019 (COVID-19) pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) claimed over 4 million lives by July 2021 and continues to pose a serious public health threat.ObjectivesOur retrospective study utilized respiratory pathogen panel (RPP) results in patients with SARS-CoV-2 to determine if coinfection (i.e. SARS-CoV-2 positivity with an additional respiratory virus) was associated with more severe presentation and outcomes.MethodsAll patients with negative influenza/respiratory syncytial virus testing who underwent RPP testing within 7 days of a positive SARS-CoV-2 test at a large, academic medical centre in New York were examined. Patients positive for SARS-CoV-2 with a negative RPP were compared with patients positive for SARS-CoV-2 and positive for a virus by RPP in terms of biomarkers, oxygen requirements and severe COVID-19 outcome, as defined by mechanical ventilation or death within 30 days.ResultsOf the 306 SARS-CoV-2-positive patients with RPP testing, 14 (4.6%) were positive for a non-influenza virus (coinfected). Compared with the coinfected group, patients positive for SARS-CoV-2 with a negative RPP had higher inflammatory markers and were significantly more likely to be admitted (P = 0.01). Severe COVID-19 outcome occurred in 111 (36.3%) patients in the SARS-CoV-2-only group and 3 (21.4%) patients in the coinfected group (P = 0.24).ConclusionsPatients infected with SARS-CoV-2 along with a non-influenza respiratory virus had less severe disease on presentation and were more likely to be admitted—but did not have more severe outcomes—than those infected with SARS-CoV-2 alone.
Kinematics of the western filament of W50
Authors: Rosado M , Sánchez-Cruces M , Ambrocio-Cruz P , Trejo D 
Published: July 2021

ABSTRACT
We study the kinematics of the western optical filament of the radio shell W50 with imaging Fabry–Perot spectroscopy using the [S ii] (λ6717 Å and λ6731 Å) line doublet. The high [S ii]/H α line ratio of this filament, as well as the complexity of the radial velocity profiles obtained in this work ensure that this filament and diffuse regions are the optical counterpart of W50 hosting the peculiar object SS 433. We derive a kinematical distance of 4.7 ± 0.5 kpc, validating a previously derived distance based on the assumption that H i or CO gas is associated with W50. Our distance estimate is in agreement with the distance to SS 433 derived from proper motions. Shock velocities of up to 120 km s−1 are estimated for the [S ii] emitting regions. We derive an age between 1.0 and 1.9 × 105 yr considering that W50 is a remnant of a supernova explosion or a bubble blown by the action of the jets of the central SS 433 source, respectively. Age values are compatible with the age of SS 433. We also estimate the energy deposited by the supernova in the interstellar medium and alternatively, the luminosity of a wind-blown bubble fed by the relativistic jets of SS 433, obtaining reasonable values. We examine the different scenarios for the formation of W50. We conclude that a supernova remnant scenario rejuvenated by the interaction of SS 433 jets, acting as a piston, evolving in a three-phase medium with photo-evaporation, describes better the different observations and theoretical models of this system.
Remote sensing of cometary bow shocks: modelled asymmetric outgassing and pickup ion observations
Authors: Alho Markku , Jarvinen Riku , Simon Wedlund Cyril , Nilsson Hans , Kallio Esa , Pulkkinen Tuija I 
Published: July 2021

ABSTRACT
Despite the long escort by the ESA Rosetta mission, direct observations of a fully developed bow shock around 67P/Churyumov–Gerasimenko have not been reported. Expanding on our previous work on indirect observations of a shock, we model the large-scale features in cometary pickup ions, and compare the results with the ESA Rosetta Plasma Consortium Ion Composition Analyser ion spectrometer measurements over the pre-perihelion portion of the escort phase. Using our hybrid plasma simulation, an empirical, asymmetric outgassing model for 67P, and varied interplanetary magnetic field (IMF) clock angles, we model the evolution of the large-scale plasma environment. We find that the subsolar bow shock standoff distance is enhanced by asymmetric outgassing with a factor of 2 to 3, reaching up to $18\,000\, \rm {km}$ approaching perihelion. We find that distinct spectral features in simulated pickup ion distributions are present for simulations with shock-like structures, with the details of the spectral features depending on shock standoff distance, heliocentric distance, and IMF configuration. Asymmetric outgassing along with IMF clock angle is found to have a strong effect on the location of the spectral features, while the IMF clock angle causes no significant effect on the bow shock standoff distance. These dependences further complicate the interpretation of the ion observations made by Rosetta. Our data-model comparison shows that the large-scale cometary plasma environment can be probed by remote sensing the pickup ions, at least when the comet’s activity is comparable to that of 67P, and the solar wind parameters are known.
Differential rotation of the solar transition region from STEREO/EUVI 30.4-nm images
Authors: Sharma Jaidev , Kumar Brajesh , Malik Anil K , Vats Hari Om 
Published: July 2021

ABSTRACT
The solar photosphere, chromosphere, and corona are known to rotate differentially as a function of latitude. To date, it is unclear whether the solar transition region also rotates differentially. In this work, we investigate the differential rotational profile of the solar transition region as a function of latitude, using solar full-disc (SFD) images at 30.4-nm wavelength recorded by the Extreme Ultraviolet Imager (EUVI) on board the Solar Terrestrial Relations Observatory(STEREO) space mission for the period from 2008–2018 (Solar Cycle 24). Our investigations show that the solar transition region rotates differentially. The sidereal rotation rate obtained in the ${\pm}5{^\circ }$ equatorial band is quite high (∼14.7 deg day−1), dropping to ∼13.6 deg day−1 towards both polar regions. We also find that rotational differentiality is low during the period of high solar activity (the rotation rate varies from 14.86–14.27 deg day−1), while it increases during the ascending and descending phases of the 24th solar cycle (the rotation rate varies from 14.56 to ∼13.56 deg day−1 in 2008 and 14.6–13.1 deg day−1 in 2018). The average sidereal rotation rate (over SFD) follows the trend of solar activity (maximum ∼14.97 deg day−1 during the peak phase of solar activity, slowly decreasing to a minimum ∼13.9 deg day−1 during ascending and descending phases of the 24th solar cycle). We also observe that the solar transition region rotates less differentially than the corona.
uGMRT detection of cluster radio emission in low-mass Planck Sunyaev–Zel’dovich clusters
Authors: Paul Surajit , Gupta Prateek , Salunkhe Sameer , Bhagat Shubham , Sonkamble Satish , Hiray Manish , Dabhade Pratik , Raychaudhury Somak 
Published: July 2021

ABSTRACT
Low-mass (M500 &lt; 5 × 1014 M⊙) galaxy clusters have been largely unexplored in radio observations, because of the inadequate sensitivity of existing telescopes. However, the upgraded Giant Metrewave Radio Telescope (uGMRT) and the Low Frequency ARray (LoFAR), with unprecedented sensitivity at low frequencies, have paved the way to study less massive clusters more closely than before. We have started the first large-scale programme to systematically search for diffuse radio emission from low-mass galaxy clusters, chosen from the Planck Sunyaev–Zel’dovich cluster catalogue. We report here the detection of diffuse radio emission from four of the 12 objects in our sample, shortlisted from the inspection of the LoFAR Two-Meter Sky Survey data release 1 (LoTSS-I), followed up by uGMRT Band 3 deep observations. The clusters PSZ2 G089 (Abell 1904) and PSZ2 G111 (Abell 1697) are detected with relic-like emission, while PSZ2 G106 is found to have an intermediate radio halo and PSZ2 G080 (Abell 2018) seems to be a halo-relic system. PSZ2 G089 and PSZ2 G080 are among the lowest-mass clusters discovered with a radio-relic and a halo-relic system, respectively. A high ($\sim \! 30{{\ \rm per\ cent}}$) detection rate, with powerful radio emission (P1.4 GHz ∼ 1023 W Hz−1) found in most of these objects, opens up prospects of studying radio emission in galaxy clusters over a wider mass range, to much lower-mass systems.