bluuebunny/crossref_metadata_2025_split huggingface dataset:
Spread of hypervirulent multidrug-resistant ST147 Klebsiella pneumoniae in patients with severe COVID-19: an observational study from Italy, 2020–21
Authors: Falcone Marco , Tiseo Giusy , Arcari Gabriele , Leonildi Alessandro , Giordano Cesira , Tempini Sara , Bibbolino Giulia , Mozzo Roberto , Barnini Simona , Carattoli Alessandra , Menichetti Francesco 
Published: December 2021

Abstract

Objectives
To report an outbreak of hypervirulent Klebsiella pneumoniae (hvKp) in COVID-19 patients.

Methods
Prospective, observational study including consecutive COVID-19 patients with hvKp infections admitted to the University Hospital of Pisa (Italy). Clinical data and outcome of patients were collected. All patients were followed-up to 30 days from the diagnosis of infection. Mortality within 30 days of the diagnosis of hvKp infection was reported. The hypermucoviscous phenotype was determined by the ‘string test’. Molecular typing was performed on three strains collected during different periods of the outbreak. The strains underwent whole genome sequencing using the Illumina MiSeq instrument. The complete circular assemblies were also obtained for the chromosome and a large plasmid using the Unicycler tool.

Results
From November 2020 to March 2021, hvKp has been isolated from 36 COVID-19 patients: 29/36 (80.6%) had infections (15 bloodstream infections, 8 ventilator-associated pneumonias and 6 complicated urinary tract infections), while 7/36 (19.4%) had colonization (3 urine, 2 rectal and 2 skin). The isolates belonged to ST147 and their plasmid carried three replicons of the IncFIB (Mar), IncR and IncHI1B types and several resistance genes, including the rmpADC genes encoding enhancers of capsular synthesis. The hvKp isolates displayed an ESBL phenotype, with resistance to piperacillin/tazobactam and ceftolozane/tazobactam and susceptibility only to meropenem and ceftazidime/avibactam. The majority of patients were treated with meropenem alone or in combination with fosfomycin. Thirty-day mortality was 48.3% (14/29).

Conclusions
ST147 ESBL-producing hvKp is associated with high mortality in COVID-19 patients. Strict microbiological surveillance and infection control measures are needed in this population.
Within-Year Effects of Prescribed Fire on Bumble Bees (Hymenoptera: Apidae) and Floral Resources
Authors: Tai T M , Kaldor A , Urbina D , Gratton C 
Published: December 2021

Abstract
Despite the importance of bumble bees (genus Bombus Latreille) for their services to natural and agricultural environments, we know little about the relationship between grassland management practices and bumble bee conservation. Prescribed fire is a common grassland maintenance tool, including in areas where endangered and threatened bumble bees are present. Thus, knowledge of the effects of prescribed fire on bumble bees is essential for designing management schemes that protect and bolster their populations. Using nonlethal surveys to record bumble bee species richness, abundance, and community composition, we evaluated the effects of spring controlled burns on summer bumble bee gynes and workers across five sites in southern Wisconsin. In addition, we explored the effects of fire on floral resources by measuring floral genus richness, abundance, ground cover, and proportion of transects containing blooming flowers in adjacent burned and unburned parcels. Prescribed fire had no measurable effects on bumble bee gyne or worker community composition, species richness, or abundance. However, consistent with previous studies prescribed fire increased floral genus richness and ground cover. The disconnect between bumble bee and floral responses to fire highlights some opportunities for improving our understanding of fire’s effects on bumble bee diapause, nest site choice, and foraging.
Whole-Body/Head Transplantation: Personal Identity, Experimental Surgery, and Bioethics
Authors: Cherry Mark J , Fan Ruiping 
Published: December 2021

AbstractThis issue of The Journal of Medicine and Philosophy brings together an international group of scholars from Hong Kong, Mainland China, and North America, critically to explore whole-body/head transplantation. The proposed procedure raises significant philosophical, ethical, and social/political questions. For example, assuming transplant is successful, who survives the surgery? Does personal identity necessarily follow the head? The contributors to this special thematic issue explore the nature and ground of personal identity, what it would mean to preserve personal identity, given such a significant set of physical changes, as well as the morality of such a procedure. As the authors make clear, careful conceptual philosophical analysis is essential for understanding whether whole-body/head transplantation is a life-saving/life-enhancing technological innovation, or a bioethical morass that should not be attempted. How we come to terms with such conceptual and moral concerns will have a significant impact on the future of medicine and medical technological innovation.
DNA Repair Pathways and Their Association With Lethal Prostate Cancer in African American and European American Men
Authors: Plym Anna , Dióssy Miklós , Szallasi Zoltan , Sartor Oliver , Silberstein Jonathan , Powell Isaac J , Rebbeck Timothy R , Penney Kathryn L , Mucci Lorelei A , Pomerantz Mark M , Kibel Adam S 
Published: December 2021

AbstractBackgroundAltered DNA damage response (DDR) has emerged as an important mechanism for the development of aggressive prostate cancer among men of European ancestry but not other ancestry groups. Because common mechanisms for aggressive disease are expected, we explored a large panel of DDR genes and pathways to demonstrate that DDR alterations contribute to development of aggressive prostate cancer in both African American and European American men.MethodsWe performed a case-case study of 764 African American and European American men with lethal or indolent prostate cancer treated at 4 US hospitals. We calculated carrier frequencies of germline pathogenic or likely pathogenic sequence variants within 306 DDR genes, summarized by DDR pathway, and compared lethal cases against indolent cases using 2-sided Fisher’s exact tests. Secondary analysis examined if carrier frequencies differed by ancestry.ResultsLethal cases were more likely to carry a pathogenic sequence variant in a DDR gene compared with indolent cases (18.5% vs 9.6%, P = 4.30 × 10−4), even after excluding BRCA2 (14.6% vs 9.6%, P = .04). The carrier frequency was similar among lethal cases of African (16.7% including and 15.8% excluding BRCA2) and lethal cases of European (19.3% including and 14.2% excluding BRCA2) ancestry. Three DDR pathways were statistically significantly associated with lethal disease: homologous recombination (P = .003), Fanconi anemia (P = .002), and checkpoint factor (P = .02).ConclusionsOur findings suggest that altered DDR is an important mechanism for aggressive prostate cancer not only in men of European but also of African ancestry. Therefore, interrogation of entire DDR pathways is needed to fully characterize and better define genetic risk of lethal disease.
Molecular characterization of Schistosoma infections in African migrants: identification of a Schistosoma haematobium-bovis hybrid in bladder biopsies
Authors: Marascio Nadia , Loria Maria Teresa , Lamberti Angelo Giuseppe , Pavia Grazia , Adams Neill James , Quirino Angela , Divenuto Francesca , Mazzitelli Maria , Greco Giuseppe , Trecarichi Enrico Maria , Perandin Francesca , Bisoffi Zeno , Webster Bonnie L , Liberto Maria Carla , Torti Carlo , Matera Giovanni 
Published: December 2021

Atypical Schistosoma haematobium eggs were found in a bladder biopsy from an African migrant with severe Schistosomiasis.
Amplification of mitochondrial (cox 1) and genomic (ITS2) DNA identified the presence of a S. haematobium-Schistosoma bovis hybrid.
Phylogenetic analysis clustered the hybrid sequence with other sequences from western Africa.
Satisfiability of constrained Horn clauses on algebraic data types: A transformation-based approach
Authors: De Angelis Emanuele , Fioravanti Fabio , Pettorossi Alberto , Proietti Maurizio 
Published: December 2021

Abstract
We address the problem of checking the satisfiability of constrained Horn clauses (CHCs) defined on algebraic data types (ADTs), such as lists and trees. We propose a new technique for transforming CHCs defined on ADTs into CHCs where the arguments of the predicates have only basic types, such as integers and booleans. Thus, our technique avoids, during satisfiability checking, the explicit use of proof rules based on induction over the ADTs. The main extension over previous techniques for ADT removal is a new transformation rule, called differential replacement, which allows us to introduce auxiliary predicates, whose definitions correspond to lemmas that are used when making inductive proofs. We present an algorithm that performs the automatic removal of ADTs by applying the new rule, together with the traditional folding/unfolding rules. We prove that, under suitable hypotheses, the set of the transformed clauses is satisfiable if and only if so is the set of the original clauses. By an experimental evaluation, we show that the use of the new rule significantly improves the effectiveness of ADT removal. We also show that our approach is competitive with respect to tools that extend CHC solvers with the use of inductive rules.
Covid-19-associated fungal osteomyelitis of jaws and sinuses: An experience-driven management protocol
Authors: Suresh Amal , Joshi Abhijit , Desai Anil Kumar , Juturu Uday , Kurian Denis Jacob , Jain Pavithra , Kulkarni R D , Kumar Niranjan 
Published: December 2021

Abstract

Invasive fungal co-infections with COVID-19 are currently being reported at an alarming rate. Our study explores the importance of early identification of the disease, probable etiopathogenesis, clinical and radiological features and a treatment protocol for COVID-19 Associated Fungal Osteomyelitis of Jaws and Sinuses (CAFOJS). A one-year prospective study from June 2020 to May 2021 was conducted among CAFOJS diagnosed patients at a tertiary care center in South India. Demographic details, COVID-19 infection and treatment history, time taken for initiation of symptoms after COVID-19 diagnosis, medical history and clinical features were recorded. All patients were managed with a standard diagnostic and intervention protocol which included pre-operative and post-operative administration of Inj. Amphotericin B 50 mg (liposomal), early aggressive surgical debridement and tab. Posaconazole GR 300 mg OD for 90 days after discharge. Thirty-nine (78%) patients were diagnosed with CAFOJS out of 50 osteomyelitis patients. 35 patients (90%) were diabetic and 21 patients (54%) were known to receive steroids during the COVID-19 treatment. Sole existence of Mucorales spp. was seen in 30 patients (77%), Aspergillus fumigatus in 2 patients (5%), Curvularia spp. in 2 patients (5%). Concomitant existence of Mucorales and Aspergillus fumigatus was reported in two patients (5%) and Candida albicans in three patients (8%). Patients underwent treatment with standard protocol and no recurrence noted. CAFOJS is a clinical entity with aggressive presentation and warrants early diagnosis and treatment.

Lay summary
Invasive fungal infections of head and neck region cause necrosis of bones affected by it, especially maxilla. Early diagnosis and treatment are advocated in such infections due to its aggressive clinical presentation compared to similar infections before COVID-19 pandemic.
Deep phase retrieval for astronomical Shack–Hartmann wavefront sensors
Authors: Guo Youming , Wu Yu , Li Ying , Rao Xuejun , Rao Changhui 
Published: December 2021

ABSTRACT
We present a high-speed deep learning-based phase retrieval approach for Shack–Hartmann wavefront sensors used in astronomical adaptive optics. It reconstructs the Zernike modal coefficients from the image captured by the wavefront sensor with a lightweight convolutional neural network. Compared to the traditional slope-based wavefront reconstruction, the proposed approach uses the image captured by the sensor directly as inputs for more high-order aberrations. Compared to the recently developed iterative phase retrieval methods, the speed is much faster with the computation time less than 1 ms for a 100-aperture configuration, which may satisfy the requirement of an astronomical adaptive optics system. Simulations have been done to demonstrate the advantages of this approach. Experiments on a 241-unit deformable-secondary-mirror AOS have also been done to validate the proposed approach.
BEBOP III. Observations and an independent mass measurement of Kepler-16 (AB) b – the first circumbinary planet detected with radial velocities
Authors: Triaud Amaury H M J , Standing Matthew R , Heidari Neda , Martin David V , Boisse Isabelle , Santerne Alexandre , Correia Alexandre C M , Acuña Lorena , Battley Matthew , Bonfils Xavier , Carmona Andrés , Collier Cameron Andrew , Cortés-Zuleta Pía , Dransfield Georgina , Dalal Shweta , Deleuil Magali , Delfosse Xavier , Faria João , Forveille Thierry , Hara Nathan C , Hébrard Guillaume , Hoyer Sergio , Kiefer Flavien , Kunovac Vedad , Maxted Pierre F L , Martioli Eder , Miller Nicola J , Nelson Richard P , Poveda Mathilde , Rein Hanno , Sairam Lalitha , Udry Stéphane , Willett Emma 
Published: December 2021

ABSTRACTThe radial velocity method is amongst the most robust and most established means of detecting exoplanets. Yet, it has so far failed to detect circumbinary planets despite their relatively high occurrence rates. Here, we report velocimetric measurements of Kepler-16A, obtained with the SOPHIE spectrograph, at the Observatoire de Haute-Provence’s 193cm telescope, collected during the BEBOP survey for circumbinary planets. Our measurements mark the first radial velocity detection of a circumbinary planet, independently determining the mass of Kepler-16 (AB) b to be $0.313 \pm 0.039\, {\rm M}_{\rm Jup}$, a value in agreement with eclipse timing variations. Our observations demonstrate the capability to achieve photon-noise precision and accuracy on single-lined binaries, with our final precision reaching $\rm 1.5~m\, s^{-1}$ on the binary and planetary signals. Our analysis paves the way for more circumbinary planet detections using radial velocities which will increase the relatively small sample of currently known systems to statistically relevant numbers, using a method that also provides weaker detection biases. Our data also contain a long-term radial velocity signal, which we associate with the magnetic cycle of the primary star.
The combined and respective roles of imaging and stellar kinematics in identifying galaxy merger remnants
Authors: Bottrell Connor , Hani Maan H , Teimoorinia Hossen , Patton David R , Ellison Sara L 
Published: December 2021

ABSTRACT
One of the central challenges to establishing the role of mergers in galaxy evolution is the selection of pure and complete merger samples in observations. In particular, while large and reasonably pure interacting galaxy pair samples can be obtained with relative ease via spectroscopic criteria, automated selection of post-coalescence merger remnants is restricted to the physical characteristics of remnants alone. Furthermore, such selection has predominantly focused on imaging data – whereas kinematic data may offer a complimentary basis for identifying merger remnants. Therefore, we examine the theoretical utility of both the morphological and kinematic features of merger remnants in distinguishing galaxy merger remnants from other galaxies. Deep classification models are calibrated and evaluated using idealized synthetic images and line-of-sight stellar velocity maps of a heterogeneous population of galaxies and merger remnants from the TNG100 cosmological hydrodynamical simulation. We show that even idealized stellar kinematic data have limited utility compared to imaging and underperforms by $2.1 \pm 0.5 {{\ \rm per\ cent}}$ in completeness and $4.7 \pm 0.4 {{\ \rm per\ cent}}$ in purity for our fiducial model architecture. Combining imaging and stellar kinematics offers a small boost in completeness (by $1.8 \pm 0.4 {{\ \rm per\ cent}}$, compared to $92.7 \pm 0.2 {{\ \rm per\ cent}}$ from imaging alone) but no change in purity ($0.1\pm 0.3 {{\ \rm per\ cent}}$ improvement compared to $92.7 \pm 0.2 {{\ \rm per\ cent}}$, evaluated with equal numbers of merger remnant and non-remnant control galaxies). Classification accuracy of all models is particularly sensitive to physical companions at separations ≲ 40 kpc and to time-since-coalescence. Taken together, our results show that the stellar kinematic data have little to offer in compliment to imaging for merger remnant identification in a heterogeneous galaxy population.
Less wrong: a more realistic initial condition for simulations of turbulent molecular clouds
Authors: Lane Henry B , Grudić Michael Y , Guszejnov Dávid , Offner Stella S R , Faucher-Giguère Claude-André , Rosen Anna L 
Published: December 2021

ABSTRACT
Simulations of isolated giant molecular clouds (GMCs) are an important tool for studying the dynamics of star formation, but their turbulent initial conditions (ICs) are uncertain. Most simulations have either initialized a velocity field with a prescribed power spectrum on a smooth density field (failing to model the full structure of turbulence) or ‘stirred’ turbulence with periodic boundary conditions (which may not model real GMC boundary conditions). We develop and test a new GMC simulation setup (called turbsphere) that combines advantages of both approaches: we continuously stir an isolated cloud to model the energy cascade from larger scales, and use a static potential to confine the gas. The resulting cloud and surrounding envelope achieve a quasi-equilibrium state with the desired hallmarks of supersonic ISM turbulence (e.g. density PDF and a ∼k−2 velocity power spectrum), whose bulk properties can be tuned as desired. We use the final stirred state as initial conditions for star formation simulations with self-gravity, both with and without continued driving and protostellar jet feedback, respectively. We then disentangle the respective effects of the turbulent cascade, simulation geometry, external driving, and gravity/MHD boundary conditions on the resulting star formation. Without external driving, the new setup obtains results similar to previous simple spherical cloud setups, but external driving can suppress star formation considerably in the new setup. Periodic box simulations with the same dimensions and turbulence parameters form stars significantly slower, highlighting the importance of boundary conditions and the presence or absence of a global collapse mode in the results of star formation calculations.
The MAVERIC Survey: The first radio and X-ray limits on the detached black holes in NGC 3201
Authors: Paduano Alessandro , Bahramian Arash , Miller-Jones James C A , Kawka Adela , Göttgens Fabian , Strader Jay , Chomiuk Laura , Kamann Sebastian , Dreizler Stefan , Heinke Craig O , Husser Tim-Oliver , Maccarone Thomas J , Tremou Evangelia , Zhao Yue 
Published: December 2021

ABSTRACT
The Galactic globular cluster (GC) NGC 3201 is the first Galactic GC observed to host dynamically confirmed stellar-mass black holes (BHs), containing two confirmed and one candidate BH. This result indicates that GCs can retain BHs, which has important implications for GC evolution. NGC 3201 has been observed as part of the MAVERIC survey of Galactic GCs. We use these data to confirm that there is no radio or X-ray detection of the three BHs, and present the first radio and X-ray limits on these sources. These limits indicate that any accretion present is at an extremely low rate and may be extremely inefficient. In particular, for the system ACS ID #21859, by assuming the system is tidally locked and any accretion is through the capture of the companion’s winds, we constrain the radiative efficiency of any accretion to ≲ 1.5 × 10−5. We also combine the radio and X-ray source catalogues from the MAVERIC survey with the existing MUSE spectroscopic surveys and the HUGS catalogue of NGC 3201 to provide a catalogue of 42 multiwavelength sources in this cluster. We identify a new red straggler source with X-ray emission, and investigate the multiwavelength properties of the sub-subgiant population in the cluster.
Prospects for differentiating extended coronal geometries in AGNs with the IXPE mission
Authors: Ursini F , Matt G , Bianchi S , Marinucci A , Dovčiak M , Zhang W 
Published: December 2021

ABSTRACT
X-ray polarimetry can potentially constrain the unknown geometrical shape of active galactic nucleous (AGN) coronae. We present simulations of the X-ray polarization signal expected from AGN coronae, assuming three different geometries, namely slab, spherical, and conical. We use the fully relativistic Monte Carlo Comptonization code monk to compute the X-ray polarization degree and angle. We explore different coronal parameters such as shape, size, location, and optical depth. Different coronal geometries give a significantly different X-ray polarization signal. A slab corona yields a high polarization degree, up to 14 per cent depending on the viewing inclination; a spherical corona yields low values, about 1–3 per cent, while a conical corona yields intermediate values. We also find a difference of 90 degrees in polarization angle between the slab corona and the spherical or conical coronae. Upcoming X-ray polarimetry missions like IXPE will allow us to observationally distinguish among different coronal geometries in AGNs for the first time.
Type Ia supernova magnitude step from the local dark matter environment
Authors: Steigerwald Heinrich , Rodrigues Davi , Profumo Stefano , Marra Valerio 
Published: December 2021

ABSTRACTResiduals in the Hubble diagram at optical wavelengths and host galaxy stellar mass are observed to correlate in type Ia supernovae (SNe Ia) (‘magnitude step’). Among possible progenitor channels for the associated explosions, those based on dark matter (DM) have attracted significant attention, including our recent proposal that ‘normal’ SNe Ia from bare detonations in sub-Chandrasekhar white dwarf stars are triggered by the passage of asteroid-mass primordial black holes (PBHs): the magnitude step could then originate from a brightness dependence on stellar properties, on DM properties, or both. Here, we present a method to estimate the local DM density and velocity dispersion of the environment of SN Ia progenitors. We find a luminosity step of $0.52\pm 0.11\,$ mag corresponding to bins of high versus low DM density in a sample of 222 low-redshift events from The Open Supernova Catalog. We investigate whether the magnitude step can be attributed to local DM properties alone, assuming asteroid-mass PBHs. Given the inverse correlation between SN Ia brightness and PBH mass, an intriguing explanation is a spatially inhomogeneous PBH mass function. If so, a strong mass segregation in the DM density-dependent PBH mass scale is needed to explain the magnitude step. While mass segregation is observed in dense clusters, it is unlikely to be realized on galactic scales. Therefore, if DM consists of asteroid-mass PBHs, the magnitude step is more likely to exist, and dominantly to be attributed to local stellar properties.