bluuebunny/crossref_metadata_2025 huggingface dataset:
Enamel cutting mechanism and performance of different dental burs: an in vitro study
Authors: Zhao Jing , Wu Di , Liu Sinan , Gong Kun , Zhang Zhijun , Zhao Jian
Published: May 2023

Tooth enamel machining is a common procedure in dental surgery, yet the cutting mechanisms and performance of different dental burs remain unclear. In the dental field, this poses challenges for dentists in selecting appropriate dental burs for specific operations. In the engineering field, this creates difficulties in understanding the cutting mechanisms of tooth enamel and designing new high-performance dental burs. Therefore, the objective of this study is to bridge the gap between medicine and engineering by comprehending the cutting mechanisms and performance of different dental burs for tooth enamel machining. This study established an enamel machining experimental system and utilized the fissure bur, diamond bur, and round bur to conduct enamel drilling and milling experiments on the occlusal, buccal/lingual, and mesial/distal surfaces of the tooth. The results indicate that, compared to the buccal/lingual and mesial/distal surfaces, the milling force is lower (p< 0.05) but the milling temperature is higher (p< 0.05) on the occlusal surface. Furthermore, the fissure bur generated the lowest drilling and milling temperatures (p< 0.05) and the best milling quality. The diamond bur generated the best drilling quality but lacked drilling precision (p< 0.05). The round bur generated the smallest drilling force (p< 0.05) but the largest milling force (p< 0.05). The analysis of the structure and cutting mechanisms of different dental burs on various tooth surfaces explains the aforementioned phenomena. Different dental burs have distinct advantages based on their structures. This study enhances the understanding of tooth enamel cutting mechanisms and dental bur machining performance in the field of medicine and engineering, which can improve the quality of dental surgery and facilitate the development of high-performance dental burs.
Study on plasticized Poly (vinylidene chloride- co- acrylonitrile) polymer electrolytes for battery applications
Authors: Vijaya B , Rani M Usha , Babu Ravi Shanker
Published: May 2023

Plasticized Poly (vinylidene chloride- co- acrylonitrile) [P(VdC-co-AN)] polymer electrolytes comprising of Lithium Perchloride (LiClO4) as complexing salt and plasticizers such as Propylene carbonate (PC) andβ-butyrolactone (βbl) is prepared by solution casting technique. Polymer electrolytes were prepared in the ratio [(x)PVdC-co-PAN+(100-x-z) Plasticizer+(z) LiClO4] and were subjected to various characterizations. X-ray Diffraction (XRD), and Fourier transform infrared spectroscopy (FTIR) were carried out to study the structural and functional groups present in the material. Impedance spectroscopy to find the ionic conductivity of the material. The maximum ionic conductivity at room temperature was exhibited by the samples containing 68% PC (9.237 × 10−4S cm−1) and 66% ofβbl (2.284 × 10−4S cm−1). Samples exhibiting higher ionic conductivity (68% PC and 66% ofβbl) are subjected to Linear sweep voltammetry and transference number measurements. The electrochemical stability is 4.5 v for the both films, whereas transference number is 0.955 and 0.94, respectively. Thermogravimetry/Differential Thermal analysis (TG/DTA) shows the prepared films doesn’t not undergo any weight loss till 220 °C (thermally stable). The surface morphology of the polymer membrane was explored through Atomic force microscopy (AFM).
NCIRF: an organ dose calculator for patients undergoing radiography and fluoroscopy
Authors: Lee Choonsik , Yeom Yeon Soo , Shin Jungwook , Streitmatter Seth W , Kitahara Cari M
Published: May 2023

Background. It is critical to monitor the radiation dose delivered to patients undergoing radiography and fluoroscopy to prevent both acute and potential long-term adverse health effects. Accurate estimation of organ doses is essential to ensuring that radiation dose is maintained As Low As Reasonably Achievable. We developed a graphical user interface-based organ dose calculation tool for pediatric and adult patients undergoing radiography and fluoroscopy examinations. Methods. Our dose calculator follows the four sequential steps. First, the calculator obtains input parameters related to patient age and gender, and x-ray source data. Second, the program creates an input file describing the anatomy and material composition of a phantom, x-ray source, and organ dose scorers for Monte Carlo radiation transport using the user input parameters. Third, a built-in Geant4 module was developed to import the input file and to calculate organ absorbed doses and skeletal fluences through Monte Carlo radiation transport. Lastly, active marrow and endosteum doses are derived from the skeletal fluences and effective dose is calculated from the organ and tissue doses. Following benchmarking with MCNP6, we conducted some benchmarking calculations calculated organ doses for an illustrative cardeiac interventional fluoroscopy and compared the results with those from an existing dose calculator, PCXMC. Results. The graphical user interface-based program was entitled National Cancer Institute dosimetry system for Radiography and Fluoroscopy (NCIRF). Organ doses calculated from NCIRF showed an excellent agreement with those from MCNP6 in the simulation of an illustrative fluoroscopy exam. In the cardiac interventional fluoroscopy exam of the adult male and female phantoms, the lungs received relatively greater doses than any other organs. PCXMC based on stylistic phantoms overall overestimated major organ doses calculated from NCIRF by up to 3.7-fold (active bone marrow). Conclusion. We developed an organ dose calculation tool for pediatric and adult patients undergoing radiography and fluoroscopy examinations. NCIRF could substantially increase the accuracy and efficiency of organ dose estimation in radiography and fluoroscopy exams.
Atomic protein structure refinement using all-atom graph representations and SE(3)-equivariant graph transformer
Authors: Wu Tianqi , Guo Zhiye , Cheng Jianlin
Published: May 2023

Motivation

The state-of-art protein structure prediction methods such as AlphaFold are being widely used to predict structures of uncharacterized proteins in biomedical research. There is a significant need to further improve the quality and nativeness of the predicted structures to enhance their usability. In this work, we develop ATOMRefine, a deep learning-based, end-to-end, all-atom protein structural model refinement method. It uses a SE(3)-equivariant graph transformer network to directly refine protein atomic coordinates in a predicted tertiary structure represented as a molecular graph.

Results

The method is first trained and tested on the structural models in AlphaFoldDB whose experimental structures are known, and then blindly tested on 69 CASP14 regular targets and 7 CASP14 refinement targets. ATOMRefine improves the quality of both backbone atoms and all-atom conformation of the initial structural models generated by AlphaFold. It also performs better than two state-of-the-art refinement methods in multiple evaluation metrics including an all-atom model quality score—the MolProbity score based on the analysis of all-atom contacts, bond length, atom clashes, torsion angles, and side-chain rotamers. As ATOMRefine can refine a protein structure quickly, it provides a viable, fast solution for improving protein geometry and fixing structural errors of predicted structures through direct coordinate refinement.

Availability and implementation

The source code of ATOMRefine is available in the GitHub repository (https://github.com/BioinfoMachineLearning/ATOMRefine). All the required data for training and testing are available at https://doi.org/10.5281/zenodo.6944368.
Worst area local Hidradenitis suppurativa Activity and Severity Index-Revised (W-HASI-R): a study evaluating construct validity
Authors: Bellefeuille Gretchen , Paiewonsky Briana , Khalid Bisma , Freese Rebecca L , Lowes Michelle A , Kirby Joslyn S , Alavi Afsaneh , Goldfarb Noah
Published: May 2023

Current validated hidradenitis suppurativa (HS) severity assessment tools are time-consuming and impractical in fast-paced, ambulatory clinic settings. This study evaluated the construct validity of the most severe or ‘worst’ area local Hidradenitis suppurativa Activity and Severity Index-Revised (W-HASI-R) as a novel target area assessment tool for clinical setting use. W-HASI-R had strong association with the International Hidradenitis Suppurativa Severity Score System and abscess and nodule count, moderate association with Hurley stage and HS physician global assessment and weak, negative association with reverse-scored Dermatology Quality Life Index. The resulting data suggest that W-HASI-R may be an option as an efficient target area assessment tool for fast-paced, ambulatory settings.
Mpox: an updated review of dermatological manifestations in the current outbreak
Authors: Maronese Carlo Alberto , Avallone Gianluca , Aromolo Italo Francesco , Spigariolo Cristina Beatrice , Quattri Eleonora , Ramoni Stefano , Carrera Carlo Giovanni , Marzano Angelo Valerio
Published: May 2023

Mpox is a disease caused by a double-stranded DNA orthopoxvirus discovered in 1958. In 2022, an outbreak on an unprecedented scale marked its transition from neglected, zoonotic disease circulating almost exclusively within African borders to sexually transmitted infection (STI) of international concern. Although phylogenetic evidence suggests progressive evolution from the strain associated with the 2018 outbreak in Nigeria, epidemiological links with previous cases have still not been completely elucidated. Clinically, mpox presents with systemic symptoms, such as fever, headache, malaise and a characteristic cutaneous eruption, similar to that of cognate viruses (e.g. smallpox). Mpox pseudopustules evolve through several stages, including umbilication and crusting, and resolve in the span of 2–3 weeks. The hallmarks that set the 2022 outbreak apart from classic mpox were a disproportionate number of cases occurring in men who have sex with men, an often localized cutaneous picture and a significant burden in terms of concomitant STIs. Investigations into the disease pathogenesis, related immune response, clinical and dermoscopic features, in addition to studies aimed at defining novel management strategies, have advanced mpox knowledge considerably. Herein, recent findings on mpox are reviewed, with a keen focus on dermatological manifestations and their implications in the current diagnostic scenario, reinforcing the pivotal role of dermatologists in managing suspect cases and preventing further spread of the contagion.
Modified artery-first approach for distal pancreatectomy with celiac axis resection
Authors: Wang Huan , Shen Shuo , Ren Yiwei , Lin Xueru , Shi Xiaohan , Gao Suizhi , Li Bo , Yin Xiaoyi , Zhang Guoxiao , Liu Wuchao , Wang Jian , Han Jiawei , Zhu Lingyu , Xu Xiongfei , Shao Zhuo , Jing Wei , Song Bin , Cheng Peng , Guo Shiwei , Zheng Kailian , Jin Gang
Published: May 2023

Background

The superior mesenteric artery-first approach has been proved superior in pancreatoduodenectomy compared with the standard procedure. It is unclear whether similar benefits could be obtained in distal pancreatectomy with celiac axis resection.

Methods

Perioperative and survival outcomes of patients who underwent distal pancreatectomy with celiac axis resection with the modified artery-first approach or traditional approach between January 2012 and September 2021 were compared.

Results

The entire cohort comprised 106 patients (modified artery-first approach, n = 35; traditional approach, n = 71). The most common complication was postoperative pancreatic fistula (n = 18, 17.0 per cent), followed by ischaemic complications (n = 17, 16.0 per cent) and surgical site infection (n = 15, 14.0 per cent). Intraoperative blood loss (400 versus 600 ml, P = 0.017) and intraoperative transfusion rate (8.6 versus 29.6 per cent, P = 0.015) were lower in the modified artery-first approach group compared with the traditional approach group. A higher number of harvested lymph nodes (18 versus 13, P = 0.030) and R0 resection rate (88.6 versus 70.4 per cent, P = 0.038) and a lower incidence of ischaemic complications (5.7 versus 21.1 per cent, P = 0.042) was observed in the modified artery-first approach group compared with the traditional approach group. In multivariable analysis, the modified artery-first approach (OR 0.006, 95 per cent c.i., 0 to 0.447; P = 0.020) was protective against ischaemic complications.

Conclusions

Compared with the traditional approach, the modified artery-first approach was associated with lower blood loss and fewer ischaemic complications, and a higher number of harvested lymph nodes and R0 resection rate. Thus, it might improve the safety, staging and prognosis of distal pancreatectomy with celiac axis resection for pancreatic cancer.
TGFβ4 alleviates the phenotype of Charcot–Marie–Tooth disease type 1A
Authors: Jeon Hyeonjin , Jang So Young , Kwak Geon , Yi Yong Weon , You Mi-Hyeon , Park Na Young , Jo Ju Hee , Yang Ji Won , Jang Hye Ji , Jeong Sun-Young , Moon Seung Kee , Doo Hyun Myung , Nahm Minyeop , Kim Donghoon , Chang Jong Wook , Choi Byung-Ok , Hong Young Bin
Published: May 2023

The duplication of the peripheral myelin protein 22 (PMP22) gene causes a demyelinating type of neuropathy, commonly known as Charcot–Marie–Tooth disease type 1A (CMT1A). Development of effective drugs for CMT1A still remains as an unmet medical need.

In the present study, we assessed the role of the transforming growth factor beta 4 (TGFβ4)/Nodal axis in the pathogenesis of CMT1A.

First, we identified PMP22 overexpression-induced Nodal expression in Schwann cells, which might be one of the downstream effectors in CMT1A. Administration of Nodal protein at the developmental stage of peripheral nerves induced the demyelinating phenotype in vivo. Second, we further isolated TGFβ4 as an antagonist that could abolish Nodal-induced demyelination. Finally, we developed a recombinant TGFβ4–fragment crystallizable (Fc) fusion protein, CX201, and demonstrated that its application had promyelinating efficacy in Schwann cells. CX201 administration improved the demyelinating phenotypes of CMT1A mouse models at both pre-symptomatic and post-symptomatic stages.

These results suggest that the TGFβ4/Nodal axis plays a crucial role in the pathogenesis of CMT1A and might be a potential therapeutic target for CMT1A.
Severe Falciparum and Vivax Malaria on the Thailand-Myanmar Border: A Review of 1503 Cases
Authors: Chu Cindy S , Stolbrink Marie , Stolady Daniel , Saito Makoto , Beau Candy , Choun Kan , Wah Tha Gay , Mu Ne , Htoo Klay , Nu Be , Keereevijit Arunrot , Wiladpaingern Jacher , Carrara Verena , Phyo Aung Pyae , Lwin Khin Maung , Luxemburger Christine , Proux Stephane , Charunwatthana Prakaykaew , McGready Rose , White Nicholas J , Nosten François
Published: May 2023

Background

The northwestern border of Thailand is an area of low seasonal malaria transmission. Until recent successful malaria elimination activities, malaria was a major cause of disease and death. Historically the incidences of symptomatic Plasmodium falciparum and Plasmodium vivax malaria were approximately similar.

Methods

All malaria cases managed in the Shoklo Malaria Research Unit along the Thailand-Myanmar border between 2000 and 2016 were reviewed.

Results

There were 80 841 consultations for symptomatic P. vivax and 94 467 for symptomatic P. falciparum malaria. Overall, 4844 (5.1%) patients with P. falciparum malaria were admitted to field hospitals, of whom 66 died, compared with 278 (0.34%) with P. vivax malaria, of whom 4 died (3 had diagnoses of sepsis, so the contribution of malaria to their fatal outcomes is uncertain). Applying the 2015 World Health Organization severe malaria criteria, 68 of 80 841 P. vivax admissions (0.08%) and 1482 of 94 467 P. falciparum admissions (1.6%) were classified as severe. Overall, patients with P. falciparum malaria were 15 (95% confidence interval, 13.2–16.8) times more likely than those with P. vivax malaria to require hospital admission, 19 (14.6–23.8) times more likely to develop severe malaria, and ≥14 (5.1–38.7) times more likely to die.

Conclusions

In this area, both P. falciparum and P. vivax infections were important causes of hospitalization, but life-threatening P. vivax illness was rare.
Diversity, distribution, and bioprospecting potentials of manglicolous yeasts: a review
Authors: Nimsi Kizhakkeyveetil AbdulSaleem , Manjusha Kozhikotte , Hatha Ammanamveetil Abdulla Mohamed , Kathiresan Kandasamy
Published: May 2023

Manglicolous yeasts are those that inhabit mangroves. Being adapted to survive extreme environmental variations, these yeasts possess traits that are desirable in terms of bioprospecting potential. Yeasts have been successfully isolated from different microhabitats within the mangrove ecosystem, including vegetation, water, sediments, and invertebrates. They have been found to be most abundant in sediments and water. Manglicolous yeasts are highly diverse unlike previously assumed. Yeasts belonging to the phyla Ascomycetes are more common in mangrove ecosystems than Basidiomycetes. Candida, Cryptococcus, Debaryomyces, Geotrichum, Kluyveromyces, Rhodotorula, Saccharomyces, and Pichia were some of the dominant yeast genera, which are cosmopolitan in distribution. New species yeasts such as Vishniacozyma changhuana and V. taiwanica are also known from mangroves. A compilation of isolation and identification methods employed for manglicolous yeast culture is provided in this review. Culture-independent approaches to understanding yeast diversities have also been introduced. The bioprospecting potentials of manglicolous yeasts have been highlighted these include enzymes, xylitol, biofuel, single-cell oil, anticancer agents, antimicrobials, and biosurfactants. Manglicolous yeast also finds application as biocontrol agents, bioremediators, single-cell proteins, food and feed, and immunostimulants. Our knowledge of the diversity and economical prospects of manglicolous yeasts is limited and likely to remain so as mangroves are disappearing fast. Therefore, this review is an attempt to give insight into these aspects.
Remaining non-isostatic effects in isostatic-gravimetric Moho determination—is it needed?
Authors: Abrehdary M , Sjöberg L E
Published: May 2023

For long time the study of the Moho discontinuity (or Moho) has been a crucial topic in inferring the dynamics of the Earth's interior, and with profitable result it is mapped by seismic data, but due to the heterogeneous distribution of such data the quality varies over the world. Nevertheless, with the advent of satellite gravity missions, it is today possible to recover the Moho constituents (i.e. Moho depth; MD and Moho density contrast; MDC) via gravity observations based on isostatic models. Prior to using gravity observations for this application it must be stripped due to the gravitational contributions of known anomalous crustal density structures, mainly density variations of oceans, glacial ice sheets and sediment basins (i.e. stripping gravity corrections). In addition, the gravity signals related mainly with masses below the crust must also be removed. The main purpose of this study is to estimate the significance of removing also remaining non-isostatic effects (RNIEs) on gravity, that is, gravity effects that remain after the stripping corrections. This is carried out by using CRUST19 seismic crustal model and employing Vening Meinesz–Moritz (VMM) gravimetric-isostatic model in recovering the Moho constituents on a global scale to a resolution of 1° × 1°. To reach this goal, we present a new model, named MHUU22, formed by the SGGUGM2 gravitational field, Earth2014 topography, CRUST1.0 and CRUST19 seismic crustal models. Particularly, this study has its main emphasis on the RNIEs on gravity and Moho constituents to find out if we can modify the stripping gravity corrections by a specific correction of the RNIEs. The numerical results illustrate that the RMS differences between MHUU22 MD and the seismic model CRUST1.0 and least-squares combined model MOHV21 are reduced by 33 and 41 per cent by applying the NIEs, and the RMS differences between MHUU22 MDC and the seismic model CRUST1.0 and least-squares combined model MDC21 are reduced by 41 and 23 per cent when the above strategy for removing the RNIEs is applied. Hence, our study demonstrates that the specific correction for the RNIEs on gravity disturbance is significant, resulting in remarkable improvements in MHUU22, which more clearly visualize several crustal structures.
The Definition, Presentation and Automatic Generation of Contextual Data in Lexicography
Authors: Domínguez Vázquez María José , Gouws Rufus H
Published: May 2023

This paper deals with several aspects of context in lexicography. Section 1 briefly mentions some different approaches to the concept context in various fields. Section 2 puts the focus on different uses and perceptions of the concept context in lexicography, contrasting it with related concepts, such as cotext, contextualization and contextual information. A more comprehensive discussion also covers different aspects of the occurrence of the concept context in dictionary research, with specific reference to central aspects of the so-called inner and outer context. Various portals, dictionaries and dictionary entries will illustrate the above-mentioned approaches. Section 3 approaches the subject from a user perspective. Section 4 addresses the question How can contextual data be extracted or generated? To answer this question, some methods and tools for (automatic) acquisition and analysis of contextual data, – in particular of the local contextual data in terms of Faber and León-Araúz (2016) – are introduced. Examples of these are lexical databases or semantic networks, like WordNet, and corpora, like Sketch Engine, or predictive methods, like Word2vec and similar ones. Some advantages and disadvantages of specific data acquisition tools used for the analysis of local contextual data are indicated. This section also contributes to a more detailed discussion of the automatic generation of the so-called local syntactic-semantic context or word environment, specifically of the building of syntactic-semantic argument patterns and their examples.
Ghost Distributions on Supersymmetric Spaces II: Basic Classical Superalgebras
Authors: Sherman Alexander
Published: May 2023

We study ghost distributions on supersymmetric spaces for the case of basic classical Lie superalgebras. We introduce the notion of interlaced pairs, which are those for which both $({\mathfrak{g}},{\mathfrak{k}})$ and $({\mathfrak{g}},{\mathfrak{k}}^{\prime})$ admit Iwasawa decompositions. For such pairs, we define a ghost algebra, generalizing the subalgebra of ${\mathcal{U}}{\mathfrak{g}}$ defined by Gorelik. We realize this algebra as an algebra of $G$-equivariant operators on the supersymmetric space itself, and for certain pairs, the “special” ones, we realize our operators as twisted-equivariant differential operators on $G/K$. We additionally show that the Harish-Chandra morphism is injective, compute its image for all rank one pairs, and provide a conjecture for the image when $({\mathfrak{g}},{\mathfrak{k}})$ is interlaced.
Pathogenesis of Aerosolized Ebola Virus Variant Makona in Nonhuman Primates
Authors: Prasad Abhishek N , Fenton Karla A , Agans Krystle N , Borisevich Viktoriya , Woolsey Courtney , Comer Jason E , Dobias Natalie S , Peel Jennifer E , Deer Daniel J , Geisbert Joan B , Lawrence William S , Cross Robert W , Geisbert Thomas W
Published: May 2023

Background

Highly pathogenic filoviruses such as Ebola virus (EBOV) hold capacity for delivery by artificial aerosols, and thus potential for intentional misuse. Previous studies have shown that high doses of EBOV delivered by small-particle aerosol cause uniform lethality in nonhuman primates (NHPs), whereas only a few small studies have assessed lower doses in NHPs.

Methods

To further characterize the pathogenesis of EBOV infection via small-particle aerosol, we challenged cohorts of cynomolgus monkeys with low doses of EBOV variant Makona, which may help define risks associated with small particle aerosol exposures.

Results

Despite using challenge doses orders of magnitude lower than previous studies, infection via this route was uniformly lethal across all cohorts. Time to death was delayed in a dose-dependent manner between aerosol-challenged cohorts, as well as in comparison to animals challenged via the intramuscular route. Here, we describe the observed clinical and pathological details including serum biomarkers, viral burden, and histopathological changes leading to death.

Conclusions

Our observations in this model highlight the striking susceptibility of NHPs, and likely humans, via small-particle aerosol exposure to EBOV and emphasize the need for further development of diagnostics and postexposure prophylactics in the event of intentional release via deployment of an aerosol-producing device.
Antibacterial effects in blood irradiated with a polychromatic device mediated through reactive oxygen species: possible involvement of haem
Authors: Willmott Thomas , Humphreys Gavin , Chappell-Jones Krista , Dickinson Mark , Lu Jian R , Hamblin Michael R , Dark Paul , McBain Andrew J
Published: May 2023

The antibacterial effects of a polychromatic light device designed for intravenous application were assessed in vitro. Staphylococcus aureus, Klebsiella pneumoniae, or Escherichia coli were exposed to a 60-min sequential light cycle comprising 365, 530, and 630 nm wavelengths in circulated sheep blood. Bacteria were quantified by viable counting. The potential involvement of reactive oxygen species in the antibacterial effect was assessed using the antioxidant N-acetylcysteine-amide. A modified device was then used to determine the effects of the individual wavelengths. Exposure of blood to the standard wavelength sequence caused small (c. 0.5 Log 10 CFU) but statistically significant reductions in viable counts for all three bacteria, which were prevented by the addition of N-acetylcysteine-amide. Bacterial inactivation did not occur in blood-free medium, but supplementation with haem restored the moderate bactericidal effect. In single-wavelength experiments, bacterial inactivation occurred only with red (630 nm) light. Concentrations of reactive oxygen species were significantly higher under light stimulation than in unstimulated controls. In summary, exposure of bacteria within blood to a cycle of visible light wavelengths resulted in small but statistically significant bacterial inactivation apparently mediated by a 630 nm wavelength only, via reactive oxygen species possibly generated by excitation of haem groups.
The dynamics of debris streams from tidal disruption events: exact solutions, critical stream density, and hydrogen recombination
Authors: Coughlin Eric R
Published: May 2023

A star destroyed by a supermassive black hole (SMBH) in a tidal disruption event (TDE) is transformed into a filamentary structure known as a tidally disrupted stellar debris stream. We show that when ideal gas pressure dominates the thermodynamics of the stream, there is an exact solution to the hydrodynamics equations that describes the stream evolution and accounts for self-gravity, pressure, the dynamical expansion of the gas, and the transverse structure of the stream. We analyse the stability of this solution to cylindrically symmetric perturbations, and show that there is a critical stream density below which the stream is unstable and is not self-gravitating; this critical density is a factor of at least 40–50 smaller than the stream density in a TDE. Above this critical density the stream is overstable, self-gravity confines the stream, the oscillation period is exponentially long, and the growth rate of the overstability scales as t1/6. The power-law growth and small power-law index of the overstability implies that the stream is effectively stable to cylindrically symmetric perturbations. We also use this solution to analyse the effects of hydrogen recombination, and suggest that even though recombination substantially increases the gas entropy, it is likely incapable of completely destroying the influence of self-gravity. We also show that the transient produced by recombination is far less luminous than previous estimates.
The PAU survey: close galaxy pairs identification and analysis
Authors: Gonzalez E J , Rodriguez F , Navarro-Gironés D , Gaztañaga E , Siudek M , García Lambas D , O’Mill A L , Renard P , Cabayol L , Carretero J , Casas R , De Vicente J , Eriksen M , Fernandez E , Garcia-Bellido J , Hildebrandt H , Miquel R , Padilla C , Sanchez E , Sevilla-Noarbe I , Tallada-Crespí P , Wittje A
Published: May 2023

Galaxy pairs constitute the initial building blocks of galaxy evolution, which is driven through merger events and interactions. Thus, the analysis of these systems can be valuable in understanding galaxy evolution and studying structure formation. In this work, we present a new publicly available catalogue of close galaxy pairs identified using photometric redshifts provided by the Physics of the Accelerating Universe Survey (PAUS). To efficiently detect them, we take advantage of the high-precision photo−z (σ68 < 0.02) and apply an identification algorithm previously tested using simulated data. This algorithm considers the projected distance between the galaxies (rp < 50 kpc), the projected velocity difference (ΔV < 3500 km s−1) and an isolation criterion to obtain the pair sample. We applied this technique to the total sample of galaxies provided by PAUS and to a subset with high-quality redshift estimates. Finally, the most relevant result we achieved was determining the mean mass for several subsets of galaxy pairs selected according to their total luminosity, colour, and redshift, using galaxy–galaxy lensing estimates. For pairs selected from the total sample of PAUS with a mean r-band luminosity 1010.6 h−2 L⊙, we obtain a mean mass of M200 = 1012.2 h−1 M⊙, compatible with the mass–luminosity ratio derived for elliptical galaxies. We also study the mass-to-light ratio M/L as a function of the luminosity L and find a lower M/L (or steeper slope with L) for pairs than the one extrapolated from the measurements in groups and galaxy clusters.
Scalable precision wide-field imaging in radio interferometry: I. uSARA validated on ASKAP data
Authors: Wilber A G , Dabbech A , Jackson A , Wiaux Y
Published: May 2023

As Part I of a paper series showcasing a new imaging framework, we consider the recently proposed unconstrained Sparsity Averaging Reweighted Analysis (uSARA) optimization algorithm for wide-field, high-resolution, high-dynamic range, monochromatic intensity imaging. We reconstruct images from real radio-interferometric observations obtained with the Australian Square Kilometre Array Pathfinder (ASKAP) and present these results in comparison to the widely used, state-of-the-art imager WSClean . Selected fields come from the ASKAP Early Science and Evolutionary Map of the Universe (EMU) Pilot surveys and contain several complex radio sources: the merging cluster system Abell 3391-95, the merging cluster SPT-CL 2023-5535, and many extended, or bent-tail, radio galaxies, including the X-shaped radio galaxy PKS 2014-558 and ‘the dancing ghosts’, known collectively as PKS 2130-538. The modern framework behind uSARA utilizes parallelization and automation to solve for the w -effect and efficiently compute the measurement operator, allowing for wide-field reconstruction over the full field-of-view of individual ASKAP beams (up to ∼3.3° each). The precision capability of uSARA produces images with both super-resolution and enhanced sensitivity to diffuse components, surpassing traditional CLEAN algorithms that typically require a compromise between such yields. Our resulting monochromatic uSARA-ASKAP images of the selected data highlight both extended, diffuse emission and compact, filamentary emission at very high resolution (up to 2.2 arcsec), revealing never-before-seen structure. Here we present a validation of our uSARA-ASKAP images by comparing the morphology of reconstructed sources, measurements of diffuse flux, and spectral index maps with those obtained from images made with WSClean .
Scalable precision wide-field imaging in radio interferometry – II. AIRI validated on ASKAP data
Authors: Wilber A G , Dabbech A , Terris M , Jackson A , Wiaux Y
Published: May 2023

Accompanying Part I, this sequel delineates a validation of the recently proposed AI for Regularization in radio-interferometric Imaging (AIRI) algorithm on observations from the Australian Square Kilometre Array Pathfinder (ASKAP). The monochromatic AIRI-ASKAP images showcased in this work are formed using the same parallelized and automated imaging framework described in Part I: ‘uSARA validated on ASKAP data’. Using a Plug-and-Play approach, AIRI differs from uSARA by substituting a trained denoising deep neural network (DNN) for the proximal operator in the regularization step of the forward–backward algorithm during deconvolution. We build a trained shelf of DNN denoisers that target the estimated image dynamic ranges of our selected data. Furthermore, we quantify variations of AIRI reconstructions when selecting the nearest DNN on the shelf versus using a universal DNN with the highest dynamic range, opening the door to a more complete framework that not only delivers image estimation but also quantifies epistemic model uncertainty. We continue our comparative analysis of source structure, diffuse flux measurements, and spectral index maps of selected target sources as imaged by AIRI and the algorithms in Part I – uSARA and WSClean. Overall, we see an improvement over uSARA and WSClean in the reconstruction of diffuse components in AIRI images. The scientific potential delivered by AIRI is evident in further imaging precision, more accurate spectral index maps, and a significant acceleration in deconvolution time, whereby AIRI is four times faster than its subiterative sparsity-based counterpart uSARA.
Asteroseismology of the DAV star KUV 08368+4026
Authors: Yang Y H , Chen Y H , Tang M Y
Published: May 2023

As a DAV star, KUV 08368+4026 was observed by Li et al. in 2009 February, 2009 December, 2010 January, and 2012 February. They extracted 30 frequencies from the reported 300 h observation data and identified 17 independent modes. Based on the frequency splitting relationship, 6 l = 1 modes and 1 l = 2 mode are identified. The seven identified modes are reliable and can be used to constrain fitting models. A large sample (7,558,272) DAV star models were established using White Dwarf Evolution Code (wdec; 2018 version). The theoretical modes are calculated and used to fit the observed modes in order to obtain a best-fitting model. The best-fitting model has an average fitting error of σRMS  = 0.71 s. The best-fitting model parameters are M*  = 0.685 ± 0.005 M⊙, Teff  = 11820 ± 40 K, log(MHe/M*)  = − 5.00 ± 0.01, and, log(MH/M*)  = − 6.90 ± 0.01. The stellar mass M* and effective temperature Teff of the best-fitting model are basically consistent with the results of the spectroscopy. The mass of the He layer is thinner than the results obtained from previous asteroseismic models. The best-fitting model has a small Carbon/Oxygen central core with an oxygen abundance of XO  = 0.76. The asteroseismological distance calculated using the luminosity of our best-fitting model is basically consistent with that of the Kiso Schmidt ultraviolet excess survey.
Redefining normal breast cell populations using long noncoding RNAs
Authors: Bitar Mainá , Rivera Isela Sarahi , Almeida Isabela , Shi Wei , Ferguson Kaltin , Beesley Jonathan , Lakhani Sunil R , Edwards Stacey L , French Juliet D
Published: May 2023

Single-cell RNAseq has allowed unprecedented insight into gene expression across different cell populations in normal tissue and disease states. However, almost all studies rely on annotated gene sets to capture gene expression levels and sequencing reads that do not align to known genes are discarded. Here, we discover thousands of long noncoding RNAs (lncRNAs) expressed in human mammary epithelial cells and analyze their expression in individual cells of the normal breast. We show that lncRNA expression alone can discriminate between luminal and basal cell types and define subpopulations of both compartments. Clustering cells based on lncRNA expression identified additional basal subpopulations, compared to clustering based on annotated gene expression, suggesting that lncRNAs can provide an additional layer of information to better distinguish breast cell subpopulations. In contrast, these breast-specific lncRNAs poorly distinguish brain cell populations, highlighting the need to annotate tissue-specific lncRNAs prior to expression analyses. We also identified a panel of 100 breast lncRNAs that could discern breast cancer subtypes better than protein-coding markers. Overall, our results suggest that lncRNAs are an unexplored resource for new biomarker and therapeutic target discovery in the normal breast and breast cancer subtypes.
ChroKit: a Shiny-based framework for interactive analysis, visualization and integration of genomic data
Authors: Croci Ottavio , Campaner Stefano
Published: May 2023

We developed ChroKit (the Chromatin toolKit), an interactive web-based framework written in R that enables intuitive exploration, multidimensional analyses, and visualization of genomic data from ChIP-Seq, DNAse-Seq or any other NGS experiment that reports the enrichment of aligned reads over genomic regions. This program takes preprocessed NGS data and performs operations on genomic regions of interest, including resetting their boundaries, their annotation based on proximity to genomic features, the association to gene ontologies, and signal enrichment calculations. Genomic regions can be further refined or subsetted by user-defined logical operations and unsupervised classification algorithms. ChroKit generates a full range of plots that are easily manipulated by point and click operations, thus allowing ‘on the fly’ re-analysis and fast exploration of the data. Working sessions can be exported for reproducibility, accountability, and easy sharing within the bioinformatics community. ChroKit is multiplatform and can be deployed on a server to enhance computational speed and provide simultaneous access by multiple users. ChroKit is a fast and intuitive genomic analysis tool suited for a wide range of users due to its architecture and its user-friendly graphical interface. ChroKit source code is available at https://github.com/ocroci/ChroKit and the Docker image at https://hub.docker.com/r/ocroci/chrokit.
Inferring ligand-receptor cellular networks from bulk and spatial transcriptomic datasets with BulkSignalR
Authors: Villemin Jean-Philippe , Bassaganyas Laia , Pourquier Didier , Boissière Florence , Cabello-Aguilar Simon , Crapez Evelyne , Tanos Rita , Cornillot Emmanuel , Turtoi Andrei , Colinge Jacques
Published: May 2023

The study of cellular networks mediated by ligand-receptor interactions has attracted much attention recently owing to single-cell omics. However, rich collections of bulk data accompanied with clinical information exists and continue to be generated with no equivalent in single-cell so far. In parallel, spatial transcriptomic (ST) analyses represent a revolutionary tool in biology. A large number of ST projects rely on multicellular resolution, for instance the Visium™ platform, where several cells are analyzed at each location, thus producing localized bulk data. Here, we describe BulkSignalR, a R package to infer ligand-receptor networks from bulk data. BulkSignalR integrates ligand-receptor interactions with downstream pathways to estimate statistical significance. A range of visualization methods complement the statistics, including functions dedicated to spatial data. We demonstrate BulkSignalR relevance using different datasets, including new Visium liver metastasis ST data, with experimental validation of protein colocalization. A comparison with other ST packages shows the significantly higher quality of BulkSignalR inferences. BulkSignalR can be applied to any species thanks to its built-in generic ortholog mapping functionality.
Replisome dysfunction upon inducible TIMELESS degradation synergizes with ATR inhibition to trigger replication catastrophe
Authors: Patel Jinal A , Zezelic Camryn , Rageul Julie , Saldanha Joanne , Khan Arafat , Kim Hyungjin
Published: May 2023

The structure of DNA replication forks is preserved by TIMELESS (TIM) in the fork protection complex (FPC) to support seamless fork progression. While the scaffolding role of the FPC to couple the replisome activity is much appreciated, the detailed mechanism whereby inherent replication fork damage is sensed and counteracted during DNA replication remains largely elusive. Here, we implemented an auxin-based degron system that rapidly triggers inducible proteolysis of TIM as a source of endogenous DNA replication stress and replisome dysfunction to dissect the signaling events that unfold at stalled forks. We demonstrate that acute TIM degradation activates the ATR-CHK1 checkpoint, whose inhibition culminates in replication catastrophe by single-stranded DNA accumulation and RPA exhaustion. Mechanistically, unrestrained replisome uncoupling, excessive origin firing, and aberrant reversed fork processing account for the synergistic fork instability. Simultaneous TIM loss and ATR inactivation triggers DNA-PK-dependent CHK1 activation, which is unexpectedly necessary for promoting fork breakage by MRE11 and catastrophic cell death. We propose that acute replisome dysfunction results in a hyper-dependency on ATR to activate local and global fork stabilization mechanisms to counteract irreversible fork collapse. Our study identifies TIM as a point of replication vulnerability in cancer that can be exploited with ATR inhibitors.
Variation in microbial feature perception in the Rutaceae family with immune receptor conservation in citrus
Authors: Trinh Jessica , Li Tianrun , Franco Jessica Y , Toruño Tania Y , Stevens Danielle M , Thapa Shree P , Wong Justin , Pineda Rebeca , de Dios Emmanuel Ávila , Kahn Tracy L , Seymour Danelle K , Ramadugu Chandrika , Coaker Gitta L
Published: May 2023

Although much is known about the responses of model plants to microbial features, we still lack an understanding of the extent of variation in immune perception across members of a plant family. In this work, we analyzed immune responses in Citrus and wild relatives, surveying 86 Rutaceae genotypes with differing leaf morphologies and disease resistances. We found that responses to microbial features vary both within and between members. Species in 2 subtribes, the Balsamocitrinae and Clauseninae, can recognize flagellin (flg22), cold shock protein (csp22), and chitin, including 1 feature from Candidatus Liberibacter species (csp22CLas), the bacterium associated with Huanglongbing. We investigated differences at the receptor level for the flagellin receptor FLAGELLIN SENSING 2 (FLS2) and the chitin receptor LYSIN MOTIF RECEPTOR KINASE 5 (LYK5) in citrus genotypes. We characterized 2 genetically linked FLS2 homologs from “Frost Lisbon” lemon (Citrus ×limon, responsive) and “Washington navel” orange (Citrus ×aurantium, nonresponsive). Surprisingly, FLS2 homologs from responsive and nonresponsive genotypes were expressed in Citrus and functional when transferred to a heterologous system. “Washington navel” orange weakly responded to chitin, whereas “Tango” mandarin (C. ×aurantium) exhibited a robust response. LYK5 alleles were identical or nearly identical between the 2 genotypes and complemented the Arabidopsis (Arabidopsis thaliana) lyk4/lyk5-2 mutant with respect to chitin perception. Collectively, our data indicate that differences in chitin and flg22 perception in these citrus genotypes are not the results of sequence polymorphisms at the receptor level. These findings shed light on the diversity of perception of microbial features and highlight genotypes capable of recognizing polymorphic pathogen features.
Validation of a patient-reported outcome measure for giant cell arteritis
Authors: Ndosi Mwidimi , Almeida Celia , Dawson Jill , Dures Emma , Greenwood Rosemary , Bromhead Alison , Guly Catherine , Stern Steve , Hill Catherine , Mackie Sarah , Robson Joanna C
Published: May 2023

Objectives

GCA is systemic vasculitis manifesting as cranial, ocular or large vessel vasculitis. A prior qualitative study developed 40 candidate items to assess the impact of GCA on health-related quality of life (HRQoL). This study aimed to determine final scale structure and measurement properties of the GCA patient reported outcome (GCA-PRO) measure.

Methods

Cross-sectional study included UK patients with clinician-confirmed GCA. They completed 40 candidate items for the GCA-PRO at times 1 and 2 (3 days apart), EQ-5D-5L, ICECAP-A, CAT-PROM5 and self-report of disease activity. Rasch and exploratory factor analyses informed item reduction and established structural validity, reliability and unidimensionality of the final GCA-PRO. Evidence of validity was also established with hypothesis testing (GCA-PRO vs other PRO scores, and between participants with ‘active disease’ vs those ‘in remission’) and test–retest reliability.

Results

The study population consisted of 428 patients: mean (s.d.) age 74.2 (7.2), 285 (67%) female; 327 (76%) cranial GCA, 114 (26.6%) large vessel vasculitis and 142 (33.2%) ocular involvement. Rasch analysis eliminated 10 candidate GCA items and informed restructuring of response categories into four-point Likert scales. Factor analysis confirmed four domains: acute symptoms (eight items), activities of daily living (seven items), psychological (seven items) and participation (eight items). The overall scale had adequate Rasch model fit (χ2 = 25.219, degrees of freedom = 24, P = 0.394). Convergent validity with EQ5D-5L, ICECAP-A and Cat-PROM5 was confirmed through hypothesis testing. Internal consistency and test–retest reliability were excellent.

Conclusion

The final GCA-PRO is a 30-item, four-domain scale with robust evidence of validity and reliability in measuring HRQoL in people with GCA.
The experimentation–accountability trade-off in innovation and industrial policy: are learning networks the solution?
Authors: Radosevic Slavo , Kanellou Despina , Tsekouras George
Published: May 2023

The exact nature of industrial/innovation (I/I) policy challenges and the best way to address them are unknown ex ante. This requires a degree of experimentation, which can be problematic in the context of an accountable public administration and leaves the question of how to reconcile the experimental nature of I/I policy with the need for public accountability, a crucial but unresolved issue. The trade-off between experimentation and accountability requires a governance model that will allow continuous feedback loops among the various stakeholders and ongoing evaluation of and adjustments to activities as programmes are implemented. We propose an ‘action learning’ approach, incorporating the governance mechanism of ‘learning networks’ to handle the problems of implementing experimental governance of new and untried I/I policies. We resolve the issue of accountability by drawing on the literature on network governance in public policy. By integrating control and learning dimensions of accountability, this approach enables us to resolve conceptually and empirically trade-offs between the need for experimentation and accountability in I/I policy.