bluuebunny/crossref_metadata_2025_split huggingface dataset:
Testing Bayesian reconstruction methods from peculiar velocities
Authors: Valade Aurélien , Libeskind Noam I , Hoffman Yehuda , Pfeifer Simon 
Published: December 2022

ABSTRACT
Reconstructing the large-scale density and velocity fields from surveys of galaxy distances is a major challenge for cosmography. The data are very noisy and sparse. Estimated distances, and thereby peculiar velocities, are strongly affected by the Malmquist-like lognormal bias. Two algorithms have been recently introduced to perform reconstructions from such data: the Bias Gaussian correction coupled with the Wiener filter (BGc/WF) and the Hamlet implementation of the Hamiltonian Monte Carlo forward modelling. The two methods are tested here against mock catalogues that mimic the Cosmicflows-3 data. Specifically the reconstructed cosmography and moments of the velocity field (monopole, dipole) are examined. A comparison is made to the ‘exact’ WF as well, namely, the WF in the unrealistic case of zero observational errors. This is to understand the limits of the WF method. The following is found. In the nearby regime ($d \lesssim 40 \, \mathrm{ \mathit{ h}}^{-1}\, {\rm Mpc}$), the two methods perform roughly equally well. Hamlet shows more contrast in the intermediate regime ($40 \lesssim d \lesssim 120 \, h^{-1}\, {\rm Mpc}$). The main differences between the two appear in the most distant regime ($d \gtrsim 120 \, h^{-1}\, {\rm Mpc}$), close to the edge of the data. Hamlet outperforms the BGc/WF in terms of contrast and tighter correlations of the density and velocity fields. Yet, close to the edge of the data, Hamlet yields a slightly biased reconstruction, which affects the multipoles of the velocity field. Such biases are missing from the BGc/WF reconstruction. In sum, both methods perform well and create reliable reconstructions with significant differences apparent when details are examined.
Common envelope evolution and triple dynamics as potential pathways to form the inner white dwarf + brown dwarf binary of the triple star system Gaia 0007−1605
Authors: Lagos Felipe , Zorotovic Monica , Schreiber Matthias R , Gänsicke B T 
Published: December 2022

ABSTRACT
The recently discovered system Gaia 0007−1605 consisting of a white dwarf (WD) with a close brown dwarf companion and a distant WD tertiary very much resembles the triple system containing the first transiting planet candidate around a WD ever discovered: WD 1856+534. We have previously argued that the inner binary in WD 1856+534 most likely formed through common envelope evolution but triple star dynamics represent an alternative scenario. Here, we analyse different formation scenarios for Gaia 0007−1605. We reconstructed the potential common envelope evolution of the system and found that assuming standard parameters for the energy budget provides a reasonable solution. In agreement with other close white dwarf + brown dwarf binaries, and in contrast to WD 1856+534, no energy sources other than orbital energy during common envelope evolution are required to understand the current configuration of the system. In addition, using analytical prescriptions for triple dynamics, we show that Von Zeipel–Lidov–Kozai oscillations might have triggered tidal migration due to high-eccentricity incursions (e ≳ 0.997). We conclude that the inner binary in Gaia 0007−1605, as its sibling WD 1856+534, formed either through common envelope evolution, triple dynamics, or a combination of both mechanisms.
Cooperative interaction between AAG and UV-DDB in the removal of modified bases
Authors: Jang Sunbok , Kumar Namrata , Schaich Mathew A , Zhong Zhou , van Loon Barbara , Watkins Simon C , Van Houten Bennett 
Published: December 2022

Abstract
UV-DDB is a DNA damage recognition protein recently discovered to participate in the removal of 8-oxo-7,8-dihydro-2′-deoxyguanosine (8-oxoG) by stimulating multiple steps of base excision repair (BER). In this study, we examined whether UV-DDB has a wider role in BER besides oxidized bases and found it has specificity for two known DNA substrates of alkyladenine glycosylase (AAG)/N-methylpurine DNA glycosylase (MPG): 1, N6-ethenoadenine (ϵA) and hypoxanthine. Gel mobility shift assays show that UV-DDB recognizes these two lesions 4–5 times better than non-damaged DNA. Biochemical studies indicated that UV-DDB stimulated AAG activity on both substrates by 4- to 5-fold. Native gels indicated UV-DDB forms a transient complex with AAG to help facilitate release of AAG from the abasic site product. Single molecule experiments confirmed the interaction and showed that UV-DDB can act to displace AAG from abasic sites. Cells when treated with methyl methanesulfonate resulted in foci containing AAG and UV-DDB that developed over the course of several hours after treatment. While colocalization did not reach 100%, foci containing AAG and UV-DDB reached a maximum at three hours post treatment. Together these data indicate that UV-DDB plays an important role in facilitating the repair of AAG substrates.
Fasting influences aquaporin expression, water transport and adipocyte metabolism in the peritoneal membrane
Authors: Costa Ines P D , Hautem Nicolas , Schiano Gugliemo , Uchida Shinichi , Nishino Tomoya , Devuyst Olivier 
Published: December 2022

ABSTRACT

Background
The water channels aquaporin-1 (AQP1) and AQP7 are abundantly expressed in the peritoneal membrane. While AQP1 facilitates water transport during peritoneal dialysis (PD), the role of AQP7, which mediates glycerol transport during fasting, remains unknown.

Methods
We investigated the distribution of AQP7 and AQP1 and used a mouse model of PD to investigate the role of AQP7 in the peritoneal membrane at baseline and after fasting.

Results
Single nucleus RNA-sequencing revealed that AQP7 was mostly detected in mature adipocytes, whereas AQP1 was essentially expressed in endothelial cells. Fasting induced significant decreases in whole body fat, plasma glucose, insulin and triglycerides, as well as higher plasma glycerol and corticosterone levels in mice, paralleled by major decreases in adipocyte size and levels of fatty acid synthase and leptin, and increased levels of hormone-sensitive lipase mRNAs in the peritoneum. Mechanistically, fasting upregulated the expression of AQP1 and AQP7 in the peritoneum, with increased ultrafiltration but no change in small solute transport. Studies based on Aqp1 and Aqp7 knockout mice and RU-486 inhibition demonstrated that the glucocorticoid induction of AQP1 mediates the increase in ultrafiltration whereas AQP7 regulates the size of adipocytes in the peritoneum.

Conclusions
Fasting induces a coordinated regulation of lipolytic and lipogenic factors and aqua(glycero)porins in the peritoneum, driving structural and functional changes. These data yield novel information on the specific roles of aquaporins in the peritoneal membrane and indicate that fasting improves fluid removal in a mouse model of PD.
On shape forming by contractile filaments in the surface of growing tissues
Authors: Fratzl Peter , Fischer F Dieter , Zickler Gerald A , Dunlop John W C 
Published: December 2022

Abstract
Growing tissues are highly dynamic, and flow on sufficiently long timescales due to cell proliferation, migration, and tissue remodeling. As a consequence, growing tissues can often be approximated as viscous fluids. This means that the shape of microtissues growing in vitro is governed by their surface stress state, as in fluid droplets. Recent work showed that cells in the near-surface region of fibroblastic or osteoblastic microtissues contract with highly oriented actin filaments, thus making the surface properties highly anisotropic, in contrast to what is expected for an isotropic fluid. Here, we develop a model that includes mechanical anisotropy of the surface generated by contractile fibers and we show that mechanical equilibrium requires contractile filaments to follow geodesic lines on the surface. Constant pressure in the fluid forces these contractile filaments to be along geodesics with a constant normal curvature. We then take this into account to determine equilibrium shapes of rotationally symmetric bodies subjected to anisotropic surface stress states and derive a family of surfaces of revolution. A comparison with recently published shapes of microtissues shows that this theory accurately predicts both the surface shape and the direction of the actin filaments on the surface.
NEUTROPHIL HETEROGENEITY IN SEPSIS: THE ROLE OF DAMAGE-ASSOCIATED MOLECULAR PATTERNS
Authors: Murao Atsushi , Aziz Monowar , Wang Ping 
Published: December 2022

ABSTRACT
Sepsis is a severe inflammatory disease syndrome caused by the dysregulated host response to infection. Neutrophils act as the first line of defense against pathogens by releasing effector molecules such as reactive oxygen species, myeloperoxidase, and neutrophil extracellular traps. However, uncontrolled activation of neutrophils and extensive release of effector molecules often cause a “friendly fire” to damage organ systems. Although neutrophils are considered a short-lived, terminally differentiated homogeneous population, recent studies have revealed its heterogeneity comprising different subsets or states implicated in sepsis pathophysiology. Besides the well-known N1 and N2 subsets of neutrophils, several new subsets including aged, antigen-presenting, reverse-migrated, intercellular adhesion molecule-1+, low-density, olfactomedin 4+, and Siglec-F+ neutrophils have been reported. These neutrophils potentially contribute to the pathogenesis of sepsis based on their proinflammatory and immunosuppressive functions. Damage-associated molecular patterns (DAMPs) are endogenous molecules to induce inflammation by stimulating pattern recognition receptors on immune cells. Different kinds of DAMPs have been shown to contribute to sepsis pathophysiology, including extracellular cold-inducible RNA-binding protein, high-mobility group box 1, extracellular histones, and heat shock proteins. In this review, we summarize the different subsets of neutrophils and their association with sepsis and discuss the novel roles of DAMPs on neutrophil heterogeneity.
Learning robotic navigation from experience: principles, methods and recent results
Authors: Levine Sergey , Shah Dhruv 
Published: December 2022

Navigation is one of the most heavily studied problems in robotics and is conventionally approached as a geometric mapping and planning problem. However, real-world navigation presents a complex set of physical challenges that defies simple geometric abstractions. Machine learning offers a promising way to go beyond geometry and conventional planning, allowing for navigational systems that make decisions based on actual prior experience. Such systems can reason about traversability in ways that go beyond geometry, accounting for the physical outcomes of their actions and exploiting patterns in real-world environments. They can also improve as more data is collected, potentially providing a powerful network effect. In this article, we present a general toolkit for experiential learning of robotic navigation skills that unifies several recent approaches, describe the underlying design principles, summarize experimental results from several of our recent papers, and discuss open problems and directions for future work.This article is part of the theme issue ‘New approaches to 3D vision’.
Stereopsis without correspondence
Authors: Read Jenny C. A. 
Published: December 2022

Stereopsis has traditionally been considered a complex visual ability, restricted to large-brained animals. The discovery in the 1980s that insects, too, have stereopsis, therefore, challenged theories of stereopsis. How can such simple brains see in three dimensions? A likely answer is that insect stereopsis has evolved to produce simple behaviour, such as orienting towards the closer of two objects or triggering a strike when prey comes within range. Scientific thinking about stereopsis has been unduly anthropomorphic, for example assuming that stereopsis must require binocular fusion or a solution of the stereo correspondence problem. In fact, useful behaviour can be produced with very basic stereoscopic algorithms which make no attempt to achieve fusion or correspondence, or to produce even a coarse map of depth across the visual field. This may explain why some aspects of insect stereopsis seem poorly designed from an engineering point of view: for example, paying no attention to whether interocular contrast or velocities match. Such algorithms demonstrably work well enough in practice for their species, and may prove useful in particular autonomous applications.
This article is part of a discussion meeting issue ‘New approaches to 3D vision’.
Looking at the Ebbinghaus illusion: differences in neurocomputational requirements, not gaze-mediated attention, explain a classic perception-action dissociation
Authors: Whitwell Robert L. , Garach Mehul A. , Goodale Melvyn A. , Sperandio Irene 
Published: December 2022

Perceiving and grasping an object present an animal with different sets of computational problems. The solution in primates entails the specialization of separate neural networks for visual processing with different object representations. This explains why the Ebbinghaus illusion minimally affects the grasping hand's in-flight aperture, which normally scales with target size, even though the size of the target disc remains misperceived. An attractive alternative account, however, posits that grasps are refractory to the illusion because participants fixate on the target and fail to attend to the surrounding context. To test this account, we tracked both limb and gaze while participants made forced-choice judgments of relative disc size in the Ebbinghaus illusion or did so in combination with grasping or manually estimating the size of one of the discs. We replicated the classic dissociation: grasp aperture was refractory to the measured illusory effect on perceived size, while judgments and manual estimates of disc size were not. Importantly, the number of display-wide saccades per second and the percentage of total fixation time or fixations directed at the selected disc failed to explain the dissociation. Our findings support the contention that object perception and goal-directed action rely on distinct visual representations.This article is part of a discussion meeting issue ‘New approaches to 3D vision’.
The protection gap under a social health protection initiative in the COVID-19 pandemic: A case study from Khyber Pakhtunkhwa, Pakistan
Authors: Khan Sheraz Ahmad , Cresswell Kathrin , Sheikh Aziz 
Published: December 2022

AbstractBackgroundSehat Sahulat Programme (SSP) is a Social Health Protection (SHP) initiative by the Government of Khyber Pakhtunkhwa (GoKP), covering inpatient services for 100% of the province’s population. In this paper, we describe SSP’s role in GoKP’s COVID-19 response and draw inferences for similar programmes in Pakistan.Methodology and methodsWe conceptualised SSP as an instrumental case study and collected three complementary data sources. First, we studied GoKP’s official documents to understand SSP’s benefits package. Then we undertook in-depth interviews and collected non-participant observations at the SSP policy and implementation levels. We recruited participants through direct (verbal and email) and indirect (invitation posters) methods.Use of maximum variation sampling enabled us to understand contrasting views from various stakeholders on SSP’s policy dimensions (i.e., coverage and financing), tensions between the policy directions (i.e., whether or not to cover COVID-19) and how policy decisions were made and implemented. We collected data from March 2021 to December 2021. Thematic analysis was conducted with the help of Nvivo12.FindingsThroughout 2020, SSP did not cover COVID-19 treatment. The insurer and GoKP officials considered the pandemic a standard exclusion to insurance coverage. One SSP official said: “COVID-19 is not covered and not relevant to us”. GoKP had stopped non-emergency services at all hospitals. When routine services restarted, the insurer did not cover COVID-19 screening tests, which were mandatory prior to hospital admission.In 2021, GoKP engaged 10 private SSP hospitals for COVID-19 treatment. The SSP Reserve Fund, rather than insurance pooled money, was used. The Reserve Fund was originally meant to cover high-cost organ transplants. In 2021, SSP had 1,002 COVID-19-related admissions, which represented 0.2% of all hospital admissions (N=544,841).An advocacy group representative called the COVID-19 care under SSP “too little too late”. In contrast, SSP officials suggested their insurance database and funds flow mechanism could help GoKP in future health emergencies.ConclusionThe commercially focused interpretation of SHP arrangements led to a protection gap in the context of COVID-19. SSP and similar programmes in other provinces of Pakistan should emphasise the notion of protection and not let commercial interests lead to protection gaps.
scTensor detects many-to-many cell–cell interactions from single cell RNA-sequencing data
Authors: Tsuyuzaki Koki , Ishii Manabu , Nikaido Itoshi 
Published: December 2022

AbstractComplex biological systems are described as a multitude of cell–cell interactions (CCIs). Recent single-cell RNA-sequencing studies focus on CCIs based on ligand–receptor (L-R) gene co-expression but the analytical methods are not appropriate to detect many-to-many CCIs.In this work, we proposescTensor, a novel method for extracting representative triadic relationships (or hypergraphs), which include ligand-expression, receptor-expression, and related L-R pairs. Through extensive studies with simulated and empirical datasets, we have shown thatscTensorcan detect some hypergraphs that cannot be detected using conventional CCI detection methods, especially when they include many-to-many relationships.scTensoris implemented as a freely available R/Bioconductor package.
Mad Hatter correctly annotates 98% of small molecule tandem mass spectra searching in PubChem
Authors: Hoffmann Martin A. , Kretschmer Fleming , Ludwig Marcus , Böcker Sebastian 
Published: December 2022

AbstractMetabolites provide a direct functional signature of cellular state. Untargeted metabolomics usually relies on mass spectrometry, a technology capable of detecting thousands of compounds in a biological sample. Metabolite annotation is executed using tandem mass spectrometry. Spectral library search is far from comprehensive, and numerous compounds remain unannotated. So-calledin silicomethods allow us to overcome the restrictions of spectral libraries, by searching in much larger molecular structure databases. Yet, after more than a decade of method development,in silicomethods still do not reach correct annotation rates that users would wish for. Here, we present a novel computational method called MadHatterfor this task. MadHattercombines CSI:FingerID results with information from the searched structure database via a metascore. Compound information includes the melting point, and the number words in the compound description starting with the letter ‘u’. We then show that MadHatterreaches a stunning 97.6% correct annotations when searching PubChem, one of the largest and most comprehensive molecular structure databases. Finally, we explain what evaluation glitches were necessary for MadHatterto reach this annotation level, what is wrong with similar metascores in general, and why metascores may screw up not only method evaluations but also the analysis of biological experiments.
Quantifying the impacts of an invasive weed on habitat quality and prey availability for tiger snakes (Notechis scutatus) in urban wetlands
Authors: Cornelis Jari , von Takach Brenton , Cooper Christine E. , Vos Jordan , Bateman Philip. W. , Lettoof Damian C. 
Published: December 2022

AbstractInvasive plants are a threat to natural ecosystems worldwide with urban wetlands being some of the most susceptible and highly modified environments of all. The tiger snake (Notechis scutatus) is a top predator that persists in urban wetlands in south-western Australia, many of which have been degraded by introduced kikuyu grass (Cenchrus clandestinus). To evaluate the potential impact of kikuyu grass on habitat quality for western tiger snakes we quantified the structural features of habitats within wetlands degraded by kikuyu grass and compared them to wetlands with native vegetation, examined tiger snake prey availability, assessed predation risk for juvenile snakes using clay models, and measured the thermal quality of the vegetation. Proliferation of kikuyu grass reduced habitat structural heterogeneity by reducing available bare ground and increasing vegetation density. This homogenisation of habitat structure had little effect on the predation risk for juveniles or the thermal properties of tiger snake shelter sites; however, one key snake prey species, the motorbike frog, had significantly lower abundance in the most impacted habitat. Habitat types with more structural complexity also offered tiger snakes more stable thermal regimes and lower predation risk. These findings indicate that the current extent of kikuyu grass invasion offers overall similar habitat quality for tiger snakes and may contribute to their persistence in urban wetlands, but they, along with their anuran prey, may befit from some increased habitat structural complexity in open areas.
Peripheral nerve conduction speed shows a disease control-dependent and -independent drop in type 1 diabetes mellitus in children
Authors: Oberhauser Sarah S. , l’Allemand Dagmar , Lütschg Jürg , Broser Philip J. 
Published: December 2022

AbstractBackground/AimNerve conduction speed (NCS) abnormalities are considered to be early signs of diabetic peripheral neuropathy. We investigated which determinants impact the NCS and how it is related to markers of metabolic control in children and young adults with diabetes mellitus.MethodFifty-four children aged five to 23 years suffering from type I diabetes mellitus were recruited into this study, which was conducted at the Children’s Hospital of Eastern Switzerland in St Gallen from March 2016 to June 2022. The metabolic control parameters were recorded and a nerve conduction study analyzing three motor nerves and one sensory nerve was performed. The data were compared to a control population of healthy children of the same height, and the height-adjusted NCS (dNCS) was analysed.ResultsFor all four nerves under investigation, a statistically significant drop in the NCS of approximately 5 m/s independent of metabolic control was found, the peroneal nerve being the most sensitive. The NCS of the peroneal nerve correlated significantly negatively with the long-term haemoglobin with bound glucose (HbA1c) and highly significantly negatively with the standard deviation of mean glucose (SD), but there was only a trend with the HbA1c and the time in range (TIR) at the time of neurography.InterpretationAll patients with diabetes mellitus showed a reduced NCS, partly independent of metabolic control. This may be due to a lack of the C-peptide, which regulates critical axonal membrane enzymes. High glucose variability clearly increases the risk of neuropathy, together with but also independently of the mean plasma glucose level.