bluuebunny/crossref_metadata_2025_split huggingface dataset:
A taxonomy of the brain’s white matter: twenty-one major tracts for the 21st century
Authors: Bullock Daniel N , Hayday Elena A , Grier Mark D , Tang Wei , Pestilli Franco , Heilbronner Sarah R 
Published: December 2021

AbstractThe functional and computational properties of brain areas are determined, in large part, by their connectivity profiles. Advances in neuroimaging and network neuroscience allow us to characterize the human brain noninvasively, but a comprehensive understanding of the human brain demands an account of the anatomy of brain connections. Long-range anatomical connections are instantiated by white matter, which itself is organized into tracts. These tracts are often disrupted by central nervous system disorders, and they can be targeted by neuromodulatory interventions, such as deep brain stimulation. Here, we characterized the connections, morphology, traversal, and functions of the major white matter tracts in the brain. There are major discrepancies across different accounts of white matter tract anatomy, hindering our attempts to accurately map the connectivity of the human brain. However, we are often able to clarify the source(s) of these discrepancies through careful consideration of both histological tract-tracing and diffusion-weighted tractography studies. In combination, the advantages and disadvantages of each method permit novel insights into brain connectivity. Ultimately, our synthesis provides an essential reference for neuroscientists and clinicians interested in brain connectivity and anatomy, allowing for the study of the association of white matter’s properties with behavior, development, and disorders.
Error Characterization and Statistical Modeling Improves Circulating Tumor DNA Detection by Droplet Digital PCR
Authors: Henriksen Tenna V , Drue Simon O , Frydendahl Amanda , Demuth Christina , Rasmussen Mads H , Reinert Thomas , Pedersen Jakob S , Andersen Claus L 
Published: December 2021

Abstract

Background
Droplet digital PCR (ddPCR) is a widely used and sensitive application for circulating tumor DNA (ctDNA) detection. As ctDNA is often found in low abundance, methods to separate low-signal readouts from noise are necessary. We aimed to characterize the ddPCR-generated noise and, informed by this, create a sensitive and specific ctDNA caller.

Methods
We built 2 novel complimentary ctDNA calling methods: dynamic limit of blank and concentration and assay-specific tumor load estimator (CASTLE). Both methods are informed by empirically established assay-specific noise profiles. Here, we characterized noise for 70 mutation-detecting ddPCR assays by applying each assay to 95 nonmutated samples. Using these profiles, the performance of the 2 new methods was assessed in a total of 9447 negative/positive reference samples and in 1311 real-life plasma samples from colorectal cancer patients. Lastly, performances were compared to 7 literature-established calling methods.

Results
For many assays, noise increased proportionally with the DNA input amount. Assays targeting transition base changes were more error-prone than transversion-targeting assays. Both our calling methods successfully accounted for the additional noise in transition assays and showed consistently high performance regardless of DNA input amount. Calling methods that were not noise-informed performed less well than noise-informed methods. CASTLE was the only calling method providing a statistical estimate of the noise-corrected mutation level and call certainty.

Conclusions
Accurate error modeling is necessary for sensitive and specific ctDNA detection by ddPCR. Accounting for DNA input amounts ensures specific detection regardless of the sample-specific DNA concentration. Our results demonstrate CASTLE as a powerful tool for ctDNA calling using ddPCR.
Insights on fault reactivation during the 2019 November 11, Mw 4.9 Le Teil earthquake in southeastern France, from a joint 3-D geological model and InSAR time-series analysis
Authors: Marconato L , Leloup P H , Lasserre C , Jolivet R , Caritg S , Grandin R , Métois M , Cavalié O , Audin L 
Published: December 2021

SUMMARY
The 2019, Mw 4.9 Le Teil earthquake occurred in southeastern France, causing substantial damage in this slow deforming region. Field observations, remote sensing and seismological studies following the event revealed that coseismic slip concentrates at shallow depth along a ∼5 km long rupture associated with surface breaks and a thrusting mechanism. We further investigate this earthquake by combining geological field mapping, 3-D geology, InSAR time-series analysis and a coseismic slip inversion. From structural, stratigraphic and geological data collected around the epicentre, we first produce a 3-D geological model of the region surrounding the rupture using the GeoModeller software. Our model includes the geometry of the geological layers and the main faults, including the La Rouvière Fault, (LRF) the Oligocene normal fault that ruptured during the earthquake. We generate a time-series of surface displacement from Sentinel-1 SAR data ranging from early 2019 January to late 2020 January using the NSBAS processing chain. The spatio-temporal patterns of surface displacement for this time span show neither a clear pre-seismic signal nor significant post-seismic transient deformation. We extract the coseismic displacement pattern from the InSAR time-series, highlighting along-strike variations of coseismic surface slip. The maximum relative displacement along the line of sight is up to ∼16 cm and is located in the southwestern part of the rupture. We invert for the slip distribution on the fault from the InSAR coseismic surface displacement field. Constraining our fault geometry from the geological model, acceptable fault dip ranges between 55° and 60°. Our model confirms the reactivation of LRF, with reverse slip at very shallow depth and two main slip patches reaching, respectively, 30 and 24 cm of slip, both around 500 m depth. We finally discuss how the 3-D fault geometry and geological structure may have impacted the slip distribution and propagation during the earthquake. This study is a step to reassess the seismic hazard of the many faults similar to the La Rouvière one along the Cévennes fault system, in a densely populated area hosting several sensitive nuclear sites.
A review on the ethnopharmacology, phytochemistry and pharmacology of Polygonum hydropiper Linn.
Authors: Bairagi Juli , Saikia Purba J , Boro Freeman , Hazarika Ajit 
Published: December 2021

Abstract

Objectives
Polygonum hydropiper is a herb with worldwide distribution, having tremendous value as traditional medicine among different communities. It is used to cure many kinds of ailments such as gynaecological disorders, ulcer, anxiety, pain, cancer, etc. The present review gives emphasis on a thorough and updated study of the botanical description and taxonomy, distribution, habitat, ethnopharmacology, phytochemical constituents, pharmacological activities and toxicological aspects of P. hydropiper.

Methods
The information included in this review was collected from different scientific databases like PubMed, ScienceDirect, Google Scholar, etc. In addition to the botanical description and taxonomy, lots of ethnomedicinal use of the water-pepper plant could be found.

Result
A good number of compounds belonging to the categories like alkaloids, carbohydrates, flavonoids, etc. were confirmed to be present in the plant. Moreover, in different studies, this plant was found to possess activities like anti-Alzheimer, antibacterial, antidementia, antifertility, neuropharmacological, sedative, anxiolytic, thrombolytic and membrane-stabilizing activity, etc. with minimal toxicity.

Conclusion
These properties may be directly related to its possession of a large number of bioactive molecules of different categories. Based on these properties, isolation of responsible compound(s), evaluation of molecular mechanisms of their action and clinical trials are recommended.
The impact of r-process heating on the dynamics of neutron star merger accretion disc winds and their electromagnetic radiation
Authors: Klion Hannah , Tchekhovskoy Alexander , Kasen Daniel , Kathirgamaraju Adithan , Quataert Eliot , Fernández Rodrigo 
Published: December 2021

ABSTRACT
Neutron star merger accretion discs can launch neutron-rich winds of &gt;10−2M⊙. This ejecta is a prime site for r-process nucleosynthesis, which will produce a range of radioactive heavy nuclei. The decay of these nuclei releases enough energy to accelerate portions of the wind by ∼0.1c. Here, we investigate the effect of r-process heating on the dynamical evolution of disc winds. We extract the wind from a 3D general relativistic magnetohydrodynamic simulation of a disc from a post-merger system. This is used to create inner boundary conditions for 2D hydrodynamic simulations that continue the original 3D simulation. We perform two such simulations: one that includes the r-process heating, and another one that does not. We follow the hydrodynamic simulations until the winds reach homology (60 s). Using time-dependent multifrequency multidimensional Monte Carlo radiation transport simulations, we then calculate the kilonova light curves from the winds with and without dynamical r-process heating. We find that the r-process heating can substantially alter the velocity distribution of the wind, shifting the mass-weighted median velocity from 0.06c to 0.12c. The inclusion of the dynamical r-process heating makes the light curve brighter and bluer at $\sim 1\, \mathrm{d}$ post-merger. However, the high-velocity tail of the ejecta distribution and the early ($\lesssim 1\, \mathrm{d}$) light curves are largely unaffected.
Atmospheric mass-loss and stellar wind effects in young and old systems – I. Comparative 3D study of TOI-942 and TOI-421 systems
Authors: Kubyshkina Daria , Vidotto Aline A , Villarreal D’Angelo Carolina , Carolan Stephen , Hazra Gopal , Carleo Ilaria 
Published: December 2021

ABSTRACT
At young ages, when radiation from the host star is high, and the planet is hot and inflated after formation, planetary atmospheric mass-loss can be extremely strong compared to older planets. In turn, stellar winds are faster and denser for young stars compared to evolved main-sequence stars. Their interaction with escaping planetary atmospheres can substantially affect atmospheric mass-loss rates, as well as the observable signatures of escaping atmospheres, with both effects expected to occur differently for young and evolved planets. We perform a comparative study of two systems around stars of similar masses but very different ages (50 Myr and 9 Gyr): TOI-942 and TOI-421. Both stars host two sub-Neptune-like planets at similar orbits and in similar mass ranges, which allows a direct comparison of the atmospheric escape and interactions with the stellar winds in the young and old systems. We perform the 3D atmospheric modelling of the four planets in TOI-942 and TOI-421 systems and make the theoretical predictions of possible observational signatures in Ly α absorption. We find that accounting for the stellar wind interacting with planetary atmospheres is crucial for the interpretation of the observations for young planets. Additionally, we show that a particular energy distribution along the XUV spectra has a minor effect on the atmospheric mass-loss rates, but it is of crucial importance for modelling the Ly α absorption and therefore for interpretation of observations.
Probing the non-thermal emission geometry of AR Sco via optical phase-resolved polarimetry
Authors: du Plessis Louis , Venter Christo , Wadiasingh Zorawar , Harding Alice K , Buckley David A H , Potter Stephen B , Meintjes P J 
Published: December 2021

ABSTRACT
AR Sco is a binary system that contains a white and red dwarf. The rotation rate of the white dwarf (WD) has been observed to slow down, analogous to rotation-powered radio pulsars; it has thus been dubbed a ‘white dwarf pulsar’. We previously fit the traditional radio pulsar rotating vector model to the linearly polarized optical data from this source, constraining the system geometry as well as the WD mass. Using a much more extensive data set, we now explore the application of the same model to binary phase-resolved optical polarimetric data, thought to be the result of non-thermal synchrotron radiation, and derive the magnetic inclination angle α and the observer angle ζ at different orbital phases. We obtain an ∼10° variation in α and ∼30° variation in ζ over the orbital period. The variation patterns in these two parameters is robust, regardless of the binning and epoch of data used. We speculate that the observer is detecting radiation from an asymmetric emission region that is a stable structure over several orbital periods. The success of this simple model lastly implies that the pitch angles of the particles are small and the pulsed, non-thermal emission originates relatively close to the WD surface.
Exoplanets in the Galactic context: planet occurrence rates in the thin disc, thick disc, and stellar halo of Kepler stars
Authors: Bashi Dolev , Zucker Shay 
Published: December 2021

ABSTRACT
In order to gain a better understanding of planet formation and evolution, it is important to examine the statistics of exoplanets in the Galactic context. By combining information on stellar elemental abundances and kinematics, we constructed separate samples of Kepler stars according to their affiliation to the Galactic components of thin disc, thick disc, and stellar halo. Using a Bayesian analysis with conjugate priors, we then investigated how planet occurrence rates differ in different regions of planet properties. We find that young, slow, and metal-rich stars, associated mainly with the thin disc, host on average more planets (especially close-in super Earths) compared to the old, fast, and metal-poor thick disc stars. We further assess the dependence between stellar properties such as spectral type and metallicity, and planet occurrence rates. The trends we find agree with those found by other authors as well. We argue that in the Galactic context, these are probably not the main properties that affect planet occurrence rates, but rather the dynamical history of stars, and especially stellar age and kinematics, impact the current distribution of planets in the Galaxy.
Destruction of AlF: a quantum study of its ground-state photodissociation
Authors: Qin Zhi , Bai Tianrui , Liu Linhua 
Published: December 2021

ABSTRACTPhotodissociation by ultraviolet photons is the key destruction pathway for aluminium monofluoride (AlF) in the envelope of the carbon star IRC +10216 from the stellar photosphere up to the outer layers. However, there is no available photodissociation data for AlF, which hampers the prediction of the abundances of Al-bearing molecules in astrochemical models. Here, we present an ab initio study of AlF photodissociation. Potential energy curves of seven singlet states for AlF were computed by the internally contracted multireference single and double configuration-interaction method and aug-cc-pCV5Z-DK basis set, along with the transition dipole moments from excited singlet states to the ground state. State-resolved cross sections for the direct photodissociation from 36 349 ground rovibrational levels ( υ″≤120, J″≤360) to six singlet excited states were calculated by the quantum mechanical method. We found that the 21Π←X 1Σ+, 31Π←X 1Σ+, and 41Π←X 1Σ+ transitions have extremely strong absorption for lower wavelengths, especially between the Lyman and  Lyman α ones. Photodissociation cross sections in local thermal equilibrium were estimated for gas temperatures from 500 to 20 000 K. Finally, the cross sections were utilized to calculate the photodissociation rates in the interstellar and blackbody radiation fields. The obtained photodissociation cross sections and rates can be used to determine the abundance of AlF in astrochemical models.
Focusing of non-linear eccentric waves in astrophysical discs – II. Excitation and damping of tightly wound waves
Authors: Lynch Elliot M 
Published: December 2021

ABSTRACT
In this paper, I develop a non-linear theory of tightly wound (highly twisted) eccentric waves in astrophysical discs, based on the averaged Lagrangian method of Whitham. Viscous dissipation is included in the theory by use of a pseudo-Lagrangian. This work is an extension of the theory developed by Lee & Goodman to 3D discs, with the addition of viscosity. I confirm that linear tightly wound eccentric waves are overstable and are excited by the presence of a shear viscosity and show that this persists for weakly non-linear waves. I find the waves are damped by shear viscosity when the wave become sufficiently non-linear, a result previously found in particulate discs. Additionally, I compare the results of this model to recent simulations of eccentric waves propagating in the inner regions of black hole discs and show that an ingoing eccentric wave can be strongly damped near the marginally stable orbit, resulting in a nearly circular disc, with a strong azimuthal variation in the disc density.
HyDRo: atmospheric retrieval of rocky exoplanets in thermal emission
Authors: Piette Anjali A A , Madhusudhan Nikku , Mandell Avi M 
Published: December 2021

ABSTRACT
Emission spectroscopy is a promising technique to observe atmospheres of rocky exoplanets, probing both their chemistry and thermal profiles. We present hydro, an atmospheric retrieval framework for thermal emission spectra of rocky exoplanets. hydro does not make prior assumptions about the background atmospheric composition, and can therefore be used to interpret spectra of secondary atmospheres with unknown compositions. We use hydro to assess the chemical constraints which can be placed on rocky exoplanet atmospheres using JWST. First, we identify the best currently known rocky exoplanet candidates for spectroscopic observations in thermal emission with JWST, finding &gt;30 known rocky exoplanets whose thermal emission will be detectable by JWST/MIRI in fewer than 10 eclipses at R ∼ 10. We then consider the observations required to characterize the atmospheres of three promising rocky exoplanets across the ∼400–800 K equilibrium temperature range: Trappist-1 b, GJ 1132 b, and LHS 3844 b. Considering a range of CO2- to H2O-rich atmospheric compositions, we find that as few as eight eclipses of LHS 3844 b or GJ 1132 b with MIRI LRS will be able to place important constraints on the chemical compositions of their atmospheres. This includes confident detections of CO2 and H2O in the case of a cloud-free CO2-rich composition, besides ruling out a bare rock scenario. Similarly, 30 eclipses of Trappist-1 b with MIRI LRS can allow detections of a cloud-free CO2-rich or CO2-H2O atmosphere. hydro will allow important atmospheric constraints for rocky exoplanets using JWST observations, providing clues about their geochemical environments.
Simultaneous borrowing and saving in microfinance
Authors: Dasgupta Dyotona , Roy Chowdhury Prabal 
Published: December 2021

AbstractThis paper provides a rationale for one of the most widely practised mechanisms by microfinance institutions (MFIs)—simultaneous borrowing and saving. Unlike the existing literature, our explanation does not involve any behavioral aspect. We study a dynamic relationship between a benevolent MFI and a borrower who is subject to an ex post moral hazard problem. The optimum contract involves simultaneous borrowing and saving—at each date, the MFI provides a small loan, the borrower invests that in a production technology, and saves the net return with the MFI. These help her to accumulate a lumpsum amount and ‘graduate’ to an improved lifetime utility which is not achievable when only credit is provided. Over time, as her savings increase, her incentive to repay increases. The optimal loan scheme is weakly progressive, i.e. weakly increasing over time. We also provide a sufficient condition for the non-existence of any incentive compatible contract.
Molecular Dosimetry of DNA Adducts in Rats Exposed to Vinyl Acetate Monomer
Authors: Hsiao Yun-Chung , Liu Chih-Wei , Hoffman Gary , Fang Caroline , Lu Kun 
Published: December 2021

Abstract
Vinyl acetate monomer (VAM) is heavily used to synthesize polymers. Previous studies have shown that inhaled VAM, being metabolized to acetaldehyde, may form DNA adducts including N2-ethylidene-deoxyguanosine (N2-EtD-dG), which may subsequently cause mutations and contribute to its carcinogenesis. Currently, there is little knowledge on the molecular dosimetry between VAM exposure and DNA adducts under dosages relevant to human exposure. In this study, 0.02, 0.1, 1, 10, 50, 200, and 600 ppm VAM were exposed to rats by inhalation for 14 days (6 h/day). The use of [13C2]-VAM allows unambiguous differentiation and quantification of the exogenous and endogenous N2-EtD-dG by highly sensitive LC-MS/MS. Our data indicate that VAM-induced exogenous DNA adducts were formed in a non-linear manner. Exogenous DNA adducts were only detected in the nasal epithelium of rats exposed to 10, 50, 200, and 600 ppm VAM, whereas endogenous adducts were found in all nasal and other tissues analyzed. In addition, ratios of exogenous/endogenous DNA adducts were less than 1 with the dose up to 50 ppm, indicating that endogenous DNA adducts are predominant at low VAM concentrations. Moreover, differential dose-response in terms of exogenous DNA adduct formation were observed between nasal respiratory and olfactory epithelium. Furthermore, the lack of exogenous DNA adducts in distant tissues, including peripheral blood mononuclear cells, liver, brain, and bone marrow, indicates that VAM and/or its metabolite do not distribute systemically to cause DNA damage in distant tissues. Together, these results provided new molecular dosimetry to improve science-based cancer risk assessments of VAM.
Comparative Transcriptome Analyses Reveal Conserved and Distinct Mechanisms of the SDHI Fungicide Benzovindiflupyr Inhibiting Colletotrichum
Authors: Liang Xiaoyu , Zou Lijun , Lian Wenxu , Wang Meng , Yang Ye , Zhang Yu 
Published: December 2021

Colletotrichum leaf disease (CLD) is an annual production concern for commercial growers worldwide. The succinate dehydrogenase inhibitor (SDHI) fungicide benzovindiflupyr shows higher bioactivity against CLD than other SDHIs. However, the mechanism underlying such difference remains unclear. In this study, benzovindiflupyr exhibits good inhibitory activity against Colletotrichum siamense and C. nymphaeae in vitro and in vivo. To reveal its mechanism for inhibiting Colletotrichum, we compared transcriptomes of C. siamense and C. nymphaeae under treatment with benzovindiflupyr and boscalid. Benzovindiflupyr exhibited higher inhibitory activity against SDH enzyme than boscalid, resulting in a greater reduction in the ATP content of Colletotrichum isolates. Most of the metabolic pathways induced in these fungicide-treated isolates were similar, indicating that benzovindiflupyr exhibited a conserved mechanism of SDHIs inhibiting Colletotrichum. At the same level of suppressive SDH activity, benzovindiflupyr activated more than three times greater gene numbers of Colletotrichum than boscalid, suggesting that benzovindiflupyr could activate distinct mechanisms against Colletotrichum. Membrane-related gene ontology terms, mainly including intrinsic components of membrane, were highly abundant for the benzovindiflupyr-treated isolates rather than boscalid-treated isolates. Only benzovindiflupyr increased the relative conductivities of hyphae, indicating that it could damage the cell membrane and increase mycelial electrolyte leakage. Thus, we proposed that the high bioactivity of benzovindiflupyr against Colletotrichum occurred by inhibiting SDH activity and damaging the cell membrane at the same time. The research improves our understanding the mode of action of SDHI fungicides against Colletotrichum.